Treatment and prevention of muscle atrophy and type 2 diabetes with inositol polyphosphate phosphatase-like 1 (inppl1) inhibitors

Abstract

The present disclosure generally relates to the treatment of subjects having muscle atrophy or at risk of developing muscle atrophy by administering an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) inhibitor to the subject., and to the treatment of subjects having type 2 diabetes or at risk of developing type 2 diabetes by administering an INPPL1 inhibitor to the subject.

Description

[0001] DOCKET NO.: 38120-4614 (11651WO01)

[0002] - 1 - Treatment And Prevention Of Muscle Atrophy And Type 2 Diabetes With Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) Inhibitors

[0003] Reference To Sequence Listing

[0004] This application includes a Sequence Listing filed electronically as an XML file named 381204614SEQ, created on April 6, 2026 with a size of 3,343,414 bytes. The Sequence Listing is incorporated herein by reference.

[0005] Field

[0006] The present disclosure generally relates to the treatment of subjects having muscle atrophy or at risk of developing muscle atrophy by administering an INPPL1 inhibitorto the subject, to methods of identifying subjects having an increased risk of developing muscle atrophy, to the treatment of subjects having type 2 diabetes or at risk of developing type 2 diabetes by administering an INPPL1 inhibitorto the subject, and to methods of identifying subjects having an increased risk of developing type 2 diabetes.

[0007] Background

[0008] Skeletal muscular atrophy, also known as muscle wasting, has symptoms including muscle weakness, myokymia, and muscular fasciculation. Skeletal muscle atrophy occurs in response to a variety of pathophysiological stimuli and contributes to profound losses of muscle mass and whole body strength. Examples of settings characterized by muscle atrophy include rare genetic diseases affecting skeletal muscle (including but not limited to muscular dystrophies, myotonic dystrophies, and mitochondrial myopathies), inflammatory muscle diseases (including but not limited to polymyositis and dermatomyositits), sarcopenia (including but not limited to age-related sarcopenia), myopathy arising secondary to environmental influences (e.g., drug-induced, alcohol-induced, among others), myopathy arising secondary to systemic diseases (e.g., thyroid-associated myopathy), and other neuromuscular conditions leading to muscle atrophy (e.g., amyotrophic lateral sclerosis, myasthenia gravis, among others). Weight loss via various mechanisms (e.g., bariatric surgery, or pharmacologically-induced) may also produce substantial loss of skeletal muscle mass and lead to muscle atrophy. Furthermore, skeletal muscle plays a crucial role in metabolic homeostasis. It is the primary site of glucose disposal, helping to regulate blood sugar levels by taking up glucose from the

[0009] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0010] - 2 -bloodstream during periods of high blood sugar. Additionally, muscle plays a significant role in the regulation of adipose tissue, primarily through the process of lipid oxidation.

[0011] Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) (a.k.a. SH2-domain containing phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2 (SHIP2)) is encoded by a 15 kb gene located at llql3.4. INPPL1 encodes the inositol phosphatase, SHIP2. SHIP2 is 1258 amino acids long, 138 kDa, and is involved in the regulation of insulin function, epidermal growth factor receptor turnover, and actin remodeling. More specifically, SHIP2 functions to dephosphorylate, and negatively regulate, the lipid second messenger phosphatidylinositol (3,4,5)P3. SHIP2 is required for the maintenance and dynamic remodeling of actin structures as well as in endocytosis, having a major impact on ligand-induced EGFR internalization and degradation. SHIP2 also participates in regulation of cortical and submembraneous actin by hydrolyzing phosphatidylinositol (3,4,5)P3 thereby regulating membrane ruffling. In addition, SHIP2 regulates cell adhesion and cell spreading and is required for HGF-mediated lamellipodium formation, cell scattering and spreading. Diseases associated with INPPL1 include opsismodysplasia and Schneckenbecken dysplasia.

[0012] Summary

[0013] The present disclosure provides methods of treating a subject having muscle atrophy, or at risk of developing muscle atrophy, the methods comprising administering an INPPL1 inhibitor to the subject.

[0014] The present disclosure provides methods of treating a subject having type 2 diabetes, or at risk of developing type 2 diabetes, the methods comprising administering an INPPL1 inhibitor to the subject.

[0015] The present disclosure also provides methods of treating a subject having muscle atrophy or at risk of developing muscle atrophy by administering a muscle atrophy therapeutic agent or muscle atrophy therapy, the methods comprising: determining or having determined whether the subject has an INPPL1 variant nucleic acid molecule by: obtaining or having obtained a biological sample from the subject; and performing or having performed a sequence analysis on the biological sample to determine if the subject has a genotype comprising the INPPL1 variant nucleic acid molecule; and administering or continuing to administerthe muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or administering an INPPL1 inhibitor to a subject that

[0016] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0017] - 3 -is INPPL1 reference, orto a subject that is heterozygous for the INPPL1 variant nucleic acid molecule; or administering or continuing to administer the muscle atrophy therapeutic agent or muscle atrophy therapy in a standard dosage amount to a subject that is homozygous for the INPPL1 variant nucleic acid molecule; wherein the presence the INPPL1 variant nucleic acid molecule indicates the subject has a decreased risk of developing muscle atrophy.

[0018] The present disclosure also provides methods of treating a subject having type 2 diabetes or at risk of developing type 2 diabetes by administering a type 2 diabetes therapeutic agent, the methods comprising: determining or having determined whether the subject has an INPPL1 variant nucleic acid molecule by: obtaining or having obtained a biological sample from the subject; and performing or having performed a sequence analysis on the biological sample to determine if the subject has a genotype comprising the INPPL1 variant nucleic acid molecule; and administering or continuing to administer the type 2 diabetes therapeutic agent in an amount that is the same as or lessthan a standard dosage amount, and / or administering an INPPL1 inhibitor to a subject that is INPPL1 reference, or to a subject that is heterozygous for the INPPL1 variant nucleic acid molecule; or administering or continuing to administer the type 2 diabetes therapeutic agent in a standard dosage amount to a subject that is homozygous for the INPPL1 variant nucleic acid molecule; wherein the presence the INPPL1 variant nucleic acid molecule indicates the subject has a decreased risk of developing type 2 diabetes.

[0019] The present disclosure also provides methods of identifying a subject having an increased risk of developing muscle atrophy, the methods comprising: determining or having determined the presence or absence of an INPPL1 variant nucleic acid molecule in a biological sample obtained from the subject; wherein: when the subject is INPPL1 reference, then the subject has an increased risk of developing muscle atrophy; and when the subject is heterozygous or homozygous for the INPPL1 variant nucleic acid molecule, then the subject has a decreased risk of developing muscle atrophy.

[0020] The present disclosure also provides methods of identifying a subject having an increased risk of developing type 2 diabetes, the methods comprising: determining or having determined the presence or absence of an INPPL1 variant nucleic acid molecule in a biological sample obtained from the subject; wherein: when the subject is INPPL1 reference, then the subject has an increased risk of developing type 2 diabetes; and when the subject is heterozygous or homozygous for the INPPL1 variant nucleic acid molecule, then the subject has a decreased risk of developing type 2 diabetes.

[0021] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0022] - 4- The present disclosure also provides muscle atrophy therapeutic agents for use in the treatment or prevention of muscle atrophy in a subject having an INPPL1 variant nucleic acid molecule.

[0023] The present disclosure also provides type 2 diabetes therapeutic agents for use in the treatment or prevention of type 2 diabetes in a subject having an INPPL1 variant nucleic acid molecule.

[0024] The present disclosure also provides INPPL1 inhibitors for use in the treatment or prevention of muscle atrophy in a subject that is INPPL1 reference or in a subject that is heterozygous for an INPPL1 variant nucleic acid molecule.

[0025] The present disclosure also provides INPPL1 inhibitors for use in the treatment or prevention of type 2 diabetes in a subject that is INPPL1 reference or in a subject that is heterozygous for an INPPL1 variant nucleic acid molecule.

[0026] Brief Description Of The Drawings

[0027] The accompanying figures, which are incorporated in and constitute a part of this specification, illustrate several features of the present disclosure and are intended to exemplify non-limiting embodiments of the present disclosure.

[0028] FIG. 1 shows loss of function of INPPL1 associates with increased creatinine levels, increased bioelectrical impedance analysis (BIA)- and dual-energy X-ray absorptiometry (DXA)-derived markers of lean mass, increased BIA-derived fat mass, and numerical increases in grip strength and MRI-derived muscle mass.

[0029] FIG. 2 shows Inppll siRNA knockdown extended p-Akt signaling in C2C12 differentiated myotubes.

[0030] FIG. 3 shows CACNG1 mAb-AAV9(W503A)-gRNA directed Cas9 editing of Inppll resulted in a reduction of mRNA levels in the tibialis anterior and EDL muscles after i.m. injection.

[0031] FIG. 4 shows the burden of loss of function and deleterious missense variants in INPPL1 associates with a lower risk of type 2 diabetes.

[0032] Description

[0033] Various terms relating to aspects of the present disclosure are used throughout the specification and claims. Such terms are to be given their ordinary meaning in the art, unless

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[0035] - 5 -otherwise indicated. Other specifically defined terms are to be construed in a manner consistent with the definitions provided herein.

[0036] Unless otherwise expressly stated, it is in no way intended that any method or aspect set forth herein be construed as requiring that its steps be performed in a specific order.

[0037] Accordingly, where a method claim does not specifically state in the claims or descriptions that the steps are to be limited to a specific order, it is in no way intended that an order be inferred, in any respect. This holds for any possible non-expressed basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, or the number or type of aspects described in the specification.

[0038] As used herein, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise.

[0039] As used herein, the term "about" means that the recited numerical value is approximate and small variations would not significantly affect the practice of the disclosed embodiments. Where a numerical value is used, unless indicated otherwise by the context, the term "about" means the numerical value can vary by ±10% and remain within the scope of the disclosed embodiments.

[0040] As used herein, the term "comprising" may be replaced with "consisting" or "consisting essentially of' in particular embodiments as desired.

[0041] As used herein, the terms "nucleic acid", "nucleic acid molecule", "nucleic acid sequence", "polynucleotide", or "oligonucleotide" can comprise a polymeric form of nucleotides of any length, can comprise DNA and / or RNA, and can be single-stranded, doublestranded, or multiple stranded. One strand of a nucleic acid also refers to its complement.

[0042] As used herein, the term "subject" includes any animal, including mammals. Mammals include, but are not limited to, farm animals (such as, for example, horses, cows, and pigs), companion animals (such as, for example, dogs and cats), laboratory animals (such as, for example, mice, rats, and rabbits), and non-human primates. In some embodiments, the subject is a human. In some embodiments, the human is a patient underthe care of a physician.

[0043] It has been observed in accordance with the present disclosure that rare INPPL1 variant nucleic acid molecules (whetherthese variants are homozygous or heterozygous in a particular subject) associate with a greater muscle mass and strength. It has also been observed in accordance with the present disclosure that rare INPPL1 variant nucleic acid molecules

[0044] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0045] - 6 - (whether these variants are homozygous or heterozygous in a particular subject) associate with a lower risk of type 2 diabetes. It is believed that INPPL1 variant nucleic acid molecules have not been associated with increased muscle mass or decreased atrophy in humans. In particular, it has been observed that pLoF (singletons) in I N PPL1 / SH I P-2 associate with increased bioimpedance-derived lean mass. In addition, it has been observed that pLoF (singletons) in IN PPL1 / SH IP-2 associate with decreased risk of type 2 diabetes. Therefore, subjects that are INPPL1 reference or heterozygous for an INPPL1 variant nucleic acid molecule may be treated with an INPPL1 inhibitor such that muscle mass is increased and / or muscle atrophy is inhibited or prevented, the symptoms thereof are reduced or prevented and / or muscle mass is increased, and / or development of symptoms is repressed or prevented. In addition, subjects that are INPPL1 reference or heterozygous for an INPPL1 variant nucleic acid molecule may be treated with an INPPL1 inhibitor such that type 2 diabetes is treated or prevented, the symptoms thereof are reduced or prevented, and / or to prevent and / or treat obesity or cardiometabolic disease (e.g. diabetes), and / or development of symptoms is repressed or prevented. It is also believed that such subjects having muscle atrophy may further be treated with one or more muscle atrophy therapeutic agents or muscle atrophy therapy that promotes skeletal muscle hypertrophy and / ortreats or inhibits muscle atrophy. It is also believed that such subjects having type 2 diabetes may further be treated with one or more type 2 diabetes therapeutic agents. In addition, the present disclosure provides methods of leveraging the presence or absence of INPPL1 variant nucleic acid molecules in subjects to identify or stratify risk is such subjects of developing muscle atrophy, or to diagnose subjects as having an increased risk of developing muscle atrophy. In addition, the present disclosure provides methods of leveraging the presence or absence of INPPL1 variant nucleic acid molecules in subjects to identify or stratify risk is such subjects of developing type 2 diabetes, or to diagnose subjects as having an increased risk of developing type 2 diabetes.

[0046] For purposes of the present disclosure, any particular subject, such as a human, can be categorized as having one of three INPPL1 genotypes: i) INPPL1 reference; ii) heterozygous for an INPPL1 variant nucleic acid molecule; or iii) homozygous for an INPPL1 variant nucleic acid molecule. A subject is INPPL1 reference when the subject does not have a copy of an INPPL1 variant nucleic acid molecule. A subject is heterozygous for an INPPL1 variant nucleic acid molecule when the subject has a single copy of an INPPL1 variant nucleic acid molecule. A

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[0048] - 7 -subject is homozygous for an INPPL1 variant nucleic acid molecule when the subject has two copies of an INPPL1 variant nucleic acid molecule.

[0049] In any of the embodiments described herein, the INPPL1 variant nucleic acid molecule can be any nucleic acid molecule (such as, a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule produced from an mRNA molecule) encoding an INPPL1 variant polypeptide having a partial loss-of-function, a complete loss-of-function, a predicted partial loss-of-function, or a predicted complete loss-of-function. A subject who has an INPPL1 polypeptide having a partial loss-of-function (or predicted partial loss-of-function) is hypomorphic for INPPL1. In some embodiments, the INPPL1 variant nucleic acid molecule may result in decreased or aberrant expression or activity of INPPL1 mRNA or polypeptide. In some embodiments, the INPPL1 variant nucleic acid molecule may be associated with a reduced in vitro response to INPPL1 ligands compared to reference INPPL1. In some embodiments, the INPPL1 variant nucleic acid molecule is a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide. In some embodiments, the INPPL1 variant nucleic acid molecule is a missense variant nucleic acid molecule. In some embodiments, the INPPL1 variant nucleic acid molecule comprises a single nucleotide polymorphism (SNP). In some embodiments, the INPPL1 variant nucleic acid molecule comprises a variation in a coding region. In some embodiments, the INPPL1 variant nucleic acid molecule does not comprise a variation in a non-coding region, except for a splice acceptor region (two bases before the start of any exon except the first). In some embodiments, the INPPL1 variant nucleic acid molecule results or is predicted to result in a premature truncation of an INPPL1 polypeptide compared to the reference INPPL1. In some embodiments, the INPPL1 variant nucleic acid molecule is a variant that is predicted to be damaging to the protein function (and hence, in this case, protective to the human) by in vitro prediction algorithms such as Polyphen, SIFT, or similar algorithms. In some embodiments, the INPPL1 variant nucleic acid molecule is a variant that causes or is predicted to cause a nonsynonymous amino acid substitution in an INPPL1 nucleic acid molecule and whose allele frequency is less than 1 / 100 alleles in the population from which the subject is selected. In some embodiments, the INPPL1 variant nucleic acid molecule is a rare missense variant (allele frequency < 0.1%; or 1 in 1,000 alleles), or a splice-site, stop-gain, start-loss, stop-loss, frameshift, or in-frame indel, or other frameshift INPPL1 variant.

[0050] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0051] - 8 - In any of the embodiments described herein, the INPPL1 variant genomic nucleic acid molecule may include one or more variations at any of the positions of chromosome 11 (i.e., positions 72,223,701-72,239,147) using the nucleotide sequence of the INPPL1 reference genomic nucleic acid molecule in the GRCh38 / hg38 human genome assembly (see, ENSG00000165458.15, ENST00000298229.7 annotated in the in the Ensembl database (URL: world wide web at "useast.ensembl.org / Homo_sapiens / Gene / Summary? g=ENSG00000165458;r=ll:72223701-72239147;transcript=ENST00000298229.7")) as a reference sequence. The sequences provided in this transcript for the INPPL1 genomic nucleic acid molecule is only an exemplary sequence. Other sequences forthe INPPL1 genomic nucleic acid molecule are also possible.

[0052] In any of the embodiments described herein, the INPPL1 variant nucleic acid molecule may comprise any one or more of the following genetic variations in the genomic nucleic acid molecule (referring to the chromosome:positions set forth in the GRCh38 / hg38 human genome assembly) listed in Table 1, or a cDNA molecule produced from the mRNA molecule.

[0053] Table 1

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[0252]

[0253] For subjects that are genotyped or determined to be INPPL1 reference, such subjects have an increased risk of developing muscle atrophy compared to subjects that are heterozygous or homozygous for an INPPL1 variant nucleic acid molecule. For subjects that are genotyped or determined to be either INPPL1 reference or heterozygous for an INPPL1 variant nucleic acid molecule, such subjects can be treated with an INPPL1 inhibitor.

[0254] For subjects that are genotyped or determined to be INPPL1 reference, such subjects have an increased risk of developing type 2 diabetes compared to subjects that are heterozygous or homozygous for an INPPL1 variant nucleic acid molecule. For subjects that are genotyped or determined to be either INPPL1 reference or heterozygous for an INPPL1 variant nucleic acid molecule, such subjects can be treated with an INPPL1 inhibitor.

[0255] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0256] - 75 - In any of the embodiments described herein, the subject in whom muscle atrophy is prevented by administering an INPPL1 inhibitor may be anyone at risk for developing muscle atrophy including, but not limited to, subjects with a genetic predisposition for developing muscle atrophy. Additional risk factors for muscle atrophy include, but are not limited to, age, inactivity or disuse, malnutrition, chronic diseases, neurological conditions, endocrine disorders, medications, alcohol and other substances, among others. Furthermore, general weight loss arising from a variety of mechanisms (e.g., bariatric surgery, medication-induced, etc.) may predispose to substantial loss of muscle loss. In some embodiments, administering an INPPL1 inhibitor to a subject having muscle atrophy may be carried out to prevent development of another occurrence of muscle atrophy in a subject who has already had muscle atrophy. In any of the embodiments described herein, the methods can be used to improve muscle atrophy.

[0257] In any of the embodiments described herein, the subject in whom type 2 diabetes is prevented by administering an INPPL1 inhibitor may be anyone at risk for developing type 2 diabetes including, but not limited to, subjects with a genetic predisposition for developing type 2 diabetes. Additional risk factors for type 2 diabetes include, but are not limited to, age (particularly after the age of 45), overweight, fat distribution, inactivity, race and ethnicity, prediabetes, and gestational diabetes. In any of the embodiments described herein, the methods can be used to improve type 2 diabetes.

[0258] In any of the embodiments described herein, the INPPL1 predicted loss-of-function polypeptide can be any INPPL1 polypeptide having a partial loss-of-function, a complete loss-of-function, a predicted partial loss-of-function, or a predicted complete loss-of-function.

[0259] Any one or more (i.e., any combination) of the INPPL1 variant nucleic acid molecules described herein can be used within any of the methods described herein to determine whether a subject has an increased or decreased risk of developing muscle atrophy. The combinations of particular variants can form a mask used for statistical analysis of the particular association of INPPL1 and an increased or decreased risk of developing muscle atrophy. In some embodiments, the mask used for statistical analysis of the particular association of INPPL1 and an increased or decreased risk of developing muscle atrophy can exclude any one or more of these INPPL1 variant nucleic acid molecules described herein.

[0260] Any one or more (i.e., any combination) of the INPPL1 variant nucleic acid molecules described herein can be used within any of the methods described herein to determine

[0261] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0262] - 76 -whether a subject has an increased or decreased risk of developing type 2 diabetes. The combinations of particular variants can form a mask used for statistical analysis of the particular association of INPPL1 and an increased or decreased risk of developing type 2 diabetes. In some embodiments, the mask used for statistical analysis of the particular association of INPPL1 and an increased or decreased risk of developing type 2 diabetes can exclude any one or more of these INPPL1 variant nucleic acid molecules described herein.

[0263] In any of the embodiments described herein, the subject can have muscle atrophy. In any of the embodiments described herein, the subject can be at risk of developing muscle atrophy. In any of the embodiments described herein, the muscle atrophy is skeletal muscle atrophy. In any of the embodiments described herein, the muscle atrophy is cardiac muscle atrophy. In some embodiments, muscle atrophy may be due to: 1) a rare genetic disease affecting skeletal muscle including, but not limited to muscular dystrophies, myotonic dystrophies, and mitochondrial myopathies; 2) inflammatory muscle diseases including, but not limited to, polymyositis and dermatomyositits; 3) sarcopenia including, but not limited to, age-related sarcopenia; 4) myopathy arising secondary to environmental influences (e.g., drug-induced, alcohol-induced, among others); 5) myopathy arising secondary to systemic diseases (e.g., thyroid-associated myopathy); and 6) other neuromuscular conditions leading to muscle atrophy (e.g., amyotrophic lateral sclerosis, myasthenia gravis, among others). Weight loss via various mechanisms (e.g., bariatric surgery, or pharmacologically-induced) may also produce substantial loss of skeletal muscle mass and lead to muscle atrophy. In some embodiments, the muscle atrophy may be due to type 2 diabetes.

[0264] In any of the embodiments described herein, the subject can have type 2 diabetes. In any of the embodiments described herein, the subject can be at risk of developing type 2 diabetes. In any of the embodiments described herein, the subject can be at any stage of T2D including insulin resistance and prediabetes. In some embodiments, the subject can have insulin resistance. In some embodiments, the subject can have prediabetes.

[0265] Muscle mass and strength can be measured by, for example: i) handgrip strength, ii) MRI-derived thigh muscle volume / perimeter, iii) DXA-derived lean / muscle mass, iv) bioimpedance-derived lean / muscle mass, v) creatinine levels, and vi) creatinine / cystatin C ratio ("sarcopenia index").

[0266] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0267] - 77 - The present disclosure provides methods of treating a subject having muscle atrophy or at risk of developing muscle atrophy, the methods comprising administering an INPPL1 inhibitor to the subject.

[0268] The present disclosure provides methods of treating a subject having type 2 diabetes or at risk of developing type 2 diabetes, the methods comprising administering an INPPL1 inhibitor to the subject.

[0269] In some embodiments, the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule. Examples of inhibitory nucleic acid molecules include, but are not limited to, antisense nucleic acid molecules, small interfering RNAs (siRNAs), and short hairpin RNAs (shRNAs). Such inhibitory nucleic acid molecules can be designed to target any region of an INPPL1 nucleic acid molecule. In some embodiments, the antisense RNA, siRNA, or shRNA hybridizes to a sequence within an INPPL1 genomic nucleic acid molecule or mRNA molecule and decreases expression of the INPPL1 polypeptide in a cell in the subject. In some embodiments, the INPPL1 inhibitor comprises an antisense molecule that hybridizes to an INPPL1 genomic nucleic acid molecule or mRNA molecule and decreases expression of the INPPL1 polypeptide in a cell in the subject. In some embodiments, the INPPL1 inhibitor comprises an siRNA that hybridizes to an INPPL1 genomic nucleic acid molecule or mRNA molecule and decreases expression of the INPPL1 polypeptide in a cell in the subject. In some embodiments, the INPPL1 inhibitor comprises an shRNA that hybridizes to an INPPL1 genomic nucleic acid molecule or mRNA molecule and decreases expression of the INPPL1 polypeptide in a cell in the subject.

[0270] In some embodiments, the INPPL1 antisense nucleic acid molecules comprise or consist of any of the nucleotide sequences represented by SEQ ID NOs: 1-850. In some embodiments, the INPPL1 siRNA molecules comprise or consist of any of the nucleotide sequences (sense and antisense strands presented one after the other) represented by SEQ ID NOs: 851-2642 (e.g., the sense strand is, for example, SEQ ID NO: 851 and the corresponding antisense strand is SEQ ID NO: 852; the sense strand is, for example, SEQ ID NO: 853 and the corresponding antisense strand is SEQ ID NO: 854; etc.).

[0271] Table 2: INPPL1 antisense molecules

[0272]

[0273]

[0274] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0275] - 78 -

[0276]

[0277]

[0278] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0279] - 79 -

[0280]

[0281]

[0282] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0283] - 80 -

[0284]

[0285]

[0286] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0287] - 81 -

[0288]

[0289]

[0290] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0291] - 82 -

[0292]

[0293]

[0294] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0295] - 83 -

[0296]

[0297]

[0298] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0299] - 84 -

[0300]

[0301]

[0302] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0303] - 85 -

[0304]

[0305]

[0306] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0307] - 86 -

[0308]

[0309]

[0310] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0311] - 87 -

[0312]

[0313] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0314] - 88 - Table 3: INPPL1 siRNA molecules

[0315]

[0316] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0317] - 89-

[0318]

[0319] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0320] - 90 -

[0321]

[0322] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0323] - 91 -

[0324]

[0325] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0326] - 92 -

[0327]

[0328] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0329] - 93 -

[0330]

[0331] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0332] - 94-

[0333]

[0334] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0335] - 95 -

[0336]

[0337] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0338] - 96 -

[0339]

[0340] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0341] - 97 -

[0342]

[0343] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0344] - 98 -

[0345]

[0346] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0347] -99-

[0348]

[0349] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0350] - 100 -

[0351]

[0352] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0353] - 101 -

[0354]

[0355] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0356] - 102 -

[0357]

[0358] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0359] - 103 -

[0360]

[0361] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0362] - 104 -

[0363]

[0364] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0365] - 105 -

[0366]

[0367] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0368] - 106 -

[0369]

[0370] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0371] - 107 -

[0372]

[0373] The inhibitory nucleic acid molecules can comprise RNA, DNA, or both RNA and DNA. The inhibitory nucleic acid molecules can also be linked or fused to a heterologous nucleic acid sequence, such as in a vector, or a heterologous label. For example, the inhibitory nucleic acid molecules can be within a vector or as an exogenous donor sequence comprising the inhibitory nucleic acid molecule and a heterologous nucleic acid sequence. The inhibitory nucleic acid molecules can also be linked or fused to a heterologous label. The label can be directly detectable (such as, for example, fluorophore) or indirectly detectable (such as, for example, hapten, enzyme, or fluorophore quencher). Such labels can be detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Such labels include, for example, radiolabels, pigments, dyes, chromogens, spin labels, and fluorescent labels. The label can also be, for example, a chemiluminescent substance; a metal-containing substance; or an enzyme, where there occurs an enzyme-dependent secondary generation of signal. The term "label" can also refer to a "tag" or hapten that can bind selectively to a conjugated molecule

[0374] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0375] - 108 -such that the conjugated molecule, when added subsequently along with a substrate, is used to generate a detectable signal. For example, biotin can be used as a tag along with an avidin or streptavidin conjugate of horseradish peroxidate (HRP) to bind to the tag, and examined using a calorimetric substrate (such as, for example, tetra methylbenzidine (TMB)) or a fluorogenic substrate to detect the presence of HRP. Exemplary labels that can be used as tags to facilitate purification include, but are not limited to, myc, HA, FLAG or3XFLAG, 6XHis or polyhistidine, glutathione-S-transferase (GST), maltose binding protein, an epitope tag, or the Fc portion of immunoglobulin. Numerous labels include, for example, particles, fluorophores, haptens, enzymes and their calorimetric, fluorogenic and chemiluminescent substrates and other labels.

[0376] The inhibitory nucleic acid molecules can comprise, for example, nucleotides or nonnatural or modified nucleotides, such as nucleotide analogs or nucleotide substitutes. Such nucleotides include a nucleotide that contains a modified base, sugar, or phosphate group, or that incorporates a non-natural moiety in its structure. Examples of non-natural nucleotides include, but are not limited to, dideoxynucleotides, biotinylated, aminated, deaminated, alkylated, benzylated, and fluorophor-labeled nucleotides.

[0377] The inhibitory nucleic acid molecules can also comprise one or more nucleotide analogs or substitutions. A nucleotide analog is a nucleotide which contains a modification to either the base, sugar, or phosphate moieties. Modifications to the base moiety include, but are not limited to, natural and synthetic modifications of A, C, G, and T / U, as well as different purine or pyrimidine bases such as, for example, pseudouridine, u racil-5-y I, hypoxanthin-9-yl (I), and 2-aminoadenin-9-yl. Modified bases include, but are not limited to, 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo (such as, for example, 5-bromo), 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine, 7-methyladenine, 8-azaguanine, 8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, and 3-deazaadenine.

[0378] Nucleotide analogs can also include modifications of the sugar moiety. Modifications to the sugar moiety include, but are not limited to, natural modifications of the ribose and

[0379] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0380] - 109 -deoxy ribose as well as synthetic modifications. Sugar modifications include, but are not limited to, the following modifications at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O-a Iky l-O-al kyl, wherein the alkyl, alkenyl, and alkynyl may be substituted or unsubstituted Ci-ioalkyl or C2-ioalkenyl, and Cz-ioalkynyl. Exemplary 2' sugar modifications also include, but are not limited to, -O[(CH2)nO]mCH3, -O(CH2)nOCH3, -O(CH2)nNH2, -O(CH2)nCH3, -O(CH2)n-ONH2, and -O(CH2)nON[(CH2)nCH3)h, where n and m, independently, are from 1 to about 10. Other modifications at the 2' position include, but are not limited to, Ci-ioalkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. Similar modifications may also be made at other positions on the sugar, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked oligonucleotides and the 5' position of 5' terminal nucleotide. Modified sugars can also include those that contain modifications at the bridging ring oxygen, such as CH2 and S. Nucleotide sugar analogs can also have sugar mimetics, such as cyclobutyl moieties in place of the pentofu ranosyl sugar.

[0381] Nucleotide analogs can also be modified at the phosphate moiety. Modified phosphate moieties include, but are not limited to, those that can be modified so that the linkage between two nucleotides contains a phosphorothioate, chiral phosphorothioate, phosphorodithioate, phosphotriester, aminoalkylphosphotriester, methyl and other alkyl phosphonates including 3'-alkylene phosphonate and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and boranophosphates. These phosphate or modified phosphate linkage between two nucleotides can be through a 3'-5' linkage or a 2'-5' linkage, and the linkage can contain inverted polarity such as 3'-5' to 5'-3' or 2' -5' to 5'-2'. Various salts, mixed salts, and free acid forms are also included. Nucleotide substitutes also include peptide nucleic acids (PNAs).

[0382] In some embodiments, the antisense nucleic acid molecules are gapmers, whereby the first one to seven nucleotides at the 5' and 3' ends each have 2'-methoxyethyl (2'-MOE) modifications. In some embodiments, the first five nucleotides at the 5' and 3' ends each have

[0383] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0384] - 110 - 2'-MOE modifications. In some embodiments, the first one to seven nucleotides at the 5' and 3' ends are RNA nucleotides. In some embodiments, the first five nucleotides at the 5' and 3' ends are RNA nucleotides. In some embodiments, each of the backbone linkages between the nucleotides is a phosphorothioate linkage.

[0385] In some embodiments, the siRNA molecules have termini modifications. In some embodiments, the 5' end of the antisense strand is phosphorylated. In some embodiments, 5'-phosphate analogs that cannot be hydrolyzed, such as 5'-(E)-vinyl-phosphonate are used.

[0386] In some embodiments, the siRNA molecules have backbone modifications. In some embodiments, the modified phosphodiester groups that link consecutive ribose nucleosides have been shown to enhance the stability and in vivo bioavailability of siRNAs The non-ester groups (-OH, =0) of the phosphodiester linkage can be replaced with sulfur, boron, or acetate to give phosphorothioate, boranophosphate, and phosphonoacetate linkages. In addition, substituting the phosphodiester group with a phosphotriester can facilitate cellular uptake of siRNAs and retention on serum components by eliminating their negative charge. In some embodiments, the siRNA molecules have sugar modifications. In some embodiments, the sugars are deprotonated (reaction catalyzed by exo- and endonucleases) whereby the 2'-hydroxyl can act as a nucleophile and attack the adjacent phosphorous in the phosphodiester bond. Such alternatives include 2'-O-methyl, 2'-O-methoxyethyl, and 2'-fluoro modifications.

[0387] In some embodiments, the siRNA molecules have base modifications. In some embodiments, the bases can be substituted with modified bases such as pseudouridine, 5'-methylcytidine, N6-methyladenosine, inosine, and N7-methylguanosine.

[0388] In some embodiments, the siRNA molecules are conjugated to lipids. Lipids can be conjugated to the 5' or 3' termini of siRNA to improve their in vivo bioavailability by allowing them to associate with serum lipoproteins. Representative lipids include, but are not limited to, cholesterol and vitamin E, and fatty acids, such as palmitate and tocopherol.

[0389] In some embodiments, a representative siRNA has the following formula:

[0390] Sense: mN*mN7i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / *mN* / 32FN /

[0391] Antisense: / 52FN / * / i2FN / *mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN*N*N

[0392] wherein: " N" is the base; "2F" is a 2'-F modification; "m" is a 2'-O-methyl modification, " I" is an internal base; and is a phosphorothioate backbone linkage.

[0393] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0394] - 111 - In any of the embodiments described herein, the inhibitory nucleic acid molecules may be administered, for example, as one- to two-hour i.v. infusions or s.c. injections. In any of the embodiments described herein, the inhibitory nucleic acid molecules may be administered at dose levels that range from about 50 mg to about 900 mg, from about 100 mg to about 800 mg, from about 150 mg to about 700 mg, or from about 175 mg to about 640 mg (2.5 to

[0395] 9.14 mg / kg; 92.5 to 338 mg / m2- based on an assumption of a body weight of 70 kg and a conversion of mg / kg to mg / m2dose levels based on a mg / kg dose multiplier value of 37 for humans).

[0396] The present disclosure also provides vectors comprising any one or more of the inhibitory nucleic acid molecules. In some embodiments, the vectors comprise any one or more of the inhibitory nucleic acid molecules and a heterologous nucleic acid. The vectors can be viral or nonviral vectors capable of transporting a nucleic acid molecule. In some embodiments, the vector is a plasmid or cosmid (such as, for example, a circular double-stranded DNA into which additional DNA segments can be ligated). In some embodiments, the vector is a viral vector, wherein additional DNA segments can be ligated into the viral genome. Expression vectors include, but are not limited to, plasmids, cosmids, retroviruses, adenoviruses, adeno-associated viruses (AAV), plant viruses such as cauliflower mosaic virus and tobacco mosaic virus, yeast artificial chromosomes (YACs), Epstein-Barr (EBV)-derived episomes, and other expression vectors known in the art.

[0397] The present disclosure also provides compositions comprising any one or more of the inhibitory nucleic acid molecules. In some embodiments, the composition is a pharmaceutical composition. In some embodiments, the compositions comprise a carrier and / or excipient. Examples of carriers include, but are not limited to, poly(lactic acid) (PLA) microspheres, poly(D, L-lactic-coglycolic-acid) (PLGA) microspheres, liposomes, micelles, inverse micelles, lipid cochleates, and lipid microtubules. A carrier may comprise a buffered salt solution such as PBS, HBSS, etc.

[0398] In some embodiments, the INPPL1 inhibitor comprises a nuclease agent that induces one or more nicks or double-strand breaks at a recognition sequence(s) or a DNA-binding protein that binds to a recognition sequence within an INPPL1 genomic nucleic acid molecule. The recognition sequence can be located within a coding region of the INPPL1 gene, or within regulatory regions that influence the expression of the gene. A recognition sequence of the DNA-binding protein or nuclease agent can be located in an intron, an exon, a promoter, an

[0399] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0400] - 112 -enhancer, a regulatory region, or any non-protein coding region. The recognition sequence can include or be proximate to the start codon of the INPPL1 gene. For example, the recognition sequence can be located about 10, about 20, about 30, about 40, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides from the start codon. As another example, two or more nuclease agents can be used, each targeting a nuclease recognition sequence including or proximate to the start codon. As another example, two nuclease agents can be used, one targeting a nuclease recognition sequence including or proximate to the start codon, and one targeting a nuclease recognition sequence including or proximate to the stop codon, wherein cleavage by the nuclease agents can result in deletion of the coding region between the two nuclease recognition sequences. Any nuclease agent that induces a nick or double-strand break into a desired recognition sequence can be used in the methods and compositions disclosed herein. Any DNA-binding protein that binds to a desired recognition sequence can be used in the methods and compositions disclosed herein.

[0401] Suitable nuclease agents and DNA-binding proteins for use herein include, but are not limited to, zinc finger protein or zinc finger nuclease (ZFN) pair, Transcription Activator-Like Effector (TALE) protein or Transcription Activator-Like Effector Nuclease (TALEN), or Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) / CRISPR-associated (Cas) systems. The length of the recognition sequence can vary, and includes, for example, recognition sequences that are about 30-36 bp for a zinc finger protein or ZFN pair, about 15-18 bp for each ZFN, about 36 bp for a TALE protein or TALEN, and about 20 bp for a CRISPR / Cas guide RNA.

[0402] In some embodiments, CRISPR / Cas systems can be used to modify an INPPL1 genomic nucleic acid molecule within a cell. The methods and compositions disclosed herein can employ CRISPR-Cas systems by utilizing CRISPR complexes (comprising a guide RNA (gRNA) complexed with a Cas protein) for site-directed cleavage of INPPL1 nucleic acid molecules.

[0403] Cas proteins generally comprise at least one RNA recognition or binding domain that can interact with gRNAs. Cas proteins can also comprise nuclease domains (such as, for example, DNase or RNase domains), DNA binding domains, helicase domains, protein-protein interaction domains, dimerization domains, and other domains. Suitable Cas proteins include, for example, a wild type Cas9 protein and a wild type Cpfl protein (such as, for example, FnCpfl). A Cas protein can have full cleavage activity to create a double-strand break in an INPPL1 genomic nucleic acid molecule or it can be a nickase that creates a single-strand break in an INPPL1 genomic nucleic acid molecule. Additional examples of Cas proteins include, but

[0404] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0405] - 113 -are not limited to, Casl, CaslB, Cas2, Cas3, Cas4, Cas5, CasSe (CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8al, Cas8a2, Cas8b, Cas8c, Cas9 (Csnl or Csxl2), CaslO, CaslOd, CasF, CasG, CasH, Csyl, Csy2, Csy3, Csel (CasA), Cse2 (CasB), Cse3 (CasE), Cse4 (CasC), Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, and Cul966, and homologs or modified versions thereof. In some embodiments, a Cas system, such as Casl2a, can have multiple gRNAs encoded into a single crRNA. Cas proteins can also be operably linked to heterologous polypeptides as fusion proteins. For example, a Cas protein can be fused to a cleavage domain, an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repressor domain. Cas proteins can be provided in any form. For example, a Cas protein can be provided in the form of a protein, such as a Cas protein complexed with a gRNA. Alternately, a Cas protein can be provided in the form of a nucleic acid molecule encoding the Cas protein, such as an RNA or DNA.

[0406] In some embodiments, targeted genetic modifications of INPPL1 genomic nucleic acid molecules can be generated by contacting a cell with a Cas protein and one or more gRNAs that hybridize to one or more gRNA recognition sequences within a target genomic locus in the INPPL1 genomic nucleic acid molecule. The gRNA recognition sequence can include or be proximate to the start codon of an INPPL1 genomic nucleic acid molecule or the stop codon of an INPPL1 genomic nucleic acid molecule. For example, the gRNA recognition sequence can be located from about 10, from about 20, from about 30, from about 40, from about 50, from about 100, from about 200, from about 300, from about 400, from about 500, or from about 1,000 nucleotides of the start codon or the stop codon.

[0407] The gRNA recognition sequences within a target genomic locus in an INPPL1 genomic nucleic acid molecule are located near a Protospacer Adjacent Motif (PAM) sequence, which is a 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease. The canonical PAM is the sequence 5'-NGG-3' where " N" is any nucleobase followed by two guanine (" G") nucleobases. gRNAs can transport Cas9 to anywhere in the genome for gene editing, but no editing can occur at any site other than one at which Cas9 recognizes PAM. In addition, 5'-NGA-3' can be a highly efficient non-canonical PAM for human cells. Generally, the PAM is about 2-6 nucleotides downstream of the DNA sequence targeted by the gRNA. The PAM can flank the gRNA recognition sequence. In some embodiments, the gRNA recognition sequence can be flanked on the 3' end by the PAM. In some embodiments, the gRNA

[0408] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0409] - 114 -recognition sequence can be flanked on the 5' end by the PAM. For example, the cleavage site of Cas proteins can be about 1 to about 10, about 2 to about 5 base pairs, or three base pairs upstream or downstream of the PAM sequence. In some embodiments (such as when Cas9 from S. pyogenes or a closely related Cas9 is used), the PAM sequence of the non-complementary strand can be 5'-NGG-3', where N is any DNA nucleotide and is immediately 3' of the gRNA recognition sequence of the non-complementary strand of the target DNA. As such, the PAM sequence of the complementary strand would be 5'-CCN-3', where N is any DNA nucleotide and is immediately 5' of the gRNA recognition sequence of the complementary strand of the target DNA.

[0410] A gRNA is an RNA molecule that binds to a Cas protein and targets the Cas protein to a specific location within an INPPL1 genomic nucleic acid molecule. An exemplary gRNA is a gRNA effective to direct a Cas enzyme to bind to or cleave an INPPL1 genomic nucleic acid molecule, wherein the gRNA comprises a DNA-targeting segment that hybridizes to a gRNA recognition sequence within the INPPL1 genomic nucleic acid molecule. Exemplary gRNAs comprise a DNA-targeting segment that hybridizes to a gRNA recognition sequence present within an INPPL1 genomic nucleic acid molecule that includes or is proximate to the start codon or the stop codon. For example, a gRNA can be selected such that it hybridizes to a gRNA recognition sequence that is located from about 5, from about 10, from about 15, from about 20, from about 25, from about 30, from about 35, from about 40, from about 45, from about 50, from about 100, from about 200, from about 300, from about 400, from about 500, or from about 1,000 nucleotides of the start codon or located from about 5, from about 10, from about 15, from about 20, from about 25, from about 30, from about 35, from about 40, from about 45, from about 50, from about 100, from about 200, from about 300, from about 400, from about 500, or from about 1,000 nucleotides of the stop codon. Suitable gRNAs can comprise from about 17 to about 25 nucleotides, from about 17 to about 23 nucleotides, from about 18 to about 22 nucleotides, or from about 19 to about 21 nucleotides. In some embodiments, the gRNAs can comprise 20 nucleotides.

[0411] The Cas protein and the gRNA form a complex, and the Cas protein cleaves the INPPL1 genomic nucleic acid molecule. The Cas protein can cleave the nucleic acid molecule at a site within or outside of the nucleic acid sequence present in the INPPL1 genomic nucleic acid molecule to which the DNA-targeting segment of a gRNA will bind. For example, formation of a CRISPR complex (comprising a gRNA hybridized to a gRNA recognition sequence and complexed

[0412] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0413] - 115 -with a Cas protein) can result in cleavage of one or both strands in or near (such as, for example, within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from) the nucleic acid sequence present in the INPPL1 genomic nucleic acid molecule to which a DNA-targeting segment of a gRNA will bind.

[0414] Such methods can result, for example, in an INPPL1 genomic nucleic acid molecule in which a region of the INPPL1 genomic nucleic acid molecule is disrupted, the start codon is disrupted, the stop codon is disrupted, or the coding sequence is disrupted or deleted.

[0415] Optionally, the cell can be further contacted with one or more additional gRNAs that hybridize to additional gRNA recognition sequences within the target genomic locus in the INPPL1 genomic nucleic acid molecule. By contactingthe cell with one or more additional gRNAs (such as, for example, a second gRNA that hybridizes to a second gRNA recognition sequence), cleavage by the Cas protein can create two or more double-strand breaks or two or more single-strand breaks.

[0416] In any of the methods of treatment or prevention described herein, the subject being treated may comprise an INPPL1 variant nucleic acid molecule. In some embodiments, the subject being treated is heterozygous for the INPPL1 variant nucleic acid molecule. In some embodiments, the subject being treated is homozygous for the INPPL1 variant nucleic acid molecule. In some embodiments, the subject being treated is INPPL1 reference. The INPPL1 variant nucleic acid molecule can be any of the INPPL1 variant nucleic acid molecules disclosed herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0417] In some embodiments, the methods of treatment or prevention further comprise detecting the presence or absence of an INPPL1 variant nucleic acid molecule in a biological sample from the subject. In some embodiments, the INPPL1 variant nucleic acid molecule can be any of the INPPL1 variant nucleic acid molecules disclosed herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0418] The present disclosure also provides methods of treating a subject with a muscle atrophy therapeutic agent or muscle atrophy therapy that treats or inhibits muscle atrophy,

[0419] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0420] - 116 -wherein the subject has muscle atrophy or is at risk of developing muscle atrophy. The methods comprise determining whetherthe subject has an INPPL1 variant nucleic acid molecule by obtaining or having obtained a biological sample from the subject, and performing or having performed a sequence analysis on the biological sample to determine if the subject has a genotype comprising the INPPL1 variant nucleic acid molecule. In some embodiments, the methods further comprise administering or continuing to administerthe muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy to the subject, and / or administering an INPPL1 inhibitorto a subject that is INPPL1 reference orto a subjectthat is heterozygous for the INPPL1 variant nucleic acid molecule. In some embodiments, the methods further comprise administering or continuing to administer the muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy to a subject that is homozygous for the INPPL1 variant nucleic acid molecule. The presence of an INPPL1 variant nucleic acid molecule indicates the subject has a decreased risk of developing muscle atrophy. In some embodiments, the subject is INPPL1 reference. In some embodiments, the subject is heterozygous for an INPPL1 variant nucleic acid molecule. In some embodiments, the subject is homozygous for an INPPL1 variant nucleic acid molecule. In any of the embodiments described herein, the INPPL1 inhibitor is an example of a muscle atrophy therapeutic agent. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0421] The present disclosure also provides methods of treating a subject with a type 2 diabetes therapeutic agent, wherein the subject has type 2 diabetes or is at risk of developing type 2 diabetes. The methods comprise determining whether the subject has an INPPL1 variant nucleic acid molecule by obtaining or having obtained a biological sample from the subject, and performing or having performed a sequence analysis on the biological sample to determine if the subject has a genotype comprising the INPPL1 variant nucleic acid molecule. In some embodiments, the methods further comprise administering or continuing to administerthe type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount to the subject, and / or administering an INPPL1 inhibitorto a subject that is INPPL1 reference orto a subject that is heterozygous forthe INPPL1 variant nucleic acid molecule. In some embodiments, the methods further comprise administering or continuing to

[0422] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0423] - 117 -administer the type 2 diabetes therapeutic agent in a standard dosage amount to a subject that is homozygous for the INPPL1 variant nucleic acid molecule. The presence of an INPPL1 variant nucleic acid molecule indicates the subject has a decreased risk of developing type 2 diabetes. In some embodiments, the subject is INPPL1 reference. In some embodiments, the subject is heterozygous for an INPPL1 variant nucleic acid molecule. In some embodiments, the subject is homozygous for an INPPL1 variant nucleic acid molecule. In any of the embodiments described herein, the INPPL1 inhibitor is an example of a type 2 diabetes therapeutic agent. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0424] For subjects that are genotyped or determined to be either INPPL1 reference or heterozygous for an INPPL1 variant nucleic acid molecule, such subjects can be administered an INPPL1 inhibitor, as described herein.

[0425] Detecting the presence or absence of an INPPL1 variant nucleic acid molecule in a biological sample from a subject and / or determining whether a subject has an INPPL1 variant nucleic acid molecule can be carried out by any of the methods described herein. In some embodiments, these methods can be carried out in vitro. In some embodiments, these methods can be carried out in situ. In some embodiments, these methods can be carried out in vivo. In any of these embodiments, the nucleic acid molecule can be present within a cell obtained from the subject.

[0426] In some embodiments, when the subject is INPPL1 reference, the subject is administered a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor. In some embodiments, when the subject is heterozygous for an INPPL1 variant nucleic acid molecule, the subject is administered a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor.

[0427] In some embodiments, when the subject is INPPL1 reference, the subject is administered a type 2 diabetes therapeutic agent in an amount that is the same as or lessthan a standard dosage amount, and / or an INPPL1 inhibitor. In some embodiments, when the subject is heterozygous for an INPPL1 variant nucleic acid molecule, the subject is administered

[0428] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0429] - 118 -a type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount, and / or an INPPL1 inhibitor.

[0430] In some embodiments, the treatment or prevention methods comprise detecting the presence or absence of a decrease in the expression of an INPPL1 variant mRNA or polypeptide in a biological sample from the subject. In some embodiments, when the subject does not have a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the subject is administered a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor. In some embodiments, when the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the subject is administered a muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy.

[0431] In some embodiments, the treatment or prevention methods comprise detecting the presence or absence of a decrease in the expression of an INPPL1 variant mRNA or polypeptide in a biological sample from the subject. In some embodiments, when the subject does not have a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the subject is administered a type 2 diabetes therapeutic agent in an amount that is the same as or lessthan a standard dosage amount, and / or an INPPL1 inhibitor. In some embodiments, when the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the subject is administered a type 2 diabetes therapeutic agent in a standard dosage amount.

[0432] The present disclosure also provides methods of treating a subject with a muscle atrophy therapeutic agent or muscle atrophy therapy that treats or inhibits muscle atrophy, wherein the subject has muscle atrophy or is at risk of developing muscle atrophy. The methods comprise determining whetherthe subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide by obtaining or having obtained a biological sample from the subject, and performing or having performed an assay on the biological sample to determine if the subject a decrease in the expression of an INPPL1 variant mRNA or polypeptide. In embodiments where the subject does not have a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the methods further comprise administering or continuing to administer the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy to the subject, and / or administering an INPPL1 inhibitor to the subject. In embodiments where the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the methods further comprise

[0433] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0434] - 119 -administering or continuing to administer the muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy to the subject. The presence of a decrease in the expression of an INPPL1 variant mRNA or polypeptide indicates the subject has a decreased risk of developing muscle atrophy. In some embodiments, the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide. In some embodiments, the subject does not have a decrease in the expression of an INPPL1 variant mRNA or polypeptide. In any of the embodiments described herein, the INPPL1 inhibitor is an example of a muscle atrophy therapeutic agent. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0435] The present disclosure also provides methods of treating a subject with a type 2 diabetes therapeutic agent, wherein the subject has type 2 diabetes or is at risk of developing type 2 diabetes. The methods comprise determining whether the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide by obtaining or having obtained a biological sample from the subject, and performing or having performed an assay on the biological sample to determine if the subject a decrease in the expression of an INPPL1 variant mRNA or polypeptide. In embodiments where the subject does not have a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the methods further comprise administering or continuing to administer the type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount to the subject, and / or administering an INPPL1 inhibitor to the subject. In embodiments where the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide, the methods further comprise administering or continuing to administer the type 2 diabetes therapeutic agent in a standard dosage amount to the subject. The presence of a decrease in the expression of an INPPL1 variant mRNA or polypeptide indicates the subject has a decreased risk of developing type 2 diabetes. In some embodiments, the subject has a decrease in the expression of an INPPL1 variant mRNA or polypeptide. In some embodiments, the subject does not have a decrease in the expression of an INPPL1 variant mRNA or polypeptide. In any of the embodiments described herein, the INPPL1 inhibitor is an example of a type 2 diabetes therapeutic agent. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic

[0436] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0437] - 120 -nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0438] Detecting a decrease in the expression of an INPPL1 variant mRNA or polypeptide can be carried out by a variety of known methods. In some embodiments, these methods can be carried out in vitro. In some embodiments, these methods can be carried out in situ. In some embodiments, these methods can be carried out in vivo. In any of these embodiments, the mRNA or polypeptide can be present within a cell obtained from the subject.

[0439] In some embodiments, the treatment or prevention methods comprise detecting the presence or absence of an INPPL1 variant polypeptide in a biological sample from the subject. In some embodiments, when the subject does not have an INPPL1 variant polypeptide, the subject is administered a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor. In some embodiments, when the subject has an INPPL1 variant polypeptide, the subject is administered a muscle atrophy therapeutic agent in standard dosage amount or muscle atrophy therapy.

[0440] In some embodiments, the treatment or prevention methods comprise detecting the presence or absence of an INPPL1 variant polypeptide in a biological sample from the subject. In some embodiments, when the subject does not have an INPPL1 variant polypeptide, the subject is administered a type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount, and / or an INPPL1 inhibitor. In some embodiments, when the subject has an INPPL1 variant polypeptide, the subject is administered a type 2 diabetes therapeutic agent in standard dosage amount.

[0441] The present disclosure also provides methods of treating a subject with a muscle atrophy therapeutic agent or muscle atrophy therapy that treats or inhibits muscle atrophy, wherein the subject has muscle atrophy or is at risk of developing muscle atrophy. The methods comprise determining whetherthe subject has an INPPL1 variant polypeptide by obtaining or having obtained a biological sample from the subject and performing or having performed an assay on the biological sample to determine if the subject has an INPPL1 variant polypeptide. When the subject does not have an INPPL1 variant polypeptide, the subject is administered the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor. When the subject has an INPPL1 variant polypeptide, the subject is administered the muscle atrophy therapeutic

[0442] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0443] - 121 -agent in a standard dosage amount or muscle atrophy therapy. The presence of an INPPL1 variant polypeptide indicates the subject has a decreased risk of developing muscle atrophy. In some embodiments, the subject has an INPPL1 variant polypeptide. In some embodiments, the subject does not have an INPPL1 variant polypeptide.

[0444] The present disclosure also provides methods of treating a subject with a type 2 diabetes therapeutic agent, wherein the subject has type 2 diabetes or is at risk of developing type 2 diabetes. The methods comprise determining whether the subject has an INPPL1 variant polypeptide by obtaining or having obtained a biological sample from the subject and performing or having performed an assay on the biological sample to determine if the subject has an INPPL1 variant polypeptide. When the subject does not have an INPPL1 variant polypeptide, the subject is administered the type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount, and / or an INPPL1 inhibitor. When the subject has an INPPL1 variant polypeptide, the subject is administered the type 2 diabetes therapeutic agent in a standard dosage amount. The presence of an INPPL1 variant polypeptide indicates the subject has a decreased risk of developing type 2 diabetes. In some embodiments, the subject has an INPPL1 variant polypeptide. In some embodiments, the subject does not have an INPPL1 variant polypeptide.

[0445] The present disclosure also provides methods of preventing a subject from developing muscle atrophy by administering a muscle atrophy therapeutic agent or muscle atrophy therapy that prevents muscle atrophy. In some embodiments, the method comprises determining whether the subject has an INPPL1 variant polypeptide by obtaining or having obtained a biological sample from the subject and performing or having performed an assay on the biological sample to determine if the subject has an INPPL1 variant polypeptide. When the subject does not have an INPPL1 variant polypeptide, the subject is administered the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor. When the subject has an INPPL1 variant polypeptide, the subject is administered the muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy. The presence of an INPPL1 variant polypeptide indicates the subject has a decreased risk of developing muscle atrophy. In some embodiments, the subject has an INPPL1 variant polypeptide. In some embodiments, the subject does not have an INPPL1 variant polypeptide.

[0446] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0447] - 122 - The present disclosure also provides methods of preventing a subject from developing type 2 diabetes by administering a type 2 diabetes therapeutic agent. In some embodiments, the method comprises determining whether the subject has an INPPL1 variant polypeptide by obtaining or having obtained a biological sample from the subject and performing or having performed an assay on the biological sample to determine if the subject has an INPPL1 variant polypeptide. When the subject does not have an INPPL1 variant polypeptide, the subject is administered the type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount, and / or an INPPL1 inhibitor. When the subject has an INPPL1 variant polypeptide, the subject is administered the type 2 diabetes therapeutic agent in a standard dosage amount. The presence of an INPPL1 variant polypeptide indicates the subject has a decreased risk of developing type 2 diabetes. In some embodiments, the subject has an INPPL1 variant polypeptide. In some embodiments, the subject does not have an INPPL1 variant polypeptide.

[0448] Detecting the presence or absence of an INPPL1 variant polypeptide in a biological sample from a subject and / or determining whether a subject has an INPPL1 variant polypeptide can be carried out by any of the methods described herein. In some embodiments, these methods can be carried out in vitro. In some embodiments, these methods can be carried out in situ. In some embodiments, these methods can be carried out in vivo. In any of these embodiments, the polypeptide can be present within a cell obtained from the subject.

[0449] In some embodiments, the INPPL1 inhibitor is a small molecule. In some embodiments, the small molecule is low molecular weight (< 900 daltons) organic compound. In some embodiments, the INPPL1 inhibitor comprises AS1949490, AS1938909, N-(pyridin-2-yl)alkanamides (see, PCT Publication WO 2012 / 169571), 1PIE, 6PTQ, 2PIQ, K149, or NGD-61338, or any combination thereof. In some embodiments, the INPPL1 inhibitor comprises an antibody. In some embodiments, the INPPL1 inhibitor comprises SHIP-2 Antibody (E-2) (Santa Cruz; catalog# sc-166641), SHIP-2 Antibody (B-9) (Santa Cruz; catalog# sc-515211), SHIP-2 Antibody (Z-16) (Santa Cruz; catalog# sc-100387), Anti-INPPL1 / SHIP2, clone 8C13 (Biomol; catalog# NSJ-RQ6359), Anti-INPPL1 / SHIP2 (Biomol), Anti-INPPL1 (Inositol Polyphosphate Phosphatase-like 1, SHIP2) (AP) (Biomol; catalog# 247667-AP.100), SHIP2 Monoclonal Antibody (T.194.8) (Thermo Fisher; catalog# MA5-14844), SHIP2 Monoclonal Antibody (8C13) (Thermo Fisher; catalog# MA5-49211), SHIP2 Polyclonal Antibody (Thermo Fisher; catalog# PA5-95562), SHIP2 Polyclonal Antibody (Thermo Fisher; catalog# PA5-83381), SHIP2 Polyclonal Antibody

[0450] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0451] - 123 - (Thermo Fisher; catalog# PA5-17383), SHIP2 Polyclonal Antibody (Thermo Fisher; catalog# PA5-87643), INPPL1 / SHIP2 Polyclonal Antibody (Thermo Fisher; catalog# A300-574A), of INPPL1 Polyclonal Antibody (Thermo Fisher; catalog# BS-7048R), or any combination thereof.. In some embodiments, the INPPL1 inhibitor comprises an siRNA. In some embodiments, the INPPL1 inhibitor comprises SHIP-2 siRNA (h) (Santa Cruz; catalog# sc-39077) or SHIP-2 siRNA (m) (Santa Cruz; catalog# sc-39078), or a combination thereof.

[0452] In some embodiments, the INPPL1 inhibitor comprises an antibody, or antigen-binding fragment thereof. In some embodiments, the antibody, or antigen-binding fragment thereof, binds specifically to human INPPL1. In some embodiments, the antibody is a fully human monoclonal antibody (mAb), or antigen-binding fragment thereof, that specifically binds and neutralizes, inhibits, blocks, abrogates, reduces, or interferes with, at least one activity of INPPL1, in particular, human INPPL1. In some embodiments, an antibody or fragment thereof can neutralize, inhibit, block, abrogate, reduce, or interfere with, an activity of INPPL1 by binding to an epitope of INPPL1 that is directly involved in the targeted activity of INPPL1. In some embodiments, an antibody or fragment thereof can neutralize, inhibit, block, abrogate, reduce, or interfere with, an activity of INPPL1 by binding to an epitope of INPPL1 that is not directly involved in the targeted activity of INPPL1, but the antibody or fragment binding thereto sterically or conformationally inhibits, blocks, abrogates, reduces, or interferes with, the targeted activity of INPPL1. In some embodiments, an antibody or fragment thereof binds to an epitope of INPPL1 that is not directly involved in the targeted activity of INPPL1 (i.e., a non-blocking antibody), but the antibody or fragment binding thereto results in the enhancement of the clearance of INPPL1 from the circulation, compared to the clearance of INPPL1 in the absence of the antibody or fragment thereof, thereby indirectly inhibiting, blocking, abrogating, reducing, or interfering with, an activity of INPPL1. Clearance of INPPL1 from the circulation can be particularly enhanced by combining two or more different nonblocking antibodies that do not compete with one another for specific binding to INPPL1. The antibodies can be full-length (for example, an IgG1 or IgG4 antibody) or may comprise only an antigen-binding portion (for example, a Fab, F(ab')z or scFv fragment), and may be modified to affect functionality, e.g., to eliminate residual effector functions (Reddy et al., J. Immunol., 2000, 164, 1925-1933). Antigen-binding fragments include, but are not limited to, a monovalent Fab', a divalent Fab2, a F(ab')2 fragment, a single-chain fragment variable (scFv), a bis-scFv, a (scFv)2, a diabody, a minibody, a nanobody, a triabody, a tetrabody, a disulfide stabilized Fv

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[0454] - 124 -protein (dsFv), a single-domain antibody (sdAb), an Ig NAR, a bispecific antibody or binding fragment thereof, a bi-specific T-cell engager (BiTE), a trispecific antibody, and chemically modified derivatives thereof. In some embodiments, the antibody is a monoclonal antibody.

[0455] In some embodiments, the antibody or antigen-binding fragment thereof specifically binds to INPPL1 with an equilibrium dissociation constant (KD) of about 7 nM or less, about 6 nM or less, about 5 nM or less, about 4 nM or less, about 3 nM or less, about 2 nM or less, or about 1 nM or less, as measured by surface plasmon resonance assay (for example, BIACORE™). In some embodiments, the antibody exhibits a KD of about 800 pM or less, about 700 pM or less; about 600 pM or less; about 500 pM or less; about 400 pM or less; about 300 pM or less; about 200 pM or less; about 100 pM or less; or about 50 pM or less.

[0456] In some embodiments, the anti-INPPL1 antibody has a modified glycosylation pattern. In some applications, modification to remove undesirable glycosylation sites may be useful, or e.g., removal of a fucose moiety to increase antibody dependent cellular cytotoxicity (ADCC) function (see, Shield et al., J. Biol. Chem., 2002, 277, 26733). In other applications, removal of N-glycosylation site may reduce undesirable immune reactions against the therapeutic antibodies or increase affinities ofthe antibodies. In yet other applications, modification of galactosylation can be made to modify complement dependent cytotoxicity (CDC).

[0457] In some embodiments, the INPPL1 inhibitor can be delivered to skeletal muscle tissue or cells by using Calcium Voltage-Gated Channel Auxiliary Subunit Gamma 1 (CACNG1) binding protein delivery systems (see, for example, PCT Publications WO 23 / 81850 and WO 23 / 81847).

[0458] The present disclosure also provides compositions comprising a combination of an antibody or antigen-binding fragment thereof and a muscle atrophy therapeutic agent.

[0459] The present disclosure also provides compositions comprising a combination of an antibody or antigen-binding fragment thereof and a type 2 diabetes therapeutic agent.

[0460] In some embodiments, the muscle atrophy therapeutic agents include but are not limited to a corticosteroid, testosterone, a Selective Androgen Receptor Modulator (SARM), a growth hormone, a growth hormone secretagogue, a myostatin inhibitor, an Activin Type II Receptor inhibitor, and a modulator ofthe activin / inhibin family of ligands and receptors, or any combination thereof.

[0461] Examples of corticosteroids include but are not limited to prednisone, dexamethasone, hydrocortisone, cortisone, fluticasone, budesonide, betamethasone, methylprednisolone, triamcinolone, prednisolone, ciclesonide, flunisolide, mometasone, mometasone esters,

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[0463] - 125 -beclomethasone, beclomethasone esters, 17-propionate ester or the 17,21-dipropionate ester, rofleponide, or any combination thereof.

[0464] Examples of SARMs include but are not limited to ostarine (enobosarm, MK2866, 822), ligandrol (LGD-4033), testolone (RAD-140), andarine (GTx-007, S4), LGD-3033, TT-701, S23, SR9009 (stenabolic), ibutamoren (MK-677, Nutrabol), GW501516 (GW1516, cardarine, endurobol), and YK-11, or any combination thereof.

[0465] Examples of growth hormones include but are not limited to somatotropin (human growth hormone or hGH), insulin-like growth factor 1 (IGF-1), growth hormone-releasing hormone (GHRH), ghrelin, somatostatin, somatropin, lonapegsomatropin, somapacitan, and somatrogon, or any combination thereof.

[0466] Examples of growth hormone secretagogues include but are not limited to sermorelin, tesamorelin, CJC-1295 + ipamorelin, macimorelin, and ibutamoren (MK-677), or any combination thereof.

[0467] Examples of myostatin inhibitors include but are not limited to trevogrumab and domagrozumab, or a combination thereof.

[0468] Examples of Activin Type II Receptor inhibitors include but are not limited to bimagrumab, LAE102, LAE103, LAE123, follistatin, SB-431542, and SB-505124, or any combination thereof.

[0469] Muscle atrophy therapies include any therapy used to reduce or manage muscle atrophy risk factors or causes including but not limited to exercise therapy and nutrition therapy. These treatment therapies may be delayed or avoided altogether by treatment with an INPPL1 inhibitor as described herein.

[0470] Furthermore, INPPL1 inhibitors can be combined with therapeutic agents that induce muscle atrophy (e.g., Glucagon-Like Peptide 1 (GLP-1) receptor agonists or combined agonists of GLP-1 receptor and Glucose-dependent Insulinotropic Polypeptide (GIP) receptor (GLP-1 / GIP)) to mitigate against muscle loss arising from such therapeutic agents.

[0471] Examples of GLP-1 receptor agonists include but are not limited to exenatide, liraglutide, dulaglutide, lixisenatide, semaglutide, tirzepatide, and albiglutide, or any combination thereof. The GLP-1 receptor agonist can be any pharmacological entity with any agonist activity to the GLP-1 receptor regardless of whether or not the GLP-1 receptor agonist has other pharmacological properties related to any other pathway or target. In some embodiments, the GLP-1 receptor agonist comprises a dual GLP-l / GIP agonist including but not

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[0473] - 126 -limited to tirzepatide, maridebart cafraglutide (MariTide), and NNC0090-2746 (RG7697), or any combination thereof. In some embodiments, the GLP-1 receptor agonist comprises a dual GLP-1 / amylin receptor agonist including but not limited to zenagamtide, CagriSema (combination of semaglutide and cagrilintide), and ASC36 / ASC35, or any combination thereof. In some embodiments, the GLP-1 receptor agonist comprises a triple GLP-l / GIP / glucagon receptor (GCGR) (GLP-l / GIP / GCGR) agonist including but not limited to retatrutide (LY3437943). In some embodiments, the GLP-1 receptor agonist comprises a dual GLP-l / GCGR agonist including but not limited to survodutide (Bl 456906) and mazdutide (IBI362), or a combination thereof.

[0474] In some embodiments, the muscle atrophy therapeutic agent or muscle atrophy therapy can be combined with an INPPL1 inhibitor.

[0475] In some embodiments, the type 2 diabetes therapeutic agents include but are not limited to an alpha-glucosidase inhibitor, a biguanide, a bile acid sequestrant, a dopamine-2 agonist, a Dipeptidyl Peptidase-4 (DPP-4) inhibitor, a meglitinide, a Sodium-Glucose Cotransporter-2 (SGLT2) inhibitor, a sulfonylurea, a thiazolidinedione (TZD), a GLP-1 receptor agonist, an insulin, an insulin sensitizer, a Proprotein Convertase Subtilisin / Kexin Type 9 (PCSK9) inhibitor, and an agent that preserves beta cell function and survival, or any combination thereof.

[0476] Examples of alpha-glucosidase inhibitors include but are not limited to acarbose, miglitol, and voglibose, or any combination thereof.

[0477] Examples of biguanides include but are not limited to metformin, phenformin, and buformin, or any combination thereof.

[0478] Examples of bile acid sequestrants include but are not limited to cholestyramine, colesevelam, and colestipol, or any combination thereof.

[0479] Examples of dopamine-2 agonists include but are not limited to bromocriptine, pergolide, cabergoline, pramipexole, ropinirole, and rotigotine, or any combination thereof.

[0480] Examples of DPP-4 inhibitors include but are not limited to alogliptin, linagliptin, saxagliptin, sitagliptin, vildagliptin, gemigliptin, anagliptin, teneligliptin, trelagliptin, omarigliptin, evogliptin, gosogliptin, dutogliptin, neogliptin, retagliptin, denagliptin, cofrogliptin, fotagliptin, prusogliptin, and cetagliptin, or any combination thereof.

[0481] Examples of meglitinides include but are not limited to nateglinide, repaglinide, and mitiglinide, or any combination thereof.

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[0483] - 127 - Examples of SGLT2 inhibitors include but are not limited to canagliflozin, dapagliflozin, empagliflozin, bexagliflozin, enavogliflozin, ertugliflozin, henagliflozin, pragliflozin, luseogliflozin, remogliflozin, rongliflozin, sergliflozin, sotagliflozin, tofogliflozin, and velagliflozin, or any combination thereof.

[0484] Examples of sulfonylureas include but are not limited to glimepiride, glipizide, glyburide, acetohexamide, carbutamide, chlorpropamide, glycyclamide, metahexamide, tolazamide, tolbutamide, glibornuride, gliclazide, gliquidone, glisoxepide, glyhexamide, phenbutamide, tolcyclamide, and glyclopyramide, or any combination thereof.

[0485] Examples of TZDs include but are not limited to rosiglitazone, pioglitazone, lobeglitazone, 5-((4-(2-(methyl-2-pyridinylamino) ethoxy)phenyl)methyl)-2,4-thiazolidinedione, troglitazone, ciglitazone, WAY-120,744, englitazone, AD 5075, and darglitazone, or any combination thereof.

[0486] Examples of insulins include but are not limited to insulin glulisine, insulin lispro, insulin aspart, insulin glargine, insulin detemir, and insulin isophane, or any combination thereof.

[0487] Examples of insulin sensitizers include but are not limited to metformin and a TZD, or a combination thereof.

[0488] Examples of PCSK9 inhibitors include but are not limited to alirocumab, evolocumab, inclisiran, lupin peptide, resveratrol, lycopene, and eugenol, or any combination thereof.

[0489] In some embodiments, the dose of the muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy can be decreased by about 10%, by about 20%, by about 30%, by about 40%, by about 50%, by about 60%, by about 70%, by about 80%, or by about 90% for subjects that are heterozygous for an INPPL1 variant nucleic acid molecule or INPPL1 reference (i.e., a less than the standard dosage amount) compared to subjects that are homozygous for an INPPL1 variant nucleic acid molecule (who may receive a standard dosage amount). In some embodiments, the dose of the muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy can be decreased by about 10%, by about 20%, by about 30%, by about 40%, or by about 50%. In some embodiments, the dose of the muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy can be decreased by about 10%, by about 20%, by about 30%, by about 40%, by about 50%, by about 60%, by about 70%, by about 80%, or by about 90% for subjects that are heterozygous for an INPPL1 variant nucleic acid molecule compared to subjects that are INPPL1 reference. In addition, subjects that are

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[0491] - 128 -heterozygous for an INPPL1 variant nucleic acid molecule can be administered the muscle atrophy therapeutic agents less frequently compared to subjects that are INPPL1 reference.

[0492] In some embodiments, the dose of the type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes can be decreased by about 10%, by about 20%, by about 30%, by about 40%, by about 50%, by about 60%, by about 70%, by about 80%, or by about 90% for subjects that are heterozygous for an INPPL1 variant nucleic acid molecule or INPPL1 reference (i.e., a less than the standard dosage amount) compared to subjects that are homozygous for an INPPL1 variant nucleic acid molecule (who may receive a standard dosage amount). In some embodiments, the dose of the type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes can be decreased by about 10%, by about 20%, by about 30%, by about 40%, or by about 50%. In some embodiments, the dose of the type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes can be decreased by about 10%, by about 20%, by about 30%, by about 40%, by about 50%, by about 60%, by about 70%, by about 80%, or by about 90% for subjects that are heterozygous for an INPPL1 variant nucleic acid molecule compared to subjects that are INPPL1 reference. In addition, subjects that are heterozygous for an INPPL1 variant nucleic acid molecule can be administered the type 2 diabetes therapeutic agents less frequently compared to subjectsthat are INPPL1 reference.

[0493] Administration of the muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy, and / or INPPL1 inhibitors can be repeated, for example, after one day, two days, three days, five days, one week, two weeks, three weeks, one month, five weeks, six weeks, seven weeks, eight weeks, two months, or three months. The repeated administration can be at the same dose or at a different dose. The administration can be repeated once, twice, three times, four times, five times, six times, seven times, eight times, nine times, ten times, or more. For example, according to certain dosage regimens a subject can receive therapy for a prolonged period of time such as, for example, 6 months, 1 year, or more.

[0494] Administration of the type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes, and / or INPPL1 inhibitors can be repeated, for example, after one day, two days, three days, five days, one week, two weeks, three weeks, one month, five weeks, six weeks, seven weeks, eight weeks, two months, or three months. The repeated administration can be at the same dose or at a different dose. The administration can be repeated once, twice, three times, four times, five times, six times, seven times, eight times, nine times, ten times, or

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[0496] - 129 -more. For example, according to certain dosage regimens a subject can receive therapy for a prolonged period of time such as, for example, 6 months, 1 year, or more.

[0497] Administration of the muscle atrophy therapeutic agents, type 2 diabetes therapeutic agents, and / or INPPL1 inhibitors can occur by any suitable route including, but not limited to, parenteral, intravenous, oral, subcutaneous, intra-arterial, intracranial, intrathecal, intraperitoneal, topical, intranasal, or intramuscular. Pharmaceutical compositions for administration are desirably sterile and substantially isotonic and manufactured under GMP conditions. Pharmaceutical compositions can be provided in unit dosage form (i.e., the dosage for a single administration). Pharmaceutical compositions can be formulated using one or more physiologically and pharmaceutically acceptable carriers, diluents, excipients, or auxiliaries. The formulation depends on the route of administration chosen. The term "pharmaceutically acceptable" means that the carrier, diluent, excipient, or auxiliary is compatible with the other ingredients of the formulation and not substantially deleterious to the recipient thereof. The terms "treat", "treating", and "treatment" and "prevent", "preventing", and "prevention" as used herein, refer to eliciting the desired biological response, such as a therapeutic and prophylactic effect, respectively. In some embodiments, a therapeutic effect comprises one or more of a decrease / reduction in muscle atrophy, a decrease / reduction in the severity of muscle atrophy (such as, for example, a reduction or inhibition of development of muscle atrophy), a decrease / reduction in symptoms and disease-related effects, delaying the onset of symptoms and disease-related effects, reducing the severity of symptoms of disease-related effects, reducing the number of symptoms and disease-related effects, reducing the latency of symptoms and disease-related effects, an amelioration of symptoms and disease-related effects, reducing secondary symptoms, reducing secondary infections, increasing latency between symptomatic episodes, increasing time to sustained progression, speeding recovery, or increasing efficacy of or decreasing resistance to alternative therapeutics, and / or an increased survival time of the affected host animal, following administration of the agent or composition comprising the agent. A prophylactic effect may comprise a complete or partial avoidance / inhibition or a delay of muscle atrophy development / progression (such as, for example, a complete or partial avoidance / inhibition or a delay), and an increased survival time of the affected host animal, following administration of a therapeutic protocol. Treatment of muscle atrophy encompasses the treatment of a subject already diagnosed as having any form of muscle atrophy at any clinical stage or manifestation, the delay of the onset or evolution or

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[0499] - 130 -aggravation or deterioration of the symptoms or signs of muscle atrophy, and / or preventing and / or reducing the severity of muscle atrophy.

[0500] The terms "treat", "treating", and "treatment" and "prevent", "preventing", and "prevention" as used herein, refer to eliciting the desired biological response, such as a therapeutic and prophylactic effect, respectively. In some embodiments, a therapeutic effect comprises one or more of a decrease / reduction in type 2 diabetes, a decrease / reduction in the severity of type 2 diabetes (such as, for example, a reduction or inhibition of development of type 2 diabetes), a decrease / reduction in symptoms and disease-related effects, delaying the onset of symptoms and disease-related effects, reducing the severity of symptoms of disease-related effects, reducing the number of symptoms and disease-related effects, reducing the latency of symptoms and disease-related effects, an amelioration of symptoms and disease-related effects, reducing secondary symptoms, reducing secondary infections, increasing latency between symptomatic episodes, increasing time to sustained progression, speeding recovery, or increasing efficacy of or decreasing resistance to alternative therapeutics, and / or an increased survival time of the affected host animal, following administration of the agent or composition comprising the agent. A prophylactic effect may comprise a complete or partial avoidance / inhibition or a delay of type 2 diabetes development / progression (such as, for example, a complete or partial avoidance / inhibition or a delay), and an increased survival time of the affected host animal, following administration of a therapeutic protocol. Treatment of type 2 diabetes encompasses the treatment of a subject already diagnosed as having any form of type 2 diabetes at any clinical stage or manifestation, the delay of the onset or evolution or aggravation or deterioration of the symptoms or signs of type 2 diabetes, and / or preventing and / or reducing the severity of type 2 diabetes.

[0501] In some embodiments, the INPPL1 inhibitor and the muscle atrophy therapeutic agent are disposed within a pharmaceutical composition. In some embodiments, the INPPL1 inhibitor is disposed within a first pharmaceutical composition and the muscle atrophy therapeutic agent is disposed within a second pharmaceutical composition. In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered simultaneously. In some embodiments, the first pharmaceutical composition is administered before the second pharmaceutical composition. In some embodiments, the first pharmaceutical composition is administered after the second pharmaceutical composition.

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[0503] - 131 - In some embodiments, the INPPL1 inhibitor and the type 2 diabetes therapeutic agent are disposed within a pharmaceutical composition. In some embodiments, the INPPL1 inhibitor is disposed within a first pharmaceutical composition and the type 2 diabetes therapeutic agent is disposed within a second pharmaceutical composition. In some embodiments, the first pharmaceutical composition and the second pharmaceutical composition are administered simultaneously. In some embodiments, the first pharmaceutical composition is administered before the second pharmaceutical composition. In some embodiments, the first pharmaceutical composition is administered after the second pharmaceutical composition.

[0504] The present disclosure also provides methods of identifying a subject having an increased risk of developing muscle atrophy. In some embodiments, the method comprises determining or having determined in a biological sample obtained from the subject the presence or absence of an INPPL1 variant nucleic acid molecule (such as a genomic nucleic acid molecule, mRNA molecule, and / or cDNA molecule). When the subject lacks an INPPL1 variant nucleic acid molecule (i.e., the subject is genotypically categorized as INPPL1 reference), then the subject has an increased risk of developing muscle atrophy. When the subject has an INPPL1 variant nucleic acid molecule (i.e., the subject is heterozygous or homozygous for an INPPL1 variant nucleic acid molecule), then the subject has a decreased risk of developing muscle atrophy. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0505] The present disclosure also provides methods of identifying a subject having an increased risk of developing type 2 diabetes. In some embodiments, the method comprises determining or having determined in a biological sample obtained from the subject the presence or absence of an INPPL1 variant nucleic acid molecule (such as a genomic nucleic acid molecule, mRNA molecule, and / or cDNA molecule). When the subject lacks an INPPL1 variant nucleic acid molecule (i.e., the subject is genotypically categorized as INPPL1 reference), then the subject has an increased risk of developing type 2 diabetes. When the subject has an INPPL1 variant nucleic acid molecule (i.e., the subject is heterozygous or homozygous for an INPPL1 variant nucleic acid molecule), then the subject has a decreased risk of developing type 2 diabetes. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an

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[0507] - 132 -mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0508] Having a single copy of an INPPL1 variant nucleic acid molecule is more protective of a subject from developing muscle atrophy than having no copies of an INPPL1 variant nucleic acid molecule. Without intending to be limited to any particular theory or mechanism of action, it is believed that a single copy of an INPPL1 variant nucleic acid molecule (i.e., heterozygous for an INPPL1 variant nucleic acid molecule) is protective of a subject from developing muscle atrophy and it is also believed that having two copies of an INPPL1 variant nucleic acid molecule (i.e., homozygous for an INPPL1 variant nucleic acid molecule) may be more protective of a subject from developing muscle atrophy, relative to a subject with a single copy. Thus, in some embodiments, a single copy of an INPPL1 variant nucleic acid molecule may not be completely protective, but instead, may be partially or incompletely protective of a subject from developing muscle atrophy. While not desiring to be bound by any particular theory, there may be additional factors or molecules involved in the development of muscle atrophy that are still present in a subject having a single copy of an INPPL1 variant nucleic acid molecule, thus resulting in less than complete protection from the development of muscle atrophy.

[0509] Having a single copy of an INPPL1 variant nucleic acid molecule is more protective of a subject from developing type 2 diabetes than having no copies of an INPPL1 variant nucleic acid molecule. Without intending to be limited to any particular theory or mechanism of action, it is believed that a single copy of an INPPL1 variant nucleic acid molecule (i.e., heterozygous for an INPPL1 variant nucleic acid molecule) is protective of a subject from developing type 2 diabetes and it is also believed that having two copies of an INPPL1 variant nucleic acid molecule (i.e., homozygous for an INPPL1 variant nucleic acid molecule) may be more protective of a subject from developing type 2 diabetes, relative to a subject with a single copy. Thus, in some embodiments, a single copy of an INPPL1 variant nucleic acid molecule may not be completely protective, but instead, may be partially or incompletely protective of a subject from developing type 2 diabetes. While not desiring to be bound by any particular theory, there may be additional factors or molecules involved in the development of type 2 diabetes that are still present in a subject having a single copy of an INPPL1 variant nucleic acid molecule, thus resulting in less than complete protection from the development of type 2 diabetes.

[0510] Determining whether a subject has an INPPL1 variant nucleic acid molecule in a biological sample from a subject and / or determining whether a subject has an INPPL1 variant

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[0512] - 133-nucleic acid molecule can be carried out by any of the methods described herein. In some embodiments, these methods can be carried out in vitro. In some embodiments, these methods can be carried out in situ. In some embodiments, these methods can be carried out in vivo. In any of these embodiments, the nucleic acid molecule can be present within a cell obtained from the subject.

[0513] In some embodiments, when a subject is identified as having an increased risk of developing muscle atrophy, the subject is administered a muscle atrophy therapeutic agent or muscle atrophy therapy, and / or an INPPL1 inhibitor, as described herein. For example, when the subject is INPPL1 reference, and therefore has an increased risk of developing muscle atrophy, the subject is administered a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or is administered an INPPL1 inhibitor. In some embodiments, when the subject is heterozygous for an INPPL1 variant nucleic acid molecule, the subject is administered the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or is administered an INPPL1 inhibitor. In some embodiments, when the subject is homozygous for an INPPL1 variant nucleic acid molecule, the subject is administered a muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy. In some embodiments, the subject is INPPL1 reference. In some embodiments, the subject is heterozygous for an INPPL1 variant nucleic acid molecule. In some embodiments, the subject is homozygous for an INPPL1 variant nucleic acid molecule.

[0514] In some embodiments, when a subject is identified as having an increased risk of developing type 2 diabetes, the subject is administered a type 2 diabetes therapeutic agent, and / or an INPPL1 inhibitor, as described herein. For example, when the subject is INPPL1 reference, and therefore has an increased risk of developing type 2 diabetes, the subject is administered a type 2 diabetes therapeutic agent in an amount that is the same as or lessthan a standard dosage amount, and / or is administered an INPPL1 inhibitor. In some embodiments, when the subject is heterozygous for an INPPL1 variant nucleic acid molecule, the subject is administered the type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount, and / or is administered an INPPL1 inhibitor. In some embodiments, when the subject is homozygous for an INPPL1 variant nucleic acid molecule, the subject is administered a type 2 diabetes therapeutic agent in a standard dosage amount or muscle atrophy therapy. In some embodiments, the subject is INPPL1 reference. In some

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[0516] - 134 -embodiments, the subject is heterozygous for an INPPL1 variant nucleic acid molecule. In some embodiments, the subject is homozygous for an INPPL1 variant nucleic acid molecule.

[0517] The present disclosure also provides methods of determining a subject's aggregate burden, or risk score, of having two or more INPPL1 variant nucleic acid molecules, and / or two or more INPPL1 variant polypeptides associated with a decreased risk of developing muscle atrophy. The aggregate burden is the sum of two or more genetic variantsthat can be carried out in an association analysis with muscle atrophy. In some embodiments, the subject is homozygous for one or more INPPL1 variant nucleic acid molecules associated with a decreased risk of developing muscle atrophy. In some embodiments, the subject is heterozygous for one or more INPPL1 variant nucleic acid molecules associated with a decreased risk of developing muscle atrophy. When the subject has a lower aggregate burden, the subject has an increased risk of developing muscle atrophy, and the subject is administered or continued to be administered the muscle atrophy therapeutic agent in an amount that isthe same as or less than the standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor. When the subject has a higher aggregate burden, the subject has a decreased risk of developing muscle atrophy and the subject is administered or continued to be administered the muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy. The higher the aggregate burden, the lower the risk of developing muscle atrophy.

[0518] The present disclosure also provides methods of determining a subject's aggregate burden, or risk score, of having two or more INPPL1 variant nucleic acid molecules, and / or two or more INPPL1 variant polypeptides associated with a decreased risk of developing type 2 diabetes. The aggregate burden is the sum of two or more genetic variants that can be carried out in an association analysis with type 2 diabetes. In some embodiments, the subject is homozygous for one or more INPPL1 variant nucleic acid molecules associated with a decreased risk of developing type 2 diabetes. In some embodiments, the subject is heterozygous for one or more INPPL1 variant nucleic acid molecules associated with a decreased risk of developing type 2 diabetes. When the subject has a lower aggregate burden, the subject has an increased risk of developing type 2 diabetes, and the subject is administered or continued to be administered the type 2 diabetes therapeutic agent in an amount that is the same as or less than the standard dosage amount, and / or an INPPL1 inhibitor. When the subject has a higher aggregate burden, the subject has a decreased risk of developing type 2 diabetes and the subject is administered or continued to be administered the type 2 diabetes therapeutic agent

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[0520] - 135 -in a standard dosage amount. The higher the aggregate burden, the lower the risk of developing type 2 diabetes.

[0521] In some embodiments, a subject's aggregate burden of having any two or more INPPL1 variant nucleic acid molecules represents a weighted sum of a plurality of any of the INPPL1 variant nucleic acid molecules. In some embodiments, the aggregate burden is calculated using at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 100, at least about 120, at least about 150, at least about 200, at least about 250, at least about 300, at least about 400, at least about 500, at least about 1,000, at least about 10,000, at least about 100,000, or at least about or more than 1,000,000 genetic variants present in or around (up to 10 Mb) the INPPL1 gene, where the genetic burden is the number of alleles multiplied by the association estimate with muscle atrophy or related outcome for each allele (e.g., a weighted polygenic burden score). In some embodiments, when the subject has an aggregate burden higher than a desired threshold score, the subject has a decreased risk of developing muscle atrophy. In some embodiments, when the subject has an aggregate burden lower than a desired threshold score, the subject has an increased risk of developing muscle atrophy.

[0522] In some embodiments, a subject's aggregate burden of having any two or more INPPL1 variant nucleic acid molecules represents a weighted sum of a plurality of any of the INPPL1 variant nucleic acid molecules. In some embodiments, the aggregate burden is calculated using at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 100, at least about 120, at least about 150, at least about 200, at least about 250, at least about 300, at least about 400, at least about 500, at least about 1,000, at least about 10,000, at least about 100,000, or at least about or more than 1,000,000 genetic variants present in or around (up to 10 Mb) the INPPL1 gene, where the genetic burden is the number of alleles multiplied by the association estimate with type 2 diabetes or related outcome for each allele (e.g., a weighted polygenic burden score). In some embodiments, when the subject has an aggregate burden higher than a desired threshold score, the subject has a decreased risk of developing type 2 diabetes. In some embodiments, when the subject has an aggregate burden lower than a desired threshold score, the subject has an increased risk of developing type 2 diabetes.

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[0524] - 136 - In some embodiments, the aggregate burden may be divided into quintiles, e.g., top quintile, second quintile, intermediate quintile, fourth quintile, and bottom quintile, wherein the top quintile of aggregate burden corresponds to the lowest risk group and the bottom quintile of aggregate burden corresponds to the highest risk group. In some embodiments, a subject having a higher aggregate burden comprises the highest weighted aggregate burdens, including, but not limited to the top 10%, top 20%, top 30%, top 40%, or top 50% of aggregate burdens from a subject population. In some embodiments, the genetic variants comprise the genetic variants having association with muscle atrophy in the top 10%, top 20%, top 30%, top 40%, or top 50% of p-value range forthe association. In some embodiments, each of the identified genetic variants comprise the genetic variants having association with muscle atrophy with p-value of no more than about 10'2, about 10‘3, about 10‘4, about 10‘5, about 10‘6, about 10'7, about 10‘8, about 10‘9, about 1010, about 10-11, about 1012, about 1013, about 1014, about or 1015. In some embodiments, the identified genetic variants comprise the genetic variants having association with muscle atrophy with p-value of less than 5 x 10‘8. In some embodiments, the identified genetic variants comprise genetic variants having association with muscle atrophy in high-risk subjects as compared to the rest of the reference population with odds ratio (OR) about 1.5 or greater, about 1.75 or greater, about 2.0 or greater, or about 2.25 or greater forthe top 20% of the distribution; or about 1.5 or greater, about 1.75 or greater, about 2.0 or greater, about 2.25 or greater, about 2.5 or greater, or about 2.75 or greater. In some embodiments, the odds ratio (OR) may range from about 1.0 to about 1.5, from about 1.5 to about 2.0, from about 2.0 to about 2.5, from about 2.5 to about 3.0, from about 3.0 to about 3.5, from about 3.5 to about 4.0, from about 4.0 to about 4.5, from about 4.5 to about 5.0, from about 5.0 to about 5.5, from about 5.5 to about 6.0, from about 6.0 to about 6.5, from about 6.5 to about 7.0, or greater than 7.0. In some embodiments, high-risk subjects have aggregate burdens in the bottom decile, quintile, or fertile in a reference population. The threshold of the aggregate burden can be determined on the basis of the nature of the intended practical application and the risk difference that would be considered meaningful for that practical application.

[0525] In some embodiments, the aggregate burden may be divided into quintiles, e.g., top quintile, second quintile, intermediate quintile, fourth quintile, and bottom quintile, wherein the top quintile of aggregate burden corresponds to the lowest risk group and the bottom quintile of aggregate burden corresponds to the highest risk group. In some embodiments, a

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[0527] - 137 -subject having a higher aggregate burden comprises the highest weighted aggregate burdens, including, but not limited to the top 10%, top 20%, top 30%, top 40%, or top 50% of aggregate burdens from a subject population. In some embodiments, the genetic variants comprise the genetic variants having association with type 2 diabetes in the top 10%, top 20%, top 30%, top 40%, or top 50% of p-value range forthe association. In some embodiments, each of the identified genetic variants comprise the genetic variants having association with type 2 diabetes with p-value of no more than about 10'2, about 10'3, about 10'4, about 10'5, about 10'6, about 10’7, about 10’8, about 10’9, about 1010, about 10n, about 1012, about 1013, about 1014, about or 1015. In some embodiments, the identified genetic variants comprise the genetic variants having association with type 2 diabetes with p-value of less than 5 x 10'8. In some embodiments, the identified genetic variants comprise genetic variants having association with type 2 diabetes in high-risk subjects as compared to the rest of the reference population with odds ratio (OR) about 1.5 or greater, about 1.75 or greater, about 2.0 or greater, or about 2.25 or greater forthe top 20% of the distribution; or about 1.5 or greater, about 1.75 or greater, about 2.0 or greater, about 2.25 or greater, about 2.5 or greater, or about 2.75 or greater. In some embodiments, the odds ratio (OR) may range from about 1.0 to about 1.5, from about 1.5 to about 2.0, from about 2.0 to about 2.5, from about 2.5 to about 3.0, from about 3.0 to about 3.5, from about 3.5 to about 4.0, from about 4.0 to about 4.5, from about 4.5 to about 5.0, from about 5.0 to about 5.5, from about 5.5 to about 6.0, from about 6.0 to about 6.5, from about 6.5 to about 7.0, or greater than 7.0. In some embodiments, high-risk subjects have aggregate burdens in the bottom decile, quintile, or tertile in a reference population. The threshold of the aggregate burden can be determined on the basis of the nature of the intended practical application and the risk difference that would be considered meaningful for that practical application.

[0528] In embodiments where the aggregate burden is determined for genetic variants of any one of INPPL1 associated with muscle atrophy, then the aggregate burden represents a subject's risk score for developing muscle atrophy. In some embodiments, the aggregate burden or risk score includes genetic variants of any two or more of the INPPL1 (or any other gene) associated with muscle atrophy to generate a polygenic risk score (PRS) for developing muscle atrophy. In some embodiments, the PRS includes the INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

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[0530] - 138 - In embodiments where the aggregate burden is determined for genetic variants of any one of INPPL1 associated with type 2 diabetes, then the aggregate burden represents a subject's risk score for developing type 2 diabetes. In some embodiments, the aggregate burden or risk score includes genetic variants of any two or more of the INPPL1 (or any other gene) associated with type 2 diabetes to generate a polygenic risk score (PRS) for developing or type 2 diabetes. In some embodiments, the PRS includes the INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0531] The present disclosure also provides methods of detecting the presence or absence of an INPPL1 variant nucleic acid molecule (i.e., a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule produced from an mRNA molecule) in a biological sample from a subject. It is understood that gene sequences within a population and mRNA molecules encoded by such genes can vary due to polymorphisms such as single-nucleotide polymorphisms.

[0532] The biological sample can be derived from any cell, tissue, or biological fluid from the subject. The biological sample may comprise any clinically relevant tissue, such as a bone marrow sample, a tumor biopsy, a fine needle aspirate, or a sample of bodily fluid, such as blood, gingival crevicular fluid, plasma, serum, lymph, ascitic fluid, cystic fluid, or urine. In some cases, the sample comprises a buccal swab. The biological sample used in the methods disclosed herein can vary based on the assay format, nature of the detection method, and the tissues, cells, or extracts that are used as the sample. A biological sample can be processed differently depending on the assay being employed. For example, when detecting any INPPL1 variant nucleic acid molecule, preliminary processing designed to isolate or enrich the biological sample for the genomic DNA can be employed. A variety of techniques may be used for this purpose. When detecting the level of any INPPL1 variant nucleic acid molecule, different techniques can be used enrich the biological sample with mRNA molecules. Various methods to detect the presence or level of an mRNA molecule orthe presence of a particular variant genomic DNA locus can be used.

[0533] In some embodiments, detecting an INPPL1 variant nucleic acid molecule in a subject comprises performing a sequence analysis on a biological sample obtained from the subject to determine whether an INPPL1 genomic nucleic acid molecule in the biological sample, and / or an INPPL1 mRNA molecule in the biological sample, and / or an INPPL1 cDNA molecule produced

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[0535] - 139 -from an mRNA molecule in the biological sample, is present in the sample. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0536] In some embodiments, the methods of detecting the presence or absence of an INPPL1 variant nucleic acid molecule (such as, for example, a genomic nucleic acid molecule, an mRNA molecule, and / or a cDNA molecule produced from an mRNA molecule) in a subject comprise performing an assay on a biological sample obtained from the subject. The assay determines whether a nucleic acid molecule in the biological sample comprises a particular nucleotide sequence.

[0537] In some embodiments, the biological sample comprises a cell or cell lysate. Such methods can further comprise, for example, obtaining a biological sample from the subject comprising an INPPL1 genomic nucleic acid molecule or mRNA molecule, and if mRNA, optionally reverse transcribing the mRNA into cDNA. Such assays can comprise, for example determining the identity of these positions of the particular INPPL1 nucleic acid molecule. In some embodiments, the method is an in vitro method.

[0538] In some embodiments, the determining step, detecting step, or sequence analysis comprises sequencing at least a portion of the nucleotide sequence of the INPPL1 genomic nucleic acid molecule, the INPPL1 mRNA molecule, or the INPPL1 cDNA molecule in the biological sample that comprises a genetic variation compared to the corresponding INPPL1 reference molecule. In some embodiments, the sequenced portion comprises one or more variations that cause a loss-of-function (partial or complete) or are predicted to cause a loss-of-function (partial or complete).

[0539] In some embodiments, the assay comprises sequencingthe entire nucleic acid molecule. In some embodiments, only an INPPL1 genomic nucleic acid molecule is analyzed. In some embodiments, only an INPPL1 mRNA is analyzed. In some embodiments, only an INPPL1 cDNA obtained from the INPPL1 mRNA is analyzed.

[0540] Alteration-specific polymerase chain reaction techniques can be used to detect mutations such as SNPs in a nucleic acid sequence. Alteration-specific primers can be used because the DNA polymerase will not extend when a mismatch with the template is present.

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[0542] - 140 - In some embodiments, the nucleic acid molecule in the sample is mRNA and the mRNA is reverse-transcribed into a cDNA prior to the amplifying step. In some embodiments, the nucleic acid molecule is present within a cell obtained from the subject.

[0543] In some embodiments, the assay comprises contacting the biological sample with a primer or probe, such as an alteration-specific primer or alteration-specific probe, that specifically hybridizes to an INPPL1 variant genomic sequence, variant mRNA sequence, or variant cDNA sequence and not the corresponding INPPL1 reference sequence under stringent conditions and determining whether hybridization has occurred.

[0544] In some embodiments, the determining step, detecting step, or sequence analysis comprises: a) amplifying at least a portion of the INPPL1 nucleic acid molecule that encodes the INPPL1 polypeptide; b) labeling the amplified nucleic acid molecule with a detectable label; c) contacting the labeled nucleic acid molecule with a support comprising an alteration-specific probe; and d) detecting the detectable label.

[0545] In some embodiments, the assay comprises RNA sequencing (RNA-Seq). In some embodiments, the assays also comprise reverse transcribing mRNA into cDNA, such as by the reverse transcriptase polymerase chain reaction (RT-PCR).

[0546] In some embodiments, the methods utilize probes and primers of sufficient nucleotide length to bind to the target nucleotide sequence and specifically detect and / or identify a polynucleotide comprising an INPPL1 variant genomic nucleic acid molecule, variant mRNA molecule, or variant cDNA molecule. The hybridization conditions or reaction conditions can be determined by the operator to achieve this result. The nucleotide length may be any length that is sufficient for use in a detection method of choice, including any assay described or exemplified herein. Such probes and primers can hybridize specifically to a target nucleotide sequence under high stringency hybridization conditions. Probes and primers may have complete nucleotide sequence identity of contiguous nucleotides within the target nucleotide sequence, although probes differing from the target nucleotide sequence and that retain the ability to specifically detect and / or identify a target nucleotide sequence may be designed by conventional methods. Probes and primers can have about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or 100% sequence identity or complementarity with the nucleotide sequence of the target nucleic acid molecule.

[0547] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0548] - 141 - Illustrative examples of nucleic acid sequencing techniques include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing. Other methods involve nucleic acid hybridization methods other than sequencing, including using labeled primers or probes directed against purified DNA, amplified DNA, and fixed cell preparations (fluorescence in situ hybridization (FISH)). In some methods, a target nucleic acid molecule may be amplified prior to or simultaneous with detection. Illustrative examples of nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA). Other methods include, but are not limited to, ligase chain reaction, strand displacement amplification, and thermophilic SDA (tSDA).

[0549] In hybridization techniques, stringent conditions can be employed such that a probe or primer will specifically hybridize to its target. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target sequence to a detectably greater degree than to other non-target sequences, such as, at least 2-fold, at least 3-fold, at least 4-fold, or more over background, including over 10-fold over background. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence to a detectably greater degree than to other nucleotide sequences by at least 2-fold. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence to a detectably greater degree than to other nucleotide sequences by at least 3-fold. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence to a detectably greater degree than to other nucleotide sequences by at least 4-fold. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence to a detectably greater degree than to other nucleotide sequences by over 10-fold over background. Stringent conditions are sequence-dependent and will be different in different circumstances.

[0550] Appropriate stringency conditions which promote DNA hybridization, for example, 6X sodium chloride / sodium citrate (SSC) at about 45°C., followed by a wash of 2X SSC at 50°C, are known or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N. Y. (1989), 6.3.1-6.3.6. Typically, stringent conditions for hybridization and detection will be those in which the salt concentration is less than about 1.5 M Na+ion, typically about 0.01 to 1.0 M Na+ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about

[0551] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0552] - 142 - 30°C for short probes (such as, for example, 10 to 50 nucleotides) and at least about 60°C for longer probes (such as, for example, greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Optionally, wash buffers may comprise about 0.1% to about 1% SDS. Duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash time will be at least a length of time sufficient to reach equilibrium.

[0553] In some embodiments, such isolated nucleic acid molecules comprise or consist of at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55, at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 2000, at least about 3000, at least about 4000, or at least about 5000 nucleotides. In some embodiments, such isolated nucleic acid molecules comprise or consist of at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, or at least about 25 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of at least about 18 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consists of at least about 15 nucleotides. In some embodiments, the isolated nucleic acid molecules consist of or comprise from about 10 to about 35, from about 10 to about 30, from about 10 to about 25, from about 12 to about 30, from about 12 to about 28, from about 12 to about 24, from about 15 to about 30, from about 15 to about 25, from about 18 to about 30, from about 18 to about 25, from about 18 to about 24, or from about 18 to about 22 nucleotides. In some embodiments, the isolated nucleic acid molecules consist of or comprise from about 18 to about 30 nucleotides. In some embodiments, the isolated nucleic acid molecules comprise or consist of at least about 15 nucleotides to at least about 35 nucleotides.

[0554] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0555] - 143 - In some embodiments, such isolated nucleic acid molecules hybridize to INPPL1 variant nucleic acid molecules (such as genomic nucleic acid molecules, mRNA molecules, and / or cDNA molecules) under stringent conditions. Such nucleic acid molecules can be used, for example, as probes, primers, alteration-specific probes, or alteration-specific primers as described or exemplified herein, and include, without limitation primers, probes, antisense RNAs, shRNAs, and siRNAs, each of which is described in more detail elsewhere herein and can be used in any of the methods described herein.

[0556] In some embodiments, the isolated nucleic acid molecules hybridize to at least about 15 contiguous nucleotides of a nucleic acid molecule that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to the INPPL1 variant nucleic acid molecule. In some embodiments, the isolated nucleic acid molecules consist of or comprise from about 15 to about 100 nucleotides, or from about 15 to about 35 nucleotides. In some embodiments, the isolated nucleic acid molecules consist of or comprise from about 15 to about 100 nucleotides. In some embodiments, the isolated nucleic acid molecules consist of or comprise from about 15 to about 35 nucleotides.

[0557] In some embodiments, the alteration-specific probes and alteration-specific primers comprise DNA. In some embodiments, the alteration-specific probes and alteration-specific primers comprise RNA.

[0558] In some embodiments, the probes and primers described herein (including alteration-specific probes and alteration-specific primers) have a nucleotide sequence that specifically hybridizes to any of the nucleic acid molecules disclosed herein, or the complement thereof. In some embodiments, the probes and primers specifically hybridize to any of the nucleic acid molecules disclosed herein under stringent conditions.

[0559] In some embodiments, the primers, including alteration-specific primers, can be used in second generation sequencing or high throughput sequencing. In some instances, the primers, including alteration-specific primers, can be modified. In particular, the primers can comprise various modifications that are used at different steps of, for example. Massive Parallel Signature Sequencing (MPSS), Polony sequencing, and 454 Pyrosequencing. Modified primers can be used at several steps of the process, including biotinylated primers in the cloning step and fluorescently labeled primers used at the bead loading step and detection step. Polony sequencing is generally performed using a paired-end tags library wherein each molecule of

[0560] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0561] - 144 - DNA template is about 135 bp in length. Biotinylated primers are used at the bead loading step and emulsion PCR. Fluorescently labeled degenerate nonamer oligonucleotides are used at the detection step. An adaptor can contain a 5'-biotin tag for immobilization of the DNA library onto streptavidin-coated beads.

[0562] The probes and primers described herein can be used to detect a nucleotide variation within any of the INPPL1 variant nucleic acid molecules disclosed herein. The primers described herein can be used to amplify any INPPL1 variant nucleic acid molecules, or a fragment thereof.

[0563] In the context of the disclosure "specifically hybridizes" means that the probe or primer (such as, for example, the alteration-specific probe or alteration-specific primer) does not hybridize to a nucleic acid sequence encoding an INPPL1 reference genomic nucleic acid molecule, an INPPL1 reference mRNA molecule, and / or an INPPL1 reference cDNA molecule.

[0564] In some embodiments, the probes (such as, for example, an alteration-specific probe) comprise a label. In some embodiments, the label is a fluorescent label, a radiolabel, or biotin.

[0565] The present disclosure also provides supports comprising a substrate to which any one or more of the probes disclosed herein is attached. Solid supports are solid-state substrates or supports with which molecules, such as any of the probes disclosed herein, can be associated. A form of solid support is an array. Another form of solid support is an array detector. An array detector is a solid support to which multiple different probes have been coupled in an array, grid, or other organized pattern. A form for a solid-state substrate is a microtiter dish, such as a standard 96-well type. In some embodiments, a multiwell glass slide can be employed that normally contains one array per well.

[0566] The genomic nucleic acid molecules, mRNA molecules, and cDNA molecules can be from any organism. For example, the genomic nucleic acid molecules, mRNA molecules, and cDNA molecules can be human or an ortholog from another organism, such as a non-human mammal, a rodent, a mouse, or a rat. It is understood that gene sequences within a population can vary due to polymorphisms such as single-nucleotide polymorphisms.

[0567] Also provided herein are functional polynucleotides that can interact with the disclosed nucleic acid molecules. Examples of functional polynucleotides include, but are not limited to, antisense molecules, aptamers, ribozymes, triplex forming molecules, and external guide sequences. The functional polynucleotides can act as effectors, inhibitors, modulators, and stimulators of a specific activity possessed by a target molecule, or the functional polynucleotides can possess a de novo activity independent of any other molecules.

[0568] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0569] - 145 - The isolated nucleic acid molecules disclosed herein can comprise RNA, DNA, or both RNA and DNA. The isolated nucleic acid molecules can also be linked or fused to a heterologous nucleic acid sequence, such as in a vector, or a heterologous label. For example, the isolated nucleic acid molecules disclosed herein can be within a vector or as an exogenous donor sequence comprising the isolated nucleic acid molecule and a heterologous nucleic acid sequence. The isolated nucleic acid molecules can also be linked or fused to a heterologous label. The label can be directly detectable (such as, for example, fluorophore) or indirectly detectable (such as, for example, hapten, enzyme, or fluorophore quencher). Such labels can be detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Such labels include, for example, radiolabels, pigments, dyes, chromogens, spin labels, and fluorescent labels. The label can also be, for example, a chemiluminescent substance; a metal-containing substance; or an enzyme, where there occurs an enzyme-dependent secondary generation of signal. The term "label" can also refer to a "tag" or hapten that can bind selectively to a conjugated molecule such that the conjugated molecule, when added subsequently along with a substrate, is used to generate a detectable signal. For example, biotin can be used as a tag along with an avidin or streptavidin conjugate of horseradish peroxidate (HRP) to bind to the tag, and examined using a calorimetric substrate (such as, for example, tetramethylbenzidine (TMB)) or a fluorogenic substrate to detect the presence of HRP. Exemplary labels that can be used as tags to facilitate purification include, but are not limited to, myc, HA, FLAG or 3XFLAG, 6Xhis or polyhistidine, glutathione-S-transferase (GST), maltose binding protein, an epitope tag, or the Fc portion of immunoglobulin. Numerous labels include, for example, particles, fluorophores, haptens, enzymes and their calorimetric, fluorogenic and chemiluminescent substrates and other labels.

[0570] Percent identity (or percent complementarity) between particular stretches of nucleotide sequences within nucleic acid molecules or amino acid sequences within polypeptides can be determined routinely using BLAST programs (basic local alignment search tools) and PowerBLAST programs (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656) or by using the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489). Herein, if reference is made to percent sequence identity, the higher percentages of sequence identity are preferred over the lower ones.

[0571] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0572] - 146 - The present disclosure also provides muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy for use in the treatment or prevention of muscle atrophy in a subject having an INPPL1 variant nucleic acid molecule. Any of the muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0573] The present disclosure also provides uses of muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy for use in the preparation of a medicament for treating or preventing muscle atrophy in a subject having an INPPL1 variant nucleic acid molecule. Any of the muscle atrophy therapeutic agents that treat, prevent, or inhibit muscle atrophy described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0574] The present disclosure also provides type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes for use in the treatment or prevention of type 2 diabetes in a subject having an INPPL1 variant nucleic acid molecule. Any of the type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0575] The present disclosure also provides uses of type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes for use in the preparation of a medicament for treating or preventing type 2 diabetes in a subject having an INPPL1 variant nucleic acid molecule. Any of the type 2 diabetes therapeutic agents that treat, prevent, or inhibit type 2 diabetes described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in

[0576] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0577] - 147 - Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0578] The present disclosure also provides INPPL1 inhibitors for use in the treatment or prevention of muscle atrophy in a subject that is INPPL1 reference or is heterozygous for an INPPL1 variant nucleic acid molecule. Any of the INPPL1 inhibitors described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0579] The present disclosure also provides INPPL1 inhibitors in the preparation of a medicament for treating or preventing muscle atrophy in a subject that is INPPL1 reference or is heterozygous for an INPPL1 variant nucleic acid molecule. Any of the INPPL1 inhibitors described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0580] The present disclosure also provides INPPL1 inhibitors for use in the treatment or prevention of type 2 diabetes in a subject that is INPPL1 reference or is heterozygous for an INPPL1 variant nucleic acid molecule. Any of the INPPL1 inhibitors described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0581] The present disclosure also provides INPPL1 inhibitors in the preparation of a medicament for treating or preventing type 2 diabetes in a subject that is INPPL1 reference or is heterozygous for an INPPL1 variant nucleic acid molecule. Any of the INPPL1 inhibitors described herein can be used herein. Any of the INPPL1 variant nucleic acid molecules disclosed herein can be used herein. In some embodiments, the INPPL1 variant nucleic acid molecule is an INPPL1 variant genomic nucleic acid molecule that comprises the genetic variation listed in Table 1, or is an mRNA molecule produced therefrom, or is a cDNA molecule produced from the mRNA molecule.

[0582] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0583] - 148 - All patent documents, websites, other publications, accession numbers and the like cited above or below are incorporated by reference in their entirety for all purposes to the same extent as if each individual item were specifically and individually indicated to be so incorporated by reference. If different versions of a sequence are associated with an accession number at different times, the version associated with the accession number at the effective filing date of this application is meant. The effective filing date means the earlier of the actual filing date or filing date of a priority application referring to the accession number if applicable. Likewise, if different versions of a publication, website or the like are published at different times, the version most recently published at the effective filing date of the application is meant unless otherwise indicated. Any feature, step, element, embodiment, or aspect of the present disclosure can be used in combination with any other feature, step, element, embodiment, or aspect unless specifically indicated otherwise. Although the present disclosure has been described in some detail by way of illustration and example for purposes of clarity and understanding, it will be apparent that certain changes and modifications may be practiced within the scope of the appended claims.

[0584] The following examples are provided to describe the embodiments in greater detail. They are intended to illustrate, not to limit, the claimed embodiments. The following examples provide those of ordinary skill in the art with a disclosure and description of how the compounds, compositions, articles, devices and / or methods described herein are made and evaluated and are intended to be purely exemplary and are not intended to limit the scope of any claims. Efforts have been made to ensure accuracy with respect to numbers (such as, for example, amounts, temperature, etc.), but some errors and deviations may be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in °C or is at ambient temperature, and pressure is at or near atmospheric.

[0585] Examples

[0586] Example 1: General Methods

[0587] Genetic association studies were performed in the University of Texas Southwestern Dallas Heart Expansion Study - Dallas Biobank (UTSW-COHEN), the United Kingdom Biobank (UKB) cohort, the UCLA Biobank (UCLA), the Colorado Biobanked and Prospective Collection Project (COLORADO), the DiscoverEHR cohort from the Geisinger Health System (GHS) MyCode Community Health Initiative, Mount Sinai BioMe Biobank cohort (SINAI), The University of

[0588] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0589] - 149 - Pennsylvania Penn Medicine BioBank (UPENN-PMBB), Malmo Diet and Cancer Study (MDCS), the Mayo Clinic Biobank (MAYO-CLINIC), the Mexico City Prospective Study (MCPS), and the Bangladesh Longitudinal Investigation of Emerging Vascular Events Study (CAMBRIDGE-BELIEVE).

[0590] The UTSW-COHEN is a population-based cohort of 13,888 African- and Hispanic-Americans in the city of Dallas. The UKB is a population-based cohort study of people aged between 40 and 69 years recruited through 22 testing centers in the UK between 2006-2010 (Sudlow et al., PLoS Med., 2015, 12, el001779). Over 430,000 European ancestry participants from UKB with available whole-exome sequencing and clinical phenotype data were included. UCLA is a hospital-based electronic health record data that provided genotypic and phenotypic data on 27,932 individuals. COLORADO is a hospital-based electronic health record database with genotypic and phenotypic data on 35,320 individuals. The GHS MyCode study Community Health Initiative is a health system-based cohort of patients from Central and Eastern Pennsylvania (USA) recruited in 2007-2019 (Carey et al., Genet. Med., 2016, 18, 906-13). Over 130,000 European ancestry participants from GHS with available whole-exome sequencing and clinical phenotype data were included. SINAI is a health-system based cohort of patients from the Mount Sinai BioMe Biobank, recruited from the Mount Sinai Health System (Abul-Husn et aL, Cell, 2019, 177, 58-69). UPENN-PMBB is a health-system based cohort of patients from the University of Pennsylvania Penn Medicine BioBank (Park et al., Genet. Med., 2020, 22, 102-111). MDCS is a Swedish population-based, prospective, observational cohort recruited between 1991 and 1996 (Berglund et aL, J. Intern. Med., 1993, 233, 45-51). The MAYO-CLINIC is a hospital-based electronic health record database with genotypic and phenotypic data on 81,132 individuals (Olson et al., BMJ Open, 2019, 9(11), e032707). The MCPS is a populationbased prospective study that included up to 159,755 individuals with phenotype and exome sequencing data (Tapia-Conyer et aL, Int. J. Epidemiol., 2006, 35, 243-9). The CAMBRIDGE-BELIEVE study is a cross-sectional study conducted in Bangladesh (Khan et aL, 2019, BMJ Open, 2019, 9:e030886).

[0591] Phenotype definitions

[0592] Baseline values for blood-based biomarkers (including creatinine, cystatin C, and others) were used in population-based cohorts. For health-system based cohorts, biomarker

[0593] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0594] - 150 -values were extracted from the electronic medical records of participants and median values were derived if two or more measurements were available for an individual.

[0595] For the analysis of serum creatinine concentration, individuals who likely have chronic kidney disease were first excluded (since kidney disease may influence creatinine levels). Such individuals were identified on the basis of various data sources, including: 1) electronic-health record or self-reported diagnoses of chronic kidney disease (including a record of renal replacement therapy), 2) measured estimated glomerular filtration rate (eGFR) less than 60 ml / min, and, if possible, 3) measured urine albumin-creatinine ratio greaterthan 30 mg / g. The creatinine-to-cystatin C ratio was derived by dividing the serum creatinine concentration by the serum cystatin C concentration (without excluding individuals with chronic kidney disease from either measurement), and mu Itiplying th is ratio by a hundred.

[0596] Thigh muscle water volume was derived from magnetic resonance imaging (MRI) data in UKB. Analysis was performed using a subset of 38,880 participants with exome sequencing data who had undergone two-point Dixon MRI using Siemens MAGNETOM Aera 1.5T clinical MRI scanners, split into six different imaging series. Whole-body Dixon MRI images for 52 subjects were manually annotated, and then used these annotations to train a multi-class segmentation deep neural-net which employed a UNet architecture with a ResNet34 backbone, and a loss function of a sum of the Jaccard Index and categorical focal loss (Akbari et al., Nat. Commun., 2022, 23, 13(1), 4844). Thigh muscle phenotypes were calculated by summing the resulting segmentation maps from the neural net for each corresponding class.

[0597] Bioelectrical impedance was assessed at baseline in UKB using a Tanita BC 418ma Body Fat Analyser device. Bioelectrical impedance-derived measures of fat and fat-free mass and body composition were used as reported by UKB.

[0598] Dual-energy X-ray absorptiometry was assessed with a Lunar iDXA Scanner. Dualenergy X-ray absorptiometry-derived measures of fat and fat-free mass and body composition were used as reported by UKB.

[0599] Hand grip strength was assessed at baseline in UKB using a Jamar J00105 hydraulic hand dynamometer. The maximum value between the right and left hand values was selected, and adjusted the maximum value for body mass index, body mass index squared, and height, with adjustment performed separately in men and women. The unadjusted maximum value between the right and left hand values was also assessed.

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[0601] - 151 - Genotype data

[0602] High coverage whole exome sequencing was performed as previously described (Dewey et al., Science, 2016, 354, aaf6814; Van Hout et al., Nature, 2020, 586, 749-756) and as summarized below. NimbleGen probes (VCRome; for part of the GHS cohort) or a modified version of the xGen design available from Integrated DNA Technologies (IDT; forthe rest of GHS and other cohorts) were used for target sequence capture of the exome. A unique 6 base pair (bp) barcode (VCRome) or 10 bp barcode (IDT) was added to each DNA fragment during library preparation to facilitate multiplexed exome capture and sequencing. Equal amounts of sample were pooled prior to exome capture. Sequencing was performed using 75 bp paired-end reads on Illumina v4 HiSeq 2500 (for part ofthe GHS cohort) or NovaSeq (forthe rest of GHS and other cohorts) instruments. Sequencing had a coverage depth (i.e., number of sequence-reads covering each nucleotide in the target areas ofthe genome) sufficient to provide greater than 20x coverage over 85% of targeted bases in 96% of VCRome samples and 20x coverage over 90% of targeted bases in 99% of IDT samples. Data processing steps included sample demultiplexing using Illumina software, alignment to the GRCh38 Human Genome reference sequence including generation of binary alignment and mapping files (BAM), processing of BAM files (e.g., marking of duplicate reads and other read mapping evaluations). Variant calling was performed using the GLNexus system (DOI: 10.1101 / 343970). Variant mapping and annotation were based on the GRCh38 Human Genome reference sequence and Ensembl v85 gene definitions using the snpEff software. The snpEff predictions that involve protein-coding transcripts with an annotated start and stop were then combined into a single functional impact prediction by selecting the most deleterious functional effect class for each gene. The hierarchy (from most to least deleterious) for these annotations was frameshift, stop-gain, stop-loss, splice acceptor, splice donor, stop-lost, in-frame indel, missense, other annotations. Predicted LOF genetic variants included: a) insertions or deletions resulting in a frameshift, b) insertions, deletions or single nucleotide variants resulting in the introduction of a premature stop codon or in the loss ofthe transcription start site or stop site, and c) variants in donor or acceptor splice sites. Missense variants were classified for likely functional impact according to the number of in silico prediction algorithms that predicted deleteriousness using SIFT (Adzhubei et al., Nat. Methods, 2010, 7, 248-9) and Polyphen2_HVAR (Adzhubei et al., Nat. Methods, 2010, 7, 248-9), LRT (Chun et al.. Genome Res., 2009, 19, 1553-61) and MutationTaster (Schwarz et al., Nat. Methods, 2010, 7, 575-6).

[0603] 119279242DOCKET NO.: 38120-4614 (11651WO01)

[0604] - 152 - Example 2: Association Analysis Results

[0605] FIG. 1 shows loss of function of INPPL1 associates with increased creatinine levels, increased bioelectrical impedance analysis (BIA)- and dual-energy X-ray absorptiometry (DXA)-derived markers of lean mass, increased BIA-derived fat mass, and numerical increases in grip strength and MRI-derived muscle mass.

[0606] FIG. 2 shows Inppll siRNA knockdown extended p-Akt signaling in C2C12 differentiated myotubes.

[0607] FIG. 3 shows CACNG1 mAb-AAV9(W503A)-gRNA directed Cas9 editing of Inppll resulted in a reduction of mRNA levels in the tibialis anterior and EDL muscles after i.m. injection (REGN10717-AAV9(W503A) capsid separately expressing an Inppll gRNA under a Pol III promoter and eGFP under under a Pol II promoter).

[0608] FIG. 4 shows the burden of loss of function and deterious missense variants in INPPL1 associates with a lower risk of type 2 diabetes.

[0609] Various modifications of the described subject matter, in addition to those described herein, will be apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. Each reference (including, but not limited to, journal articles, U. S. and non-U. S. patents, patent application publications, international patent application publications, gene bank accession numbers, and the like) cited in the present application is incorporated herein by reference in its entirety and for all purposes.

[0610] 119279242

Claims

DOCKET NO.: 38120-4614 (11651WO01)- 153 - What is Claimed is:

1. A method of treating a subject having muscle atrophy or at risk of developing muscle atrophy, the method comprising administering an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) inhibitor to the subject.

2. The method of claim 1, wherein the muscle atrophy is skeletal muscle atrophy.

3. The method of claim 1, wherein the muscle atrophy is cardiac muscle atrophy.

4. The method of claim 1, wherein the subject has: i) a muscular dystrophy, a myotonic dystrophy, or a mitochondrial myopathy; ii) an inflammatory muscle disease; iii) a sarcopenia; iv) a myopathy arising secondary to an environmental influence; v) a myopathy arising secondary to a systemic disease; vi) a neuromuscular condition leading to muscle atrophy; or vii) a weight loss mechanism.

5. The method of claim 4, wherein:the inflammatory muscle disease comprises polymyositis or dermatomyositits; the sarcopenia comprises age-related sarcopenia;the myopathy arising secondary to an environmental influence comprises drug-induced or alcohol-induced;the myopathy arising secondary to a systemic disease comprises thyroid-associated myopathy;the neuromuscular condition leading to muscle atrophy comprises amyotrophic lateral sclerosis or myasthenia gravis; andthe weight loss mechanism comprises bariatric surgery or pharmacologically-induced.

6. The method of any one of claims 1 to 5, wherein the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an INPPL1 nucleic acid molecule.

7. The method of claim 6, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), and / or a short hairpin RNA (shRNA).

8. The method of claim 7, wherein the inhibitory nucleic acid molecule comprises an siRNA.

9. The method of claim 7, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule.

10. The method of any one of claims 1 to 9, wherein the subject is also administered a muscle atrophy therapeutic agent or muscle atrophy therapy.119279242DOCKET NO.: 38120-4614 (11651WO01)- 154 - 11. The method of any one of claims 1 to 10, further comprising detecting the presence or absence of an INPPL1 variant nucleic acid molecule in a biological sample from the subject.

12. The method of claim 11, further comprising administering a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy to the subject when the INPPL1 variant nucleic acid molecule is absent from the biological sample.

13. The method of claim 11, further comprising administering a muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy to the subject when the subject is heterozygous for the INPPL1 variant nucleic acid molecule.

14. The method of any one of claims 11 to 13, wherein the INPPL1 variant nucleic acid molecule comprises a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, and / or a variant that encodes a truncated INPPL1 variant polypeptide.

15. The method of any one of claims 11 to 13, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

16. A method of treating a subject having type 2 diabetes or at risk of developing type 2 diabetes, the method comprising administering an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) inhibitor to the subject.

17. The method of claim 16, wherein the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an INPPL1 nucleic acid molecule.

18. The method of claim 17, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), and / or a short hairpin RNA (shRNA).

19. The method of claim 18, wherein the inhibitory nucleic acid molecule comprises an siRNA.

20. The method of claim 18, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule.

21. The method of any one of claims 16 to 20, wherein the subject is also administered a type 2 diabetes therapeutic agent.

22. The method of any one of claims 16 to 21, further comprising detecting the presence or absence of an INPPL1 variant nucleic acid molecule in a biological sample from the subject.119279242DOCKET NO.: 38120-4614 (11651WO01)- 155 - 23. The method of claim 22, further comprising administering a type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount to the subject when the INPPL1 variant nucleic acid molecule is absent from the biological sample.

24. The method of claim 22, further comprising administering a type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount to the subject when the subject is heterozygous for the INPPL1 variant nucleic acid molecule.

25. The method of any one of claims 22 to 24, wherein the INPPL1 variant nucleic acid molecule comprises a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, and / or a variant that encodes a truncated INPPL1 variant polypeptide.

26. The method of any one of claims 22 to 24, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

27. A method of treating a subject having muscle atrophy or at risk of developing muscle atrophy by administering a muscle atrophy therapeutic agent or muscle atrophy therapy, the method comprising:determining or having determined whether the subject has an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) variant nucleic acid molecule, by:obtaining or having obtained a biological sample from the subject; andperforming or having performed a sequence analysis on the biological sample to determine if the subject has a genotype comprising the INPPL1 variant nucleic acid molecule; andadministering or continuing to administer the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitor to a subject that is INPPL1 reference;administering or continuing to administer the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy, and / or an INPPL1 inhibitorto a subject that is heterozygous forthe INPPL1 variant nucleic acid molecule; oradministering or continuing to administer the muscle atrophy therapeutic agent in a standard dosage amount or muscle atrophy therapy to a subject that is homozygous forthe INPPL1 variant nucleic acid molecule;119279242DOCKET NO.: 38120-4614 (11651WO01)- 156 - wherein the presence of the INPPL1 variant nucleic acid molecule indicatesthe subject has a decreased risk of developing muscle atrophy.

28. The method of claim 27, wherein the muscle atrophy is skeletal muscle atrophy.

29. The method of claim 27, wherein the muscle atrophy is cardiac muscle atrophy.

30. The method of claim 27, wherein the subject has: i) a muscular dystrophy, a myotonic dystrophy, or a mitochondrial myopathy; ii) an inflammatory muscle disease; iii) a sarcopenia; iv) a myopathy arising secondary to an environmental influence; v) a myopathy arising secondary to a systemic disease; vi) a neuromuscular condition leading to muscle atrophy; or vii) a weight loss mechanism.

31. The method of claim 30, wherein:the inflammatory muscle disease comprises polymyositis or dermatomyositits; the sarcopenia comprises age-related sarcopenia;the myopathy arising secondary to an environmental influence comprises drug-induced or alcohol-induced;the myopathy arising secondary to a systemic disease comprises thyroid-associated myopathy;the neuromuscular condition leading to muscle atrophy comprises amyotrophic lateral sclerosis or myasthenia gravis; andthe weight loss mechanism comprises bariatric surgery or pharmacologically-induced.

32. The method of any one of claims 27 to 31, wherein the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an INPPL1 nucleic acid molecule.

33. The method of claim 32, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), and / or a short hairpin RNA (shRNA).

34. The method of claim 33, wherein the inhibitory nucleic acid molecule comprises an siRNA.

35. The method of claim 33, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule.

36. The method of any one of claims 27 to 35, wherein the subject is heterozygous forthe INPPL1 variant nucleic acid molecule, and the subject is administered or continued to be administered the muscle atrophy therapeutic agent in an amount that isthe same as or less than a standard dosage amount or muscle atrophy therapy and the INPPL1 inhibitor.119279242DOCKET NO.: 38120-4614 (11651WO01)- 157 - 37. The method of any one of claims 1 to 35, wherein the subject is INPPL1 reference, and the subject is administered or continued to be administered the muscle atrophy therapeutic agent in an amount that is the same as or less than a standard dosage amount or muscle atrophy therapy and the INPPL1 inhibitor.

38. The method of any one of claims 27 to 37, wherein the INPPL1 variant nucleic acid molecule comprises a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, and / or a variant that encodes a truncated INPPL1 variant polypeptide.

39. The method of any one of claims 27 to 37, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

40. A method of treating a subject having type 2 diabetes or at risk of developing type 2 diabetes by administering a type 2 diabetes, the method comprising:determining or having determined whether the subject has an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) variant nucleic acid molecule, by:obtaining or having obtained a biological sample from the subject; andperforming or having performed a sequence analysis on the biological sample to determine if the subject has a genotype comprising the INPPL1 variant nucleic acid molecule; andadministering or continuing to administer the type 2 diabetes therapeutic agent in an amount that is the same as or lessthan a standard dosage amount, and / or an INPPL1 inhibitor to a subject that is INPPL1 reference;administering or continuing to administer the type 2 diabetes therapeutic agent in an amount that is the same as or lessthan a standard dosage amount, and / or an INPPL1 inhibitor to a subject that is heterozygous forthe INPPL1 variant nucleic acid molecule; or administering or continuing to administer the type 2 diabetes therapeutic agent in a standard dosage amount to a subject that is homozygous forthe INPPL1 variant nucleic acid molecule;wherein the presence of the INPPL1 variant nucleic acid molecule indicatesthe subject has a decreased risk of developing type 2 diabetes.

41. The method of claim 40, wherein the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an INPPL1 nucleic acid molecule.119279242DOCKET NO.: 38120-4614 (11651WO01)- 158 - 42. The method of claim 41, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), and / or a short hairpin RNA (shRNA).

43. The method of claim 42, wherein the inhibitory nucleic acid molecule comprises an siRNA.

44. The method of claim 42, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule.

45. The method of any one of claims 40 to 44, wherein the subject is heterozygous forthe INPPL1 variant nucleic acid molecule, and the subject is administered or continued to be administered the type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount and the INPPL1 inhibitor.

46. The method of any one of claims 40 to 44, wherein the subject is INPPL1 reference, and the subject is administered or continued to be administered the type 2 diabetes therapeutic agent in an amount that is the same as or less than a standard dosage amount and the INPPL1 inhibitor.

47. The method of any one of claims 40 to 46, wherein the INPPL1 variant nucleic acid molecule comprises a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, and / or a variant that encodes a truncated INPPL1 variant polypeptide.

48. The method of any one of claims 40 to 46, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

49. A method of identifying a subject having an increased risk of developing muscle atrophy, the method comprising:determining or having determined the presence or absence of an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) variant nucleic acid molecule in a biological sample obtained from the subject;wherein:when the subject is INPPL1 reference, then the subject has an increased risk of developing muscle atrophy; andwhen the subject is heterozygous or homozygous for the INPPL1 variant nucleic acid molecule, then the subject has a decreased risk of developing muscle atrophy.119279242DOCKET NO.: 38120-4614 (11651WO01)- 159 - 50. The method of claim 49, wherein the muscle atrophy is skeletal muscle atrophy.

51. The method of claim 49, wherein the muscle atrophy is cardiac muscle atrophy.

52. The method of claim 49, wherein the subject has: i) a muscular dystrophy, a myotonic dystrophy, or a mitochondrial myopathy; ii) an inflammatory muscle disease; iii) a sarcopenia; iv) a myopathy arising secondary to an environmental influence; v) a myopathy arising secondary to a systemic disease; vi) a neuromuscular condition leading to muscle atrophy; or vii) a weight loss mechanism.

53. The method of claim 52, wherein:the inflammatory muscle disease comprises polymyositis or dermatomyositits; the sarcopenia comprises age-related sarcopenia;the myopathy arising secondary to an environmental influence comprises drug-induced or alcohol-induced;the myopathy arising secondary to a systemic disease comprises thyroid-associated myopathy;the neuromuscular condition leading to muscle atrophy comprises amyotrophic lateral sclerosis or myasthenia gravis; andthe weight loss mechanism comprises bariatric surgery or pharmacologically-induced.

54. The method of any one of claims 49 to 53, wherein the INPPL1 variant nucleic acid molecule is a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide.

55. The method of any one of claims 49 to 53, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

56. A method of identifying a subject having an increased risk of developing type 2 diabetes, the method comprising:determining or having determined the presence or absence of an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) variant nucleic acid molecule in a biological sample obtained from the subject;wherein:when the subject is INPPL1 reference, then the subject has an increased risk of developing type 2 diabetes; and119279242DOCKET NO.: 38120-4614 (11651WO01)- 160 - when the subject is heterozygous or homozygous for the INPPL1 variant nucleic acid molecule, then the subject has a decreased risk of developing type 2 diabetes.

57. The method of claim 56, wherein the INPPL1 variant nucleic acid molecule is a splicesite variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide.

58. The method of claim 56, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

59. A muscle atrophy therapeutic agent for use in the treatment or prevention of muscle atrophy in a subject having an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) variant nucleic acid molecule.

60. The muscle atrophy therapeutic agent for use of claim 59, wherein the muscle atrophy is skeletal muscle atrophy.

61. The muscle atrophy therapeutic agent for use of claim 59, wherein the muscle atrophy is cardiac muscle atrophy.

62. The muscle atrophy therapeutic agent for use of claim 59, wherein the subject has: i) a muscular dystrophy, a myotonic dystrophy, or a mitochondrial myopathy; ii) an inflammatory muscle disease; iii) a sarcopenia; iv) a myopathy arising secondary to an environmental influence; v) a myopathy arising secondary to a systemic disease; vi) a neuromuscular condition leading to muscle atrophy; or vii) a weight loss mechanism.

63. The muscle atrophy therapeutic agent for use of claim 62, wherein:the inflammatory muscle disease comprises polymyositis or dermatomyositits; the sarcopenia comprises age-related sarcopenia;the myopathy arising secondary to an environmental influence comprises drug-induced or alcohol-induced;the myopathy arising secondary to a systemic disease comprises thyroid-associated myopathy;the neuromuscular condition leading to muscle atrophy comprises amyotrophic lateral sclerosis or myasthenia gravis; andthe weight loss mechanism comprises bariatric surgery or pharmacologically-induced.119279242DOCKET NO.: 38120-4614 (11651WO01)- 161 - 64. The muscle atrophy therapeutic agent for use of any one of claims 59 to 63, wherein the INPPL1 variant nucleic acid molecule is a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide.

65. The muscle atrophy therapeutic agent for use of any one of claims 59 to 63, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

66. The muscle atrophy therapeutic agent for use of any one of claims 59 to 65, wherein the muscle atrophy therapeutic agent comprises a corticosteroid, testosterone, a Selective Androgen Receptor Modulator (SARM), a growth hormone, a growth hormone secretagogue, a myostatin inhibitor, an Activin Type II Receptor inhibitor, or a modulator of the activin / inhibin family of ligands and receptors, or any combination thereof.

67. The muscle atrophy therapeutic agent for use of claim 66, wherein:the corticosteroid comprises prednisone, dexamethasone, hydrocortisone, cortisone, fluticasone, budesonide, betamethasone, methylprednisolone, triamcinolone, prednisolone, ciclesonide, flunisolide, mometasone, a mometasone ester, beclomethasone, a beclomethasone ester, 17-propionate ester or the 17,21-dipropionate ester, or rofleponide, or any combination thereof;the SARM comprises ostarine, ligandrol, testolone, andarine, LGD-3033, TT-701, S23, SR9009, ibutamoren, GW501516, or YK-11, or any combination thereof;the growth hormone comprises somatotropin, insulin-like growth factor 1 (IGF-1), growth hormone-releasing hormone (GHRH), ghrelin, somatostatin, somatropin, lonapegsomatropin, somapacitan, or somatrogon, or any combination thereof;the growth hormone secretagogue comprises sermorelin, tesamorelin, CJC-1295 and ipa morelin, macimorelin, or ibutamoren, or any combination thereof;the myostatin inhibitor comprises trevogrumab or domagrozumab, or a combination thereof; andthe Activin Type II Receptor inhibitor comprises bimagrumab, LAE102, LAE103, LAE123, fol I istatin, SB-431542, or SB-505124, or any combination thereof.

68. The muscle atrophy therapeutic agent for use of any one of claims 59 to 67, wherein the subject is also treated with a therapeutic agent that induces muscle atrophy.

69. The muscle atrophy therapeutic agent for use of claim 68, wherein the therapeutic agent that induces muscle atrophy comprises a Glucagon-like Peptide 1 (GLP-1) receptor119279242DOCKET NO.: 38120-4614 (11651WO01)- 162 -agonist, or a combined agonist of GLP-1 receptor and Glucose-dependent Insulinotropic Polypeptide (GIP) receptor (GLP-l / GIP).

70. The muscle atrophy therapeutic agent for use of claim 69, wherein the GLP-1 receptor agonist comprises exenatide, liraglutide, dulaglutide, lixisenatide, semaglutide, or albiglutide, or any combination thereof, and the GLP-l / GIP comprises tirzepatide.

71. A type 2 diabetes therapeutic agent for use in the treatment or prevention of type 2 diabetes in a subject having an Inositol Polyphosphate Phosphatase-Like 1 (INPPL1) variant nucleic acid molecule.

72. The type 2 diabetes therapeutic agent for use of claim 71, wherein the INPPL1 variant nucleic acid molecule is a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide.

73. The type 2 diabetes therapeutic agent for use of claim 71 or claim 72, wherein the INPPL1 variant nucleic acid molecule comprisesthe genetic variation listed in Table 1.

74. The type 2 diabetes therapeutic agent for use of any one of claims 71 to 73, wherein the type 2 diabetes therapeutic agent comprises an alpha-glucosidase inhibitor, a biguanide, a bile acid sequestra nt, a dopamine-2 agonist, a Dipeptidyl Peptidase-4 (DPP-4) inhibitor, a meglitinide, a Sodium-Glucose Cotransporter-2 (SGLT2) inhibitor, a sulfonylurea, a thiazolidinedione (TZD), a Glucagon-like Peptide 1 (GLP-1) receptor agonist, an insulin, an insulin sensitizer, a Proprotein Convertase Su btil isin / Kexin Type 9 (PCSK9) inhibitor, or an agent that preserves beta cell function and survival, or any combination thereof.

75. The type 2 diabetes therapeutic agent for use of claim 74, wherein:the alpha-glucosidase inhibitor comprises acarbose, miglitol, or voglibose, or any combination thereof;the biguanide comprises metformin, phenformin, or buformin, or any combination thereof;the bile acid sequestrant comprises cholestyramine, colesevelam, or colestipol, or any combination thereof;the dopamine-2 agonist comprises bromocriptine, pergolide, cabergoline, pramipexole, ropinirole, or rotigotine, or any combination thereof;the DPP-4 inhibitor comprises alogliptin, linagliptin, saxagliptin, sitagliptin, vildagliptin, gemigliptin, anagliptin, teneligliptin, trelagliptin, omarigliptin, evogliptin, gosogliptin,119279242DOCKET NO.: 38120-4614 (11651WO01)- 163 -dutogliptin, neogliptin, retagliptin, denagliptin, cofrogliptin, fotagliptin, prusogliptin, or cetagliptin, or any combination thereof;the meglitinide comprises nateglinide, repaglinide, or mitiglinide, or any combination thereof;the SGLT2 inhibitor comprises canagliflozin, dapagliflozin, empagliflozin, bexagliflozin, enavogliflozin, ertugliflozin, henagliflozin, pragliflozin, luseogliflozin, remogliflozin, rongliflozin, sergliflozin, sotagliflozin, tofogliflozin, or velagliflozin, or any combination thereof;the sulfonylurea comprises glimepiride, glipizide, glyburide, acetohexamide, carbutamide, chlorpropamide, glycyclamide, metahexamide, tolazamide, tolbutamide, glibornuride, gliclazide, gliquidone, glisoxepide, glyhexamide, phenbutamide, tolcyclamide, or glyclopyramide, or any combination thereof;the TZD comprises rosiglitazone, pioglitazone, lobeglitazone, 5-((4-(2-(methyl-2-pyridinylamino) ethoxy)phenyl)methyl)-2,4-thiazolidinedione, troglitazone, ciglitazone, WAY-120,744, englitazone, AD 5075, or darglitazone, or any combination thereof;the insulin comprises insulin glulisine, insulin lispro, insulin aspart, insulin glargine, insulin detemir, or insulin isophane, or any combination thereof;the PCSK9 inhibitor comprises alirocumab, evolocumab, inclisiran, lupin peptide, resveratrol, lycopene, or eugenol, or any combination thereof; andthe GLP-1 receptor agonist comprises exenatide, liraglutide, dulaglutide, lixisenatide, semaglutide, a Ibiglutide, tirzepatide, maridebart cafraglutide, NNC0090-2746, zenagamtide, ASC36 / ASC35, retatrutide, survodutide, mazdutide, or a combination of semaglutide and cagrilintide, or any combination thereof.

76. An Inositol Polyphosphate Phosphatase-Like l (INPPLl) inhibitor for use in the treatment or prevention of muscle atrophy in a subject that is INPPL1 reference or is heterozygous for an INPPL1 variant nucleic acid molecule.

77. The INPPL1 inhibitor for use of claim 76, wherein the muscle atrophy is skeletal muscle atrophy.

78. The INPPL1 inhibitor for use of claim 76, wherein the muscle atrophy is cardiac muscle atrophy.

79. The INPPL1 inhibitor for use of claim 76, wherein the subject has: i) a muscular dystrophy, a myotonic dystrophy, or a mitochondrial myopathy; ii) an inflammatory muscle disease; iii) a sarcopenia; iv) a myopathy arising secondary to an environmental influence; v) a119279242DOCKET NO.: 38120-4614 (11651WO01)- 164 -myopathy arising secondary to a systemic disease; vi) a neuromuscular condition leading to muscle atrophy; or vii) a weight loss mechanism.

80. The INPPL1 inhibitor for use of claim 79, wherein:the inflammatory muscle disease comprises polymyositis or dermatomyositits; the sarcopenia comprises age-related sarcopenia;the myopathy arising secondary to an environmental influence comprises drug-induced or alcohol-induced;the myopathy arising secondary to a systemic disease comprises thyroid-associated myopathy;the neuromuscular condition leading to muscle atrophy comprises amyotrophic lateral sclerosis or myasthenia gravis; andthe weight loss mechanism comprises bariatric surgery or pharmacologically-induced.

81. The INPPL1 inhibitor for use of any one of claims 76 to 80, wherein the INPPL1 variant nucleic acid molecule is a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide.

82. The INPPL1 inhibitor for use of any one of claims 76 to 80, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

83. The INPPL1 inhibitor for use of any one of claims 76 to 82, wherein the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an INPPL1 nucleic acid molecule.

84. The INPPL1 inhibitor for use of claim 83, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), and / or a short hairpin RNA (shRNA).

85. The INPPL1 inhibitor for use of claim 84, wherein the inhibitory nucleic acid molecule comprises an siRNA.

86. The INPPL1 inhibitor for use of claim 84, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule.

87. An Inositol Polyphosphate Phosphatase-Like l (INPPLl) inhibitor for use in the treatment or prevention of type 2 diabetes in a subject that is INPPL1 reference or is heterozygous for an INPPL1 variant nucleic acid molecule.119279242DOCKET NO.: 38120-4614 (11651WO01)- 165 - 88. The INPPL1 inhibitor for use of claim 87, wherein the INPPL1 variant nucleic acid molecule is a splice-site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, a missense variant, an in-frame indel variant, or a variant that encodes a truncated INPPL1 variant polypeptide.

89. The INPPL1 inhibitor for use of claim 87, wherein the INPPL1 variant nucleic acid molecule comprises the genetic variation listed in Table 1.

90. The INPPL1 inhibitor for use of any one of claims 87 to 89, wherein the INPPL1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an INPPL1 nucleic acid molecule.

91. The INPPL1 inhibitor for use of claim 90, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), and / or a short hairpin RNA (shRNA).

92. The INPPL1 inhibitor for use of claim 91, wherein the inhibitory nucleic acid molecule comprises an siRNA.

93. The INPPL1 inhibitor for use of claim 91, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule.119279242

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