Methods for the treatment of Hunter syndrome

Abstract

Certain embodiments provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising an ETV:IDS protein.

Description

[0001] METHODS FOR THE TREATMENT OF HUNTER SYNDROME

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This application claims priority to U.S. Provisional Application Serial No. 62 / 971,758, filed February 7, 2020, U.S. Provisional Application Serial No. 63 / 091,704, filed October 14, 2020, U.S. Provisional Application Serial No. 63 / 111,586, filed November 9, 2020, and U.S. Provisional Application Serial No. 63 / 135,974, filed January 11, 2021. The entire content of the applications referenced above are hereby incorporated by reference herein.

[0004] BACKGROUND

[0005] Hunter syndrome, or MPS II, is a rare, X-linked recessive disorder caused by IDS gene mutations. Insufficient iduronate 2-sulfatase (IDS) activity leads to accumulation of the glycosaminoglycans (GAGs) heparan sulfate (HS) and dermatan sulfate (DS) and to lysosomal dysfunction in multiple organs and tissues. Approximately two-thirds of patients display a neuronopathic phenotype (nMPS II). A recombinant form of IDS has been approved to treat Hunter syndrome, but it has little effect on the brain due to difficulties in delivering the recombinant enzyme across the blood-brain barrier (BBB). Accordingly, there is a need for more effective therapies that treat both the peripheral and central nervous system (CNS) symptoms of Hunter syndrome. Additionally, there is a need for new methods and biomarkers for evaluating disease activity and treatment response for such newly developed therapeutics.

[0006] SUMMARY

[0007] Accordingly, certain embodiments described herein provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising an ETVTDS protein described herein.

[0008] Certain embodiments also provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising an ETV:IDS protein described herein, wherein administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome. In certain embodiments, the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0009] In certain embodiments, the pharmaceutical composition further comprises a pharmaceutically acceptable excipient (e.g., a pharmaceutically acceptable carrier).

[0010] In certain embodiments, the pharmaceutical composition is administered weekly.

[0011] In certain embodiments, the pharmaceutical composition is administered to the subject intravenously.

[0012] In certain embodiments, the therapeutically effective dose (e.g., a safe and therapeutically effective dose) is evaluated by examining the subject post-treatment using one or more assessments selected from the group consisting of a biomarker assessment, a safety assessment, a neurocognitive assessment, a clinical assessment, a functional assessment and a quality of life assessment.

[0013] In certain embodiments, the administration of the pharmaceutical composition treats one or more symptoms of Hunter syndrome (e.g., a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal abnormality) in the subject. Thus, in certain embodiments, the administration of the pharmaceutical composition changes one or more disease associated parameters for the subject. In certain embodiments, the parameter is a parameter described herein. In certain embodiments, the parameter is evaluated using a biomarker assessment, a safety assessment, a neurocognitive assessment, a clinical assessment, a functional assessment or a quality of life assessment. In certain embodiments, the parameter is evaluated using an assessment described herein.

[0014] In certain embodiments, the duration of response in relation to the parameter change is at least about 2 weeks, 4 weeks, 6, weeks, 8 weeks, 10 weeks, 12 weeks, 14, weeks, 16 weeks, 18 weeks, 20 weeks, 24 weeks, 26 weeks, 28 weeks, 30 weeks, 32 weeks, 36 weeks or more. In certain embodiments, the duration of response is at least about 24 weeks.

[0015] In certain embodiments, the method further comprises adjusting the dose of the pharmaceutical composition based on a parameter described herein. Certain embodiments also provide method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 3 mg / kg, and wherein the protein comprises: (a) a first Fc polypeptide linked to an iduronate 2- sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and (b) a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0016] Certain embodiments provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 7.5 mg / kg, and wherein the protein comprises: (a) a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and (b) a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0017] Certain embodiments provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 15 mg / kg, and wherein the protein comprises: (a) a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and (b) a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0018] Certain embodiments provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 30 mg / kg of protein, and wherein the protein comprises: (a) a first Fc polypeptide linked to an iduronate 2- sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and (b) a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0019] In certain embodiments, the second Fc polypeptide specifically binds to the transferrin receptor.

[0020] In certain embodiments, the IDS amino acid sequence has at least 90% identity to SEQ ID NO:70.

[0021] In certain embodiments, the IDS amino acid sequence has at least 90% identity to SEQ ID NO:90.

[0022] In certain embodiments, the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 90, 170 and 174.

[0023] In certain embodiments, the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 170 and 174.

[0024] In certain embodiments, the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:90, 170 and 174.

[0025] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 91, 171, 175, 213, 215 or 217. In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 91, 171 or 175. In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 213, 215 or 217.

[0026] In certain embodiments, the IDS amino acid sequence is linked to the N-terminus of the first Fc polypeptide.

[0027] In certain embodiments, the second Fc polypeptide comprises Leu at position 380; Ala at position 389; and Ser at position 390. In certain embodiments, the second Fc polypeptide comprises Glu at position 380; Ala at position 389; and Asn at position 390. In certain embodiments, the second Fc polypeptide comprises Trp at position 380; Ser at position 389; and Ser at position 390. In certain embodiments, the second Fc polypeptide comprises Leu at position 380; Ser at position 389; and Ser at position 390.

[0028] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 92. In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 189.

[0029] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 95. In certain embodiments, the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO:95.

[0030] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 191. In certain embodiments, the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO: 191.

[0031] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 168.

[0032] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 207.

[0033] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 169.

[0034] In certain embodiments, the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 199.

[0035] Certain embodiments also provide a pharmaceutical composition comprising a protein for use in a method of treating Hunter syndrome, the method comprising administering a therapeutically effective dose of the pharmaceutical composition to a subject in need thereof, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0036] Certain embodiments also provide the use of a protein in the preparation of a medicament for treating Hunter syndrome by administering a therapeutically effective dose of the medicament to a subject in need thereof, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0037] BRIEF DESCRIPTION OF THE FIGURES

[0038] Figure 1. Brain HS / DS (GAG) accumulation in IDS KO mice relative to age matched control. For each age grouping, wildtype (WT) is shown on the left and IDS KO is shown on the right.

[0039] Figures 2A-2D. Lysosomal lipids (GM2, GM3, BMP and GlcCer) accumulate in the brains of IDS KO mice relative to their age matched controls. In Figures 2B-2D, for each age grouping, the bar representing WT is shown on the left and bar representing IDS KO is shown on the right.

[0040] Figure 3. Elevated levels of BMP observed in the serum of IDS KO mice relative to their age matched controls. For each age grouping, the bar representing wildtype (WT) is shown on the left and bar representing IDS KO is shown on the right.

[0041] Figure 4. Elevated levels of lysosomal lipids (Gdla / b, GM3, BMP and GlcCer) observed in the CSF of IDS KO mice relative to their age matched controls. For each age grouping, the bar representing wildtype (WT) is shown on the left, and bar representing IDS KO is shown on the right.

[0042] Figures 5A-5B. Peripheral administration of ETVTDS (4 week treatment) corrects (Figure 5A) brain and (Figure 5B) CSF GAG accumulation in IDS KO mice. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; * p ≤

[0043] 0.05, ** p ≤ 0.01, *** p ≤ 0.001, and **** p ≤ 0.0001.

[0044] Figure 6. Peripheral administration of ETVTDS (4 week treatment) corrects lysosomal lipid (gangliosides) accumulation in IDS KO brains. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; * p ≤ 0.05, ** p ≤ 0.01, *** p ≤

[0045] 0.001, and **** p ≤ 0.0001.

[0046] Figures 7A-7B. Peripheral administration of ETVTDS (4 week treatment) corrects lysosomal lipid (GlcCer) accumulation in IDS KO brains. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; * p ≤ 0.05, ** p ≤ 0.01, *** p < 0.001, and **** p ≤ 0.0001.

[0047] Figure 8. Peripheral administration of ETV:IDS (4 week treatment) corrects lysosomal lipid (BMP) accumulation in IDS KO brains. The graph displays mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; * p ≤ 0.05, ** p ≤ 0.01, *** p ≤

[0048] 0.001, and **** p ≤ 0.0001.

[0049] Figure 9. Heat map illustrating lipid levels in brains of IDS KO mice treated with vehicle, ETVTDS or Elaprase (idursulfase). Fold change as compared to WT.

[0050] Figure 10. Peripheral administration of ETVTDS corrects TREM2 accumulation in IDS KO brains. The graph displays mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; **** p 0.0001.

[0051] Figure 11. Peripheral administration of ETV:IDS reduces accumulation of CSF soluble TREM2 (sTrem2) levels in IDS KO; TfRmu / huKI mice.

[0052] Figures 12A-12C. Serum (Figure 12A), brain (Figure 12B) and CSF (Figure 12C) HS / DS (GAG) accumulation in IDS KO mice treated with vehicle or 3, 10, 20, or 40 mg / kg ETVTDS.

[0053] Figures 13A-13C. Peripheral administration of ETVTDS corrects GM3 (Figure 13 A), GlcCer (Figure 13B) and BMP (Figure 13C) accumulation in brains of IDS KO mice treated with 3, 10, 20, or 40 mg / kg ETV:IDS, as compared to IDS KO mice treated with vehicle.

[0054] Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; * p ≤ 0.05, ** p ≤ 0.01, *** p ≤ 0.001, and **** p ≤ 0.0001.

[0055] Figures 14A-14B. Administration of ETVTDS reduces the levels of individual GAG species (D0S0, D0A0 and D0a4) in brain (Figure 14A) and CSF (Figure 14B) from IDS KO mice, as compared to IDS KO mice treated with vehicle. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; ** p ≤ 0.01, *** p ≤ 0.001, and **** p ≤ 0.0001.

[0056] Figure 15A. GAG levels in microglia, astrocytes, and neurons isolated from IDS KO; TfRmu / huKi mice relative to TfRmu / huKI controls (n=3-5 mice per group). All data are displayed as mean ± SEM; unpaired student’s t-test p< 0.05*, 0.001***.

[0057] Figure 15B. Distribution of ETVTDS in FACS-enriched neuron, astrocyte, and microglia cell populations at 2-hours post dose in vehicle-treated TfRmu / huKI and ETVTDS (40 mg / kg) treated IDS KO; TfRmu / huKI mice; n=4 mice per group. Graph displays mean ± SEM; two-way ANOVA with Sidak’s test; ** p ≤ 0.01, *** p ≤ 0.001, and **** p ≤ 0.0001.

[0058] Figure 16. Reduction of GAG accumulation in neurons, astrocytes, and microglia from IDS KO; TfRmu / huKI mice dosed intravenously with 40 mg / kg ETV:IDS once a week for four weeks. Data are displayed as mean ± SEM; one-way ANOVA with Tukey’s multiple comparison test, * p ≤ 0.05, ** p ≤ 0.01, **** p ≤0.0001.

[0059] Figure 17. Reduction of ganglioside accumulation in neurons, astrocytes, and microglia from IDS KO; TfRmu / huKI mice dosed intravenously with 40 mg / kg ETV:IDS once a week for four weeks. Data are displayed as mean ± SEM; one-way ANOVA with Tukey’s multiple comparison test, * p ≤ 0.05, ** p ≤ 0.01, **** p ≤0.0001.

[0060] Figure 18. Reduction of glucosylceramide accumulation in neurons, astrocytes, and microglia from IDS KO; TfRmu / huKI mice dosed intravenously with 40 mg / kg ETVTDS once a week for four weeks. Data are displayed as mean ± SEM; one-way ANOVA with Tukey’s multiple comparison test, * p ≤ 0.05, ** p ≤ 0.01, **** p ≤0.0001.

[0061] Figure 19. Rescue of BMP alterations in neurons, astrocytes, and microglia from IDS KO; TfRmu / huKI mice dosed intravenously with 40 mg / kg ETV:IDS once a week for four weeks. Data are displayed as mean ± SEM; one-way ANOVA with Tukey’s multiple comparison test, * p ≤ 0.05, ** p ≤ 0.01, **** p <0.0001.

[0062] Figure 20. H&E staining (top panel) and MALDI MS images (middle and bottom panels) of coronal brain sections of wild-type and IDS KO; TfRmu / huKI mice after four, weekly doses of vehicle, idursulfase or ETVTDS. The middle panel shows the distribution of the signal at m / z 1382.816, corresponding to GM2 (d36: 1); and the bottom panel shows the distribution of the signal at m / z 1179.738, corresponding to GM3 (d36: 1). Images depict the relative intensity of each signal from 0-100%.

[0063] Figure 21. Immunofluorescent images of brain tissue from TfRmu / huKI and IDS KO; TfRmu / huKimicethat were treated with vehicle, ETVTDS or idursulfase. The brain tissue was stained for DAPI and CD68. Magnification is 20x, and the images represent hippocampus (top panel), cortex (middle panel), and striatum (bottom panel).

[0064] Figure 22. Dose-dependent reduction in brain GAGs following ETVTDS treatment. GAG levels in brain from IDS KO; TfRmu / huKI mice were measured 7 days after the last dose of ETVTDS or idursulfase and compared to vehicle treatment and TfRmu / huKI mice; n=5 per group. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; **** p < 0.0001. Values calculated include fold over TfRmu / hukΐ, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; TfRmu / huKI mice.

[0065] Figure 23. Dose-dependent reduction in CSF GAGs following ETV:IDS treatment.

[0066] GAG levels in CSF from IDS KO; TfRmu / huKI mice were measured 7 days after the last dose of ETV:IDS or idursulfase and compared to vehicle treatment and TfRmu / huKI mice; n=4-5 per group. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; **** p < 0.0001. Values calculated include fold over TfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO;TfRmu huKI mice.

[0067] Figure 24. Reduction in liver GAGs following ETV:IDS and Idursulfase treatment. GAG levels in liver from IDS KO; TfRmu / huKI mice were measured 7 days after the last dose of ETV:IDS or idursulfase and compared to vehicle treatment and TfRmu / huKI mice; n=5 per group. Graphs display mean ± SEM and are represented in log scale. Values calculated include Fold over xfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; TfRmu / lluKI mice.

[0068] Figures 25A-25C. Reduction of brain lysosomal lipid accumulation following ETV:IDS treatment. Brain levels of (Figure 25A) glucosylceramide and (Figure 25C) bis(monoacylglycerol)phosphate (BMP) and brain (top panel) and CSF (bottom panel) levels of gangliosides (Figure 25B) from IDS KO; TfRmu / huKI mice were measured 7 days after their last dose of ETV:IDS or idursulfase and compared to vehicle treatment and xfRmu / huKI mice; n=5 per group. Graphs display mean ± SEM and p values: one-way ANOVA with Dunnett multiple comparison test; * p < 0.05, ** p < 0.01, *** p < 0.001, and **** p < 0.0001. Values calculated include Fold over xfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; xfRmu / huKI mice.

[0069] Figure 26. Dose-dependent reduction in brain Trem2 levels following ETV:IDS treatment. Levels of Trem2 were assessed using an MSD-based assay in brains of IDS KO; TfRmu / huKI mice 7 days after their last dose of ETV:IDS or idursulfase and compared to vehicle treatment and xfRmu / huKI mice; n=5 per group. Graphs display mean ± SEM and p values: oneway ANOVA with Dunnett multiple comparison test; * p < 0.05, *** p < 0.001, and **** p < 0.0001. Values calculated include fold over xfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; xfRmu / huKI mice.

[0070] Figures 27A-27B. Reduction in brain and CSF GAG accumulation following ETV:IDS treatment. GAG levels were evaluated in the brain (Figure 27A) and CSF (Figure 27B) of mice treated with 1 mg / kg or 3 mg / kg ETV:IDS for 13 weekly doses and compared to vehicle treatment and TfRmu / hukΐ mice. Values calculated include fold over TfRmu / hukΐ, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; TfRmu / huKI mice (**p<0.01; ****p<o.0001; error bars = SEM).

[0071] Figures 28A-28B. Reduction in peripheral GAG accumulation following ETV:IDS treatment. GAG levels were evaluated in the liver (Figure 28A) and urine (Figure 28B) of mice treated with 1 mg / kg or 3 mg / kg ETV:IDS for 13 weekly doses and compared to vehicle treatment and TfRmu / huKI mice. Urine GAG levels were normalized to creatinine. Values calculated include fold over TfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; xfRmu / huKI mice (**** p<0.0001; error bars = SEM).

[0072] Figure 29. Reduction in brain lysosomal lipid accumulation following ETV:IDS treatment. Lysosomal lipids glucosyl ceramides (left panel), GM3 (middle panel) and BMP (right panel) were evaluated in the brains of mice treated with 1 mg / kg or 3 mg / kg ETV:IDS for 13 weekly doses and compared to vehicle treatment and xfRmu / huKI mice. Values calculated include fold over xfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; XfRmu / huKI mice (****p<0.0001; error bars = SEM).

[0073] Figure 30. Reduction in CSF lysosomal lipid accumulation following ETV:IDS treatment. Lysosomal lipids glucosyl ceramides (left panel), GM3 (middle panel) and BMP (right panel) were evaluated in the CSF of mice treated with 1 mg / kg or 3 mg / kg ETV:IDS for 13 weekly doses and compared to vehicle treatment and xfRmu / humice. Values calculated include fold over XfRmu / hu, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; XfRmu / humice (*p<0.05; ***p<0.001; ****p<0.0001; error bars = SEM).

[0074] Figures 31A-31C. Scatter plots of Nf-L concentrations in wild-type and IDS knockout mice at 3, 6, and 9 months of age. Nf-L levels in serum and CSF of 9-month old mice are illustrated in Figures 31A and 3 IB, respectively. Nf-L levels in CSF of mice cohorts at different ages are illustrated in Figure 31C. Data are displayed as mean + / - SEM with p values obtained by unpaired t test analysis.

[0075] Figure 32. Reduction in CSF Neurofilament Light Chain (Nf-L) following administration of ETV:IDS. Levels of Neurofilament Light chain (Nf-L) were evaluated in the CSF of mice treated with 1 mg / kg or 3 mg / kg ETV:IDS for 13 weekly doses and compared to vehicle treatment and xfRmu / huKI mice. Values calculated include Fold over xfRmu / huKI, percent treatment efficiency, and percent reduction from vehicle treated IDS KO; xfRmu / huKI mice. One outlier was removed from TfRmu / huvehicle treated and 3 mg / kg ETV:IDS treated groups as determined by Grubbs test or ROUT method (*p< .05; ***p<0.001; error bars = SEM).

[0076] Figure 33. ETVTDS reduces peripheral and CNS GAGs. GAG levels were evaluated in the liver, brain and CSF of Ids KO;TfRmu / humice and compared to vehicle treatment and non- diseased TfRmu / humice. Graphs display mean ± SEM: one-way ANOVA with Tukey’s multiple comparison test; * p < 0.05, ** p < 0.01, *** p < 0.001, and **** p < 0.0001.

[0077] Figure 34. ETVTDS reduces serum and CSF Nf-L levels. Nf-L levels were evaluated in the serum (left panel) and CSF (right panel) of Ids KO;TfRmu / humice and compared to vehicle treatment and non-diseased TfRmu / humice. Graphs display mean ± SEM: one-way ANOVA with Tukey’s multiple comparison test; * p < 0.05, ** p < 0.01, *** p < 0.001, and **** p < 0.0001.

[0078] Figure 35. ETVTDS improves certain neurobehavioral deficits in Ids KO;TfRmu / humice. Proportion of mice that successfully completed the running trials on the accelerated treadmill (Fisher exact or Chi-square test). Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p< .001, *** p<0.0005, and **** p< .OOOl.

[0079] Figure 36. ETVTDS improves certain neurobehavioral deficits in Ids KO;TfRmu / humice. Latency to descend the pole averaged across 3 trials (linear mixed-effects model). Graph displays mean ± SEM. Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p<0.001, *** p<0.0005, and **** p< .OOOl.

[0080] Figure 37. ETVTDS improves certain neurobehavioral deficits in Ids KO;TfRmu / humice. Levels of startle inhibition were calculated in the pre-pulse inhibition assay (linear model). Graph displays mean ± SEM. Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p<0.001, *** p<0.0005, and **** p< .OOOl.

[0081] Figure 38. ETVTDS normalizes certain neurobehavioral deficits in Ids KO;TfRmu / humice. In the active place avoidance assay, mice are trained to avoid an unmarked aversive zone (orange) where a mild foot shock was presented upon entrance in the zone. The number of entrances in the aversive zone was measured during each phase of testing (Linear mixed-effects model to assess treatment effect in Ids KO;TfRmu / humice). Graph displays mean ± SEM. Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p< .001, *** p<0.0005, and **** p< .OOOl. Figure 39. ETV:IDS normalizes certain neurobehavioral deficits in Ids KO;TfRmu / humice. Number of entrances in the aversive zone from the third trial and the reinstatement trial (Wilcoxon sum rank test). Graphs display mean ± SEM except. Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p<0.001, *** p<0.0005, and **** p< .0001

[0082] Figure 40. ETV:IDS normalizes certain neurobehavioral deficits in Ids KO;TfRmu / humice. Classification of performance based on number of entrances in the aversive zone during the reinstatement trial; poor (>1), good (1), top (0). Fisher’s exact test. Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p< .001, *** p<0.0005, and **** p<0.0001.

[0083] Figure 41. The three mice treatment cohorts were observed to have similar pain response in the hot plate assay and proper avoidance of the aversive location in the visual cliff assay. The hind paw withdrawal was measured in the hot plate test to assess supraspinal nociception (Wilcoxon rank sum test, ns) (left panel). Visual function of the mice was assessed by evaluating their preference toward the shallow over the deep zones in the visual cliff test (Chi-square test, ns) (right panel). Graphs display mean ± SEM. Comparison of vehicle treated TfRmu / humice and Ids KO;TfRmu / humice, or as indicated by brackets; * p<0.05, ** p< .001, *** p<0.0005, and **** p< .0001

[0084] Figure 42. ETVTDS improves auricular abnormalities of Ids KO;TfRmu / humice. Representative H&E photomicrographs of the ear canal from vehicle-treated TfRmu / hu, vehicle- treated Ids KO;TfRmu / humice, and ETVTDS-treated Ids KO;TfRmu / humice. The tympanic bulla (TB) in the examined Ids KO;TfRmu / humice had effusion and / or chronic otitis media as evidenced by the presence of cellular debris and exudate (black arrowhead) and expansion of the tympanic membrane (TM) by inflammatory cell infiltrates (higher magnification in panel a). Higher magnification of the lining of the TB (panel b) showed the submucosa (SM) of the TB epithelium (EP) was expanded by edema or dense connective tissue (fibrosis); EAM = external auditory canal; BM = bone marrow cells. Fibrous polyps were also evident (yellow arrowheads).

[0085] Figure 43. ETVTDS improves the facial morphology of Ids KO;TfRmu / humice. Qualitative assessment of the severity of an animal’s shortened, broadened snout (arrowhead). Representative images of each facial score is shown on the left panel. Graphs display the number of mice within each category: Fisher’s exact test; **** p < 0.0001. Figure 44. ETV:IDS improves skeletal abnormalities in Ids KO;TfRmu / humice. Representative image of the femur defining the regions of interest for analysis of cortical and trabecular bone; representative cross sectional images from vehicle-treated TfRmu / hu( / / = 5), vehicle-treated Ids KO;TfRmu / humice (n = 5), and ETV:IDS-treated Ids KO;TfRmu / humice (n = 5)·

[0086] Figure 45. ETV:IDS improves skeletal abnormalities in Ids KO;TfRmu / humice. Quantitative analysis from the micro-CT scans of the femur trabecular. Graphs display mean ± SEM: one-way ANOVA with Tukey’s multiple comparison test; * p ≤ 0.05, *** p ≤ 0.001, and

[0087] **** p ≤ 0.0001.

[0088] Figure 46. ETV:IDS improves skeletal abnormalities in Ids KO;TfRmu / humice. (Quantitative analysis from the micro-CT scans of the femur cortical bone. Graphs display mean ± SEM: one-way ANOVA with Tukey’s multiple comparison test; * p ≤ 0.05, *** p ≤ 0.001, and **** p ≤ 0.0001.

[0089] Figure 47. Scheme showing assessments for a nonrandomized, multicenter, prospective, observational study of patients diagnosed with MPS II.

[0090] Figure 48. Scheme showing dosing escalation and assessments for a Phase 1 / 2 study of patients diagnosed with MPS II. To Be Determined1(TBD1): Subjects within sub-cohorts B1 and B2 may undergo dose escalation based on Cohort A and Cohort B safety and biomarker results; however, dosing will not exceed 30 mg / kg. TBD2: Dosing for Cohort C will be determined based on Cohort A and Cohort B safety and biomarker results.

[0091] Figure 49. ETV:IDS statistically reduces CSF GAG (heparan sulfate, dermatan sulfate) levels in MPS II patients after four weekly doses. P-values were determined by T-test comparison of mean percent change from baseline.

[0092] Figures 50A-50B. Heparan sulfate (Fig. 50A) and dermatan sulfate (Fig. 50B) levels in CSF from MPS II patients after 12 weekly doses of ETVTDS. Normal range (black circle) determined using 30 adult CSF samples (range 10-90 percentile); adult and child CSF GAG levels are similar (Hendriksz et al., Mol. Genet. Metab. Rep., 5:103-106 (2015)). P-values were determined by T-test comparison of mean percent change from baseline.

[0093] Figures 51A-51B. Heparan sulfate (Fig. 51 A) and dermatan sulfate (Fig. 5 IB) levels in urine from MPS II patients after 8 weekly doses of ETVTDS. P-values were determined by T- test comparison of mean percent change from baseline. Figures 52A-52B. GM3 (Fig. 52A) and BMP (Fig. 52B) levels in CSF from MPS II patients after 8 weekly doses of ETV:IDS. Individual patient data is shown on the left and Group Mean % change from baseline (D BL) is shown on the right. P-values were determined by T-test comparison of mean percent change from baseline.

[0094] DETAILED DESCRIPTION

[0095] Hunter syndrome, specifically the neurocognitive phenotype, remains a significant unmet medical need. Described herein is the evaluation of a specific enzyme replacement therapy termed ETVTDS, which has the capability of crossing the BBB and treating both the peripheral and CNS manifestations of Hunter syndrome, including neurobehavioral deficits, auditory deficits and musculoskeletal abnormalities. Exemplary ETVTDS proteins are described herein, and disease activity and therapeutic response to ETVTDS may be evaluated using a series of assessments (e.g., one or more assessments), including biomarker, safety, neurocognitive, clinical, functional, and quality of life assessments. For example, exploration of CSF, serum, and urine biomarkers described herein, including glycosaminoglycan (GAG) species, indicators of CNS lysosomal lipid accumulation (sphingolipids, gangliosides, and bis(monoacylglycerol)phosphate (BMP) species), microglial activation and neuroinflammation (sTREM2; cytokines), and neuroaxonal neurofilament light chain (Nf-L) may be used to identify and evaluate safe and therapeutically effective doses of ETVTDS. In some embodiments, changes in the CSF, serum, and urine biomarkers described herein can occur after switching to treatment with ETV:IDS from an intravenous idursulfase treatment (e.g. Elaprase).

[0096] Also described herein is an exploration of therapeutically effective doses of ETVTDS, or a pharmaceutical composition including the same, which significantly reduce CSF GAG levels in patients with Hunter syndrome. In some embodiments, the administered doses of ETVTDS result in normalization of CSF GAG levels. Furthermore, as described herein, the administered doses can have a beneficial impact on CSF lysosomal lipid levels, as well as urine GAG levels in the patients.

[0097] Biomarkers Assessments

[0098] Disease activity and therapeutic response to ETVTDS may be evaluated using a series of biomarkers described herein. In particular, these biomarkers include the accumulation of glycosaminoglycans (GAGs) and specific lipids (i.e., sphingolipids, gangliosides, and BMPs) in a subject having Hunter syndrome, as well as the accumulation of Nf-L and TREM2, which may be measured based on sTREM2 levels. Additionally, increased concentrations of cytokines may also be used as a biomarker for neuroinflammation. Thus, the concentration of one or more of these molecules / lipids / proteins may be evaluated and compared relative to a baseline level or control (e.g., a baseline pre-treatment level as described herein). In certain embodiments, the assessment is performed, e.g., 6 months, 12 months and / or 18 months after treatment initiation.

[0099] In certain embodiments, administration of a pharmaceutical composition comprising ETVTDS reduces levels of one or more analytes in a sample from the subject as compared to a control, wherein the one or more analytes are selected from the group consisting of a GAG, Nf- L, sTREM2, a cytokine, a BMP, a ganglioside and a sphingolipid. In certain embodiments, administration of a pharmaceutical composition comprising ETVTDS reduces levels of one or more analytes in a sample from the subject by at least about 10%, 15%, 20%, 25%, or 30% as compared to a control, wherein the one or more analytes are selected from the group consisting of a GAG, Nf-L, sTREM2, a cytokine, a BMP, a ganglioside and a sphingolipid. In certain embodiments, the control is a Hunter syndrome patient that was not administered the pharmaceutical composition. In certain embodiments, the control is the subject prior to treatment.

[0100] In certain embodiments, administration of the pharmaceutical composition reduces levels of one or more analytes in a sample from the subject to baseline levels, wherein the one or more analytes are selected from the group consisting of a GAG, Nf-L, sTREM2, a cytokine, a BMP, a ganglioside and a sphingolipid. In certain embodiments, the baseline levels are measured in a sample from a healthy individual. In certain embodiments, the baseline levels are measured in a sample from a subject that does not have Hunter syndrome.

[0101] As used herein, the phrase “sample” or “physiological sample” is meant to refer to a biological sample obtained from a subject that contains an analyte of interest, such as a polysaccharide, protein and / or lipid. Thus, the sample may be evaluated at, e.g., the molecular, lipid or protein level. In certain embodiments, the physiological sample comprises tissue, cerebrospinal fluid (CSF), urine, blood, serum, or plasma. In certain embodiments, the sample comprises tissue, such as brain, liver, kidney, lung or spleen. The sample may include a fluid.

[0102] In certain embodiments, the sample comprises CSF. In certain embodiments, the sample comprises blood and / or plasma. In certain embodiments, the sample comprises serum. In certain embodiments, the sample comprises CNS tissue (e.g., brain tissue). In certain embodiments, administration of the pharmaceutical composition reduces levels of one or more analytes in an organ, tissue or fluid (e.g., blood, plasma, serum, CSF or urine) of the subject, as compared to a control, wherein the one or more analytes are selected from the group consisting of a GAG, Nf-L, sTREM2, a cytokine, a BMP, a ganglioside and a sphingolipid. In certain embodiments, administration of the pharmaceutical composition reduces levels of one or more analytes in an organ, tissue or fluid (e.g., blood, plasma, serum, CSF or urine) of the subject by at least about 10%, 15%, 20%, 25%, or 30%, as compared to a control, wherein the one or more analytes are selected from the group consisting of a GAG, Nf-L, sTREM2, a cytokine, a BMP, a ganglioside and a sphingolipid. In certain embodiments, the control is a Hunter syndrome patient that was not administered the pharmaceutical composition. In certain embodiments, the control is the subject prior to treatment. For example, in certain embodiments, administration of the pharmaceutical composition reduces levels of one or more analytes in the CSF of the subject by at least about 10%, 15%, 20%, 25%, or 30%, wherein the reduction is relative to the level of the corresponding one or more analytes in the subject prior to the administration, wherein the one or more analytes are selected from the group consisting of a GAG, Nf-L, sTREM2, a cytokine, a BMP, a ganglioside and a sphingolipid.

[0103] In certain embodiments, administration of the pharmaceutical composition reduces levels of one or more analytes in an organ, tissue or fluid (e.g., CSF, blood, plasma, serum or urine) of the subject to baseline levels, wherein the one or more analytes are selected from the group consisting of a GAG, Nf-L, sTREM2, a cytokine, a BMP, a ganglioside, and a sphingolipid. In certain embodiments, the baseline levels are measured in a healthy individual. In certain embodiments, the baseline levels are measured in a subject that does not have Hunter syndrome.

[0104] Glycosaminoglycans (GAGs)

[0105] Insufficient or absent IDS enzyme activity leads to the accumulation of the glycosaminoglycans (GAGs) heparan sulfate (HS; D0A0 and D0S0) and dermatan sulfate (DS; D0a4) in the CNS and periphery, as well as lysosome dysfunction in multiple organs and tissues. Accordingly, the concentration of total GAGs or the concentration of one or more GAG species may be evaluated in a subject having Hunter syndrome (e.g., in a post-treatment sample from a subject administered ETV:IDS). Quantification of GAG concentration levels may be performed using methods known in the art, for example, using a liquid chromatography mass spectrometry (LCMS) assay (see, e.g., the Examples). In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a GAG in an organ, tissue or fluid of the subject are reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in an organ, tissue or fluid of the subject, to baseline levels ( e.g . levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0106] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the CNS of the subject, as compared to a control. In certain embodiments, levels of a GAG in the CNS of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the CNS of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0107] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the CSF of the subject, as compared to a control. In certain embodiments, levels of a GAG in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a GAG in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a GAG in the CSF of the subject is relative to the CSF levels of the GAG in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 4 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels of heparan sulfate in the CSF of the subject by at least 80% after at least 4 weekly doses, wherein the reduction is relative to the CSF heparan sulfate levels in the subject prior to administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 4 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 8 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the CSF of the subject by at least about 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 12 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels heparan sulfate in the CSF of the subject by at least 70% after at least 12 weekly doses, wherein the reduction is relative to the CSF heparan sulfate levels in the subject prior to administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the GAG in the CSF of the subject by at least about 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 12 weekly doses. In certain embodiments, the administration of the pharmaceutical composition normalizes levels of a GAG in the CSF of the subject, i.e. reduces levels of a GAG in the CSF of the subject to baseline levels measured in a healthy subject or a subject that does not have Hunter syndrome. In certain embodiments, the reduction or normalization of a GAG in the CSF of the subject occurs after switching the subject’s administered therapy from intravenous idursulfase ( e.g . Elaprase) to the pharmaceutical composition comprising ETV:IDS.

[0108] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the serum of the subject, as compared to a control. In certain embodiments, levels of a GAG in the serum of the subject are reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the reduction of a GAG in the serum of the subject is relative to the serum levels of the GAG in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the serum of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0109] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject, as compared to a control. In certain embodiments, levels of a GAG in the urine of the subject are reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a GAG in the urine of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a GAG in the urine of the subject is relative to the urine levels of the GAG in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject by at least about 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 4 weekly doses, wherein the reduction is relative to the urine levels of the GAG in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the GAG in the urine of the subject by at least about 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 4 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject by at least about 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the urine levels of the GAG in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the GAG in the urine of the subject by at least about 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 8 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject to baseline levels measured in a healthy subject or a subject that does not have Hunter syndrome. In certain embodiments, the reduction of a GAG in the urine of the subject occurs after switching the subject’s administered therapy from intravenous idursulfase ( e.g . Elaprase) to the pharmaceutical composition comprising ETV:IDS.

[0110] In certain embodiments, total GAG levels are reduced. In certain embodiments, heparan sulfate levels are reduced (e.g., D0A0 and / or D0S0 levels are reduced). In certain embodiments, dermatan sulfate levels are reduced (e.g., D0a4 levels are reduced).

[0111] Neurofilament light (Nf-L)

[0112] As used herein, the term “Nf-L” refers to neurofilament light chain (also referred to as neurofilament light chain polypeptide, neurofilament light polypeptide, and neurofilament light protein) that is encoded by the gene NEFL. As used herein, an “Nf-L protein” refers to a native ( / .£., wild-type) Nf-L protein. In some embodiments, an Nf-L protein is a human Nf-L protein having the sequence identified in UniprotKB accession number P07196.

[0113] As described herein, increased levels of Nf-L are indicative of downstream pathology in subjects having Hunter syndrome. Accordingly, the concentration of Nf-L may be evaluated in a subject having Hunter syndrome (e.g., in a post-treatment sample from a subject administered ETV:IDS). Nf-L levels can be measured using an assay known in the art or described herein. For example, assays for detecting and measuring levels of protein expression include, e.g., western blot analysis, immunofluorescence, immunohistochemistry (e.g, of tissue arrays), MesoScale Discovery (MSD) method, etc.

[0114] In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of Nf-L in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0115] In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in the CNS of the subject, as compared to a control. In certain embodiments, levels of Nf-L in the CNS of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in the CNS of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0116] In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in the CSF of the subject, as compared to a control. In certain embodiments, levels of Nf-L in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of Nf-L in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of Nf-L in the CSF of the subject is relative to the CSF Nf-L level in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome). In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in the serum of the subject, as compared to a control. In certain embodiments, levels of Nf-L in the serum of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of Nf-L in the serum of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of Nf-L in the serum of the subject is relative to the serum Nf-L level in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of Nf-L in the serum of the subject to baseline levels ( e.g . levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0117] TREM2

[0118] As used herein, the term “TREM2 protein” refers to a triggering receptor expressed on myeloid cells 2 protein that is encoded by the gene Trem2. As used herein, a “TREM2 protein” refers to a native (i.e., wild-type) TREM2 protein. In some embodiments, a TREM2 protein is a human TREM2 protein having the sequence identified in UniprotKB accession number Q9NZC2.

[0119] The TREM2 gene encodes a 230 amino acid-length protein that includes an extracellular domain, a transmembrane region and a short cytoplasmic tail (see, UniProtKB Q9NZC2; NCB1 Reference Sequence: NP 061838.1). The extracellular region, encoded by exon 2, is composed of a single type V Ig-SF domain, containing three potential N-glycosylation sites. The putative transmembrane region contains a charged lysine residue. The cytoplasmic tail of TREM2 lacks signaling motifs and is thought to signal through the signaling adaptor molecule DAP12 / TYROBP and through DAPIO. TREM2 is found on the surface of osteoclasts, immature dendritic cells, and macrophages. In the central nervous system, TREM2 is exclusively expressed in microglia.

[0120] TREM2 may be cleaved by a disintegrin and metalloproteinase (ADAM) proteases (e.g., ADAM 10 and ADAM 17), which results in the release of soluble TREM2 (sTREM2) into the extracellular environment. As described herein, increased levels of TREM2 are indicative of downstream pathology (e.g., microglial activation and neuroinflammation) in subjects having Hunter syndrome. Accordingly, the concentration of TREM2 / sTREM2 may be evaluated in a subject having Hunter syndrome (e.g., in a post-treatment sample from a subject administered ETV:IDS). TREM2 or sTREM2 levels can be measured using an assay known in the art or described herein. For example, assays for detecting and measuring levels of protein expression include, e.g., western blot analysis, immunofluorescence, immunohistochemistry (e.g, of tissue arrays), MesoScale Discovery (MSD) method, etc.

[0121] In certain embodiments, the administration of the pharmaceutical composition reduces levels of TREM2 or sTREM2 in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of TREM2 or sTREM2 in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of TREM2 or sTREM2 in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0122] In certain embodiments, the administration of the pharmaceutical composition reduces levels of TREM2 or sTREM2 in the CSF of the subject, as compared to a control. In certain embodiments, levels of TREM2 or sTREM2 in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the reduction of TREM2 or sTREM2 in the CSF of the subject is relative to the CSF TREM2 or sTREM2 level in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of TREM2 or sTREM2 in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0123] Lysosomal Lipids

[0124] As described herein, increased levels of BMPs, sphingolipids (e.g., GlcCer) and gangliosides (e.g., GD3, GDla / b, GM2 and GM3) are indicative of downstream pathology in subjects having Hunter syndrome. Accordingly, the concentration of one or more of these lysosomal lipids may be evaluated in a subject having Hunter syndrome (e.g., in a post-treatment sample from a subject administered ETV:IDS). The concentration of these lipids may be measured using an assay known in the art or described herein (e.g, by mass spectrometry).

[0125] In certain embodiments, the administration of the pharmaceutical composition reduces levels of one or more of a BMP, a sphingolipid or a ganglioside in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of one or more of a BMP, a sphingolipid or a ganglioside in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of one or more of a BMP, a sphingolipid or a ganglioside in an organ, tissue or fluid of the subject, to baseline levels ( e.g . levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0126] BMPs

[0127] Bis(monoacylglycero)phosphates (BMPs) refer to a class of an anionic phospholipids. BMPs are enriched in internal membranes of multivesicular endosomes and lysosomes and are thought to play a role in glycosphingolipid degradation and cholesterol transport (see, Kobayashi et al., Nat. Cell Biol. 1 (1999) 113-118). Particular BMP species are described herein, and include but are not limited to, BMP (44:12), BMP (36:2), BMP (di20:4), BMP (di22:6) and BMP (dil8:l) (see also , e.g., the Examples and Figures).

[0128] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a BMP in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a BMP in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a BMP in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0129] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a BMP in the CSF of the subject, as compared to a control. In certain embodiments, levels of a BMP in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a BMP in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a BMP in the CSF of the subject is relative to the CSF levels of the BMP in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels of a BMP in the CSF of the subject by at least about 10%, 15%,

[0130] 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the BMP in the subject prior to administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the BMP in the CSF of the subject by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a BMP in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome). In certain embodiments, the reduction of a BMP in the CSF of the subject occurs after switching the subject’s administered therapy from intravenous idursulfase (e.g. Elaprase) to the pharmaceutical composition comprising ETV:IDS. In certain embodiments, the BMP is a BMP di 18:1 species.

[0131] Sphingolipids

[0132] As described herein, increased levels of certain sphingolipids, such as glucosylceramide (GlcCer), are indicative of downstream pathology in subjects having Hunter syndrome. GlcCer is a glycosphingolipid (ceramide and oligosaccharide) or oligoglyeosylceramide with one or more sialic acids linked on the sugar chain. Particular GlcCer species, include but are not limited to, GlcCer (d34:0), GlcCer (d34:l), GlcCer (d36:l), GlcCer (d42:l), GlcCer (dl8:l, 16:0), GlcCer (dl8:l, 18:0), GlcCer (dl8:2, 18:0), GlcCer (dl8:l, 20:0), GlcCer (dl8:2, 20:0), GlcCer (dl8:l, 22:0), GlcCer (dl 8:1, 22:1), GlcCer (dl8:2, 22:0), GlcCer (dl8:l, 24:1) or GlcCer (dl8:l, 24:0) (see also , e.g. , the Examples and Figures).

[0133] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a sphingolipid (e.g., a GlcCer) in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a sphingolipid (e.g., a GlcCer) in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a sphingolipid (e.g., a GlcCer) in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0134] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a sphingolipid (e.g., a GlcCer) in the CSF of the subject, as compared to a control. In certain embodiments, levels of a sphingolipid (e.g., a GlcCer) in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a sphingolipid (e.g., a GlcCer) in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a sphingolipid ( e.g . a GlcCer) in the CSF of the subject is relative to the CSF sphingolipid level in the subject prior to the administration.

[0135] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a sphingolipid (e.g., a GlcCer) in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0136] Gangliosides

[0137] Gangliosides are a type of glycosphingolipid. As described herein, increased levels of certain gangliosides, such as (GD3, GDla / b, GM2 and GM3), are indicative of downstream pathology in subjects having Hunter syndrome.

[0138] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a ganglioside (e.g., a GD3, GDla / b, GM2 or GM3 species) in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a ganglioside in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a ganglioside in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0139] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a ganglioside (e.g., a GD3, GDla / b, GM2 or GM3 species) in the CSF of the subject, as compared to a control. In certain embodiments, levels of a ganglioside in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a ganglioside (e.g., a GD3, GDla / b, GM2 or GM3 species) in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a ganglioside in the CSF of the subject is relative to the CSF levels of the ganglioside in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels of a ganglioside in the CSF of the subject by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the ganglioside in the subject prior to administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the ganglioside in the CSF of the subject by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a ganglioside in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome). In certain embodiments, the reduction of a ganglioside in the CSF of the subject occurs after switching the subject’s administered therapy from intravenous idursulfase (e.g. Elaprase) to the pharmaceutical composition comprising ETV:IDS.

[0140] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GD3 species. Particular GD3 species, include but are not limited to, e.g., GD3 (d34:l), GD3 (d36:l), GD3 (d38:l), GD3 (d39:l), GD3 (d40:l), GD3 (d42:2) or GD3 (d42:l). (see also , e.g. , the Examples and Figures).

[0141] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GD3 species in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a GD3 species in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GD3 species in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0142] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GD3 species in the CSF of the subject, as compared to a control. In certain embodiments, levels of a GD3 species in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a GD3 species in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a GD3 in the CSF of the subject is relative to the CSF levels of the GD3 in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GD3 species in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0143] Gang!ioskles GDla and GDlb are glycosphingolipids. Particular GDla / b species are described herein, such as GDla / b (d36:l) and GDla / b (d38:l) (see also , e.g. , the Examples and Figures).

[0144] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GDla / b species in an organ, tissue or fluid of the subject, as compared to a control.

[0145] In certain embodiments, levels of a GDla / b species in an organ, tissue or fluid of the subject is reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GDla / b species in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0146] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GDla / b species in the CSF of the subject, as compared to a control. In certain embodiments, levels of a GDla / b species in the CSF of the subject is reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a GDla / b species in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a GDla / b in the CSF of the subject is relative to the CSF levels of the GDla / b in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GDla / b species in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0147] Ganglioside Monosialic 2 (GM2) is a glycosphingolipid. Particular GM2 species are described herein, such as GM2 (d38:l) or GM2 (d36:l) (see also , e.g. , the Examples and Figures).

[0148] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM2 species in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a GM2 species in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM2 species in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0149] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM2 species in the CSF of the subject, as compared to a control. In certain embodiments, levels of a GM2 species in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a GM2 species in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a GM2 in the CSF of the subject is relative to the CSF levels of the GM2 in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM2 species in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0150] Similar to GM2, Ganglioside Monosialic 3 (GM3) is also a class of glycospbingolipids. Particular GM3 species, include but are not limited to, (d34:l), GM3 (d36:l), GM3 (d38:l),

[0151] GM3 (d40:l), GM3 (d41:l), GM3 (d42:2), GM3 (d42:l), GM3 (d43:0), GM3 (d44:l) or GM3 (d44:2) (see also , e.g. , the Examples and Figures).

[0152] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM3 species in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a GM3 species in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM3 species in an organ, tissue or fluid of the subject, to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0153] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM3 species in the CSF of the subject, as compared to a control. In certain embodiments, levels of a GM3 species in the CSF of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, levels of a GM3 species in the CSF of the subject is reduced by at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control, after at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20 or more weekly doses. In certain embodiments, the reduction of a GM3 in the CSF of the subject is relative to the CSF levels of the GM3 in the subject prior to the administration. For example, in certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM3 species in the CSF of the subject by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the GM3 species in the subject prior to administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of the GM3 species in the CSF of the subject by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a GM3 species in the CSF of the subject to baseline levels ( e.g . levels measured in a healthy subject or a subject that does not have Hunter syndrome). In certain embodiments, the reduction of a GM3 species in the CSF of the subject occurs after switching the subject’s administered therapy from intravenous idursulfase (e.g. Elaprase) to the pharmaceutical composition comprising ETV:IDS.

[0154] Cytokines

[0155] As described herein, increased levels of certain cytokines are indicative of neuroinflammation. Accordingly, the concentration of one or more of these cytokines may be evaluated in a subject having Hunter syndrome (e.g., in a post-treatment sample from a subject administered ETV:IDS). For example, cytokines such as interleukin (IL) 1-b, tumor necrosis factor alpha (TNF-a), monocyte chemoattractant protein 1 (MCP-1), stromal cell-derived factor 1 alpha (SDF-Ia), IL-Ra, macrophage inflammatory protein 1 beta (MIP-Ib), IL-8, and vascular endothelial growth factor (VEGF) may be evaluated. The concentration of these cytokines may be measured using an assay known in the art or described herein.

[0156] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in an organ, tissue or fluid of the subject, as compared to a control. In certain embodiments, levels of a cytokine in an organ, tissue or fluid of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in an organ, tissue or fluid of the subject, to baseline levels ( e.g . levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0157] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in the CSF of the subject, as compared to a control. In certain embodiments, levels of a cytokine in the CSF of the subject are reduced by at least about 10%, 15%, 20%,

[0158] 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the reduction of a cytokine in the CSF of the subject is relative to the CSF levels of the cytokine in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in the CSF of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0159] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in the serum of the subject, as compared to a control. In certain embodiments, levels of a cytokine in the serum of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the reduction of a cytokine in the serum of the subject is relative to the serum levels of the cytokine in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in the serum of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome).

[0160] In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in the urine of the subject, as compared to a control. In certain embodiments, levels of a cytokine in the urine of the subject are reduced by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, as compared to a control. In certain embodiments, the reduction of a cytokine in the urine of the subject is relative to the urine levels of the cytokine in the subject prior to the administration. In certain embodiments, the administration of the pharmaceutical composition reduces levels of a cytokine in the urine of the subject to baseline levels (e.g. levels measured in a healthy subject or a subject that does not have Hunter syndrome). Certain Manifestations of Disease

[0161] In addition to the correction of certain biomarkers, a therapeutically effective dose of a pharmaceutical composition described herein may also be used for the treatment of particular manifestations of Hunter syndrome, including neurobehavioral deficits, auditory deficits and / or musculoskeletal abnormalities associated with the disease (see, e.g., Example 9).

[0162] Accordingly, certain embodiments of the invention provide a method of treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal abnormality in a subject with Hunter syndrome, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising a protein, wherein the protein comprises: (a) a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and (b) a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0163] Changes in, or stabilization of, a manifestation of Hunter syndrome (e.g., a neurobehavioral deficit, an auditory deficit, and / or a musculoskeletal abnormality) may also be used to evaluate disease activity and therapeutic response to ETVTDS. For example, one or more assessments, such as one or more assessments described herein, may be used to evaluate a parameter(s) associated with a given manifestation. In certain embodiments, the parameter is measured relative to a baseline level. In certain embodiments, the baseline level of a parameter is the parameter level for the subject prior to administration of the pharmaceutical composition.

[0164] Neurobehavioral Deficits

[0165] Approximately two-thirds of Hunter syndrome patients display the neuronopathic form of the disease, which in addition to earlier presentation of the somatic disease, is characterized by progressive, debilitating neurobehavioral deficits, which include but are not limited to, motor skill deficits, cognitive deficits (e.g., learning and memory deficits) and sensorimotor gating deficits (e.g., attention and inhibitory function deficits).

[0166] In certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETVTDS may be used to treat a neurobehavioral deficit in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s neurobehavioral capabilities relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s neurobehavioral capabilities, relative to a baseline level (e.g., as measured by an assessment described herein).

[0167] In certain embodiments, the neurobehavioral deficit is a motor skill deficit, such as a gross and / or fine motor skill deficit. Thus, in certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETVTDS may be used to treat a gross and / or fine motor deficit in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s gross and / or fine motor capabilities relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s gross and / or fine motor capabilities, relative to a baseline level (e.g., as measured by an assessment described herein).

[0168] In certain embodiments, the neurobehavioral deficit is an agility deficit. Thus, in certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETVTDS may be used to treat an agility deficit in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s agility capabilities relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s agility capabilities, relative to a baseline level (e.g., as measured by an assessment described herein).

[0169] In certain embodiments, the neurobehavioral deficit is a cognitive deficit, such as a learning deficit (e.g., spatial learning deficit) or a memory deficit. Thus, in certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETVTDS may be used to treat a cognitive deficit in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s cognitive capabilities relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s cognitive capabilities, relative to a baseline level (e.g., as measured by an assessment described herein).

[0170] In certain embodiments, the neurobehavioral deficit is a sensorimotor gating deficit, which is associated with both attention and inhibitory function in a subject. Thus, in certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETV:IDS may be used to treat a sensorimotor gating deficit in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s sensorimotor gating capabilities relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s sensorimotor gating capabilities, relative to a baseline level (e.g., as measured by an assessment described herein).

[0171] Auditory Deficits

[0172] Progressive conductive and sensorineural hearing loss, resulting from GAG accumulation in the middle ear and recurrent otitis, are common in Hunter syndrome patients.

[0173] In certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETV:IDS may be used to treat an auditory deficit, such as conductive or sensorineural hearing loss, in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s auditory capabilities relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s auditory capabilities, relative to a baseline level (e.g., as measured by an assessment described herein).

[0174] In certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETV:IDS may be used to reduce middle ear effusion and / or otitis media in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the amount of middle ear effusion and / or otitis media in a subject relative to a baseline level, e.g., as measured by an assessment described herein.

[0175] In certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETV:IDS may be used to treat an auricular abnormality in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes the subject’s auricular features relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s auricular features, relative to a baseline level (e.g., as measured by an assessment described herein). Musculoskeletal Abnormalities

[0176] A series of musculoskeletal abnormalities are commonly found in Hunter syndrome patients, including disproportional short stature, joint stiffness / contractures, thoracolumbar kyphosis, hip dysplasia, and dysostosis multiplex.

[0177] In certain embodiments, a therapeutically effective dose of a pharmaceutical composition comprising ETV:IDS may be used to treat a musculoskeletal abnormality (e.g., a skeletal abnormality) in a subject having Hunter syndrome. In certain embodiments, the administration of the pharmaceutical composition changes a musculoskeletal feature(s) in the subject relative to a baseline level, e.g., as measured by an assessment described herein. In certain embodiments, the administration of the pharmaceutical composition prevents further deterioration of the subject’s musculoskeletal abnormality, relative to a baseline level (e.g., as measured by an assessment described herein).

[0178] Neurocognitive Assessments

[0179] Disease activity and therapeutic response to ETV:IDS may be evaluated using one or more neurocognitive assessments, such as the Vineland Adaptive Behavior Scales, Second Edition (Vineland-II), the Bayley Scales of Infant and Toddler Development, Third Edition (BSID-III), and the Kaufman Assessment Battery for Children, Second Edition (KABC-II).

[0180] In certain embodiments, changes in a neurocognitive assessment are relative to a baseline (e.g., from a subject who has not undergone treatment; from a subject prior to treatment; or from an age-matched control subject that does not have Hunter syndrome). In certain embodiments, the baseline is from the subject prior to treatment and the assessment is performed, e.g., at 2 months, 6 months, 12 months and / or 18 months after treatment initiation.

[0181] The Vineland-II is a standardized assessment tool used to aid in diagnosing and classifying an individual’s intellectual and developmental disabilities and other disorders (Sparrow et al., Vineland adaptive behavior scales: interview edition, survey form manual.

[0182] Circle Pines, MN: American Guidance Service; 1984; Sparrow et al., Vineland adaptive behavior scales: second edition (Vineland II), survey interview form / caregiver rating form. Livonia, MN: Pearson Assessments; 2005). The content and scales of Vineland-II are organized within a 3-domain structure: Communication, Daily Living, and Socialization. In addition, Vineland-II offers a Motor Skills domain. Within this assessment, the caregiver-reported scale may be used to measure behaviors in the domains associated with typical development, such as communication and daily living, socialization, and motor skills.

[0183] In certain embodiments, the administration of the pharmaceutical composition changes the subject’s intellectual and / or developmental disabilities / disorders relative to a baseline level, as measured by Vineland-II. In certain embodiments, the administration of the pharmaceutical composition prevents the subject’s intellectual and / or developmental disabilities / disorders, as measured by Vineland-II, from deteriorating relative to a baseline level.

[0184] The BSID-III is a standard series of measurements used to assess the development of infants and toddlers aged 1 to 42 months (Bayley, Bayley scales of infant and toddler development: administration manual. San Antonio, TX: Harcourt Assessment; 2006). Measurements may include 3 main subtests: the Cognitive Scale, the Language Scale, and the Motor Scale. Raw age-normed and age-equivalent scores may be used to calculate a DQ. In certain embodiments, the BSID-III is performed for patients who have a developmental age of 42 months or younger based on the Vineland-II.

[0185] In certain embodiments, the administration of the pharmaceutical composition changes the subject’s DQ, as measured by BSID-III, relative to a baseline level. In certain embodiments, the administration of the pharmaceutical composition prevents the subject’s DQ, as measured by BSID-III, from deteriorating relative to a baseline level.

[0186] The KABC-II is an individually administered measure of the cognitive processing abilities of children and adolescents aged 3 through 18 years. Raw age-normed and age- equivalent scores (e.g., nonverbal ability score) may be used to calculate a DQ. In certain embodiments, the KABC-II is performed for patients who have a developmental age of >42 months based on the Vineland-II.

[0187] In certain embodiments, the administration of the pharmaceutical composition changes the subject’s DQ, as measured by KABC-II, relative to a baseline level. In certain embodiments, the administration of the pharmaceutical composition prevents the subject’s DQ, as measured by KABC-II, from deteriorating relative to a baseline level.

[0188] Clinical Assessments

[0189] Disease activity and therapeutic response to ETVTDS may also be evaluated using patient diaries and / or one or more clinical assessments described herein. Additionally, as described below, these tools may also be used to evaluate the safety and tolerability of the therapeutic (e.g., to identify adverse events (AEs) associated with ETV:IDS administration). In certain embodiments, the baseline is from, e.g., the subject prior to treatment, from a subject who has not undergone treatment; or from an age-matched control subject that does not have Hunter syndrome. In certain embodiments, the assessment is performed at, e.g., 2 weeks, 3 weeks, 1 month, 2 months, 4 months, 6 months, 12 months, 18 months, and / or 24 months or longer after treatment initiation.

[0190] Medical Histories and Patient Diaries

[0191] Medical histories may be reviewed to identify and collect information about the subject’s presentation, diagnosis, comorbidities, disease-related medical events and symptoms, and medications used to manage symptoms. For example, medical histories may include but are not limited to histories of acute, chronic, and infectious disease; surgical and oncological histories; reproductive status; any conditions affecting major body systems; any cognitive or behavioral assessments or interventions; and demographic data, including year of birth, sex, race, and ethnicity. This information may be considered in conjunction with a patient diary.

[0192] Physical Examinations

[0193] Physical examinations, including age-appropriate neurologic examinations, may also be performed to evaluate disease activity and therapeutic response to ETVTDS, as well as safety / tolerability to the composition. For example, symptom-oriented physical / neurological examination may be performed (e.g., to assess patient symptoms or safety laboratory abnormalities). Physical examinations may also include measurement of vital signs (e.g., blood pressure, pulse rate, respiratory rate and body temperature) body weight and height, and liver and spleen volume.

[0194] In certain embodiments, the physical and / or neurologic examination does not identify new symptoms post treatment in the subject, as compared to pre-treatment symptoms in the subject. In certain embodiments, the physical and / or neurologic examination identifies a reduced number of symptoms post treatment in the subject, as compared to pre-treatment symptoms in the subject.

[0195] In certain embodiments, the administration of the pharmaceutical composition does not change the subject’s vital signs, relative to a baseline level. In certain embodiments, the administration of the pharmaceutical composition improves the subject’s vital signs, relative to a baseline level. In certain embodiments, the subject’s post-treatment vital signs are within a normal range (e.g., relative to a healthy subject that does not have Hunter syndrome).

[0196] In certain embodiments, the administration of the pharmaceutical composition changes the subject’s liver volume relative to a baseline level, as assessed by MRI or ultrasound. In certain embodiments, the administration of the pharmaceutical composition reduces the subject’s liver volume by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, relative to a baseline level, as assessed by MRI or ultrasound.

[0197] In certain embodiments, the administration of the pharmaceutical composition changes the subject’s spleen volume relative to a baseline level, as assessed by MRI or ultrasound. In certain embodiments, the administration of the pharmaceutical composition reduces the subject’s spleen volume by at least about 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or more, relative to a baseline level, as assessed by MRI or ultrasound.

[0198] Laboratory Tests

[0199] Standard laboratory tests (chemistry, hematology, and urinalysis) may be performed at baseline and / or at varying time-points post-treatment initiation. For example, a coagulation panel; a complete blood count (for platelet count); CSF cell counts, protein, and glucose from CSF samples; and urinalysis may be performed.

[0200] In certain embodiments, the administration of the pharmaceutical composition does not change the subject’s results for one or more of these standard tests, relative to a baseline level.

[0201] In certain embodiments, the subject’s post-treatment results for one or more of these standard tests are within a normal range (e.g., relative to a healthy subject that does not have Hunter syndrome).

[0202] Functional Assessments

[0203] Disease activity and therapeutic response to ETV:IDS may also be evaluated using one or more functional assessments described herein. For example, Individualized Educational Plans (IEPs) and / or Individualized Family Service Plan (IFSPS) may be performed at baseline and / or at varying time-points post-treatment initiation. An audiology assessment may also be performed at baseline and / or at varying time-points post-treatment (e.g., an auditory brainstem response (ABR) assessment or a standard hearing test). Additionally, a subject’s toileting abilities percentage (TAP) may also be assessed at baseline and / or at varying time-points post- treatment. In certain embodiments, the baseline is from, e.g., the subject prior to treatment, from a subject who has not undergone treatment; or from an age-matched control subject that does not have Hunter syndrome. In certain embodiments, the assessment is performed, e.g., at 2 months, 6 months, 12 months and / or 18 months after treatment initiation.

[0204] In certain embodiments, the administration of the pharmaceutical composition improves or maintains the subject’s qualitative IEP trajectories in cognitive categories or behavioral categories relative to a baseline level. In certain embodiments, the administration of the pharmaceutical composition improves or maintains the subject’s qualitative IFSPS trajectories in cognitive categories or behavioral categories relative to a baseline level.

[0205] In certain embodiments, the subject’s qualitative IEP trajectories in cognitive categories or behavioral categories relative to a baseline level do not significantly worsen post-treatment with the pharmaceutical composition. In certain embodiments, the administration of the pharmaceutical composition does not significantly worsen the subject’s qualitative IFSPS trajectories in cognitive categories or behavioral categories relative to a baseline level do not significantly worsen post-treatment with the pharmaceutical composition.

[0206] In certain embodiments, the administration of the pharmaceutical composition improves or maintains the subject’s toileting abilities percentage (TAP) relative to a baseline level. In certain embodiments, the subject’s TAP relative to a baseline level does not significantly worsen post-treatment with the pharmaceutical composition.

[0207] In certain embodiments, the administration of the pharmaceutical composition improves or maintains the subject’s hearing relative to a baseline level, as assessed by ABR or a standard hearing test. In certain embodiments, the subject’s hearing relative to a baseline level does not significantly worsen post-treatment with the pharmaceutical composition, as assessed by ABR or a standard hearing test.

[0208] Quality of Life Assessments

[0209] Disease activity and therapeutic response to ETVTDS may also be evaluated using one or more quality of life assessments described herein. For example, the Child Health Questionnaire Parent Form 28 (CHQ-PF28), the Infant and Toddler Quality of Life™ (ITQOL), and / or the Pediatric Quality of Life Inventory™ Family Impact Module (PedsQL™-FIM) assessments may be performed at baseline and / or at varying time-points post-treatment initiation. In certain embodiments, the baseline is from, e.g., the subject prior to treatment, from a subject who has not undergone treatment; or from an age-matched control subject that does not have Hunter syndrome. In certain embodiments, the assessment is performed, e.g., at 2 months, 6 months, 12 months and / or 18 months after treatment initiation.

[0210] The CHQ-PF28 is a generic person-reported outcome measurement that may be used to assess health-related quality of life for children and adolescents from 5 through 18 years of age. The ITQOL is a generic person-reported outcome measurement to assess health-related quality of life for children aged 2 months to 5 years (Raat et al. Reliability and validity of the Infant and Toddler Quality of Life Questionnaire (ITQOL) in a general population and respiratory disease sample. Qual Life Res. 2007;16(3):445-60). This instrument is an extension of the CHQ-PF28 for younger patients. The ITQOL may be used for patients under age 5 years. The PedsQL-FIM is a multidimensional instrument that was designed to measure the impact of pediatric chronic health conditions on parents and the family. The PedsQL-FIM measures parent self-reported physical, emotional, social, and cognitive functioning, communication, and worry. The module also measures parent-reported family daily activities and family relationships.

[0211] In certain embodiments, the administration of the pharmaceutical composition improves or maintains the subject’s quality of life, e.g., as assessed by CHQ-PF28, ITQOL and / or PedsQL-FIM, relative to a baseline level. In certain embodiments, the subject’s quality of life, e.g., as assessed by CHQ-PF28, ITQOL and / or PedsQL-FIM, relative to a baseline level, does not significantly worsen post-treatment with the pharmaceutical composition.

[0212] Safety and Tolerability Assessments

[0213] The safety and tolerability of ETVTDS at a given dosage may be evaluated using certain assessments described herein. For example, certain biomarker and clinical assessments may be used to evaluate subjects that have been administered a pharmaceutical composition comprising ETVTDS. Additionally, the frequency and severity of adverse events (AEs) may also be monitored.

[0214] For example, in certain embodiments, a subject administered the pharmaceutical composition may be evaluated using a combination of clinical assessments, including but not limited to, vital sign measurement, physical examination, including neurological examination, diagnostic testing, laboratory assessments (e.g., hematology, serum clinical chemistry, urinalysis, and coagulation), and characterization of immunogenicity of the protein in serum (measured by the incidence of anti-drug antibodies (AD As) relative to baseline). Additionally, the total GAG concentration (normalized to creatinine) in urine may also be monitored as a safety parameter.

[0215] In certain embodiments the pharmacokinetics (PK) of the ETV:IDS are evaluated. For example, PK parameters may include, but are not be limited to, the following: Cmax; Trough concentration (Cmin); Tmax; Area under the concentration-time curve from time zero to the time of last quantifiable concentration (Auco-iast); Area under the concentration-time curve over a dosing interval (AUCO-T); Apparent terminal elimination rate constant (lz); Apparent terminal elimination tl / 2; and Accumulation ratio.

[0216] In certain embodiments, the urine total GAG concentration (normalized to creatinine) does not increase relative to a baseline level after administration of the pharmaceutical composition (e.g., the urine total GAG concentration does not increase relative to pre-treatment levels in the subject). In certain embodiments, the urine total GAG concentration (normalized to creatinine) increases by less than about 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%,

[0217] 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% relative to a baseline level after administration of the pharmaceutical composition. In certain embodiments, the urine total GAG concentration (normalized to creatinine) decreases relative to a baseline level after administration of the pharmaceutical composition. In certain embodiments, the stabilization or decrease in urine total GAG concentration in the subject supports safety of the administered dose.

[0218] In certain embodiments, prior to administration of the pharmaceutical composition, the subject had received recombinant idursulfase enzyme replacement therapy. In certain embodiments, the subject has pre-existing AD As against IDS prior to administration of the pharmaceutical composition. In certain embodiments, the subject’s pre-existing titer of antidrug antibodies against IDS is greater than 100, 150, 200, 300, 400, 500, 1,000, 5,000, 25,000, 50,000, 75,000, 100,000, 500,000, 1,000,000, 10,000,000 or more. In certain embodiments, the subject’s pre-existing titer of anti-drug antibodies against IDS ranges from 189 to greater than 11 million. In certain embodiments, the subject’s pre-existing titer of anti-drug antibodies against IDS is greater than 11 million.

[0219] In certain embodiments, the incidence of AD As does not increase relative to a baseline level after administration of the pharmaceutical composition (e.g., the incidence of AD As does not increase relative to pre-treatment levels in the subject). In certain embodiments, the incidence of AD As increases by less than about 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1% relative to a baseline level after administration of the pharmaceutical composition. In certain embodiments, the formation of new AD As or increase in existing AD As relative to a baseline level does not significantly diminish the efficacy of treatment with the pharmaceutical composition.

[0220] As used herein, an adverse event refers to any untoward medical occurrence associated the use of the pharmaceutical composition, and includes, e.g., any unfavorable and unintended signs, symptoms or disease; any new disease or exacerbation of an existing disease; recurrence of an intermittent medical condition not present at baseline; and any deterioration in a laboratory value or other clinical test that is associated with symptoms or leads to a change in concomitant treatment. For example, AEs include infusion related reactions (IRRs), such as allergic reactions and anaphylaxis.

[0221] As used herein, a “serious adverse event (SAE)” is any AE that meets any of the following criteria: is fatal; is life-threatening; requires or prolongs patient hospitalization; results in persistent or significant disability / incapacity {i.e., the AE results in substantial disruption of the patient’s ability to conduct normal life functions); or is a significant medical event (e.g., may jeopardize the patient or may require medical / surgical intervention to prevent one or more outcomes listed above).

[0222] AEs may also be categorized by severity (i.e., the intensity of the AE). For example, an AE may be considered: mild (i.e., easily tolerated, causes minimal discomfort, and does not interfere with everyday activities); moderate (i.e., causes sufficient discomfort to interfere with normal everyday activities; or severe (i.e., medically significant event that causes marked limitation or inability to perform daily activities).

[0223] In certain embodiments, a subject administered the pharmaceutical composition does not experience an adverse event (e.g., an AE associated with the administration or the composition). In certain embodiments, adverse events (AEs) in subjects administered the pharmaceutical composition are uncommon. In certain embodiments, AEs in subjects administered the pharmaceutical composition are rare or very rare. For example, in certain embodiments, the frequency of AEs in subjects administered the pharmaceutical composition are less than about 1 / 100, or less than about 1 / 1,000, or less than about 1 / 10,000.

[0224] In certain embodiments, a subject administered the pharmaceutical composition does not experience a serious adverse event (SAE), such as an untoward medical occurrence that, e.g., results in death, is life threatening, requires inpatient hospitalization or prolongation of existing hospitalization, or results in significant disability or incapacity. In certain embodiments, serious adverse events (SAEs) in subjects administered the pharmaceutical composition are uncommon. In certain embodiments, serious adverse events (SAEs) in subjects administered the pharmaceutical composition are rare or very rare. For example, in certain embodiments, the frequency of SAEs in subjects administered the pharmaceutical composition are less than about 1 / 100, or less than about 1 / 1,000, or less than about 1 / 10,000.

[0225] In certain embodiments, a subject administered the pharmaceutical composition does not experience a severe AE. In certain embodiments, severe AEs in subjects administered the pharmaceutical composition are uncommon. In certain embodiments, severe AEs in subjects administered the pharmaceutical composition are rare or very rare. For example, in certain embodiments, the frequency of severe AEs in subjects administered the pharmaceutical composition are less than about 1 / 100, or less than about 1 / 1,000, or less than about 1 / 10,000.

[0226] In certain embodiments, a subject does not experience an IRR, such as an allergic reaction or anaphylaxis, upon administration of the pharmaceutical composition. In certain embodiments, the subject does not experience an allergic reaction. In certain embodiments, the subject does not experience anaphylaxis. In certain embodiments, IRRs in subjects administered the pharmaceutical composition are uncommon. In certain embodiments, IRRs in subjects administered the pharmaceutical composition are rare or very rare. For example, in certain embodiments, the frequency of IRRs in subjects administered the pharmaceutical composition are less than about 1 / 100, or less than about 1 / 1,000, or less than about 1 / 10,000.

[0227] In certain embodiments, the pharmaceutical composition is administered to the subject without pretreatment or co-administration of medication for an infusion-related reaction (IRR). Such medications include, but are not limited to, an anti-histamine, an anti-pyretic, and a corticosteroid.

[0228] In certain embodiments, a subject experiences an IRR upon administration of the pharmaceutical composition. In certain embodiments, the pharmaceutical composition is administered to the subject with pretreatment or co-administration of medication for an infusion- related reaction (IRR). In certain embodiments, a medication for an IRR is administered to the subject post-treatment of the pharmaceutical composition.

[0229] Certain embodiments also provide a method of resolving an infusion-related reaction (IRR) in a subject receiving treatment for Hunter syndrome, comprising administering one or more agents useful for treating an IRR (e.g., selected from the group consisting of an anti- histamine, an anti-pyretic, and a corticosteroid), wherein the subject is being administered or was administered a therapeutically effective dose of the pharmaceutical composition (e.g., at least about 7.5 mg / kg). In certain embodiments, the IRR is a fever. In certain embodiments, the method of resolving the IRR comprises administering to the subject acetaminophen and diphenhydramine.

[0230] Subjects

[0231] The term “subject,” “individual,” and “patient,” as used interchangeably herein, refers to a mammal, including but not limited to humans, non-human primates, rodents (e.g., rats, mice, and guinea pigs), rabbits, cows, pigs, horses, and other mammalian species. In certain embodiments described herein, the subject is a human subject.

[0232] In certain embodiments, the subject is a male subject.

[0233] In certain embodiments, the subject is from about 1 month to 30 years of age. In certain embodiments, the subject is from about 6 months to 30 years of age. In certain embodiments, the subject is from about 1 to 30 years of age. In certain embodiments, the subject is from about 1 to 25 years of age. In certain embodiments, the subject is from about 1 to 18 years of age. In certain embodiments, the subject is from about 2 to 18 years of age. In certain embodiments, the subject is from about 2 to 15 years of age. In certain embodiments, the subject is from about 2 to 10 years of age. In certain embodiments, the subject is from about 5 to 10 years of age. In certain embodiments, the subject is less than 4 years of age. In certain embodiments, the subject is less than 2 years of age. In certain embodiments, the subject is less than 1 year of age. In certain embodiments, the subject is more than 1 year of age. In certain embodiments, the subject is about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17 or 18 years of age.

[0234] In certain embodiments, the subject has a weight of > 5 kg. In certain embodiments, the subject has a weight of > 9 kg. In certain embodiments, the subject has a weight of > 15 kg. In certain embodiments, the subject has a weight of > 19 kg. In certain embodiments, the subject has a weight of > 23 kg. In certain embodiments, the subject has a weight of > 27 kg. In certain embodiments, the subject has a weight of > 32 kg. In certain embodiments, the subject has a weight of > 36 kg. In certain embodiments, the subject has a weight of > 41 kg. In certain embodiments, the subject has a weight of > 45 kg. In certain embodiments, the subject has a weight of > 50 kg.

[0235] In certain embodiments, the subject has neuronopathic Hunter syndrome, also referred to as neuronopathic MPSII (nMPSII). In certain embodiments, the subject has non-neuronopathic Hunter syndrome. In certain embodiments, the subject has Hunter syndrome with an unknown neuronopathic phenotype.

[0236] In certain embodiments, prior to administration of the pharmaceutical composition, the subject had received recombinant idursulfase enzyme replacement therapy (e.g., for more than 4 months, more than 6 months, more than 1 year, more than 18 months, more than 2 years, or longer).

[0237] In certain embodiments, the subject has a neurobehavioral deficit. In certain embodiments, the subject has a motor skills deficit. In certain embodiments, the subject has a cognitive deficit. In certain embodiments, the subject has a sensorimotor deficit.

[0238] In certain embodiments, the subject has impaired or delayed development (e.g., mental or physical development). In certain embodiments, the subject has a development quotient (DQ) < 85. In certain embodiments, the subject has a DQ < 80. In certain embodiments, the subject has a DQ < 75. In certain embodiments, the subject has a DQ < 70. In certain embodiments, the subject has a DQ < 65. In certain embodiments, the subject has a DQ < 60. In certain embodiments, the subject has a DQ < 65. In certain embodiments, the subject has a DQ < 60.

[0239] In certain embodiments, the subject has a DQ < 55. In certain embodiments, the subject has a DQ < 50.

[0240] In certain embodiments, the subject has a decline of at least 5 points in DQ within a period of about 6 months or longer. In certain embodiments, the subject has a decline of at least 7.5 points in DQ within a period of about 6 months or longer. In certain embodiments, the subject has a decline of at least 10 points in DQ within a period of about 6 months or longer. In certain embodiments, the subject has a decline of at least 15 points in DQ within a period of about 6 months or longer. In certain embodiments, the subject has a decline of at least 20 points in DQ within a period of about 6 months or longer. In certain embodiments, the subject has a decline of at least 25 points in DQ within a period of about 6 months or longer. In certain embodiments, DQ declines within a period of about 9, 12, 18, or 24 mo or longer.

[0241] In certain embodiments, the subject has an auditory deficit.

[0242] In certain embodiments, the subject has a musculoskeletal abnormality.

[0243] In certain embodiments, the subject has a documented mutation in the IDS gene. In certain embodiments, the subject has been diagnosed as having reduced IDS enzyme activity. In certain embodiments, subject has been diagnosed with Hunter syndrome based on reduced IDS enzyme activity and a documented mutation in the IDS gene. In certain embodiments, the subject has a same genetic mutation in the IDS gene as a blood relative with confirmed neuronopathic Hunter Syndrome / nMPS II. In certain embodiments, the subject has neuronopathic Hunter syndrome / nMPS II or has a same genetic mutation in the IDS gene as a blood relative with confirmed neuronopathic Hunter Syndrome / nMPS II.

[0244] In certain embodiments, a subject administered the pharmaceutical composition, or a sample therefrom, is evaluated using an assessment described herein. In certain embodiments, parameters or certain assessment results are compared to a control or baseline levels. Depending on the type of parameter being evaluated or the assessment being performed, the control or baseline level may vary. For example, in certain embodiments, the term “control” may refer to a heathy subject or a subject that does not have Hunter syndrome (or a sample therefrom). Alternatively, the term “control” may refer to a Hunter syndrome patient that was not administered the pharmaceutical composition or to the subject prior to treatment (or a sample therefrom). Similarly, a “baseline level” may refer to a level or a range of levels that is measured in, e.g., a healthy individual or in a subject that does not have Hunter syndrome. In certain other embodiments described herein, a “baseline level” may also refer to a level or a range of levels in a Hunter syndrome patient that was not administered the pharmaceutical composition or in the subject prior to administration of the pharmaceutical composition.

[0245] In certain embodiments, a control value or baseline level may be established using data from a population of control subjects. In some embodiments, the population of subjects is matched to a test subject according to one or more patient characteristics such as age, sex, ethnicity, or other criteria. In some embodiments, the control value is established using the same type of sample from the population of subjects (e.g., a sample comprising blood or PBMCs) as is used for assessing the level of lipids / proteins in the test subject.

[0246] It is within the skill of the art to identify the appropriate control or baseline level depending on the parameter being evaluated.

[0247] Administration and Therapeutically Effective Doses

[0248] A pharmaceutical composition described herein may be administered to a subject at a therapeutically effective amount or dose, e.g., a safe and therapeutically effect amount or dose.

[0249] In certain embodiments, a therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase. In certain embodiments, a therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase beta. In certain embodiments, the therapeutically effective dose is from about 1 mg / kg to about 40 mg / kg of protein. In certain embodiments, the therapeutically effective dose is from about 1 mg / kg to about 30 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 1 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 3 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 7.5 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 10 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 15 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 20 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 30 mg / kg of protein. In certain embodiments, the therapeutically effective dose is about 40 mg / kg of protein.

[0250] In certain embodiments, such a dose described herein is a safe and therapeutically effective dose (e.g., as determined using an assessment described herein, such as stabilization or decrease in urine total GAG concentration in the subject).

[0251] In certain embodiments, the pharmaceutical composition is administered weekly.

[0252] In some embodiments, a protein molecule described herein has an enzymatic activity of at least about 500 units (U) / mg, about 1,000 U / mg, or at least about 1,500, 2,000, 2,500, 3,000, 3,500, 4,000, 4,500, 5,000, 6,000, 7,000, 8,000, 9,000, or 10,000 U / mg. In some embodiments, the enzymatic activity is at least about 11,000 U / mg, or at least about 12,000, 13,000, 14,000, 15,000, 16,000, 17,000, 18,000, 19,000, 20,000, 25,000, 30,000, 35,000, 40,000, 45000, or

[0253] 50,000 U / mg; or anywhere in a range of about 500 U / mg to about 50,000 U / mg.

[0254] Dosages may be varied according to several factors, including the chosen route of administration, the formulation of the composition, patient response, the severity of the condition, the subject’s weight, the subject’s age, the subject’s head size and / or ratio of head size to height, and the judgment of the prescribing physician. The dosage can be increased or decreased over time, as required by an individual patient. In some embodiments, a patient initially is given a low dose, which is then increased to an efficacious dosage tolerable to the patient. Determination of an effective amount is well within the capability of those skilled in the art.

[0255] In various embodiments, a pharmaceutical composition described herein is administered parenterally. In some embodiments, the pharmaceutical composition is administered intravenously. Intravenous administration can be by infusion, e.g., over a period of from about 10 to about 30 minutes, or over a period of at least 1 hour, 2 hours, 3 hours, 4 hours, 6 hours, 8 hours, or 10 hours. In some embodiments, the pharmaceutical composition is administered intravenously over a period of from about 20 minutes to 6 hours, or from about 30 minutes to 4 hours. In some embodiments, the pharmaceutical composition is administered as an intravenous bolus. Combinations of infusion and bolus administration may also be used.

[0256] ETVrIDS Protein Molecules

[0257] Certain methods described herein provide a method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising a fusion protein described herein. These fusion proteins may be referenced herein as an enzyme transport vehicle (ETV) in conjunction with the an iduronate 2-sulfatase (IDS) enzyme, or ETVTDS. ETVTDS proteins, which may be used in a method described herein, are discussed below and are described in WO 2019 / 070577, which is incorporated by reference herein for all purposes.

[0258] Certain Fusion Proteins Comprising IDS Enzymes

[0259] Described below are certain embodiments of fusion proteins that include an IDS enzyme, or a catalytically active variant or fragment of a wild-type IDS (e.g, a wild-type human IDS), linked to an Fc polypeptide; these fusion proteins may be included in a pharmaceutical composition described herein for the treatment of Hunter syndrome. In some cases, the protein includes a dimeric Fc polypeptide, where one of the Fc polypeptide monomers is linked to the IDS enzyme. The Fc polypeptides can increase enzyme half-life and, in some cases, can be modified to confer additional functional properties onto the protein. Also described herein are fusion proteins that facilitate delivery of an IDS enzyme across the blood-brain barrier (BBB). These proteins comprise an Fc polypeptide and a modified Fc polypeptide that form a dimer, and an IDS enzyme linked to the Fc region and / or the modified Fc region. The modified Fc region can specifically bind to a BBB receptor such as a transferrin receptor (TfR).

[0260] In some aspects, a fusion protein described herein comprises: (i) an Fc polypeptide, which may contain modifications (e.g, one or more modifications that promote heterodimerization) or may be a wild-type Fc polypeptide; and an IDS enzyme; and (ii) an Fc polypeptide, which may contain modifications (e.g, one or more modifications that promote heterodimerization) or may be a wild-type Fc polypeptide; and optionally an IDS enzyme. In some embodiments, one or both Fc polypeptides may contain modifications that result in binding to a blood-brain barrier (BBB) receptor, e.g., a TfR. An IDS enzyme incorporated into the fusion protein is catalytically active, i.e., it retains the enzymatic activity that is deficient in Hunter syndrome.

[0261] In some embodiments, a fusion protein comprising an IDS enzyme and optionally a modified Fc polypeptide that binds to a BBB receptor, e.g, a TfR-binding Fc polypeptide, comprises a catalytically active fragment or variant of a wild-type IDS. In some embodiments, the IDS enzyme is a variant or a catalytically active fragment of an IDS protein that comprises the amino acid sequence of any one of SEQ ID NOS: 69, 70, 90, 170, and 174. In some embodiments, a catalytically active variant or fragment of an IDS enzyme has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or greater of the activity of the wild-type IDS enzyme.

[0262] In some embodiments, an IDS enzyme, or a catalytically active variant or fragment thereof, that is present in a fusion protein described herein, retains at least 25% of its activity compared to its activity when not joined to an Fc polypeptide or a TfR-binding Fc polypeptide. In some embodiments, an IDS enzyme, or a catalytically active variant or fragment thereof, retains at least 10%, or at least 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95%, of its activity compared to its activity when not joined to an Fc polypeptide or a TfR-binding Fc polypeptide. In some embodiments, an IDS enzyme, or a catalytically active variant or fragment thereof, retains at least 80%, 85%, 90%, or 95% of its activity compared to its activity when not joined to an Fc polypeptide or a TfR-binding Fc polypeptide. In some embodiments, fusion to an Fc polypeptide does not decrease the activity of the IDS enzyme, or catalytically active variant or fragment thereof. In some embodiments, fusion to a TfR-binding Fc polypeptide does not decrease the activity of the IDS enzyme.

[0263] I. Fc Polypeptide Modifications For Blood-Brain Barrier (BBB) Receptor Binding

[0264] In some aspects, the fusion proteins are capable of being transported across the blood- brain barrier (BBB). Such a protein comprises a modified Fc polypeptide that binds to a BBB receptor. BBB receptors are expressed on BBB endothelia, as well as other cell and tissue types. In some embodiments, the BBB receptor is transferrin receptor (TfR).

[0265] Amino acid residues designated in various Fc modifications, including those introduced in a modified Fc polypeptide that binds to a BBB receptor, e.g, TfR, are numbered herein using EU index numbering. Any Fc polypeptide, e.g, an IgGl, IgG2, IgG3, or IgG4 Fc polypeptide, may have modifications, e.g., amino acid substitutions, in one or more positions as described herein.

[0266] A modified (e.g, enhancing heterodimerization and / or BBB receptor-binding) Fc polypeptide present in a fusion protein described herein can have at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to a native Fc region sequence or a fragment thereof, e.g, a fragment of at least 50 amino acids or at least 100 amino acids, or greater in length. In some embodiments, the native Fc amino acid sequence is the Fc region sequence of SEQ ID NO: 1. In some embodiments, the native Fc amino acid sequence is the Fc region sequence of SEQ ID NO: 183. In some embodiments, the modified Fc polypeptide has at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to amino acids 1- 110 of SEQ ID NO: 1; to amino acids 1-110 of SEQ ID NO: 183; to amino acids 111-217 of SEQ ID NO: 1, to amino acids 111-216 of SEQ ID NO: 183, or a fragment thereof, e.g., a fragment of at least 50 amino acids or at least 100 amino acids, or greater in length.

[0267] In some embodiments, a modified (e.g, enhancing heterodimerization and / or BBB receptor-binding) Fc polypeptide comprises at least 50 amino acids, or at least 60, 65, 70, 75, 80, 85, 90, or 95 or more, or at least 100 amino acids, or more, that correspond to a native Fc region amino acid sequence. In some embodiments, the modified Fc polypeptide comprises at least 25 contiguous amino acids, or at least 30, 35, 40, or 45 contiguous amino acids, or 50 contiguous amino acids, or at least 60, 65, 70, 75, 80 85, 90, or 95 or more contiguous amino acids, or 100 or more contiguous amino acids, that correspond to a native Fc region amino acid sequence, such as SEQ ID NO:l or 183.

[0268] In some embodiments, the domain that is modified for BBB receptor-binding activity is a human Ig CH3 domain, such as an IgGl CH3 domain. The CH3 domain can be of any IgG subtype, i.e., from IgGl, IgG2, IgG3, or IgG4. In the context of IgGl antibodies, a CH3 domain refers to the segment of amino acids from about position 341 to about position 447 as numbered according to the EU numbering scheme.

[0269] In some embodiments, a modified (e.g, BBB receptor-binding) Fc polypeptide present in a fusion protein described herein comprises at least one, two, or three substitutions; and in some embodiments, at least four, five, six, seven, eight, or nine substitutions at amino acid positions 384, 386, 387, 388, 389, 390, 413, 416, and 421, according to the EU numbering scheme.

[0270] FcRn binding sites

[0271] In certain aspects, modified ( e.g. , BBB receptor-binding) Fc polypeptides, or Fc polypeptides present in a fusion protein described herein that do not specifically bind to a BBB receptor, can also comprise an FcRn binding site. In some embodiments, the FcRn binding site is within the Fc polypeptide or a fragment thereof.

[0272] In some embodiments, the FcRn binding site comprises a native FcRn binding site. In some embodiments, the FcRn binding site does not comprise amino acid changes relative to the amino acid sequence of a native FcRn binding site. In some embodiments, the native FcRn binding site is an IgG binding site, e.g, a human IgG binding site. In some embodiments, the FcRn binding site comprises a modification that alters FcRn binding.

[0273] In some embodiments, an FcRn binding site has one or more amino acid residues that are mutated, e.g, substituted, wherein the mutation(s) increase serum half-life or do not substantially reduce serum half-life (i.e., reduce serum half-life by no more than 25% compared to a counterpart modified Fc polypeptide having the wild-type residues at the mutated positions when assayed under the same conditions). In some embodiments, an FcRn binding site has one or more amino acid residues that are substituted at positions 250-256, 307, 380, 428, and 433- 436, according to the EU numbering scheme.

[0274] In some embodiments, one or more residues at or near an FcRn binding site are mutated, relative to a native human IgG sequence, to extend serum half-life of the modified polypeptide. In some embodiments, mutations are introduced into one, two, or three of positions 252, 254, and 256. In some embodiments, the mutations are M252Y, S254T, and T256E. In some embodiments, a modified Fc polypeptide further comprises the mutations M252Y, S254T, and T256E. In some embodiments, a modified Fc polypeptide comprises a substitution at one, two, or all three of positions T307, E380, and N434, according to the EU numbering scheme. In some embodiments, the mutations are T307Q and N434A. In some embodiments, a modified Fc polypeptide comprises mutations T307A, E380A, and N434A. In some embodiments, a modified Fc polypeptide comprises substitutions at positions T250 and M428, according to the EU numbering scheme. In some embodiments, the modified Fc polypeptide comprises mutations T250Q and / or M428L. In some embodiments, a modified Fc polypeptide comprises substitutions at positions M428 and N434, according to the EU numbering scheme. In some embodiments, the modified Fc polypeptide comprises mutations M428L and N434S. In some embodiments, a modified Fc polypeptide comprises an N434S or N434A mutation.

[0275] II. Transferrin Receptor-Binding Fc Polypeptides

[0276] This section describes generation of modified Fc polypeptides described herein that bind to transferrin receptor (TfR) and are capable of being transported across the blood-brain barrier (BBB).

[0277] Tfll-binding Fc polypeptides comprising mutations in the CH3 domain

[0278] In some embodiments, a modified Fc polypeptide that specifically binds to TfR comprises substitutions in a CH3 domain. In some embodiments, a modified Fc polypeptide comprises a human Ig CH3 domain, such as an IgG CH3 domain, that is modified for TfR- binding activity. The CH3 domain can be of any IgG subtype, i.e., from IgGl, IgG2, IgG3, or IgG4. In the context of IgG antibodies, a CH3 domain refers to the segment of amino acids from about position 341 to about position 447 as numbered according to the EU numbering scheme.

[0279] In some embodiments, a modified Fc polypeptide that specifically binds to TfR binds to the apical domain of TfR and may bind to TfR without blocking or otherwise inhibiting binding of transferrin to TfR. In some embodiments, binding of transferrin to TfR is not substantially inhibited. In some embodiments, binding of transferrin to TfR is inhibited by less than about 50% (e.g, less than about 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5%). In some embodiments, binding of transferrin to TfR is inhibited by less than about 20% (e.g, less than about 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, or 1%).

[0280] In some embodiments, a modified Fc polypeptide that specifically binds to TfR comprises at least two, three, four, five, six, seven, eight, or nine substitutions at positions 384, 386, 387, 388, 389, 390, 413, 416, and 421, according to the EU numbering scheme. Illustrative substitutions that may be introduced at these positions are shown in Tables 4 and 5. In some embodiments, the amino acid at position 388 and / or 421 is an aromatic amino acid, e.g, Trp, Phe, or Tyr. In some embodiments, the amino acid at position 388 is Trp. In some embodiments, the aromatic amino acid at position 421 is Trp or Phe.

[0281] In some embodiments, at least one position as follows is substituted: Leu, Tyr, Met, or Val at position 384; Leu, Thr, His, or Pro at position 386; Val, Pro, or an acidic amino acid at position 387; an aromatic amino acid, e.g, Trp at position 388; Val, Ser, or Ala at position 389; an acidic amino acid, Ala, Ser, Leu, Thr, or Pro at position 413; Thr or an acidic amino acid at position 416; or Trp, Tyr, His, or Phe at position 421. In some embodiments, the modified Fc polypeptide may comprise a conservative substitution, e.g., an amino acid in the same charge grouping, hydrophobicity grouping, side chain ring structure grouping (e.g, aromatic amino acids), or size grouping, and / or polar or non-polar grouping, of a specified amino acid at one or more of the positions in the set. Thus, for example, He may be present at position 384, 386, and / or position 413. In some embodiments, the acidic amino acid at position one, two, or each of positions 387, 413, and 416 is Glu. In other embodiments, the acidic amino acid at one, two or each of positions 387, 413, and 416 is Asp. In some embodiments, two, three, four, five, six, seven, or all eight of positions 384, 386, 387, 388, 389, 413, 416, and 421 have an amino acid substitution as specified in this paragraph.

[0282] In some embodiments, an Fc polypeptide that is modified as described in the preceding two paragraphs comprises a native Asn at position 390. In some embodiments, the modified Fc polypeptide comprises Gly, His, Gin, Leu, Lys, Val, Phe, Ser, Ala, or Asp at position 390. In some embodiments, the modified Fc polypeptide further comprises one, two, three, or four substitutions at positions comprising 380, 391, 392, and 415, according to the EU numbering scheme. In some embodiments, Trp, Tyr, Leu, or Gin may be present at position 380. In some embodiments, Ser, Thr, Gin, or Phe may be present at position 391. In some embodiments, Gin, Phe, or His may be present at position 392. In some embodiments, Glu may be present at position 415.

[0283] In certain embodiments, the modified Fc polypeptide comprises two, three, four, five, six, seven, eight, nine, ten, or eleven positions selected from the following: Trp, Leu, or Glu at position 380; Tyr or Phe at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser, Ala, Val, or Asn at position 389; Ser or Asn at position 390; Thr or Ser at position 413; Glu or Ser at position 415; Glu at position 416; and / or Phe at position 421. In some embodiments, the modified Fc polypeptide comprises all eleven positions as follows: Trp, Leu, or Glu at position 380; Tyr or Phe at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser, Ala, Val, or Asn at position 389; Ser or Asn at position 390; Thr or Ser at position 413; Glu or Ser at position 415; Glu at position 416; and / or Phe at position 421.

[0284] In certain embodiments, the modified Fc polypeptide comprises Leu or Met at position 384; Leu, His, or Pro at position 386; Val at position 387; Trp at position 388; Val or Ala at position 389; Pro at position 413; Thr at position 416; and / or Trp at position 421. In some embodiments, the modified Fc polypeptide further comprises Ser, Thr, Gin, or Phe at position 391. In some embodiments, the modified Fc polypeptide further comprises Trp, Tyr, Leu, or Gin at position 380 and / or Gin, Phe, or His at position 392. In some embodiments, Trp is present at position 380 and / or Gin is present at position 392. In some embodiments, the modified Fc polypeptide does not have a Trp at position 380.

[0285] In other embodiments, the modified Fc polypeptide comprises Tyr at position 384; Thr at position 386; Glu or Val and position 387; Trp at position 388; Ser at position 389; Ser or Thr at position 413; Glu at position 416; and / or Phe at position 421. In some embodiments, the modified Fc polypeptide comprises a native Asn at position 390. In certain embodiments, the modified Fc polypeptide further comprises Trp, Tyr, Leu, or Gin at position 380; and / or Glu at position 415. In some embodiments, the modified Fc polypeptide further comprises Trp at position 380 and / or Glu at position 415.

[0286] In additional embodiments, the modified Fc polypeptide further comprises one, two, or three substitutions at positions comprising 414, 424, and 426, according to the EU numbering scheme. In some embodiments, position 414 is Lys, Arg, Gly, or Pro; position 424 is Ser, Thr, Glu, or Lys; and / or position 426 is Ser, Trp, or Gly.

[0287] In some embodiments, the modified Fc polypeptide comprises one or more of the following substitutions: Trp at position 380; Thr at position 386; Trp at position 388; Val at position 389; Thr or Ser at position 413; Glu at position 415; and / or Phe at position 421, according to the EU numbering scheme.

[0288] In some embodiments, the modified Fc polypeptide has at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to amino acids 111-217 of any one of SEQ ID NOS:4-68, 73-76, 81-84, and 95-167 (e.g, SEQ ID NOS: 12-16, 36, and 38-68). In some embodiments, the modified Fc polypeptide has at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to amino acids 111-216 of any one of SEQ ID NOS: 184-198 and 200-206 (e.g, SEQ ID NOS: 184, 190, 192 and 200). In some embodiments, the modified Fc polypeptide has at least 70% identity, at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:4-68, 73-76, 81-84, 95- 167, 184-198 and 200-206 (e.g., SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200). In some embodiments, the modified Fc polypeptide comprises the amino acids at EU index positions 384-390 and / or 413-421 of any one of SEQ ID NOS:4-68, 73-76, 81-84, 95-167, 184- 198 and 200-206 (e.g., SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200). In some embodiments, the modified Fc polypeptide comprises the amino acids at EU index positions 380-390 and / or 413-421 of any one of SEQ ID NOS:4-68, 73-76, 81-84, 95-167, 184-198 and 200-206 (e.g., SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200). In some embodiments, the modified Fc polypeptide comprises the amino acids at EU index positions 380-392 and / or 413-426 of any one of SEQ ID NOS:4-68, 73-76, 81-84, 95-167, 184-198 and 200-206 (e.g,

[0289] SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200).

[0290] In some embodiments, the modified Fc polypeptide has at least 75% identity, at least 80% identity, at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:4-68, 73-76, 81-84, 95-167, 184-198 and 200-206 (e.g, SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200), and further comprises at least five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, or sixteen of the positions, numbered according to the EU index, as follows: Trp, Tyr, Leu, Gin, or Glu at position 380; Leu, Tyr, Met, or Val at position 384; Leu, Thr, His, or Pro at position 386; Val, Pro, or an acidic amino acid at position 387; an aromatic amino acid, e.g, Trp, at position 388; Val, Ser, or Ala at position 389; Ser or Asn at position 390; Ser, Thr, Gin, or Phe at position 391; Gin, Phe, or His at position 392; an acidic amino acid, Ala, Ser, Leu, Thr, or Pro at position 413; Lys, Arg, Gly or Pro at position 414; Glu or Ser at position 415; Thr or an acidic amino acid at position 416; Trp, Tyr, His or Phe at position 421; Ser, Thr, Glu or Lys at position 424; and Ser, Trp, or Gly at position 426.

[0291] In some embodiments, the modified Fc polypeptide comprises the amino acid sequence of any one of SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200. In other embodiments, the modified Fc polypeptide comprises the amino acid sequence of any one of SEQ ID NOS: 12-16, 36, 38-68, 184, 190, 192 and 200, but in which one, two, or three amino acids are substituted.

[0292] In some embodiments, the modified Fc polypeptide comprises additional mutations such as the mutations described below, including, but not limited to, a knob mutation (e.g, T366W as numbered with reference to EU numbering), hole mutations (e.g, T366S, L368A, and Y407V as numbered with reference to EU numbering), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered with reference to EU numbering), and / or mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme). By way of illustration, SEQ ID NOS: 73 -76, 81-84, 92, 95-169, 185-189, 191, 193-199, and 201-207 provide non-limiting examples of modified Fc polypeptides with mutations in the CH3 domain (e.g, clones CH3C.35.20.1, CH3C.35.23.2, CH3C.35.23.3, CH3C.35.23.4, CH3C.35.21.17.2, and CH3C.35.23) comprising one or more of these additional mutations.

[0293] In some embodiments, the modified Fc polypeptide comprises a knob mutation (e.g, T366W as numbered with reference to EU numbering) and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:73, 96, 108, 120, 132, 144, 156, 185, 193, 201. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:73, 96, 108, 120, 132, 144, 156, 185, 193 and 201.

[0294] In some embodiments, the modified Fc polypeptide comprises a knob mutation (e.g, T366W as numbered with reference to EU numbering) and mutations that modulate effector function (e.g, L234A, L235A, and / or P329G (e.g, L234A and L235A) as numbered with reference to EU numbering), and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:74, 92, 97, 98, 109, 110, 121, 122, 133, 134, 145, 146, 157, 158, 168, 169, 186, 191, 194, 195, 199, 202, 203, and 207. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:74, 92, 97, 98, 109, 110, 121, 122, 133, 134, 145, 146, 157, 158, 168, 169, 186, 191, 194, 195, 199, 202, 203, and 207.

[0295] In some embodiments, the modified Fc polypeptide comprises a knob mutation (e.g, T366W as numbered with reference to EU numbering) and mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:75, 99, 111, 123, 135, 147, 159, 187, 196, and 204. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:75, 99, 111, 123, 135, 147, 159, 187, 196 and 204. In some embodiments, the modified Fc polypeptide comprises a knob mutation ( e.g ., T366W as numbered with reference to EU numbering), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered with reference to EU numbering), and mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:76,

[0296] 100, 101, 112, 113, 124, 125, 136, 137, 148, 149, 160, 161, 188, 197, 198, 205, and 206. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:76, 100, 101, 112, 113, 124, 125, 136, 137, 148, 149, 160, 161, 188, 197, 198, 205, and 206.

[0297] In some embodiments, the modified Fc polypeptide comprises hole mutations (e.g, T366S, L368A, and Y407V as numbered with reference to EU numbering) and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:81,

[0298] 102, 114, 126, 138, 150, and 162. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:81, 102, 114, 126, 138, 150, and 162.

[0299] In some embodiments, the modified Fc polypeptide comprises hole mutations (e.g, T366S, L368A, and Y407V as numbered with reference to EU numbering) and mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered with reference to EU numbering), and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:82, 103, 104, 115, 116, 127, 128, 139, 140, 151, 152, 163, and 164. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS: 82, 103, 104, 115, 116, 127, 128, 139, 140, 151, 152, 163, and 164.

[0300] In some embodiments, the modified Fc polypeptide comprises hole mutations (e.g, T366S, L368A, and Y407V as numbered with reference to EU numbering) and mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and has at least 85% identity, at least 90% identity, at least 95%, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity identity to the sequence of any one of SEQ ID NOS: 83, 105, 117, 129, 141, 153, and 165. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:83, 105, 117, 129, 141, 153, and 165.

[0301] In some embodiments, the modified Fc polypeptide comprises hole mutations ( e.g ., T366S, L368A, and Y407V as numbered with reference to EU numbering), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered with reference to EU numbering), and mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 84, 106, 107, 118, 119, 130, 131, 142, 143, 154, 155, 166, and 167. In some embodiments, the modified Fc polypeptide comprises the sequence of any one of SEQ ID NOS:84, 106, 107, 118, 119, 130, 131, 142, 143, 154, 155, 166, and 167.

[0302] In some embodiments, a modified Fc polypeptide that specifically binds to TfR comprises at least two, three, four, five, six, seven, or eight substitutions at positions 345, 346, 347, 349, 437, 438, 439, and 440, according to the EU numbering scheme. In some embodiments, the modified Fc polypeptide comprises Gly at position 437; Phe at position 438; and / or Asp at position 440. In some embodiments, Glu is present at position 440. In certain embodiments, the modified Fc polypeptide comprises at least one substitution at a position as follows: Phe or lie at position 345; Asp, Glu, Gly, Ala, or Lys at position 346; Tyr, Met, Leu, lie, or Asp at position 347; Thr or Ala at position 349; Gly at position 437; Phe at position 438; His Tyr, Ser, or Phe at position 439; or Asp at position 440. In some embodiments, two, three, four, five, six, seven, or all eight of positions 345, 346, 347, 349, 437, 438, 439, and 440 and have a substitution as specified in this paragraph. In some embodiments, the modified Fc polypeptide may comprise a conservative substitution, e.g, an amino acid in the same charge grouping, hydrophobicity grouping, side chain ring structure grouping (e.g, aromatic amino acids), or size grouping, and / or polar or non-polar grouping, of a specified amino acid at one or more of the positions in the set. III. Additional Fc Polypeptide Mutations

[0303] In some aspects, a fusion protein described herein comprises two Fc polypeptides that may each comprise independently selected modifications or may be a wild-type Fc polypeptide, e.g., a human IgGl Fc polypeptide. In some embodiments, one or both Fc polypeptides contains one or more modifications that confer binding to a blood-brain barrier (BBB) receptor, e.g, transferrin receptor (TfR). Non-limiting examples of other mutations that can be introduced into one or both Fc polypeptides include, e.g, mutations to increase serum stability or serum half- life, to modulate effector function, to influence glycosylation, to reduce immunogenicity in humans, and / or to provide for knob and hole heterodimerization of the Fc polypeptides.

[0304] In some embodiments, the Fc polypeptides present in the fusion protein independently have an amino acid sequence identity of at least about 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% to a corresponding wild-type Fc polypeptide (e.g, a human IgGl, IgG2, IgG3, or IgG4 Fc polypeptide).

[0305] In some embodiments, the Fc polypeptides present in the fusion protein include knob and hole mutations to promote heterodimer formation and hinder homodimer formation. Generally, the modifications introduce a protuberance (“knob”) at the interface of a first polypeptide and a corresponding cavity (“hole”) in the interface of a second polypeptide, such that the protuberance can be positioned in the cavity so as to promote heterodimer formation and thus hinder homodimer formation. Protuberances are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains (e.g, tyrosine or tryptophan). Compensatory cavities of identical or similar size to the protuberances are created in the interface of the second polypeptide by replacing large amino acid side chains with smaller ones (e.g, alanine or threonine). In some embodiments, such additional mutations are at a position in the Fc polypeptide that does not have a negative effect on binding of the polypeptide to a BBB receptor, e.g, TfR.

[0306] In one illustrative embodiment of a knob and hole approach for dimerization, position 366 (numbered according to the EU numbering scheme) of one of the Fc polypeptides present in the fusion protein comprises a tryptophan in place of a native threonine. The other Fc polypeptide in the dimer has a valine at position 407 (numbered according to the EU numbering scheme) in place of the native tyrosine. The other Fc polypeptide may further comprise a substitution in which the native threonine at position 366 (numbered according to the EU numbering scheme) is substituted with a serine and a native leucine at position 368 (numbered according to the EU numbering scheme) is substituted with an alanine. Thus, one of the Fc polypeptides of a fusion protein described herein has the T366W knob mutation and the other Fc polypeptide has the Y407V mutation, which is typically accompanied by the T366S and L368A hole mutations.

[0307] In some embodiments, modifications to enhance serum half-life may be introduced.

[0308] For example, in some embodiments, one or both Fc polypeptides present in a fusion protein described herein may comprise a tyrosine at position 252, a threonine at position 254, and a glutamic acid at position 256, as numbered according to the EU numbering scheme. Thus, one or both Fc polypeptides may have M252Y, S254T, and T256E substitutions. Alternatively, one or both Fc polypeptides may have M428L and N434S substitutions, as numbered according to the EU numbering scheme. Alternatively, one or both Fc polypeptides may have an N434S or N434A substitution.

[0309] In some embodiments, one or both Fc polypeptides present in a fusion protein described herein may comprise modifications that reduce effector function, i.e., having a reduced ability to induce certain biological functions upon binding to an Fc receptor expressed on an effector cell that mediates the effector function. Examples of antibody effector functions include, but are not limited to, Clq binding and complement dependent cytotoxicity (CDC), Fc receptor binding, antibody-dependent cell-mediated cytotoxicity (ADCC), antibody-dependent cell-mediated phagocytosis (ADCP), down-regulation of cell surface receptors (e.g, B cell receptor), and B-cell activation. Effector functions may vary with the antibody class. For example, native human IgGl and IgG3 antibodies can elicit ADCC and CDC activities upon binding to an appropriate Fc receptor present on an immune system cell; and native human IgGl, IgG2, IgG3, and IgG4 can elicit ADCP functions upon binding to the appropriate Fc receptor present on an immune cell.

[0310] In some embodiments, one or both Fc polypeptides present in a fusion protein described herein may also be engineered to contain other modifications for heterodimerization, e.g, electrostatic engineering of contact residues within a CH3-CH3 interface that are naturally charged or hydrophobic patch modifications.

[0311] In some embodiments, one or both Fc polypeptides present in a fusion protein described herein may include additional modifications that modulate effector function. In some embodiments, one or both Fc polypeptides present in a fusion protein described herein may comprise modifications that reduce or eliminate effector function. Illustrative Fc polypeptide mutations that reduce effector function include, but are not limited to, substitutions in a CH2 domain, e.g., at positions 234 and 235, according to the EU numbering scheme. For example, in some embodiments, one or both Fc polypeptides can comprise alanine residues at positions 234 and 235. Thus, one or both Fc polypeptides may have L234A and L235A (LALA) substitutions.

[0312] Additional Fc polypeptide mutations that modulate an effector function include, but are not limited to, the following: position 329 may have a mutation in which proline is substituted with a glycine or arginine or an amino acid residue large enough to destroy the Fc / Fcy receptor interface that is formed between proline 329 of the Fc and tryptophan residues Trp 87 and Trp 110 of FcyRIII. Additional illustrative substitutions include S228P, E233P, L235E, N297A, N297D, and P331S, according to the EU numbering scheme. Multiple substitutions may also be present, e.g., L234A and L235A of a human IgGl Fc region; L234A, L235A, and P329G of a human IgGl Fc region; S228P and L235E of a human IgG4 Fc region; L234A and G237A of a human IgGl Fc region; L234A, L235A, and G237A of a human IgGl Fc region; V234A and G237A of a human IgG2 Fc region; L235A, G237A, and E318A of a human IgG4 Fc region; and S228P and L236E of a human IgG4 Fc region, according to the EU numbering scheme. In some embodiments, one or both Fc polypeptides may have one or more amino acid substitutions that modulate ADCC, e.g, substitutions at positions 298, 333, and / or 334, according to the EU numbering scheme.

[0313] In some embodiments, the C’ terminal Lys residue is removed or not present in an Fc polypeptide described herein ( i.e ., the Lys residue at position 447, according to the EU numbering scheme).

[0314] Illustrative Fc polypeptides comprising additional mutations

[0315] By way of non-limiting example, one or both Fc polypeptides present in a fusion protein described herein may comprise additional mutations including a knob mutation (e.g, T366W as numbered according to the EU numbering scheme), hole mutations (e.g, T366S, L368A, and Y407V as numbered according to the EU numbering scheme), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered according to the EU numbering scheme), and / or mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme).

[0316] In some embodiments, an Fc polypeptide may have a knob mutation ( e.g ., T366W as numbered according to the EU numbering scheme) and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS:l, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200 may be modified to have a knob mutation.

[0317] In some embodiments, an Fc polypeptide may have a knob mutation (e.g., T366W as numbered according to the EU numbering scheme), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered according to the EU numbering scheme), and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS:l, 4-68, 183, 184, 190, 192, and 200 may be modified to have a knob mutation and mutations that modulate effector function.

[0318] In some embodiments, an Fc polypeptide may have a knob mutation (e.g, T366W as numbered according to the EU numbering scheme), mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS:l, 4-68, 183, 184, 190, 192, and 200 may be modified to have a knob mutation and mutations that increase serum stability or serum half-life.

[0319] In some embodiments, an Fc polypeptide may have a knob mutation (e.g, T366W as numbered according to the EU numbering scheme), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered according to the EU numbering scheme), mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS:l, 4-68, 183, 184, 190, 192, and 200 may be modified to have a knob mutation, mutations that modulate effector function, and mutations that increase serum stability or serum half-life.

[0320] In some embodiments, an Fc polypeptide may have hole mutations ( e.g ., T366S, L368A, and Y407V as numbered according to the EU numbering scheme) and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4- 68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200 may be modified to have hole mutations.

[0321] In some embodiments, an Fc polypeptide may have hole mutations (e.g., T366S, L368A, and Y407V as numbered according to the EU numbering scheme), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered according to the EU numbering scheme), and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200 may be modified to have hole mutations and mutations that modulate effector function.

[0322] In some embodiments, an Fc polypeptide may have hole mutations (e.g, T366S, L368A, and Y407V as numbered according to the EU numbering scheme), mutations that increase serum or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200 may be modified to have hole mutations and mutations that increase serum stability or serum half-life.

[0323] In some embodiments, an Fc polypeptide may have hole mutations ( e.g ., T366S, L368A, and Y407V as numbered according to the EU numbering scheme), mutations that modulate effector function (e.g., L234A, L235A, and / or P329G (e.g., L234A and L235A) as numbered according to the EU numbering scheme), mutations that increase serum stability or serum half-life (e.g, (i) M252Y, S254T, and T256E as numbered with reference to EU numbering, or (ii) N434S with or without M428L as numbered according to the EU numbering scheme), and at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200. In some embodiments, an Fc polypeptide having the sequence of any one of SEQ ID NOS: 1, 4-68, 183, 184, 190, 192, and 200 may be modified to have hole mutations, mutations that modulate effector function, and mutations that increase serum stability or serum half-life.

[0324] IV. Illustrative Fusion Proteins Comprising An IDS Enzyme

[0325] In some aspects, a fusion protein described herein comprises a first Fc polypeptide that is linked to an IDS enzyme, an IDS enzyme variant, or a catalytically active fragment thereof; and a second Fc polypeptide that forms an Fc dimer with the first Fc polypeptide. In some embodiments, the first Fc polypeptide and / or the second Fc polypeptide does not include an immunoglobulin heavy and / or light chain variable region sequence or an antigen-binding portion thereof. In some embodiments, the first Fc polypeptide is a modified Fc polypeptide and / or the second Fc polypeptide is a modified Fc polypeptide. In some embodiments, the second Fc polypeptide is a modified Fc polypeptide. In some embodiments, the modified Fc polypeptide contains one or more modifications that promote its heterodimerization to the other Fc polypeptide. In some embodiments, the modified Fc polypeptide contains one or more modifications that reduce effector function. In some embodiments, the modified Fc polypeptide contains one or more modifications that extend serum half-life. In some embodiments, the modified Fc polypeptide contains one or more modifications that confer binding to a blood-brain barrier (BBB) receptor, e.g, transferrin receptor (TfR).

[0326] In other aspects, a fusion protein described herein comprises a first polypeptide chain that comprises a modified Fc polypeptide that specifically binds to a BBB receptor, e.g, TfR, and a second polypeptide chain that comprises an Fc polypeptide which dimerizes with the modified Fc polypeptide to form an Fc dimer. An IDS enzyme may be linked to either the first or the second polypeptide chain. In some embodiments, the IDS enzyme is linked to the second polypeptide chain. In some embodiments, the protein comprises two IDS enzymes, each linked to one of the polypeptide chains. In some embodiments, the Fc polypeptide may be a BBB receptor-binding polypeptide that specifically binds to the same BBB receptor as the modified Fc polypeptide in the first polypeptide chain. In some embodiments, the Fc polypeptide does not specifically bind to a BBB receptor.

[0327] In some embodiments, a fusion protein described herein comprises a first polypeptide chain comprising a modified Fc polypeptide that specifically binds to TfR and a second polypeptide chain that comprises an Fc polypeptide, wherein the modified Fc polypeptide and the Fc polypeptide dimerize to from an Fc dimer. In some embodiments, the IDS enzyme is linked to the first polypeptide chain. In some embodiments, the IDS enzyme is linked to the second polypeptide chain. In some embodiments, the Fc polypeptide does not specifically bind to a BBB receptor, e.g., TfR.

[0328] In some embodiments, a fusion protein described herein comprises a first polypeptide chain that comprises a modified Fc polypeptide that binds to TfR and comprises a T366W (knob) substitution; and a second polypeptide chain that comprises an Fc polypeptide comprising T366S, L368A, and Y407V (hole) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide further comprises L234A and L235A (LALA) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide further comprises M252Y, S254T, and T256E (YTE) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide further comprises L234A and L235A (LALA) substitutions and M252Y, S254T, and T256E (YTE) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide comprises human IgGl wild-type residues at positions 234, 235, 252, 254, 256, and 366.

[0329] In some embodiments, the modified Fc polypeptide comprises the knob, LALA, and / or YTE mutations as specified for any one of SEQ ID NOS:73-76, 95-101, 108-113, 120-125, 132- 137, 144-149, 156-161, 185-188, 191, 193-198, and 201-206, and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the respective sequence; or comprises the sequence of any one of SEQ ID NOS: 73-76, 95-101, 108-113, 120-125, 132-137, 144-149, 156-161, 185-188, 191, 193-198, and 201-206. In some embodiments, the Fc polypeptide comprises the hole, LALA, and / or YTE mutations as specified for any one of SEQ ID NOS:77-80 and 208-211 and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the respective sequence; or comprises the sequence of any one of SEQ ID NOS: 77-80 and 208-211. In some embodiments, the modified Fc polypeptide comprises any one of SEQ ID NOS:73-76, 95-101, 108-113, 120- 125, 132-137, 144-149, and 156-161, and the Fc polypeptide comprises any one of SEQ ID NOS:77-80. In some embodiments, the modified Fc polypeptide comprises any one of SEQ ID NOS: 185-188, 191, 193-198 and 201-206, and the Fc polypeptide comprises any one of SEQ ID NOS: 208-211. In some embodiments, the N-terminus of the modified Fc polypeptide and / or the Fc polypeptide includes a portion of an IgGl hinge region (e.g, DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the modified Fc polypeptide has at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:92, 168, and 169, or comprises the sequence of any one of SEQ ID NOS:92, 168, and 169. In some embodiments, the modified Fc polypeptide has at least 85%, at least 90%, or at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 189, 199, and 207, or comprises the sequence of any one of SEQ ID NOS: 189, 199, and 207.

[0330] In some embodiments, a fusion protein described herein comprises a first polypeptide chain that comprises a modified Fc polypeptide that binds to TfR and comprises T366S, L368A, and Y407V (hole) substitutions; and a second polypeptide chain that comprises an Fc polypeptide comprising a T366W (knob) substitution. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide further comprises L234A and L235A (LALA) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide further comprises M252Y, S254T, and T256E (YTE) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide further comprises L234A and L235A (LALA) substitutions and M252Y, S254T, and T256E (YTE) substitutions. In some embodiments, the modified Fc polypeptide and / or the Fc polypeptide comprises human IgGl wild-type residues at positions 234, 235, 252, 254, 256, and 366.

[0331] In some embodiments, the modified Fc polypeptide comprises the hole, LALA, and / or YTE mutations as specified for any one of SEQ ID NOS:81-84, 102-107, 114-119, 126-131, 138-143, 150-155, and 162-167 and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the respective sequence; or comprises the sequence of any one of SEQ ID NOS: 81- 84, 102-107, 114-119, 126-131, 138-143, 150-155, and 162-167. In some embodiments, the Fc polypeptide comprises the knob, LALA, and / or YTE mutations as specified for any one of SEQ ID NOS: 85-88 and has at least 85% identity, at least 90% identity, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to the respective sequence; or comprises the sequence of any one of SEQ ID NOS:85-88. In some embodiments, the modified Fc polypeptide comprises any one of SEQ ID NOS: 81-84, 102-107, 114-119, 126-131, 138-143, 150-155, and 162-167, and the Fc polypeptide comprises any one of SEQ ID NOS:85-88. In some embodiments, the N-terminus of the modified Fc polypeptide and / or the Fc polypeptide includes a portion of an IgGl hinge region (e.g., DKTHTCPPCP;

[0332] SEQ ID NO: 89).

[0333] In some embodiments, an IDS enzyme present in a fusion protein described herein is linked to a polypeptide chain that comprises an Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 77-80 and 208-211, or comprises the sequence of any one of SEQ ID NOS: 77-80 and 208-211 (e.g., as a fusion polypeptide). In some embodiments, the IDS enzyme is linked to the Fc polypeptide by a linker, such as a flexible linker, and / or a hinge region or portion thereof (e.g, DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the IDS enzyme comprises a sequence having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:90, 170, and 174, or comprises the sequence of any one of SEQ ID NOS:90, 170, and 174. In some embodiments, the IDS sequence linked to the Fc polypeptide has at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:91, 93, 171, 172, 175, 176, and 212-217 or comprises the sequence of any one of SEQ ID NOS: 91, 93, 171, 172, 175, 176, and 212-217. In some embodiments, the fusion protein comprises a modified Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 73-76, 95-101, 108-113, 120-125, 132-137, 144-149, 156-161, 185-188, 191, 193-198, and 201-206, or comprises the sequence of any one of SEQ ID NOS: 73-76, 95-101, 108-113, 120-125, 132-137, 144-149, 156-161, 185-188, 191, 193-198, and 201-206. In some embodiments, the N-terminus of the Fc polypeptide and / or the modified Fc polypeptide includes a portion of an IgGl hinge region (e.g., DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the modified Fc polypeptide has at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:92, 168, and 169, or comprises the sequence of any one of SEQ ID NOS:92, 168, and 169. In some embodiments, the modified Fc polypeptide has at least 85%, at least 90%, or at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 189, 199, and 207, or comprises the sequence of any one of SEQ ID NOS: 189, 199, and 207.

[0334] In some embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:91, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 145 and 168 (e.g, SEQ ID NO: 168). In other embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:91, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 109 and 169 (e.g, SEQ ID NO: 169).

[0335] In some embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:215, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS:202 and 207 (e.g, SEQ ID NO:207). In other embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:215, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 194 and 199 (e.g, SEQ ID NO: 199).

[0336] In some embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO: 171, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 145 and 168 (e.g, SEQ ID NO: 168). In other embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO: 171, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 109 and 169 (e.g, SEQ ID NO: 169).

[0337] In some embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:213, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS:202 and 207 (e.g, SEQ ID NO:207). In other embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:213, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 194 and 199 (e.g, SEQ ID NO: 199). In some embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO: 175, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 145 and 168 ( e.g ., SEQ ID NO: 168). In other embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO: 175, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 109 and 169 (e.g., SEQ ID NO: 169).

[0338] In some embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:217, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS:202 and 207 (e.g., SEQ ID NO:207). In other embodiments, the fusion protein comprises an IDS-Fc fusion polypeptide comprising the sequence of SEQ ID NO:217, and a modified Fc polypeptide comprising the sequence of any one of SEQ ID NOS: 194 and 199 (e.g, SEQ ID NO: 199).

[0339] In some embodiments, an IDS enzyme present in a fusion protein described herein is linked to a polypeptide chain that comprises an Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 85-88, or comprises the sequence of any one of SEQ ID NOS: 85-88 (e.g, as a fusion polypeptide). In some embodiments, the IDS enzyme is linked to the Fc polypeptide by a linker, such as a flexible linker, and / or a hinge region or portion thereof (e.g, DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the IDS enzyme comprises a sequence having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:90, 170, and 174, or comprises the sequence of any one of SEQ ID NOS:90, 170, and 174. In some embodiments, the IDS sequence linked to the Fc polypeptide has at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:94, 173, and 177, or comprises the sequence of any one of SEQ ID NOS:94, 173, and 177. In some embodiments, the fusion protein comprises a modified Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 81-84, 102-107, 114-119, 126-131, 138-143, 150-155, and 162-167, or comprises the sequence of any one of SEQ ID NOS: 81-84, 102-107, 114-119, 126- 131, 138-143, 150-155, and 162-167. In some embodiments, the N-terminus ofthe Fc polypeptide and / or the modified Fc polypeptide includes a portion of an IgGl hinge region (e.g., DKTHTCPPCP; SEQ ID NO:89).

[0340] In some embodiments, an IDS enzyme present in a fusion protein described herein is linked to a polypeptide chain that comprises a modified Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 73-76, 95-101, 108-113, 120-125, 132-137, 144-149, 156-161, 185-188, 191, 193-198, and 201-206, or comprises the sequence of any one of SEQ ID NOS: 73-76, 95-101, 108-113, 120-125, 132-137, 144-149, 156-161, 185- 188, 191, 193-198, and 201-206 (e.g, as a fusion polypeptide). In some embodiments, the IDS enzyme is linked to the modified Fc polypeptide by a linker, such as a flexible linker, and / or a hinge region or portion thereof (e.g, DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the IDS enzyme comprises a sequence having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:90, 170, and 174, or comprises the sequence of any one of SEQ ID NOS:90, 170, and 174. In some embodiments, the fusion protein comprises an Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:77-80, or comprises the sequence of any one of SEQ ID NOS:77-80. In some embodiments, the fusion protein comprises an Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:208-211, or comprises the sequence of any one of SEQ ID NOS:208-211. In some embodiments, the N-terminus of the modified Fc polypeptide and / or the Fc polypeptide includes a portion of an IgGl hinge region (e.g, DKTHTCPPCP; SEQ ID NO:89).

[0341] In some embodiments, an IDS enzyme present in a fusion protein described herein is linked to a polypeptide chain that comprises a modified Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS: 81-84, 102-107, 114-119, 126-131, 138-143, 150-155, and 162-167, or comprises the sequence of any one of SEQ ID NOS: 81-84, 102-107, 114-119, 126-131, 138-143, 150-155, and 162-167 (e.g, as a fusion polypeptide). In some embodiments, the IDS enzyme is linked to the modified Fc polypeptide by a linker, such as a flexible linker, and / or a hinge region or portion thereof (e.g, DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the IDS enzyme comprises a sequence having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:90, 170, and 174, or comprises the sequence of any one of SEQ ID NOS: 90, 170, and 174. In some embodiments, the fusion protein comprises an Fc polypeptide having at least 85%, at least 90%, at least 95% identity, at least 96% identity, at least 97% identity, at least 98% identity, or at least 99% identity to any one of SEQ ID NOS:85-88, or comprises the sequence of any one of SEQ ID NOS:85-88. In some embodiments, the N-terminus of the modified Fc polypeptide and / or the Fc polypeptide includes a portion of an IgGl hinge region (e.g., DKTHTCPPCP; SEQ ID NO:89).

[0342] V. IDS Enzymes Linked To Fc Polypeptides

[0343] In some embodiments, a fusion protein described herein comprises two Fc polypeptides as described herein and one or both of the Fc polypeptides may further comprise a partial or full hinge region. The hinge region can be from any immunoglobulin subclass or isotype. An illustrative immunoglobulin hinge is an IgG hinge region, such as an IgGl hinge region, e.g, human IgGl hinge amino acid sequence EPKSCDKTHTCPPCP (SEQ ID NO:71) or a portion thereof (e.g, DKTHTCPPCP; SEQ ID NO:89). In some embodiments, the hinge region is at the N-terminal region of the Fc polypeptide.

[0344] In some embodiments, an Fc polypeptide is joined to the IDS enzyme by a linker, e.g, a peptide linker. In some embodiments, the Fc polypeptide is joined to the IDS enzyme by a peptide bond or by a peptide linker, e.g. , is a fusion polypeptide. The peptide linker may be configured such that it allows for the rotation of the IDS enzyme relative to the Fc polypeptide to which it is joined; and / or is resistant to digestion by proteases. Peptide linkers may contain natural amino acids, unnatural amino acids, or a combination thereof. In some embodiments, the peptide linker may be a flexible linker, e.g, containing amino acids such as Gly, Asn, Ser, Thr, Ala, and the like. Such linkers are designed using known parameters and may be of any length and contain any number of repeat units of any length (e.g, repeat units of Gly and Ser residues). For example, the linker may have repeats, such as two, three, four, five, or more Gly4-Ser (SEQ ID NO: 179) repeats or a single Gly4-Ser (SEQ ID NO: 179). In some embodiments, the peptide linker may include a protease cleavage site, e.g, that is cleavable by an enzyme present in the central nervous system.

[0345] In some embodiments, the IDS enzyme is joined to the N-terminus of the Fc polypeptide, e.g, by a Gly4-Ser linker (SEQ ID NO: 179) or a (Gly4-Ser)2 linker (SEQ ID NO: 180). In some embodiments, the Fc polypeptide may comprise a hinge sequence or partial hinge sequence at the N-terminus that is joined to the linker or directly joined to the IDS enzyme.

[0346] In some embodiments, the IDS enzyme is joined to the C-terminus of the Fc polypeptide, e.g., by a Gly4-Ser linker (SEQ ID NO: 179) or a (Gly4-Ser)2 linker (SEQ ID NO:180). In some embodiments, the C-terminus of the Fc polypeptide is directly joined to the IDS enzyme.

[0347] In some embodiments, the IDS enzyme is joined to the Fc polypeptide by a chemical cross-linking agent. Such conjugates can be generated using well-known chemical cross-linking reagents and protocols. For example, there are a large number of chemical cross-linking agents that are known to those skilled in the art and useful for cross-linking the polypeptide with an agent of interest. For example, the cross-linking agents are heterobifunctional cross-linkers, which can be used to link molecules in a stepwise manner. Heterobifunctional cross-linkers provide the ability to design more specific coupling methods for conjugating proteins, thereby reducing the occurrences of unwanted side reactions such as homo-protein polymers. A wide variety of heterobifunctional cross-linkers are known in the art, including N-hydroxysuccinimide (NHS) or its water soluble analog N-hydroxysulfosuccinimide (sulfo-NHS), succinimidyl 4-(N- maleimidomethyl)cyclohexane-l-carboxylate (SMCC), m-maleimidobenzoyl-N- hydroxysuccinimide ester (MBS); N-succinimidyl (4-iodoacetyl) aminobenzoate (SIAB), succinimidyl 4-(p-maleimidophenyl)butyrate (SMPB), 1 -ethyl-3 -(3- dimethylaminopropyl)carbodiimide hydrochloride (EDC); 4-succinimidyloxycarbonyl-a-methyl- a-(2-pyridyldithio)-toluene (SMPT), N-succinimidyl 3-(2-pyridyldithio)propionate (SPDP), and succinimidyl 6-[3-(2-pyridyldithio)propionate]hexanoate (LC-SPDP). Those cross-linking agents having N-hydroxysuccinimide moieties can be obtained as the N- hydroxysulfosuccinimide analogs, which generally have greater water solubility. In addition, those cross-linking agents having disulfide bridges within the linking chain can be synthesized instead as the alkyl derivatives so as to reduce the amount of linker cleavage in vivo. In addition to the heterobifunctional cross-linkers, there exist a number of other cross-linking agents including homobifunctional and photoreactive cross-linkers. Disuccinimidyl subcrate (DSS), bismaleimidohexane (BMH) and dimethylpimelimidate. 2HC1 (DMP) are examples of useful homobifunctional cross-linking agents, and bis-[B-(4-azidosalicylamido)ethyl]disulfide (BASED) and N-succinimidyl-6(4'-azido-2'-nitrophenylamino)hexanoate (SANPAH) are examples of useful photoreactive cross-linkers. Certain Embodiments

[0348] Embodiment 1. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising a protein, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386;

[0349] Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0350] Embodiment 2. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose (e.g., a safe and therapeutically effective dose) of a pharmaceutical composition comprising a protein, wherein administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386;

[0351] Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0352] Embodiment 3. The method of any one of embodiments 1-2, wherein the therapeutically effective dose (e.g., safe and therapeutically effective dose) is from about 3 mg / kg to about 30 mg / kg of protein.

[0353] Embodiment 4. The method of embodiment 3 or 115, wherein the therapeutically effective dose (e.g., a safe and therapeutically effective dose) is about 3 mg / kg of protein.

[0354] Embodiment 5. The method of embodiment 3 or 115, wherein the therapeutically effective dose (e.g., a safe and therapeutically effective dose) is about 7.5 mg / kg of protein.

[0355] Embodiment 6. The method of embodiment 3 or 115, wherein the therapeutically effective dose (e.g., a safe and therapeutically effective dose) is about 15 mg / kg of protein. Embodiment 7. The method of embodiment 3 or 115, wherein the therapeutically effective dose (e.g., a safe and therapeutically effective dose) is about 30 mg / kg of protein.

[0356] Embodiment 8. The method of any one of embodiments 1-7 or 112-150, wherein the pharmaceutical composition is administered weekly.

[0357] Embodiment 9. The method of any one of embodiments 1-8, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable excipient (e.g., a pharmaceutically acceptable carrier).

[0358] Embodiment 10. The method of any one of embodiments 1-9, wherein the second Fc polypeptide specifically binds to the transferrin receptor.

[0359] Embodiment 11. The method of any one of embodiments 1-10, wherein the IDS amino acid sequence comprises an amino acid sequence having at least 90% identity to SEQ ID NO:70.

[0360] Embodiment 12. The method of embodiment 11, wherein the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 170 and 174.

[0361] Embodiment 13. The method of embodiment 11, wherein the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 90, 170 and 174.

[0362] Embodiment 14. The method of any one of embodiments 1-13, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 91, 171 or 175.

[0363] Embodiment 15. The method of any one of embodiments 1-13, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 213, 215, or 217.

[0364] Embodiment 16. The method of any one of embodiments 1-15, wherein the IDS amino acid sequence is linked to the N-terminus of the first Fc polypeptide.

[0365] Embodiment 17. The method of any one of embodiments 1-16, wherein the second Fc polypeptide comprises: a. Leu at position 380; b. Ala at position 389; and c. Ser at position 390.

[0366] Embodiment 18. The method of any one of embodiments 1-16, wherein the second Fc polypeptide comprises: a. Glu at position 380; b. Ala at position 389; and c. Asn at position 390.

[0367] Embodiment 19. The method of any one of embodiments 1-16, wherein the second Fc polypeptide comprises: a. Trp at position 380; b. Ser at position 389; and c. Ser at position 390.

[0368] Embodiment 20. The method of any one of embodiments 1-16, wherein the second Fc polypeptide comprises: a. Leu at position 380; b. Ser at position 389; and c. Ser at position 390.

[0369] Embodiment 21. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 92.

[0370] Embodiment 22. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 189.

[0371] Embodiment 23. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 95.

[0372] Embodiment 24. The method of embodiment 23, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO:95.

[0373] Embodiment 25. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 191.

[0374] Embodiment 26. The method of embodiment 25, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO: 191.

[0375] Embodiment 27. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 168. Embodiment 28. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 207.

[0376] Embodiment 29. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 169.

[0377] Embodiment 30. The method of any one of embodiments 1-10, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 199.

[0378] Embodiment 31. The method of any one of embodiments 1-30 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the CSF of the subject to baseline levels measured in a healthy subject or in a subject that does not have Hunter syndrome, wherein the one or more analytes are selected from the group consisting of a glycosaminoglycan (GAG), neurofilament light (Nf-L), soluble triggering receptor expressed on myeloid cells 2 (sTREM2), a bis(monoacylglycerol) phosphate (BMP), a ganglioside and a sphingolipid.

[0379] Embodiment 32. The method of embodiment 31, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the CSF of the subject to baseline levels.

[0380] Embodiment 33. The method of embodiment 31 or 32, wherein the administration of the pharmaceutical composition reduces levels of Nf-L in the CSF of the subject to baseline levels.

[0381] Embodiment 34. The method of any one of embodiments 31-33, wherein the administration of the pharmaceutical composition reduces levels of sTREM2 in the CSF of the subject to baseline levels.

[0382] Embodiment 35. The method of any one of embodiments 31-34, wherein the administration of the pharmaceutical composition reduces levels of a BMP in the CSF of the subject to baseline levels.

[0383] Embodiment 36. The method of any one of embodiments 31-35, wherein the administration of the pharmaceutical composition reduces levels of a ganglioside in the CSF of the subject to baseline levels. Embodiment 37. The method of any one of embodiments 31-36, wherein the administration of the pharmaceutical composition reduces levels of a sphingolipid in the CSF of the subject to baseline levels.

[0384] Embodiment 38. The method of any one of embodiments 1-30 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the CSF of the subject by at least about 10%, 15%, 20%, 25%, or 30%, wherein the reduction is relative to the level of the corresponding one or more analytes in the subject prior to the administration, wherein the one or more analytes are selected from the group consisting of neurofilament light (Nf-L), soluble triggering receptor expressed on myeloid cells 2 (sTREM2), a bis(monoacylglycerol) phosphate (BMP), a ganglioside, and a sphingolipid.

[0385] Embodiment 39. The method of embodiment 38, wherein the administration of the pharmaceutical composition reduces levels of the one or more analytes in the CSF of the subject to baseline levels, measured in a healthy subject or in a subject that does not have Hunter syndrome.

[0386] Embodiment 40. The method of any one of embodiments 1-39 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the serum of the subject by at least about 30%, 40%, 50%, 60%, or 70% relative to the level of the corresponding one or more analytes in the serum of the subject prior to the administration, wherein the one or more analytes are selected from the group consisting of a GAG and Nf-L.

[0387] Embodiment 41. The method of embodiment 40, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the serum of the subject to baseline levels (e.g., as measured in a healthy subject or in a subject that does not have Hunter syndrome).

[0388] Embodiment 42. The method of embodiment 40 or 41, wherein the administration of the pharmaceutical composition reduces levels of Nf-L in the serum of the subject to baseline levels (e.g., as measured in a healthy subject or in a subject that does not have Hunter syndrome).

[0389] Embodiment 43. The method of any one of embodiments 1-42 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject by at least about 30%, 40%, 50%, 60%, or 70% relative to the level of the GAG in the urine of the subject prior to the administration. Embodiment 44. The method of embodiment 43, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject to baseline levels.

[0390] Embodiment 45. The method of any one of embodiments 1-44 or 112-150, wherein the administration of the pharmaceutical composition improves or maintains the subject’s toileting abilities percentage (TAP) relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition.

[0391] Embodiment 46. The method of any one of embodiments 1-45 or 112-150, wherein the administration of the pharmaceutical composition improves or maintains the subject’s qualitative individualized educational plan (IEP) trajectories in cognitive categories or behavioral categories relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition.

[0392] Embodiment 47. The method of any one of embodiments 1-46 or 112-150, wherein the administration of the pharmaceutical composition improves or maintains the subject’s hearing relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition, as assessed by an auditory brainstem response (ABR) assessment or a standard hearing test.

[0393] Embodiment 48. The method of any one of embodiments 1-47 or 112-150, wherein the administration of the pharmaceutical composition changes the subject’s liver volume relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition, as assessed by MRI or ultrasound.

[0394] Embodiment 49. The method of any one of embodiments 1-48 or 112-150, wherein the administration of the pharmaceutical composition changes the subject’s spleen volume relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition, as assessed by MRI or ultrasound.

[0395] Embodiment 50. The method of any one of embodiments 1-49 or 112-150, wherein the subject is a male subject.

[0396] Embodiment 51. The method of any one of embodiments 1-50 or 112-150, wherein the subject is from about 2 to 18 years of age.

[0397] Embodiment 52. The method of any one of embodiments 1-50 or 112-150, wherein the subject is from about 2 to 10 years of age.

[0398] Embodiment 53. The method of any one of embodiments 1-50 or 112-150, wherein the subject is from about 5 to 10 years of age.

[0399] Embodiment 54. The method of any one of embodiments 1-50 or 112-150, wherein the subject is less than 4 years of age.

[0400] Embodiment 55. The method of any one of embodiments 1-54 or 112-150, wherein the subject has a weight of > 15 kg.

[0401] Embodiment 56. The method of any one of embodiments 1-54 or 112-150, wherein the subject has a weight of > 19 kg.

[0402] Embodiment 57. The method of any one of embodiments 1-56 or 112-150, wherein the subject has a development quotient (DQ) < 85.

[0403] Embodiment 58. The method of any one of embodiments 1-57 or 112-150, wherein the subject has a decline of at least 10 points in development quotient (DQ) within a period of about 6 months or longer.

[0404] Embodiment 59. The method of any one of embodiments 1-58 or 112-150, wherein the subject has a same genetic mutation in the IDS gene as a blood relative with confirmed neuronopathic Hunter syndrome (nMPS II).

[0405] Embodiment 60. The method of any one of embodiments 1-58 or 112-150, wherein the subject has neuronopathic Hunter syndrome (nMPS II) or has a same genetic mutation in the IDS gene as a blood relative with confirmed neuronopathic Hunter syndrome (nMPS II).

[0406] Embodiment 61. The method of any one of embodiments 1-60 or 112-150, wherein the pharmaceutical composition is administered to the subject intravenously.

[0407] Embodiment 62. The method of embodiment 61, wherein the subject does not experience an infusion-related reaction (IRR) upon administration of the pharmaceutical composition.

[0408] Embodiment 63. The method of embodiment 62, wherein IRR is an allergic reaction.

[0409] Embodiment 64. The method of embodiment 62, wherein IRR is anaphylaxis.

[0410] Embodiment 65. The method of any one of embodiments 62-64, wherein the pharmaceutical composition is administered to the subject without pretreatment or coadministration of medication for an infusion-related reaction (IRR).

[0411] Embodiment 66. The method of embodiment 61, wherein the pharmaceutical composition is administered to the subject with pretreatment or co-administration of medication for an infusion-related reaction (IRR).

[0412] Embodiment 67. The method of embodiment 65 or 66, wherein the medication for infusion-related reaction is one or more selected from the group consisting of: an anti-histamine, an anti-pyretic, and a corticosteroid.

[0413] Embodiment 68. The method of any one of embodiments 1-67 or 112-150, wherein the urine total GAG concentration (normalized to creatinine) increases by less than 20% relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

[0414] Embodiment 69. The method of any one of embodiments 1-67 or 112-150, wherein the urine total GAG concentration (normalized to creatinine) does not increase relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

[0415] Embodiment 70. The method of any one of embodiments 1-67 or 112-150, wherein the urine total GAG concentration (normalized to creatinine) decreases relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

[0416] Embodiment 71. The method of any one of embodiments 69 or 70, wherein the stabilization or decrease in urine total GAG concentration in the subject supports safety of the administered dose.

[0417] Embodiment 72. The method of any one of embodiments 1-71 or 112-150, wherein the incidence of anti-drug antibodies (AD As) does not increase relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

[0418] Embodiment 73. The method of any one of embodiments 1-71 or 112-150, wherein the incidence of anti-drug antibodies (AD As) increases by less than 10% relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

[0419] Embodiment 74. The method of any one of embodiments 1-73 or 112-150, wherein the frequency of serious adverse events (SAEs) is less than about 1 / 1000.

[0420] Embodiment 75. The method of any one of embodiments 1-73 or 112-150, wherein the incidence of severe SAEs is less than about 1 / 1000.

[0421] Embodiment 76. The method of any one of embodiments 1-75 or 112-150, wherein the therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase. Embodiment 77. The method of any one of embodiments 1-75 or 112-150, wherein the therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase-beta.

[0422] Embodiment 78. The method of any one of embodiments 1-77 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 4 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to administration.

[0423] Embodiment 79. The method of embodiment 78, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 4 weekly doses.

[0424] Embodiment 80. The method of any one of embodiments 1-77 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to administration.

[0425] Embodiment 81. The method of embodiment 80, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 8 weekly doses.

[0426] Embodiment 82. The method of any one of embodiments 1-77 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 12 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to administration.

[0427] Embodiment 83. The method of embodiment 82, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 12 weekly doses.

[0428] Embodiment 84. The method of any one of embodiments 78-83, wherein administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome. Embodiment 85. The method of any one of embodiments 1-84 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 4 weekly doses, wherein the reduction is relative to the urine levels of the GAG in the subject prior to administration.

[0429] Embodiment 86. The method of embodiment 85, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 4 weekly doses.

[0430] Embodiment 87. The method of any one of embodiments 1-84 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the urine levels of the GAG in the subject prior to administration.

[0431] Embodiment 88. The method of embodiment 87, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 8 weekly doses.

[0432] Embodiment 89. The method of any one of embodiments 85-88, wherein administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the urine of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome.

[0433] Embodiment 90. The method of any one of embodiments 78-89, wherein the GAG is heparan sulfate.

[0434] Embodiment 91. The method of embodiment 90, wherein administration of the pharmaceutical composition reduces levels heparan sulfate in the CSF of the subject by at least 80% after at least 4 weekly doses, wherein the reduction is relative to the CSF heparan sulfate levels in the subject prior to administration.

[0435] Embodiments 92. The method of embodiment 90, wherein administration of the pharmaceutical composition reduces levels heparan sulfate in the CSF of the subject by at least 70% after at least 12 weekly doses, wherein the reduction is relative to the CSF heparan sulfate levels in the subject prior to administration.

[0436] Embodiment 93. The method of any one of embodiments 78-89, wherein the GAG is dermatan sulfate. Embodiment 94. The method of any one of embodiments 1-93 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a ganglioside in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the ganglioside in the subject prior to administration.

[0437] Embodiment 95. The method of embodiment 94, wherein the administration of the pharmaceutical composition reduces levels of the ganglioside in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses.

[0438] Embodiment 96. The method of embodiment 94 or 95, wherein the ganglioside is GM3.

[0439] Embodiment 97. The method of any one of embodiments 1-96 or 112-150, wherein the administration of the pharmaceutical composition reduces levels of a BMP in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the BMP in the subject prior to administration.

[0440] Embodiment 98. The method of embodiment 97, wherein the administration of the pharmaceutical composition reduces levels of the BMP in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses.

[0441] Embodiment 99. The method of embodiment 97 or 98, wherein the BMP is a BMP di 18:1 species.

[0442] Embodiment 100. The method of any one of embodiments 1-99 or 112-150, wherein prior to the administration of the pharmaceutical composition, the subject had received recombinant idursulfase enzyme replacement therapy.

[0443] Embodiment 101. The method of any one of embodiments 1-100 or 112-150, wherein the subject has pre-existing anti-drug antibodies against IDS prior to administration of the pharmaceutical composition.

[0444] Embodiment 102. The method of embodiment 101, wherein the subject’s titer of antidrug antibodies against IDS ranges from 189 to greater than 11 million.

[0445] Embodiment 103. The method of embodiment 102, wherein the subject’s titer of antidrug antibodies against IDS is greater than 11 million.

[0446] Embodiment 104. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 3 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0447] Embodiment 105. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 7.5 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0448] Embodiment 106. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 15 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0449] Embodiment 107. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 30 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0450] Embodiment 108. The method of any one of embodiments 104-107, wherein the protein is comprised in a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient.

[0451] Embodiment 109. A method of resolving an infusion-related reaction (IRR) in a subject receiving treatment for Hunter syndrome, comprising administering one or more agents selected from the group consisting of an anti-histamine, an anti-pyretic, and a corticosteroid, wherein the subject is being administered or was administered a pharmaceutical composition comprising a protein at a dose of at least about 7.5 mg / kg of protein, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0452] Embodiment 110. The method of embodiment 109, wherein the IRR is a fever.

[0453] Embodiment 111. The method of embodiment 109 or 110, wherein method of resolving the IRR comprises administering to the subject acetaminophen and diphenhydramine.

[0454] Embodiment 112. A method of treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal abnormality in a subject with Hunter syndrome, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising a protein, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386;

[0455] Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0456] Embodiment 113. The method of embodiment 112, wherein the therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase. Embodiment 114. The method of embodiment 112, wherein the therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase-beta.

[0457] Embodiment 115. The method of embodiment 112 or 113, wherein the therapeutically effective dose is from about 3 mg / kg to about 30 mg / kg of protein.

[0458] Embodiment 116. The method of any one of embodiments 112-115, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable excipient (a pharmaceutically acceptable carrier).

[0459] Embodiment 117. The method of any one of embodiments 112-116, wherein the second Fc polypeptide specifically binds to the transferrin receptor.

[0460] Embodiment 118. The method of any one of embodiments 112-117, wherein the IDS amino acid sequence comprises an amino acid sequence having at least 90% identity to SEQ ID NO:70.

[0461] Embodiment 119. The method of embodiment 118, wherein the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 90, 170 and 174.

[0462] Embodiment 120. The method of any one of embodiments 112-119, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 91, 171 or 175.

[0463] Embodiment 121. The method of any one of embodiments 112-119, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 213, 215, or 217.

[0464] Embodiment 122. The method of any one of embodiments 112-121, wherein the IDS amino acid sequence is linked to the N-terminus of the first Fc polypeptide.

[0465] Embodiment 123. The method of any one of embodiments 112-122, wherein the second Fc polypeptide comprises: d. Leu at position 380; e. Ala at position 389; and f. Ser at position 390.

[0466] Embodiment 124. The method of any one of embodiments 112-122, wherein the second Fc polypeptide comprises: d. Glu at position 380; e. Ala at position 389; and f. Asn at position 390.

[0467] Embodiment 125. The method of any one of embodiments 112-122, wherein the second Fc polypeptide comprises: d. Trp at position 380; e. Ser at position 389; and f. Ser at position 390.

[0468] Embodiment 126. The method of any one of embodiments 112-122, wherein the second Fc polypeptide comprises: d. Leu at position 380; e. Ser at position 389; and f. Ser at position 390.

[0469] Embodiment 127. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 92.

[0470] Embodiment 128. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 189.

[0471] Embodiment 129. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 95.

[0472] Embodiment 130. The method of embodiment 129, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO:95.

[0473] Embodiment 131. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 191.

[0474] Embodiment 132. The method of embodiment 131, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO: 191. Embodiment 133. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 168.

[0475] Embodiment 134. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 207.

[0476] Embodiment 135. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 169.

[0477] Embodiment 136. The method of any one of embodiments 112-117, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 199.

[0478] Embodiment 137. The method of any one of embodiments 112-136, which is a method of treating a neurobehavioral deficit.

[0479] Embodiment 138. The method of embodiment 137, wherein the neurobehavioral deficit is a motor skill deficit.

[0480] Embodiment 139. The method of embodiment 138, wherein the motor skill deficit is a fine motor skill deficit.

[0481] Embodiment 140. The method of embodiment 138, wherein the motor skill deficit is a gross motor skill deficit.

[0482] Embodiment 141. The method of embodiment 137, wherein the neurobehavioral deficit is an agility deficit.

[0483] Embodiment 142. The method of embodiment 137, wherein the neurobehavioral deficit is a cognitive deficit.

[0484] Embodiment 143. The method of embodiment 142, wherein the cognitive deficit is a learning or memory deficit.

[0485] Embodiment 144. The method of embodiment 137, wherein the neurobehavioral deficit is a sensorimotor gating deficit.

[0486] Embodiment 145. The method of any one of embodiments 112-136, which is a method of treating an auditory deficit. Embodiment 146. The method of embodiment 145, wherein administration of the pharmaceutical composition reduces middle ear effusion and / or otitis media in the subject, relative to a baseline level.

[0487] Embodiment 147. The method of embodiment 146, wherein the baseline level of a parameter is the parameter level for the subject prior to administration of the pharmaceutical composition.

[0488] Embodiment 148. The method of any one of embodiments 112-136, which is a method of treating a musculoskeletal abnormality.

[0489] Embodiment 149. The method of embodiment 148, wherein the musculoskeletal abnormality is a skeletal abnormality.

[0490] Embodiment 150. The method of any one of embodiments 112-149, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the CSF of the subject by at least about 10%, 15%, 20%, 25%, or 30%, wherein the reduction is relative to the level of the corresponding one or more analytes in the subject prior to the administration, wherein the one or more analytes are selected from the group consisting of a glycosaminoglycan (GAG), neurofilament light (Nf-L), soluble triggering receptor expressed on myeloid cells 2 (sTREM2), a bis(monoacylglycerol) phosphate (BMP), a ganglioside, and a sphingolipid.

[0491] Embodiment 151. An agent for use in resolving an infusion-related reaction (IRR), the method comprising administering the agent to a subject in need thereof, wherein the agent is selected from the group consisting of an anti-histamine, an anti-pyretic, and a corticosteroid, wherein the subject is being administered or was administered a pharmaceutical composition comprising a protein at a dose of at least about 7.5 mg / kg of protein, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0492] Embodiment 152. Use of an agent in the preparation of a medicament for resolving an infusion-related reaction (IRR), by administering the medicament to a subject in need thereof, wherein the agent is selected from the group consisting of an anti -histamine, an anti-pyretic, and a corticosteroid, wherein the subject is being administered or was administered a pharmaceutical composition comprising a protein at a dose of at least about 7.5 mg / kg of protein, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0493] Embodiment 153. A therapeutically effective dose of a pharmaceutical composition comprising a protein for use in treating Hunter syndrome in a subject in need thereof, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0494] Embodiment 154. The use of a therapeutically effective dose of a pharmaceutical composition comprising a protein in the preparation of a medicament for treating Hunter syndrome, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0495] Embodiment 155. A therapeutically effective dose of a pharmaceutical composition comprising a protein for use in treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal deficit in a subject with Hunter syndrome, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0496] Embodiment 156. The use of a therapeutically effective dose of a pharmaceutical composition comprising a protein in the preparation of a medicament for treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal deficit in a subject with Hunter syndrome, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0497] Embodiment 157. A pharmaceutical composition comprising a protein for use in a method of treating Hunter syndrome, the method comprising administering a therapeutically effective dose of the pharmaceutical composition to a subject in need thereof, wherein administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0498] Embodiment 158. Use of a protein in the preparation of a medicament for treating Hunter syndrome, by administering a therapeutically effective dose of the medicament to a subject in need thereof, wherein administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0499] Embodiment 159. The pharmaceutical composition of embodiment 157 or the use of embodiment 158, wherein the therapeutically effective dose is from about 3 mg / kg to about 30 mg / kg of protein.

[0500] Embodiment 160. A pharmaceutical composition comprising a protein for use in a method of treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal deficit associated with Hunter syndrome, the method comprising administering a therapeutically effective dose of the pharmaceutical composition to the subject, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421.

[0501] Embodiment 161. Use of a protein in the preparation of a medicament for treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal deficit associated with Hunter syndrome, by administering a therapeutically effective dose of the medicament to a subject in need thereof, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: Trp, Leu, or Glu at position 380; Tyr at position 384; Thr at position 386; Glu at position 387; Trp at position 388; Ser or Ala at position 389; Ser or Asn at position 390; Thr at position 413; Glu at position 415; Glu at position 416; and Phe at position 421. Embodiment 162. The pharmaceutical composition of embodiment 160 or the use of embodiment 161, wherein the therapeutically effective dose is from about 3 mg / kg to about 30 mg / kg of protein.

[0502] Certain Definitions

[0503] The terms “control” or “control sample” refer to any sample appropriate to the detection technique employed. The control sample may contain the products of the detection technique employed or the material to be tested. Further, the controls may be positive or negative controls.

[0504] The term “subject,” “individual,” and “patient,” as used interchangeably herein, refer to a mammal, including but not limited to humans, non-human primates, rodents ( e.g ., rats, mice, and guinea pigs), rabbits, cows, pigs, horses, and other mammalian species. In one embodiment, the patient is a human.

[0505] The term “pharmaceutically acceptable excipient” refers to a non-active pharmaceutical ingredient that is biologically or pharmacologically compatible for use in humans or animals, such as but not limited to a buffer, carrier, or preservative.

[0506] The term “administer” refers to a method of delivering agents (e.g., an LSD therapeutic agent, such as an ETV therapy described herein), compounds, or compositions (e.g, pharmaceutical composition) to the desired site of biological action. These methods include, but are not limited to, oral, topical delivery, parenteral delivery, intravenous delivery, intradermal delivery, intramuscular delivery, intrathecal delivery, colonic delivery, rectal delivery, or intraperitoneal delivery. In one embodiment, the polypeptides described herein are administered intravenously.

[0507] As used herein, “treatment” (and grammatical variations thereof such as “treat” or “treating”) refers to clinical intervention to alter the natural course of the individual being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include, but are not limited to, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.

[0508] The phrase “effective amount” means an amount of a compound described herein that (i) treats or prevents the particular disease, condition, or disorder, (ii) attenuates, ameliorates, or eliminates one or more symptoms of the particular disease, condition, or disorder, or (iii) prevents or delays the onset of one or more symptoms of the particular disease, condition, or disorder described herein.

[0509] A “therapeutically effective amount” of a substance / molecule disclosed herein may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the substance / molecule, to elicit a desired response in the individual. A therapeutically effective amount encompasses an amount in which any toxic or detrimental effects of the substance / molecule are outweighed by the therapeutically beneficial effects. A “prophylactically effective amount” refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically, but not necessarily, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount would be less than the therapeutically effective amount.

[0510] The terms “obtaining a sample from a patient”, “obtained from a patient” and similar phrasing, is used to refer to obtaining the sample directly from the patient, as well as obtaining the sample indirectly from the patient through an intermediary individual ( e.g ., obtaining the sample from a courier who obtained the sample from a nurse who obtained the sample from the patient).

[0511] An “iduronate sulfatase,” “iduronate-2-sulfatase,” or “IDS” as used herein refers to iduronate 2-sulfatase (EC 3.1.6.13), which is an enzyme involved in the lysosomal degradation of the glycosaminoglycans heparan sulfate and dermatan sulfate. Deficiency of IDS is associated with Mucopolysaccharidosis II, also known as Hunter syndrome. The term “IDS” as used herein as a component of a protein that comprises an Fc polypeptide is catalytically active and encompasses functional variants, including allelic and splice variants, of a wild-type IDS or a fragment thereof. The sequence of human IDS isoform I, which is the human sequence designated as the canonical sequence, is available under UniProt entry P22304 and is encoded by the human IDS gene at Xq28. The full-length sequence is provided as SEQ ID NO:69. A “mature” IDS sequence as used herein refers to a form of a polypeptide chain that lacks the signal and propeptide sequences of the naturally occurring full-length polypeptide chain. The amino acid sequence of a mature human IDS polypeptide is provided as SEQ ID NO:70, which corresponds to amino acids 34-550 of the full-length human sequence. A “truncated” IDS sequence as used herein refers to a catalytically active fragment of the naturally occurring full- length polypeptide chain. The amino acid sequence of an exemplary truncated human IDS polypeptide is provided as SEQ ID NO:90, which corresponds to amino acids 26-550 of the full- length human sequence. The structure of human IDS has been well -characterized. An illustrative structure is available under PDB accession code 5FQL. The structure is also described in Nat. Comm. 8:15786 doi: 10.1038 / ncommsl5786, 2017. Non-human primate IDS sequences have also been described, including chimpanzee (UniProt entry K7BKV4) and rhesus macaque (UniProt entry H9FTX2). A mouse IDS sequence is available under Uniprot entry Q08890. An IDS variant has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the activity of the corresponding wild-type IDS or fragment thereof, e.g., when assayed under identical conditions. A catalytically active IDS fragment has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the activity of the corresponding full-length IDS or variant thereof, e.g, when assayed under identical conditions.

[0512] An “IDS enzyme variant” refers to a functional variant, including allelic and splice variants, of a wild-type IDS enzyme or a fragment thereof, where the IDS enzyme variant has at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the activity of the corresponding wild-type IDS enzyme or fragment thereof, e.g, when assayed under identical conditions.

[0513] A “transferrin receptor” or “TfR” as used herein refers to transferrin receptor protein 1. The human transferrin receptor 1 polypeptide sequence is set forth in SEQ ID NO:72. Transferrin receptor protein 1 sequences from other species are also known (e.g, chimpanzee, accession number XP_003310238.1; rhesus monkey, NP_001244232.1; dog, NP_001003111.1; cattle, NP_001193506.1; mouse, NP_035768.1; rat, NP_073203.1; and chicken, NP_990587.1). The term “transferrin receptor” also encompasses allelic variants of exemplary reference sequences, e.g, human sequences, that are encoded by a gene at a transferrin receptor protein 1 chromosomal locus. Full-length transferrin receptor protein includes a short N-terminal intracellular region, a transmembrane region, and a large extracellular domain. The extracellular domain is characterized by three domains: a protease-like domain, a helical domain, and an apical domain. The apical domain sequence of human transferrin receptor 1 is set forth in SEQ ID NO: 178.

[0514] A “fusion protein” or “[IDS enzyme]-Fc fusion protein” as used herein refers to a dimeric protein comprising a first Fc polypeptide that is linked (e.g, fused) to an IDS enzyme, an IDS enzyme variant, or a catalytically active fragment thereof (i.e., an “[IDS]-Fc fusion polypeptide”); and a second Fc polypeptide that forms an Fc dimer with the first Fc polypeptide. The second Fc polypeptide may also be linked ( e.g ., fused) to an IDS enzyme, an IDS enzyme variant, or a catalytically active fragment thereof. The first Fc polypeptide and / or the second Fc polypeptide may be linked to the IDS enzyme, IDS enzyme variant, or catalytically active fragment thereof by a peptide bond or by a polypeptide linker. The first Fc polypeptide and / or the second Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that promote its heterodimerization to the other Fc polypeptide. The first Fc polypeptide and / or the second Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that confer binding to a transferrin receptor. The first Fc polypeptide and / or the second Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that reduce effector function. The first Fc polypeptide and / or the second Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that extend serum half-life.

[0515] A “fusion polypeptide” or “[IDS enzyme]-Fc fusion polypeptide” as used herein refers to an Fc polypeptide that is linked (e.g., fused) to an IDS enzyme, an IDS enzyme variant, or a catalytically active fragment thereof. The Fc polypeptide may be linked to the IDS enzyme, IDS enzyme variant, or catalytically active fragment thereof by a peptide bond or by a polypeptide linker. The Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that promote its heterodimerization to another Fc polypeptide. The Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that confer binding to a transferrin receptor. The Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that reduce effector function. The Fc polypeptide may be a modified Fc polypeptide that contains one or more modifications that extend serum half- life.

[0516] As used herein, the term “Fc polypeptide” refers to the C-terminal region of a naturally occurring immunoglobulin heavy chain polypeptide that is characterized by an Ig fold as a structural domain. An Fc polypeptide contains constant region sequences including at least the CH2 domain and / or the CH3 domain and may contain at least part of the hinge region. In general, an Fc polypeptide does not contain a variable region.

[0517] A “modified Fc polypeptide” refers to an Fc polypeptide that has at least one mutation, e.g, a substitution, deletion or insertion, as compared to a wild-type immunoglobulin heavy chain Fc polypeptide sequence, but retains the overall Ig fold or structure of the native Fc polypeptide.

[0518] The term “FcRn” refers to the neonatal Fc receptor. Binding of Fc polypeptides to FcRn reduces clearance and increases serum half-life of the Fc polypeptide. The human FcRn protein is a heterodimer that is composed of a protein of about 50 kDa in size that is similar to a major histocompatibility (MHC) class I protein and a P2-microglobulin of about 15 kDa in size.

[0519] As used herein, an “FcRn binding site” refers to the region of an Fc polypeptide that binds to FcRn. In human IgG, the FcRn binding site, as numbered using the EU index, includes T250, L251, M252, 1253, S254, R255, T256, T307, E380, M428, H433, N434, H435, and Y436.

[0520] These positions correspond to positions 20 to 26, 77, 150, 198, and 203 to 206 of SEQ ID NO:l.

[0521] As used herein, a “native FcRn binding site” refers to a region of an Fc polypeptide that binds to FcRn and that has the same amino acid sequence as the region of a naturally occurring Fc polypeptide that binds to FcRn.

[0522] The terms “CH3 domain” and “CH2 domain” as used herein refer to immunoglobulin constant region domain polypeptides. For purposes of this application, a CH3 domain polypeptide refers to the segment of amino acids from about position 341 to about position 447 as numbered according to EU, and a CH2 domain polypeptide refers to the segment of amino acids from about position 231 to about position 340 as numbered according to the EU numbering scheme and does not include hinge region sequences. CH2 and CH3 domain polypeptides may also be numbered by the IMGT (ImMunoGeneTics) numbering scheme in which the CH2 domain numbering is 1-110 and the CH3 domain numbering is 1-107, according to the IMGT Scientific chart numbering (IMGT website). CH2 and CH3 domains are part of the Fc region of an immunoglobulin. An Fc region refers to the segment of amino acids from about position 231 to about position 447 as numbered according to the EU numbering scheme, but as used herein, can include at least a part of a hinge region of an antibody. An illustrative hinge region sequence is the human IgGl hinge sequence EPKSCDKTHTCPPCP (SEQ ID NO:71).

[0523] “Naturally occurring,” “native” or “wild type” is used to describe an object that can be found in nature as distinct from being artificially produced. For example, a nucleotide sequence present in an organism (including a virus), which can be isolated from a source in nature and which has not been intentionally modified in the laboratory, is naturally occurring. Furthermore, “wild-type” refers to the normal gene, or organism found in nature without any known mutation. For example, the terms “wild-type,” “native,” and “naturally occurring” with respect to a CH3 or CH2 domain are used herein to refer to a domain that has a sequence that occurs in nature.

[0524] As used herein, the term “mutant” with respect to a mutant polypeptide or mutant polynucleotide is used interchangeably with “variant.” A variant with respect to a given wild- type CH3 or CH2 domain reference sequence can include naturally occurring allelic variants. A “non-naturally” occurring CH3 or CH2 domain refers to a variant or mutant domain that is not present in a cell in nature and that is produced by genetic modification, e.g., using genetic engineering technology or mutagenesis techniques, of a native CH3 domain or CH2 domain polynucleotide or polypeptide. A “variant” includes any domain comprising at least one amino acid mutation with respect to wild-type. Mutations may include substitutions, insertions, and deletions.

[0525] The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids.

[0526] Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g, hydroxyproline, g-carboxyglutamate and O- phosphoserine. “Amino acid analogs” refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g. , homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g, norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. “Amino acid mimetics” refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that function in a manner similar to a naturally occurring amino acid.

[0527] Naturally occurring a-amino acids include, without limitation, alanine (Ala), cysteine (Cys), aspartic acid (Asp), glutamic acid (Glu), phenylalanine (Phe), glycine (Gly), histidine (His), isoleucine (He), arginine (Arg), lysine (Lys), leucine (Leu), methionine (Met), asparagine (Asn), proline (Pro), glutamine (Gin), serine (Ser), threonine (Thr), valine (Val), tryptophan (Trp), tyrosine (Tyr), and combinations thereof. Stereoisomers of a naturally-occurring a-amino acids include, without limitation, D-alanine (D-Ala), D-cysteine (D-Cys), D-aspartic acid (D- Asp), D-glutamic acid (D-Glu), D-phenylalanine (D-Phe), D-histidine (D-His), D-isoleucine (D- Ile), D-arginine (D-Arg), D-lysine (D-Lys), D-leucine (D-Leu), D-methionine (D-Met), D- asparagine (D-Asn), D-proline (D-Pro), D-glutamine (D-Gln), D-serine (D-Ser), D-threonine (D-Thr), D-valine (D-Val), D-tryptophan (D-Trp), D-tyrosine (D-Tyr), and combinations thereof.

[0528] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission.

[0529] The terms “polypeptide” and “peptide” are used interchangeably herein to refer to a polymer of amino acid residues in a single chain. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non- naturally occurring amino acid polymers. Amino acid polymers may comprise entirely L-amino acids, entirely D-amino acids, or a mixture of L and D amino acids.

[0530] The term “protein” as used herein refers to either a polypeptide or a dimer ( i.e , two) or multimer {i.e., three or more) of single chain polypeptides. The single chain polypeptides of a protein may be joined by a covalent bond, e.g., a disulfide bond, or non-covalent interactions.

[0531] The term “conservative substitution,” “conservative mutation,” or “conservatively modified variant” refers to an alteration that results in the substitution of an amino acid with another amino acid that can be categorized as having a similar feature. Examples of categories of conservative amino acid groups defined in this manner can include: a “charged / polar group” including Glu (Glutamic acid or E), Asp (Aspartic acid or D), Asn (Asparagine or N), Gin (Glutamine or Q), Lys (Lysine or K), Arg (Arginine or R), and His (Histidine or H); an “aromatic group” including Phe (Phenylalanine or F), Tyr (Tyrosine or Y), Trp (Tryptophan or W), and (Histidine or H); and an “aliphatic group” including Gly (Glycine or G), Ala (Alanine or A), Val (Valine or V), Leu (Leucine or L), He (Isoleucine or I), Met (Methionine or M), Ser (Serine or S), Thr (Threonine or T), and Cys (Cysteine or C). Within each group, subgroups can also be identified. For example, the group of charged or polar amino acids can be sub-divided into sub-groups including: a “positively-charged sub-group” comprising Lys, Arg and His; a “negatively-charged sub-group” comprising Glu and Asp; and a “polar sub-group” comprising Asn and Gin. In another example, the aromatic or cyclic group can be sub-divided into subgroups including: a “nitrogen ring sub-group” comprising Pro, His and Trp; and a “phenyl subgroup” comprising Phe and Tyr. In another further example, the aliphatic group can be subdivided into sub-groups, e.g, an “aliphatic non-polar sub-group” comprising Val, Leu, Gly, and Ala; and an “aliphatic slightly-polar sub-group” comprising Met, Ser, Thr, and Cys. Examples of categories of conservative mutations include amino acid substitutions of amino acids within the sub-groups above, such as, but not limited to: Lys for Arg or vice versa, such that a positive charge can be maintained; Glu for Asp or vice versa, such that a negative charge can be maintained; Ser for Thr or vice versa, such that a free -OH can be maintained; and Gin for Asn or vice versa, such that a free -ML· can be maintained. In some embodiments, hydrophobic amino acids are substituted for naturally occurring hydrophobic amino acid, e.g., in the active site, to preserve hydrophobicity.

[0532] The terms “identical” or percent “identity,” in the context of two or more polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues, e.g, at least 60% identity, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% or greater, that are identical over a specified region when compared and aligned for maximum correspondence over a comparison window, or designated region, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.

[0533] For sequence comparison of polypeptides, typically one amino acid sequence acts as a reference sequence, to which a candidate sequence is compared. Alignment can be performed using various methods available to one of skill in the art, e.g, visual alignment or using publicly available software using known algorithms to achieve maximal alignment. Such programs include the BLAST programs, ALIGN, ALIGN-2 (Genentech, South San Francisco, Calif.) or Megalign (DNASTAR). The parameters employed for an alignment to achieve maximal alignment can be determined by one of skill in the art. For sequence comparison of polypeptide sequences for purposes of this application, the BLASTP algorithm standard protein BLAST for aligning two proteins sequence with the default parameters is used.

[0534] The terms “corresponding to,” “determined with reference to,” or “numbered with reference to” when used in the context of the identification of a given amino acid residue in a polypeptide sequence, refers to the position of the residue of a specified reference sequence when the given amino acid sequence is maximally aligned and compared to the reference sequence. Thus, for example, an amino acid residue in a modified Fc polypeptide “corresponds to” an amino acid in SEQ ID NO: 1, when the residue aligns with the amino acid in SEQ ID NO: 1 when optimally aligned to SEQ ID NO: 1. The polypeptide that is aligned to the reference sequence need not be the same length as the reference sequence. The term “polynucleotide” and “nucleic acid” interchangeably refer to chains of nucleotides of any length, and include DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and / or their analogs, or any substrate that can be incorporated into a chain by DNA or RNA polymerase. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. Examples of polynucleotides contemplated herein include single- and double-stranded DNA, single- and double-stranded RNA, and hybrid molecules having mixtures of single- and double-stranded DNA and RNA.

[0535] A “binding affinity” as used herein refers to the strength of the non-covalent interaction between two molecules, e.g., a single binding site on a polypeptide and a target, e.g, transferrin receptor, to which it binds. Thus, for example, the term may refer to 1 : 1 interactions between a polypeptide and its target, unless otherwise indicated or clear from context. Binding affinity may be quantified by measuring an equilibrium dissociation constant (KD), which refers to the dissociation rate constant (kd, time'1) divided by the association rate constant (ka, time'1M''). KD can be determined by measurement of the kinetics of complex formation and dissociation, e.g., using Surface Plasmon Resonance (SPR) methods, e.g, a Biacore™ system; kinetic exclusion assays such as KinExA®; and BioLayer interferometry (e.g, using the ForteBio®Octet®platform). As used herein, “binding affinity” includes not only formal binding affinities, such as those reflecting 1:1 interactions between a polypeptide and its target, but also apparent affinities for which KD’S are calculated that may reflect avid binding.

[0536] As used herein, the term “specifically binds” or “selectively binds” to a target, e.g,

[0537] TfR, when referring to an engineered TfR-binding polypeptide, TfR-binding peptide, or TfR- binding antibody as described herein, refers to a binding reaction whereby the engineered TfR- binding polypeptide, TfR-binding peptide, or TfR-binding antibody binds to the target with greater affinity, greater avidity, and / or greater duration than it binds to a structurally different target. In typical embodiments, the engineered TfR-binding polypeptide, TfR-binding peptide, or TfR-binding antibody has at least 5 -fold, 10-fold, 50-fold, 100-fold, 1,000-fold, 10,000-fold, or greater affinity for a specific target, e.g, TfR, compared to an unrelated target when assayed under the same affinity assay conditions. The term “specific binding,” “specifically binds to,” or “is specific for” a particular target (e.g, TfR), as used herein, can be exhibited, for example, by a molecule having an equilibrium dissociation constant KD for the target to which it binds of, e.g, 10-4M or smaller, e.g, 10-5M, 10-6M, 10-7M, 10-8M, 10-9M, 10-10M, 10-11M, or 10-12M. In some embodiments, an engineered TfR-binding polypeptide, TfR-binding peptide, or TfR- binding antibody specifically binds to an epitope on TfR that is conserved among species, ( e.g ., structurally conserved among species), e.g., conserved between non-human primate and human species (e.g, structurally conserved between non-human primate and human species). In some embodiments, an engineered TfR-binding polypeptide, TfR-binding peptide, or TfR-binding antibody may bind exclusively to a human TfR.

[0538] The term “variable region” or “variable domain” refers to a domain in an antibody heavy chain or light chain that is derived from a germline Variable (V) gene, Diversity (D) gene, or Joining (J) gene (and not derived from a Constant (Cμ and Cδ) gene segment), and that gives an antibody its specificity for binding to an antigen. Typically, an antibody variable region comprises four conserved “framework” regions interspersed with three hypervariable “complementarity determining regions.”

[0539] The terms “antigen-binding portion” and “antigen-binding fragment” are used interchangeably herein and refer to one or more fragments of an antibody that retains the ability to specifically bind to an antigen via its variable region. Examples of antigen-binding fragments include, but are not limited to, a Fab fragment (a monovalent fragment consisting of the VL,

[0540] VH, CL, and CH1 domains), a F(ab’)2 fragment (a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region), a single chain Fv (scFv), a disulfide- linked Fv (dsFv), complementarity determining regions (CDRs), a VL (light chain variable region), and a VH (heavy chain variable region).

[0541] The following Examples are intended to be non-limiting.

[0542] EXAMPLE 1 : Effect of peripheral administration of / CIV: IDS on brain GAG and lysosomal lipids in IDS KO x TfRmuhumice.

[0543] As described below, the effects of peripheral administration of ETVTDS on brain GAG and lysosomal lipids in IDS KO x TfRmuhumice was investigated.

[0544] Materials and Methods

[0545] Animal Care

[0546] Mice were housed under a 12-hour light / dark cycle and had access to water and standard rodent diet (LabDiet® #25502, Irradiated) ad libitum. Mouse strains

[0547] A previously described, IDS KO mice on a B6N background were obtained from The Jackson Laboratories (JAX strain 024744). Development and characterization of the TfRmu / huKI mouse line harboring the human TfR apical domain knocked into the mouse receptor was previously described (U.S. Patent No. 10,143,187). TfRmu / humale mice were bred to female IDS heterozygous mice to generate IDS KO x TfRmu / humice. All mice used in this study were males. Administration and tissue collection

[0548] 2 month old IDS KO x TfRmu / humice were injected i.v. with idursulfase (14.2 mg / kg body weight), or ETVTDS (40 mg / kg body weight) once every week for 4 weeks (n=8) (see, Example 6 for ETVTDS). 2 month-old littermate TfRmu / humice, injected i.v. with saline once every week for 4 weeks (n=5) were used as controls. For the 7-day cohort, animals were sacrificed 7 days following the first. For the 28-day cohort, animals were sacrificed 7 days following fourth weekly dose.

[0549] For terminal sample collection, animals were deeply anesthetized via intraperitoneal (i.p.) injection of 2.5% Avertin. For CSF collection, a sagittal incision was made at the back of the animal’s skull, subcutaneous tissue and muscle was separated to expose the cisterna magna and a pre-pulled glass capillary tube was used to puncture the cisterna magna to collect CSF.

[0550] CSF was transferred to a Low Protein LoBind Eppendorf tube and centrifuged at 12,700 rpm for 10 minutes at 4°C. CSF was transferred to a fresh tube and snap frozen on dry ice. Lack of blood contamination in mouse CSF was confirmed by measuring the absorbance of the samples at 420 nm. Blood was collected via cardiac puncture for serum collection. For serum collection, blood was allowed to clot at room temperature for at least 30 minutes. Tubes were then centrifuged at 12,700 rpm for 7 minutes at 4°C. Serum was transferred to a fresh tube and flash-frozen on dry ice. Animals were transcardially perfused with ice-cold PBS using a peristaltic pump (Gilson Inc. Minipuls Evolution). The brain and liver were dissected and flash-frozen on dry ice.

[0551] Tissue Preparation: GAG extraction and processing

[0552] Brain and liver tissue samples and CSF were collected as described above. Brain and liver tissue were homogenized using a TissueLyser from Qiagen. Tissue homogenate was then transferred to a 96-well deep plate and sonicated using a 96-tip sonicator (Q Sonica). A BCA protein assay was performed to quantify total protein, and 20 mg liver and 100 mg brain per sample were subjected to LC-MS / MS sample preparation. 3 mί was used per sample for CSF. Briefly, heparan and dermatan sulfate derived disaccharides were generated by digesting tissue homogenates using a combination of Heparinases I, II, III and Chondriotinase B. Digests were mixed with acetonitrile and subjected to LC-MS / MS as described below.

[0553] LCMS assay for GAG

[0554] Quantification of GAG was performed by liquid chromatography (Shimadzu Nexera X2 system, Shimadzu Scientific Instrument, Columbia, MD, USA) coupled to electrospray mass spectrometry (Sciex QTRAP 6500+, Sciex, Framingham, MA, USA). For each analysis, sample was injected on a ACQUITY UPLC BEH Amide 1.7 mm, 2.1x150 mm column (Waters Corporation) using a flow rate of 0.55 mL / minute with a column temperature of 55°C. Mobile phases A and B consisted of water with 10 mM ammonium formate and 0.1% formic acid, and acetonitrile with 0.1% formic acid, respectively. A gradient was programmed as follows: 0.0-0.5 minutes at 80%B, 0.5-3.5 minutes from 80%B to 50%B, 3.5-4.0 minutes 50%B to 80%B, 4.0- 4.5 minutes hold at 80%B. Electrospray ionization was performed in the negative-ion mode applying the following settings: curtain gas at 25; collision gas was set at medium; ion spray voltage at -4500; temperature at 600°C; ion source Gas 1 at 50; ion source Gas 2 at 60. Data acquisition was performed using Analyst 1.6.3 (Sciex) in multiple reaction monitoring mode (MRM), with dwell time 50 (msec) for each species, collision energy (CE) was set at -30; declustering potential (DP) at -80; entrance potential (EP) at -10; collision cell exit potential (CXP) at -10. GAGs were detected as [M-H]- using the following MRM transitions: D0A0 at m / z 378.1>87.0; D0S0 at m / z 416.1>138.0; D0a4 at m / z 458.1>300.0; D4UA-2S-GlcNCOEt-6S (Iduron Ltd, Manchester, UK) at m / z 472.0 (in source fragment ion) >97.0 was used as internal standard. Individual disaccharide species were identified based on their retention times and MRM transitions using commercially available reference standards (Iduron Ltd). GAGs were quantified by the peak area ratio of D0A0, D0S0 and D0a4 to the internal standard using Multi Quant 3.0.2 (Sciex). Reported GAG amounts were normalized to total protein levels as measured by a BCA assay (Pierce).

[0555] Tissue Preparation: Lipid extraction from brain tissue

[0556] Frozen brain tissues (20 ± 2 mg) were transferred into dry ice 2 mL Safe-Lock Eppendorf tube (Eppendorf Cat#022600044) and kept in dry ice containing a 5mm stainless steel bead (QIAGEN Cat#69989) and 400 mΐ of MS-grade methanol containing internal standards. The tissues were homogenized with Tissuelyser for 30 sec at 25 Hz (in the cold room). The samples were then centrifuged for 20 min at 21,000xg at 4°C. The methanol supernatant was transferred into new eppendorf vials and were left at -20°C for 1 hour to allow for further precipitation of proteins. The samples were then centrifuged for 10 min at 21,000xg at 4°C. 200uL of the methanol supernatant was transferred into a LCMS 96 well-plate and dry down under nitrogen and then resuspended in lOOuL of ACN / IPA / H20 (92.5 / 5 / 2.5) with 5 mM ammonium formate and 0.5% formic acid for GlcCer analysis. The rest of the supernatant was transferred, without disturbing pellet, into a separate LCMS 96 well-plate for analysis of BMP and ganglioside species. The samples were either directly run on LCMS or stored at -80°C. LCMS assay for BMP and ganglioside s

[0557] BMP and gangliosides analyses were performed by liquid chromatography (Shimadzu Nexera X2 system, Shimadzu Scientific Instrument, Columbia, MD, USA) coupled to electrospray mass spectrometry (Sciex QTRAP 6500+, Sciex, Framingham, M A, USA). For each analysis, 5 pL of sample was injected on a BEH C18 1.7 pm, 2.1><100 mm column (Waters Corporation, Milford, Massachusetts, USA) using a flow rate of 0.25 mL / min at 55°C. Mobile phase A consisted of 60:40 acetonitrile / water (v / v) with 10 mM ammonium acetate Mobile phase B consisted of 90:10 isopropyl alcohol / acetonitrile (v / v) with 10 mM ammonium acetate. The gradient was programmed as follows: 0.0-0.01 min from 45% B to 99% B, 0.1-3.0 min at 99% B, 3.0-3.01 min to 45% B, and 3.01-3.50 min at 45% B. Electrospray ionization was performed in negative ion mode applying the following settings: curtain gas at 30; collision gas was set at medium; ion spray voltage at -4500; temperature at 600°C; ion source Gas 1 at 50; ion source Gas 2 at 60. Data acquisition was performed using Analyst 1.6.3 (Sciex) in multiple reaction monitoring mode (MRM), with the following parameters: dwell time (msec) for each species reported in the Table A, collision energy (CE) at -50, declustering potential (DP) at -80; entrance potential (EP) at -10, and collision cell exit (CXP) potential at -15. BMP and gangliosides species were quantified using the non endogenous internal standards BMP di 14:0 and GM3 (d36:l (d5)). Quantification was performed using MultiQuant 3.02 (Sciex). BMP and gangliosides concentration were normalized to either total protein amount, tissue weight or volume. Protein concentration was measured using the bicinchoninic acid (BCA) assay (Pierce, Rockford, IL, USA). Table A. Acquisition parameters information for the BMP and ganghosides assay.

[0558] LCMS assay for GlcCer and GalCer

[0559] G1 ucosy 1 cerami de and galactosylceramide analyses were performed by liquid chromatography (Shimadzu Nexera X2 system, Shimadzu Scientific Instrument, Columbia, MD, USA) coupled to electrospray mass spectrometry' (Sciex QTRAP 6500+ Sciex, Framingham, MA, USA). For each analysis, 10 pL of sample was injected on a HALO i 111.1C 2,0 pm, 3.0 * 150 mm column (Advanced Materials Technology, PN 91813-701) using a flow rate of 0.45 mL / min at 45°C. Mobile phase A consisted of 92.5 / 5 / 2.5 ACN / IPA / H20 with 5 rnM ammonium formate and 0.5% formic Acid. Mobile phase B consisted of 92.5 / 5 / 2.5 H20 / IPA / ACN with 5 rnM ammonium formate and 0,5% formic Acid. The gradient was programmed as follows: 0,0- 3.1 min at 100% B, 3.2 min at 95% B, 5.7 min at 85% B, hold to 7.1 min at 85% B, drop to 0%

[0560] B at 7.25min and hold to 8.75 min, ramp back to 100% at 10.65 min and hold to 11 min. Electrospray ionization was performed in the positive-ion mode applying the following settings: curtain gas at 25; collision gas was set at medium; ion spray voltage at 5500; temperature at 350°C; ion source Gas 1 at 55; ion source Gas 2 at 60. Data acquisition was performed using Analyst 1.6 (Sciex) in multiple reaction monitoring mode (MRM) with the following parameters: dwell time (msec) and collision energy (CE) for each species reported in Table B, declustering potential (DP) at 45; entrance potential (EP) at 10; and collision ceil exit potential (CXP) at 12.5. Lipids were quantified using a mixture of isotope labeled internal standards as reported in Table B. Glucosylceramide and Galactosylceramide were identified based on their retention times and MRM properties of commercially available reference standards (Avanti Polar Lipids, Birmingham, AL, USA). Quantification was performed using Multi Quant 3.02 (Sciex). Metabolites were normalized to either total protein amount, tissue weight or volume. Table B: Acquisition parameters information for GlcCer and GalCer Assay. Mass spectrometry analysis of Eicosanoids

[0561] Eicosanoid analyses were performed by liquid chromatography (Shimadzu Nexera X2 system, Shimadzu Scientific Instrument, Columbia, MD, USA) coupled to electrospray mass spectrometry (Sciex QTRAP 6500+, Sciex, Framingham, MA, USA). For each analysis, 5 pL of sample was injected on a BEH CIS 1.7 pm, 2.1 * 100 mm column (Waters Corporation, Milford, Massachusetts, USA) using a flow rate of 0.6 tnL / min at 40°C. Mobile phases were composed as follows: A = w¾ter + 0.1% acetic acid, and B = 90=10 acetonitril e / isopropyl alcohol (v / v). The gradient was programmed as follows: 0.0-1.0 min at 25% B; 1.0-8.5 min to 95% B; 8.50-8.51 min at 95%B; 8.51-10.00 min at 25% B. Electrospray ionization was performed in negative ion mode applying the following settings: curtain gas at 30; collision gas w¾s set at medium; ion spray voltage at -4500; temperature at 600°C; ion source Gas 1 at 50; ion source Gas 2 at 60. Data acquisition was performed using Analyst 1.6.3 (Sciex) in multiple reaction monitoring mode (MRM), with the following parameters: dwell time (msec), collision energy (CE), and declustering potential (DP) for each species reported in Table C; entrance potential (EP) at -10; and collision cell exit potential (CXP) at -12. Eicosanoids were quantified using a mixture of non endogenous, deuterated internal standards as reported in Table C. Eicosanoids were identified based on their retention times and MRM properties of commercially available reference standards (Avanti Polar Lipids, Birmingham, AL, USA). Quantification was performed using Multi Quant 3.02 (Sciex) and Skyline. Metabolites were normalized to either total protein amount, tissue weight or volume. Protein concentration was measured using the bicinchoninic acid (BCA) assay (Pierce, Rockford, IL, USA).

[0562] Table C. Acquisition parameters information for Eicosanoid Assay.

[0563] Lipidomics analysis

[0564] Lipid analyses were performed by liquid chromatography (Shimadzu Nexera X2 system, Shimadzu Scientific Instrument, Columbia, MD, USA) coupled to electrospray mass spectrometry (QTRAP 6500+, Sciex, Framingham, MA, USA). For each analysis, 5 pL of sample was injected on aBEH CIS 1.7 pm, 2.1 xlOO mm column (Waters Corporation, Milford, Massachusetts, USA) using a flow rate of 0.25 mL / min at 55°C. For positive ionization mode, mobile phase A consisted of 60:40 acetonitrile / water (v / v) with 10 mM ammonium formate + 0.1% formic acid; mobile phase B consisted of 90; 10 isopropyl alcohol / acetonitrile (v / v) with 10 mM ammonium formate + 0,1% formic acid. For negative ionization mode, mobile phase A consisted of 60:40 acetonitrile / water (v / v) with 10 mM ammonium acetate; mobile phase B consisted of 90:10 isopropyl alcohol / acetonitrile (v / v) with 10 mM ammonium acetate. The gradient w7as programmed as follows: 0.0-8.0 min from 45% B to 99% B, 8.0-9.0 min at 99%

[0565] B, 9.0-9.1 min to 45% B, and 9.1-10.0 min at 45% B. Electrospray ionization was performed in either positive or negative ion mode applying the following settings: curtain gas at 30; collision gas was set at medium; ion spray voltage at 5500 (positive mode) or 4500 (negative mode), temperature at 250°C (positive mode) or 600°C (negative mode); ion source Gas 1 at 50; ion source Gas 2 at 60. Data acquisition w?as performed using Analyst 1.6.3 (Sciex) in multiple reaction monitoring mode (MRM), with the following parameters: dwell time (msec) and collision energy (CE) for each species reported in Table D (negative mode) or Table E (positive mode); declustering potential (DP) at 80 (positive mode) and at -80 (negative mode); entrance potential (EP) at 10 (positive mode) or -10 (negative mode); and collision cell exit, potential (CXP) at 12.5 (positive mode) or -12.5 (negative mode). Lipids were quantified using a mixture of non-endogenous internal standards as reported in Tables D and E. Lipids w?ere identified based on their retention times and MRM properties of commercially available reference standards (Avanii Polar Lipids, Birmingham, AL, USA). Quantification was performed using Multi Quant 3.02 (Sciex). Metabolites were normalized to either total protein amount or cell number. Table D. Acquisition parameters information for Lipidomics Assay in negative mode.

[0566] 111

[0567] i 1

[0568] Ί 1

[0569] J i 1

[0570] Ί 1 Table E. Acquisition parameters information for Lipidomics Assay in positive mode.

[0571]

[0572]

[0573]

[0574]

[0575]

[0576] Homogenization of ETV:IDS brain tissue and Trem2 analysis of ETV:IDS brain tissue and CSF

[0577] 50 mg tissue was homogenized in 500 pL IX CST buffer (Cell Signaling Technology 9803S) made with complete Protease Inhibitor (Roche #04693132001) and PhosStop (Roche 04906837001) using the Qiagen TissueLyzer II (Cat No. / ID: 85300) for 2 rounds of 3 minutes at 30Hz. Homogenate was incubated on ice for 20 minutes and spun at 21,100 g for 30 minutes at 4°C. Subsequent lysate was transferred to a clean 96-well deep plate, and a BCA was performed to quantify total protein amounts. Samples were then stored at -80 °C until assay use.

[0578] For Trem2 analysis in brain tissue and soluble Trem2 (sTrem2) analysis in CSF, an MSD GOLD 96w small spot streptavidin plate (MSD L45SA) was prepared for Trem2 assay by coating with lug / mL biotinylated sheep anti -mouse antibody (R&D Systems BAF1729) overnight at 4°C. The next day, the MSD plate was rinsed with tris buffered saline with triton (TBST) and blocked for two hours using 3% bovine serum albumin in TBST, while shaking at 600rpm. The MSD plate was again rinsed again with TBST, and brain lysates were diluted 5x in blocking solution and added to the MSD plate to incubate for 1 hour at 600rpm. Following the next TBST rinse, sulfotagged sheep anti-mouse antibody (R&D Systems AF1729) was added to the plate and incubated for 1 hour, again at 600rpm, and a final rinse was conducted before adding 2X MSD read buffer diluted in water. The plate was then read using the MSD Meso Sector S600. The Trem2 signal was normalized to the protein concentration and plotted with GraphPad Prism.

[0579] Abbreviations

[0580] BMP=bis(monoacylglycerol)phosphate; ETV:IDS=enzyme transport vehicle: iduronate 2-sulfatase; GlcCer=glucosylceramide; GalCer=galactosyl ceramide; IDS=iduronate 2-sulfatase; KI=knock-in; KO=knockout; TfRmu / hu=chimeric human / mouse transferrin receptor. Results

[0581] To determine whether the robust GAG reduction observed in brain translated to correction of downstream disease-relevant pathology, the ability of ETVTDS to correct secondary lysosomal storage was assessed. Four weekly activity-equivalent doses of ETVTDS or idursulfase were intravenously administered to IDS KO; TfRmu / huKI mice, and the levels of a panel of lysosomal lipids, including gangliosides, glucosylceramide, and bis(monoacylglycerol)phosphate, were measured using liquid chromatography-tandem mass spectrometry (LCMS). Significant accumulation of lysosomal lipids was observed in the brains of IDS KO; TfRmu / huKI mice compared with wild-type controls. Following 4 weekly doses of 40 mg / kg, ETVTDS was highly effective in lowering lysosomal lipids in the brain, completely reducing levels of these lipids to that seen in wild-type mice. Treatment with an activity- equivalent dose of idursulfase, however, failed to reduce levels of these lysosomal lipids in the brain. Together, these data demonstrate that ETVTDS effectively corrects secondary lysosomal storage in addition to its proximal effects on GAG accumulation.

[0582] In particular Figures 5A-5B show peripheral administration of ETVTDS (4 week treatment) corrects (Figure 5A) brain and (Figure 5B) CSF GAG accumulation in IDS KO mice. A 58% reduction in brain GAG was observed with peripheral administration of ETVTDS compared to a 14% reduction with an activity equivalent dose of Elaprase. Additionally, a 66% reduction in CSF GAG was observed with peripheral administration of ETVTDS compared to a 27% reduction with an activity equivalent dose of Elaprase (one outlier omitted for ETVTDS group). Figures 14A-14B illustrate the reduction of individual GAG species (D00S0, D00A0, D00a4) in the brain and CSF. In a follow-up study, CSF GAGs were reduced three times over WT at a dosing of 40 mg / kg of ETVTDS.

[0583] Figure 6 shows peripheral administration of ETVTDS (4 week treatment) corrected lysosomal lipid (gangliosides) accumulation in IDS KO brains.

[0584] Figures 7A-7B show that peripheral administration of ETVTDS (4 week treatment) corrected lysosomal lipid (GlcCer) accumulation in IDS KO brains. Correction of brain GlcCer accumulation with peripheral administration of ETVTDS was observed, while no change was observed in galactosyl ceramides (GalCer).

[0585] Figure 8 shows that peripheral administration of ETVTDS (4 week treatment) corrected lysosomal lipid (BMP) accumulation in IDS KO brains.

[0586] Figure 9 shows a heat map illustrating lipid levels in brains of IDS KO mice treated with vehicle, ETV:IDS or Elaprase (idursulfase). This heat map was generated using modified data from Table 2. Specifically, the data in Table 2 was modified with a cutoff, converting values between 0.9 and 1.1 to 1, in order to show differences greater than 10%.

[0587] Figure 10 shows that peripheral administration of ETVTDS corrected TREM2 accumulation in IDS KO brains.

[0588] Figure 11 illustrates that an increase in CSF sTrem2 levels was observed in IDS KO; TfRmu / hujQmjce reiative to a TfRmu / huKI mice cohort.Treatment with ETVTDS reduced the accumulation of CSF sTrem2 levels in the IDS KO; TfRmu / huKI mice.

[0589] Table 1 provides a summary of the GlcCer species analyzed, with the levels represented as fold over WT.

[0590] Table 2 provides data for lipid levels in brains of IDS KO mice treated with vehicle, ETVTDS or Elaprase (fold changes over WT).

[0591] EXAMPLE 2. Measurement of brain GAG, lysosomal lipids, and neurofilament light chain (Nf- L) in IDS KO mice at 3, 6 and 9 months of age

[0592] As described below, brain GAG, lysosomal lipid, and neurofilament light chain (Nf-L) levels were investigated in WT and IDS KO mice at 3, 6 and 9 months of age.

[0593] Materials and Methods

[0594] Animals used in this study were cared for as described herein (Example 1). Tissues were sampled, and lipid and GAG levels were measured using methods described herein (Example 1). Nf-L levels were measured as described below.

[0595] Methods for CSF and Serum Analysis of Nf-L

[0596] Using Quanterix Simoa Neurofilament-Light (NF-L) Sample Diluent (Quanterix 102252), cerebrospinal fluid (CSF) was diluted lOOx and serum was diluted 4x before being added to Simoa 96-well microplate (Quanterix 101457). NF-light assay was carried out according to Simoa NF-Light Advantage Kit (Quanterix 1031086) instructions using Simoa detector reagent and bead reagent (Quanterix 103159 and 102246, respectively). After incubation of samples with detector and bead reagent at 30°C, 800rpm for 30 minutes, the sample plate was washed with Simoa Wash Buffer A (Quanterix 103078) on Simoa Microplate Washer according to Quanterix two step protocol. SBG reagent (Quanterix 102250) was subsequently added, and samples were incubated at 30°C, 800rpm for 10 minutes. The 2-step washer protocol was continued, with the sample beads being twice resuspended in Simoa Wash Buffer B (Quanterix 103079) before final aspiration of buffer. Sample NF-L levels were measured using the NF-Light analysis protocol on the Quanterix SR-X instrument and interpolated against a calibration curve provided with the Quanterix assay kit.

[0597] Results

[0598] Brain HS / DS (GAG) accumulation at ages 3, 6, and 9 months in IDS KO mice relative to age-matched WT controls was measured (Figure 1). GAG accumulation was significantly higher in the IDS KO mice at all ages tested.

[0599] Lysosomal lipid accumulation (GM1, GM2, GM3, BMP, GlcCer and GD3) in the brains of IDS KO mice relative to age-matched WT controls was also measured (Figures 2A-2D). GM1 (d36: 1) showed similar levels in both IDS KO and WT mice (Figures 2A and 2B), whereas levels of GM2 (36:1), GM3 (36:1), BMP (36:2), GlcCer (34:1), and GD (39:1) all showed between 1.7 and 5.5 fold increases over WT animals (Figures 2A-2D). Similar to GD3 (39:1), GD3 (36: 1) also is increased in the IDS KO (2 fold on average).

[0600] Elevated levels of BMP in the serum of IDS KO mice relative to their age-matched controls were also observed. In particular, BMP (36:2) and BMP (44: 12) were increased particularly in the 9 month serum samples taken in IDS KO mice as compared to WT controls (Figure 3).

[0601] Elevated levels of lysosomal lipids (Gdla / b, GM3, BMP and GlcCer) were observed in the CSF of 9 month old IDS KO mice relative to WT age-matched controls (Figure 4).

[0602] Nf-L is a useful marker for neurodegeneration (Norgren et al. 2003. Brain Research 987(l):25-31), but it has not previously been associated with Hunter syndrome / MPSII. Nf-L concentrations in serum and CSF of 9-month old IDS KO mice were elevated relative to a same- age cohort of wild-type mice (Figures 31 A, 3 IB). The relative difference in Nf-L levels in CSF increased with the age of the mice cohorts, with the largest difference in Nf-L levels observed in the 9-month old mice cohort groups (Figure 31C). These results indicate that Nf-L can also be useful as a disease-related and treatment-responsive biomarker in mouse models of Hunter syndrome. EXAMPLE 3. Effect of peripheral administration ofETV.TDS on GAG and lysosomal lipids in IDS KO x TfRmuhumice

[0603] The effect of varying doses of ETV:IDS on GAG and lysosomal lipids in IDS KO x TfRmuhumice was examined.

[0604] Materials and Methods

[0605] Animal Care

[0606] Mice were housed under a 12-hour light / dark cycle and had access to water and standard rodent diet (LabDiet® #25502, Irradiated) ad libitum.

[0607] Mouse strains

[0608] The IDS KO x TfRmu / humice used in this study are described in Example 1 above. All mice used in this study were males.

[0609] Administration and Sample Collection

[0610] 2-3 month old IDS KO x TfRmu / humice were injected i.v. with saline, idursulfase (14.2 mg / kg body weight), or ETV:IDS (3, 10, 20, or 40 mg / kg body weight) once every week for 4 weeks (n=5-8) (see, Example 6 for ETVTDS). 2-3 month-old littermate TfRmu / humice, injected i.v. with saline once every week for 4 weeks (n=5) were used as controls. Animals were sacrificed 7 days following last 4-week dose.

[0611] For terminal sample collection, animals were deeply anesthetized via intraperitoneal (i.p.) injection of 2.5% Avertin. For CSF collection, a sagittal incision was made at the back of the animal’s skull, subcutaneous tissue and muscle was separated to expose the cisterna magna and a pre-pulled glass capillary tube was used to puncture the cisterna magna to collect CSF.

[0612] CSF was transferred to a Low Protein LoBind Eppendorf tube and centrifuged at 12,700 rpm for 10 minutes at 4°C. CSF was transferred to a fresh tube and snap frozen on dry ice. Lack of blood contamination in mouse CSF was confirmed by measuring the absorbance of the samples at 420 nm. Blood was collected via cardiac puncture for serum collection. For serum collection, blood was allowed to clot at room temperature for at least 30 minutes. Tubes were then centrifuged at 12,700 rpm for 7 minutes at 4°C. Serum was transferred to a fresh tube and flash-frozen on dry ice. Animals were transcardially perfused with ice-cold PBS using a peristaltic pump (Gilson Inc. Minipuls Evolution). The brain was dissected and flash-frozen on dry ice.

[0613] Tissue Preparation and LCMS Assay

[0614] Tissue preparation and LCMS assays were performed using methods similar to those described in Example 1.

[0615] Results

[0616] A dose-dependent decrease in serum brain and CSF GAGs was observed (Figures 12A- 12C) for mice receiving ETV:IDS. Notably, serum GAGs were corrected down to wildtype levels.

[0617] Importantly, there was a substantial reduction in brain lysosomal lipids (GM3, GlcCer and BMP), even at the lowest ETV:IDS dose (3 mg / kg) tested (Figures 13A-13C). Because lipid accumulation in IDS-deficient mice is believed to be a functional result of the GAG accumulation, these results may suggest that functional restoration of lysosomal function in the brain can be achieved even with GAG levels that are elevated relative to WT mice.

[0618] EXAMPLE 4. Effect of peripheral administration ofETVdDS on GAG and lysosomal lipids in specific CNS cell types of IDS KO x TfRmuhumice

[0619] A protocol was developed to isolate enriched populations of neurons, astrocytes, and microglial cells from brain tissue. The enriched populations from IDS KO x TfRmuhumice were then used to investigate the effect of varying doses of ETVTDS on GAG and lysosomal.

[0620] Materials and Methods

[0621] Animal Care

[0622] Mice were housed under a 12-hour light / dark cycle and had access to water and standard rodent diet (LabDiet® #25502, Irradiated) ad libitum.

[0623] Mouse strains

[0624] The TfRmu / humice and IDS KO x TfRmu / humice used in this study are described in Example 1 above. All mice used in this study were males.

[0625] Administration and Sample Collection

[0626] 2-3 month old IDS KO x TfRmu / humice were injected i.v. with saline or ETV:IDS (40 mg / kg body weight) once every week for 4 weeks (n=4-6 per treatment) (see, Example 6 for ETVTDS). 2-3 month-old littermate TfRmu / humice, injected i.v. with saline once every week for 4 weeks (n=4-6) were used as controls. Animals were sacrificed 7 days following last 4-week dose. For terminal sample collection, animals were deeply anesthetized via intraperitoneal (i.p.) injection of 2.5% Avertin. For CSF collection, a sagittal incision was made at the back of the animal’s skull, subcutaneous tissue and muscle was separated to expose the cistema magna and a pre-pulled glass capillary tube was used to puncture the cisterna magna to collect CSF.

[0627] CSF was transferred to a Low Protein LoBind Eppendorf tube and centrifuged at 12,700 rpm for 10 minutes at 4°C. CSF was transferred to a fresh tube and snap frozen on dry ice. Lack of blood contamination in mouse CSF was confirmed by measuring the absorbance of the samples at 420 nm. Blood was collected via cardiac puncture for serum collection. For serum collection, blood was allowed to clot at room temperature for at least 30 minutes. Tubes were then centrifuged at 12,700 rpm for 7 minutes at 4°C. Serum was transferred to a fresh tube and flash-frozen on dry ice. Animals were transcardially perfused with ice-cold PBS using a peristaltic pump (Gilson Inc. Minipuls Evolution). The brain was dissected and flash-frozen on dry ice.

[0628] CNS Cell Type Isolation

[0629] To prepare a single cell suspension for sorting CNS cells, mice were perfused with PBS, brains dissected and processed into a single cell suspension according to the manufacturers’ protocol using the adult brain dissociation kit (Miltenyi Biotec 130-107-677). Cells were Fc blocked (Biolegend #101320, 1 : 100) and stained for flow cytometric analysis with Fixable Viability Stain BV510 (BD Biosciences #564406, 1:100) to exclude dead cells, CDllb-BV421 (BD Biosciences 562605, 1:100), CD31-PerCP Cy5.5 (BD Biosciences #562861, 1:100), 01- 488 (Thermo / eBio #14-6506-82, 1:37.5), Thyl-PE (R&D #FAB7335P, 1:100), and EAAT2-633 (Alomone #AGC-022-FR, 1:50). Cells were washed with PBS / 1% BSA and strained through a lOOpm filter before sorting CD1 lb+ microglia, EAAT2+ astrocytes, and Thyl+ neurons on a FACS Aria III (BD Biosciences) with a lOOpm nozzle. In order to achieve pure populations of astrocytes, microglia, and neurons negative gates were set to remove 01+ and CD31+ cells which are predominantly oligodendrocytes and endothelial cells respectively. Sorted cells were either pelleted or collected directly into lysis buffers, and then processed for downstream analysis including qRT-PCR, RNAseq, or glycomics as described in the relevant methods disclosed herein. Cell numbers were used to calculate pg GAG / cell.

[0630] Cell lysate preparation and LCMS assays for measurement of GAGs, BMPs, gangliosides, GlcCer, and GalCer were performed using methods similar to those described in Example 1. Distribution analysis of ETV:IDS across CNS cell types

[0631] Live cells in sheath fluid (-1.5 ml) were sorted directly into 150 mL 5% CHAPS buffer for lysis, final concentration of CHAPS 0.5%. Samples were concentrated with Amicon Ultra 30KDa filters. Five (5) pL of sample or recombinant ETV:IDS dilution series was run with an IgG (human) AlphaLIS A Detection Kit (PerkinElmer #AL205C) per the manufacturer’ s instructions and read on an EnVision™ plate reader. Sample concentrations were interpolated from the standard curve generated using ETV:IDS and normalized to total cell input number.

[0632] Results

[0633] To confirm the enrichment and purity of isolated cell populations, gene expression profiles for each of the sorted populations were analyzed using RNA-Seq and qRT-PCR and compared to known profiles (data not shown). A strong enrichment of corresponding cell-type specific genes in isolated populations and a reduction in gene markers of endothelial cells and oligodendrocytes was observed (data not shown). This collective data demonstrates that highly pure populations of neurons, astrocytes, and microglia were obtained.

[0634] The cell-type specific distribution and efficacy of ETV:IDS in the brains of IDS KO; TfRmu / huKI mice were subsequently assessed.

[0635] GAG levels in enriched CNS cell populations were quantified as described by LC-MS / MS. Figure 15A illustrates that GAG levels were elevated in microglia, astrocytes, and neurons isolated from IDS KO; TfRmu / huKI mice relative to TfRmu / huKI controls, demonstrating substrate accumulation across all three CNS cell types when IDS expression was knocked-out (n=3-5 mice per group). The IDS KO; TfRmu / huKI mice (n=4 mice per group) were dosed intravenously with 40 mg / kg ETV:IDS, and enzyme concentration was assessed across CNS cell populations two hours post-dose. Figure 15B illustrates that significant accumulation of ETVTDS was observed in neurons, astrocytes, and microglia, demonstrating that ETVTDS effectively distributes to the brain parenchyma and is taken up by key CNS cell types. All data are displayed as mean ± SEM; unpaired student’s t-test p≤ 0.05*, 0.001***.

[0636] Next, IDS KO; TfRmu / huKI mice were dosed with 40 mg / kg ETVTDS intravenously once a week for four weeks, and LC-MS / MS was used to assess the ability of ETVTDS to reduce GAG accumulation in all three CNS cell types. Figure 16 illustrates that ETV:IDS treatment reduced GAG levels in neurons, astrocytes, and microglia to levels comparable to that seen in wild-type mice following repeated administration. Data are displayed as mean ± SEM; one-way ANOVA with Tukey’s multiple comparison test, * p ≤ 0.05, ** p ≤ 0.01. The data demonstrates that ETVTDS enables the delivery of IDS past the cerebral endothelium to brain cells and that this delivery is sufficient for efficacy across key CNS cell types.

[0637] ETVTDS treatment also reduced the secondary accumulation of the lysosomal lipids including gangliosides (Figure 17), glucosylceramides (Figure 18), and bis(monoacylglycerol)phosphate (BMP) (Figure 19) in CNS cell types of interest (e.g., neurons, astrocytes, microglial cells). These data illustrate that treatment with ETVTDS corrects secondary lysosomal dysfunction in addition to primary GAG storage in CNS cell types.

[0638] EXAMPLE 5. Spatial distribution of accumulated lipid species and correction of lipid accumulation by E TV: IDS

[0639] The effect of varying doses of ETV:IDS on the spatial distribution of lysosomal lipids and on microglial activation in IDS KO x TfRmuhumice was examined.

[0640] Mouse strains and Administration

[0641] The TfRmu / humice and IDS KO x TfRmu / humice used in this study are described in Example 1 above. All mice used in this study were males. The mice were administered saline, idursulfase, or ETV:IDS (40 mg / kg body weight) and sacrificed for tissue analysis as described in Example 1 (see, Example 6 for ETVTDS).

[0642] Mass-spectrometry based imaging of ganglioside levels

[0643] Brain tissue was flash frozen on aluminum foil that was slowly lowered into liquid nitrogen for approximately 10 seconds. Frozen brains were stored at -80°C until ready for use. Prior to sectioning, the brains were placed in a cryostat chamber to equilibrate the tissues to -20°C. Brains were cut on a cryostat (Leica Biosystems, Buffalo Grove, IL) into 12 pm thick sections and thaw-mounted onto indium -tix oxide (ITO) coated slides (Delta Technologies, Loveland, CO). Two brain levels were collected at approximately +0.72mm and -1.82mm from Bregma. Plates with sections designated for IMS were washed three times with chilled (about 4 °C) 50 mM ammonium formate and allowed to dry at room temperature prior to matrix application. Additional sections were obtained for H&E staining. After staining, digital micrographs were obtained via a slide scanner (Leica Biosystems, Buffalo Grove, IL). For matrix application, the plates were coated with 1,5-diaminonaphthalene (DAN) MALDI matrix via sublimation (Hankin et al. 2007. Journal of the American Society for Mass Spectrometry 18:1646-1652; Thomas etal. 2012. Analytical Chemistry 84:2048-2054). Briefly, 100 mg of recrystallized DAN was placed in the bottom of a glass sublimation apparatus (Chemglass Life Sciences, Vineland, NJ). The apparatus was placed on a metal heating block set to 130 °C, and DAN was sublimated onto the tissue surface for 4 minutes at a pressure of less than 25 mTorr. Approximately 1.8 mg of DAN was applied to each slide, determined by weighing the slide before and after matrix application. The coated plates were then placed in a Petri dish, flushed with nitrogen gas, and stored at -80°C for two days prior to MS analysis (Yang el al. 2019. International Journal of Mass Spectrometry 437:3-9).

[0644] For imaging mass spectrometry, the plates were allowed to equilibrate to room temperature prior to removal from the sealed Petri dish. The brain sections were imaged on a Solarix 15T FT-ICR MS (Bruker Daltonics, Billerica, MA), equipped with a SmartBeam II 2 kHz frequency tripled Nd:YAG laser (355 nm). Images were acquired at 100 pm spatial resolution in negative ion mode. Each pixel is the average of 1000 laser shots using the small laser focus setting and random -walking within the 100 pm pixel. The mass spectrometer was externally calibrated with a series of phosphorus clusters (Sladkova etal. 2009. Rapid Communications in Mass Spectrometry 23 :3114-3118). Data were collected from m / z 600 - 3,000 with a time-domain file size of 1 M (FID length = 1.3631 sec), resulting in a resolving power of 153,000 at m / z 1041. Images were generated using Fleximaging 3.0 (Bruker Daltonics, Billerica, MA). Gangliosides were identified by accurate mass, with the mass accuracies typically bette...

Claims

CLAIMSWhat is claimed is:

1. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising a protein, wherein administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the cerebrospinal fluid (CSF) of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

2. The method of claim 1, wherein the therapeutically effective dose is from about 3 mg / kg to about 30 mg / kg of protein.

3. The method of claim 2, wherein the therapeutically effective dose is about 3 mg / kg of protein.

4. The method of claim 2, wherein the therapeutically effective dose is about 7.5 mg / kg of protein.

5. The method of claim 2, wherein the therapeutically effective dose is about 15 mg / kg of protein.

6. The method of claim 2, wherein the therapeutically effective dose is about 30 mg / kg of protein.

7. The method of any one of claims 1-6, wherein the pharmaceutical composition is administered weekly.

8. The method of any one of claims 1-7, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable excipient.

9. The method of any one of claims 1-8, wherein the second Fc polypeptide specifically binds to the transferrin receptor.

10. The method of any one of claims 1-9, wherein the IDS amino acid sequence comprises an amino acid sequence having at least 90% identity to SEQ ID NO:70.

11. The method of claim 10, wherein the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 90, 170 and 174.

12. The method of any one of claims 1-11, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 91, 171 or 175.

13. The method of any one of claims 1-11, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 213, 215, or 217.

14. The method of any one of claims 1-13, wherein the IDS amino acid sequence is linked to the N-terminus of the first Fc polypeptide.

15. The method of any one of claims 1-14, wherein the second Fc polypeptide comprises: a. Leu at position 380; b. Ala at position 389; and c. Ser at position 390.

16. The method of any one of claims 1-14, wherein the second Fc polypeptide comprises: a. Glu at position 380; b. Ala at position 389; and c. Asn at position 390.

17. The method of any one of claims 1-14, wherein the second Fc polypeptide comprises: a. Trp at position 380; b. Ser at position 389; and c. Ser at position 390.

18. The method of any one of claims 1-14, wherein the second Fc polypeptide comprises: a. Leu at position 380; b. Ser at position 389; and c. Ser at position 390.

19. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 92.

20. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 189.

21. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 95.

22. The method of claim 21, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO:95.

23. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 191.

24. The method of claim 23, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO: 191.

25. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 168.

26. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 207.

27. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 169.

28. The method of any one of claims 1-9, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 199.

29. The method of any one of claims 1-28, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the CSF of the subject by at least about 10%, 15%, 20%, 25%, or 30%, wherein the reduction is relative to the level of the corresponding one or more analytes in the subject prior to the administration, wherein the one ormore analytes are selected from the group consisting of neurofilament light (Nf-L), soluble triggering receptor expressed on myeloid cells 2 (sTREM2), a bis(monoacylglycerol) phosphate (BMP), a ganglioside, and a sphingolipid.

30. The method of claim 29, wherein the administration of the pharmaceutical composition reduces levels of the one or more analytes in the CSF of the subject to baseline levels, measured in a healthy subject or in a subject that does not have Hunter syndrome.

31. The method of any one of claims 1-30, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the serum of the subject by at least about 30%, 40%, 50%, 60%, or 70% relative to the level of the corresponding one or more analytes in the serum of the subject prior to the administration, wherein the one or more analytes are selected from the group consisting of a GAG and Nf-L.

32. The method of claim 31, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the serum of the subject to baseline levels, measured in a healthy subject or in a subject that does not have Hunter syndrome.

33. The method of claim 31, wherein the administration of the pharmaceutical composition reduces levels of Nf-L in the serum of the subject to baseline levels, measured in a healthy subject or in a subject that does not have Hunter syndrome.

34. The method of any one of claims 1-33, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject by at least about 30%, 40%, 50%, 60%, or 70% relative to the level of the GAG in the urine of the subject prior to the administration.

35. The method of claim 34, wherein the administration of the pharmaceutical composition reduces levels of a GAG in the urine of the subject to baseline levels, measured in a healthy subject or in a subject that does not have Hunter syndrome.

36. The method of any one of claims 1-35, wherein the administration of the pharmaceutical composition improves or maintains the subject’s toileting abilities percentage (TAP) relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition.

37. The method of any one of claims 1-36, wherein the administration of the pharmaceutical composition improves or maintains the subject’s qualitative individualized educational plan (IEP) trajectories in cognitive categories or behavioral categories relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition.

38. The method of any one of claims 1-37, wherein the administration of the pharmaceutical composition improves or maintains the subject’s hearing relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition, as assessed by an auditory brainstem response (ABR) assessment or a standard hearing test.

39. The method of any one of claims 1-38, wherein the administration of the pharmaceutical composition changes the subject’s liver volume relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition, as assessed by MRI or ultrasound.

40. The method of any one of claims 1-39, wherein the administration of the pharmaceutical composition changes the subject’s spleen volume relative to a baseline level measured for the subject prior to administration of the pharmaceutical composition, as assessed by MRI or ultrasound.

41. The method of any one of claims 1-40, wherein the subject is a male subject.

42. The method of any one of claims 1-41, wherein the subject is from about 2 to 18 years of age.

43. The method of any one of claims 1-41, wherein the subject is from about 2 to 10 years of age.

44. The method of any one of claims 1-41, wherein the subject is from about 5 to 10 years of age.

45. The method of any one of claims 1-41, wherein the subject is less than 4 years of age.

46. The method of any one of claims 1-45, wherein the subject has a weight of > 15 kg.

47. The method of any one of claims 1-45, wherein the subject has a weight of > 19 kg.

48. The method of any one of claims 1-47, wherein the subject has a development quotient(DQ) < 85.

49. The method of any one of claims 1-48, wherein the subject has a decline of at least 10 points in development quotient (DQ) within a period of about 6 months or longer.

50. The method of any one of claims 1-49, wherein the subject has neuronopathic Hunter syndrome (nMPS II) or has a same genetic mutation in the IDS gene as a blood relative with confirmed neuronopathic Hunter syndrome (nMPS II).

51. The method of any one of claims 1-50, wherein the pharmaceutical composition is administered to the subject intravenously.

52. The method of claim 51, wherein the subject does not experience an infusion-related reaction (IRR) upon administration of the pharmaceutical composition.

53. The method of claim 52, wherein IRR is an allergic reaction.

54. The method of claim 52, wherein IRR is anaphylaxis.

55. The method of any one of claims 52-54, wherein the pharmaceutical composition is administered to the subject without pretreatment or co-administration of medication for aninfusion-related reaction (IRR).

56. The method of claim 51, wherein the pharmaceutical composition is administered to the subject with pretreatment or co-administration of medication for an infusion-related reaction (IRR).

57. The method of claim 55 or 56, wherein the medication for infusion-related reaction is one or more selected from the group consisting of: an anti-histamine, an anti-pyretic, and a corticosteroid.

58. The method of any one of claims 1-57, wherein the urine total GAG concentration (normalized to creatinine) does not increase relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

59. The method of any one of claims 1-57, wherein the urine total GAG concentration (normalized to creatinine) decreases relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

60. The method of claim 58 or 59, wherein the stabilization or decrease in urine total GAG concentration in the subject supports safety of the administered dose.

61. The method of any one of claims 1-60, wherein the incidence of anti-drug antibodies (AD As) does not increase relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

62. The method of any one of claims 1-60, wherein the incidence of anti-drug antibodies (AD As) increases by less than 10% relative to a baseline level after administration of the pharmaceutical composition, wherein the baseline level is measured for the subject prior to administration of the pharmaceutical composition.

63. The method of any one of claims 1-62, wherein the frequency of serious adverse events (SAEs) is less than about 1 / 1000.

64. The method of any one of claims 1-63, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 4 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to administration.

65. The method of claim 64, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 4 weekly doses.

66. The method of any one of claims 1-63, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to administration.

67. The method of claim 66, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 8 weekly doses.

68. The method of any one of claims 1-63, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 12 weekly doses, wherein the reduction is relative to the CSF levels of the GAG in the subject prior to administration.

69. The method of claim 68, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the CSF of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 12 weekly doses.

70. The method of any one of claims 1-69, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 4 weekly doses, wherein the reduction is relative to the urine levels of the GAG in the subject prior to administration.

71. The method of claim 70, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 4 weekly doses.

72. The method of any one of claims 1-69, wherein the administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the urine levels of the GAG in the subject prior to administration.

73. The method of claim 72, wherein the administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the urine of the subject by at least 50%, 60%, 70%, 75%, 80%, 85%, or 90% after 8 weekly doses.

74. The method of any one of claims 70-73, wherein administration of the pharmaceutical composition reduces levels of the glycosaminoglycan (GAG) in the urine of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome.

75. The method of any one of claims 64-74, wherein the GAG is heparan sulfate.

76. The method of claim 75, wherein administration of the pharmaceutical composition reduces levels heparan sulfate in the CSF of the subject by at least 80% after at least 4 weekly doses, wherein the reduction is relative to the CSF heparan sulfate levels in the subject prior to administration.

77. The method of claim 75, wherein administration of the pharmaceutical composition reduces levels heparan sulfate in the CSF of the subject by at least 70% after at least 12 weeklydoses, wherein the reduction is relative to the CSF heparan sulfate levels in the subject prior to administration.

78. The method of any one of claims 64-74, wherein the GAG is dermatan sulfate.

79. The method of any one of claims 1-78, wherein the administration of the pharmaceutical composition reduces levels of a ganglioside in the CSF of the subject by at least 10%, 15%,20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the ganglioside in the subject prior to administration.

80. The method of claim 79, wherein the administration of the pharmaceutical composition reduces levels of the ganglioside in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses.

81. The method of claim 79 or 80, wherein the ganglioside is GM3.

82. The method of any one of claims 1-81, wherein the administration of the pharmaceutical composition reduces levels of a BMP in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% after at least 8 weekly doses, wherein the reduction is relative to the CSF levels of the BMP in the subject prior to administration.

83. The method of claim 82, wherein the administration of the pharmaceutical composition reduces levels of the BMP in the CSF of the subject by at least 10%, 15%, 20%, 25%, 30%,40%, 50%, 60%, 70%, 80%, or 90% after 8 weekly doses.

84. The method of claim 82 or 83, wherein the BMP is a BMP di 18:1 species.

85. The method of any one of claims 1-84, wherein prior to the administration of the pharmaceutical composition, the subject had received recombinant idursulfase enzyme replacement therapy.

86. The method of any one of claims 1-85, wherein the subject had pre-existing anti-drug antibodies against IDS prior to administration of the pharmaceutical composition.

87. The method of claim 86, wherein the subject’s titer of anti-drug antibodies against IDS ranges from 189 to greater than 11 million.

88. The method of claim 87, wherein the subject’s titer of anti-drug antibodies against IDS is greater than 11 million.

89. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 3 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

90. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 7.5 mg / kg, and wherein the protein comprises:a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

91. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 15 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415;x. Glu at position 416; and xi. Phe at position 421.

92. A method of treating Hunter syndrome in a subject in need thereof, comprising administering to the subject a protein at a weekly dose of about 30 mg / kg, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 89; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

93. The method of any one of claims 89-92, wherein the protein is comprised in a pharmaceutical composition that further comprises a pharmaceutically acceptable excipient.

94. A method of resolving an infusion-related reaction (IRR) in a subject receiving treatment for Hunter syndrome, comprising administering one or more agents selected from the group consisting of an anti-histamine, an anti-pyretic, and a corticosteroid, wherein the subject is being administered or was administered a pharmaceutical composition comprising a protein at a dose of at least about 7.5 mg / kg of protein, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; andb. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 89; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

95. The method of claim 94, wherein the IRR is a fever.

96. The method of claim 94 or 95, wherein method of resolving the IRR comprises administering to the subject acetaminophen and diphenhydramine.

97. A method of treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal abnormality in a subject with Hunter syndrome, comprising administering to the subject a therapeutically effective dose of a pharmaceutical composition comprising a protein, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388;vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi . Phe at position 421.

98. The method of claim 97, wherein the therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase.

99. The method of claim 97, wherein the therapeutically effective dose comprises an amount of the protein that is activity equivalent to a standard of care dose for recombinant idursulfase- beta.

100. The method of claim 97 or 98, wherein the therapeutically effective dose is from about 3 mg / kg to about 30 mg / kg of protein.

101. The method of any one of claims 97-100, wherein the pharmaceutical composition further comprises a pharmaceutically acceptable excipient.

102. The method of any one of claims 97-101, wherein the second Fc polypeptide specifically binds to the transferrin receptor.

103. The method of any one of claims 97-102, wherein the IDS amino acid sequence comprises an amino acid sequence having at least 90% identity to SEQ ID NO:70.

104. The method of claim 103, wherein the IDS amino acid sequence comprises a sequence selected from the group consisting of SEQ ID NOs:70, 90, 170 and 174.

105. The method of any one of claims 97-104, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 91, 171 or 175.

106. The method of any one of claims 97-104, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises the amino acid sequence of SEQ ID NO: 213, 215, or 217.

107. The method of any one of claims 97-106, wherein the IDS amino acid sequence is linked to the N-terminus of the first Fc polypeptide.

108. The method of any one of claims 97-107, wherein the second Fc polypeptide comprises: a. Leu at position 380; b. Ala at position 389; and c. Ser at position 390.

109. The method of any one of claims 97-107, wherein the second Fc polypeptide comprises: a. Glu at position 380; b. Ala at position 389; and c. Asn at position 390.

110. The method of any one of claims 97-107, wherein the second Fc polypeptide comprises: a. Trp at position 380; b. Ser at position 389; and c. Ser at position 390.

111. The method of any one of claims 97-107, wherein the second Fc polypeptide comprises: a. Leu at position 380; b. Ser at position 389; and c. Ser at position 390.

112. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 92.

113. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 189.

114. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 95.

115. The method of claim 114, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO:95.

116. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 191.

117. The method of claim 116, wherein the second Fc polypeptide further comprises SEQ ID NO: 89, wherein SEQ ID NO: 89 is attached to the N-terminus of SEQ ID NO: 191.

118. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 168.

119. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 207.

120. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 175; and the second Fc polypeptide comprises SEQ ID NO: 169.

121. The method of any one of claims 97-102, wherein the first Fc polypeptide linked to the IDS amino acid sequence comprises SEQ ID NO: 217; and the second Fc polypeptide comprises SEQ ID NO: 199.

122. The method of any one of claims 97-121, which is a method of treating a neurobehavioral deficit.

123. The method of claim 122, wherein the neurobehavioral deficit is a motor skill deficit.

124. The method of claim 123, wherein the motor skill deficit is a fine motor skill deficit.

125. The method of claim 123, wherein the motor skill deficit is a gross motor skill deficit.

126. The method of claim 122, wherein the neurobehavioral deficit is an agility deficit.

127. The method of claim 122, wherein the neurobehavioral deficit is a cognitive deficit.

128. The method of claim 127, wherein the cognitive deficit is a learning or memory deficit.

129. The method of claim 122, wherein the neurobehavioral deficit is a sensorimotor gating deficit.

130. The method of any one of claims 97-121, which is a method of treating an auditory deficit.

131. The method of claim 130, wherein administration of the pharmaceutical composition reduces middle ear effusion and / or otitis media in the subject, relative to a baseline level.

132. The method of claim 131, wherein the baseline level of a parameter is the parameter level for the subject prior to administration of the pharmaceutical composition.

133. The method of any one of claims 97-121, which is a method of treating a musculoskeletal abnormality.

134. The method of claim 133, wherein the musculoskeletal abnormality is a skeletal abnormality.

135. The method of any one of claims 97-134, wherein the administration of the pharmaceutical composition reduces levels of one or more analytes in the CSF of the subject by at least about 10%, 15%, 20%, 25%, or 30%, wherein the reduction is relative to the level of the corresponding one or more analytes in the subject prior to the administration, wherein the one or more analytes are selected from the group consisting of a glycosaminoglycan (GAG), neurofilament light (Nf-L), soluble triggering receptor expressed on myeloid cells 2 (sTREM2), a bis(monoacylglycerol) phosphate (BMP), a ganglioside, and a sphingolipid.

136. A pharmaceutical composition comprising a protein for use in a method of treating Hunter syndrome, the method comprising administering a therapeutically effective dose of the pharmaceutical composition to a subject in need thereof, wherein administration of the pharmaceutical composition reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413;ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

137. Use of a protein in the preparation of a medicament for treating Hunter syndrome by administering a therapeutically effective dose of the medicament to a subject in need thereof, wherein administration of the medicament reduces levels of a glycosaminoglycan (GAG) in the CSF of the subject to a baseline level measured in a healthy subject or a subject that does not have Hunter syndrome, and wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

138. A pharmaceutical composition comprising a protein for use in a method of treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal deficit associated with Hunter syndrome, the method comprising administering a therapeutically effective dose of the pharmaceutical composition to a subject in need thereof, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; andb. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; and xi. Phe at position 421.

139. Use of a protein in the preparation of a medicament for treating a neurobehavioral deficit, an auditory deficit and / or a musculoskeletal deficit associated with Hunter syndrome, by administering a therapeutically effective dose of the medicament to a subject in need thereof, wherein the protein comprises: a. a first Fc polypeptide linked to an iduronate 2-sulfatase (IDS) amino acid sequence, an IDS variant amino acid sequence, or a catalytically active fragment thereof; and b. a second Fc polypeptide comprising the following amino acid residues, according to EU numbering: i. Trp, Leu, or Glu at position 380; ii. Tyr at position 384; iii. Thr at position 386; iv. Glu at position 387; v. Trp at position 388; vi. Ser or Ala at position 389; vii. Ser or Asn at position 390; viii. Thr at position 413; ix. Glu at position 415; x. Glu at position 416; andxi. Phe at position 421.

140. The pharmaceutical composition of claim 136 or 138 or the use of claim 137 or 139, wherein the therapeutically effective dose is from about 3 mg / kg to about 30 mg / kg of protein.