Tataxin-sensitive lipid markers for monitoring ataxin replacement therapy

Abstract

The present disclosure is based, at least in part, on providing a set of markers, also referred to herein as FXN-sensitive lipid markers (or FSLMs), whose respective levels are positively or negatively correlated to ataxin (FXN) levels in a cell. Thus, these FSLMs may be used to determine, assess, and / or monitor the effectiveness of FXN replacement therapy in a subject.

Description

[0001] Related applications

[0002] This application claims priority to U.S. Provisional Application No. 63 / 340,412, filed May 10, 2022, and U.S. Provisional Application No. 63 / 351,380, filed June 11, 2022. The entire contents of each of the above applications are incorporated herein by reference.

[0003] sequence list

[0004] This application contains a sequence list that has been electronically submitted in ASCII format, and is hereby incorporated in its entirety by reference. The ASCII copy created on May 8, 2023, is named 130197-01320_SL.xml and has a size of 16,411 bytes. Background Technology

[0005] Mitochondrial diseases are a group of disorders caused by dysfunctional mitochondria, organelles that store potential energy in the form of adenosine triphosphate (ATP) molecules and are present in every cell of the human body except mature red blood cells.

[0006] Friedreich ataxia (FRDA) is the most common inherited ataxia in humans and is caused by a deficiency of the mitochondrial protein frataxin (FXN), specifically human frataxin (hFXN). In the United States, FRDA is a rare disease with an estimated incidence of 1 in 29,000, a carrier frequency of approximately 1 in 85, and about 4,000–5,000 reported cases. FRDA is a progressive, multisystemic disease that typically begins in mid-childhood. Patients experience a variety of symptoms, including progressive neurological and cardiac dysfunction. Other clinical manifestations may include scoliosis, fatigue, diabetes, vision impairment, and hearing loss. The inheritance is autosomal recessive and is primarily caused by a hereditary GAA triplet amplification in the first intron of both alleles of the hFXN gene. This triplet amplification causes transcriptional repression of the FRDA gene, resulting in very low levels of hFXN in patients. hFXN heterozygotes typically have about 50% of the normal hFXN levels but are phenotypically normal. hFXN levels in whole blood of heterozygotes and patients with FRDA have been shown to be stable over time at approximately 45–70 pg / μl and approximately 5–25 pg / μl, respectively (Plasterer et al., 2013).

[0007] Currently, there are no FDA-approved FRDA treatments. Antioxidants and iron chelation are not very effective, and despite treatment, patients often experience progressive loss of motor control and death, with cardiomyopathy being the leading cause of death.

[0008] Protein replacement therapy is a recognized approach for metabolic diseases such as diabetes, lysosomal storage disorders, and hemophilia. Studies in patient-derived cell and animal models have demonstrated that functional FXN replacement can correct or improve FRDA disease phenotypes. However, there is a need in the field for reliable and effective assays to measure the clinical response and efficacy of FXN replacement. Summary of the Invention

[0009] In one aspect, this disclosure is based at least in part on providing a set of biomarkers, also referred to herein as FXN-sensitive lipid biomarkers (FSLMs), the levels of which are positively or negatively correlated with levels of conamin (FXN) in cells or subjects (e.g., samples from subjects).

[0010] In some embodiments, the FSLM of this disclosure is conversely modulated by FXN gene ablation or FXN deficiency followed by FXN protein replacement in a subject. Therefore, the FSLM of this disclosure is associated with both FXN deficiency and, conversely, FXN replacement in a subject. The FSLM of this disclosure has been found to be sensitive to FXN levels and is considered a biomarker for FXN deficiency and FXN replacement therapy.

[0011] Therefore, any one or more of the FSLMs provided herein can serve as alternative biomarkers for FXN levels in subjects. For example, the FSLMs provided herein can be used to assess or monitor the progression of FXN deficiency in subjects, as described herein. Furthermore, the FSLMs provided herein can be used to assess and / or monitor FXN replacement therapies, for example, to determine, assess, and / or monitor the efficacy of FXN replacement therapies in subjects, as described herein.

[0012] In some embodiments, the efficacy of FXN replacement therapy, for example, in subjects, can be determined, evaluated, and / or monitored based on analysis of one or more FXN lipid profiles in samples obtained from the subject before, during, and / or after administration or initiation of FXN replacement therapy. Based on the results of the FXN replacement lipid profile analysis, adjustments can be made to the FXN replacement therapy in the subject, such as, for example, initiating FXN replacement therapy in the subject, increasing the dose and / or frequency of administration of FXN replacement therapy, decreasing the dose and / or frequency of administration of FXN replacement therapy, or discontinuing FXN replacement therapy.

[0013] Therefore, in some aspects, this disclosure provides a method for evaluating the efficacy of acoagulant (FXN) replacement therapy, the method comprising: (a) determining a baseline FSLM(-) lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy; (b) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (c) comparing the FXN-substituted lipid profile determined in step (b) with the baseline FXN(-) lipid profile determined in step (a); and (d) determining the efficacy of the FXN replacement therapy based on the comparison in step (c); wherein the one or more FSLMs are selected from the group consisting of: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations; ether phospholipids; phosphatidylcholine (PC), cholesterol esters (CE); and diglycerides (DG).

[0014] In some aspects, this disclosure also provides a method for evaluating the efficacy of acoagulant (FXN) replacement therapy, the method comprising: (a) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (b) comparing the subject FXN-substituted lipid profile determined in step (a) with a reference FXN lipid profile for one or more FSLMs; and (c) determining the efficacy of the FXN replacement therapy based on the comparison in step (b); wherein one or more FSLMs are selected from the group consisting of one or more of the following: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations; ether phospholipids; phosphatidylcholine (PC); cholesterol esters (CE); and diglycerides (DG).

[0015] In some embodiments, the reference FXN lipid profile is a baseline FXN(-) lipid profile for one or more FSLMs. In some embodiments, a baseline FXN(-) lipid profile for one or more FSLMs is determined from samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy. In some embodiments, the method further includes determining a baseline FXN(-) lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy.

[0016] In some embodiments, one or more FSLMs are selected from the group consisting of one or more triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation. In some embodiments, one or more FSLMs are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs are selected from the group consisting of: TG48:1, TG48:2, TG49:1, TG49:2, TG49:4, TG50:1, TG50:3, TG51:1, TG51:2, TG51:3, TG52:3, TG53:2 and TG56:8.

[0017] In some embodiments, one or more FSLMs are selected from one or more ether phospholipids. In some embodiments, one or more ether phospholipids include one or more ether diacylglycerol phosphoric acid choline (PCO-). In some embodiments, one or more PCOs are selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-20:0 / 22:6), PC(O-20:1 / 22:6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:2 / 20:6 ... PCO-24:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, and PCO-44:7 and PCO-46:8. In some embodiments, one or more PCO- are selected from the group consisting of: PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-18:1 / 18:2), PC(O-22:2 / 20:4), and PC(O-24:2 / 20:4). In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0018] In some embodiments, one or more FSLMs are selected from one or more phosphatidylcholine (PC) compounds. In some embodiments, one or more PCs are selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, and PC42:7. In some embodiments, one or more PCs are selected from the group consisting of: PC(15:0 / 22:6) and PC(16:0 / 14:0). In some embodiments, one or more PCs are selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0). In some embodiments, one or more PCs are PC (18:2 / 18:3).

[0019] In some embodiments, one or more FSLMs are selected from one or more cholesterol esters (CEs). In some embodiments, one or more CEs are selected from the group consisting of CE16:0 and CE20:5. In some embodiments, one or more CEs are CE14:1.

[0020] In some embodiments, one or more FSLMs are selected from one or more diglycerides (DG). In some embodiments, one or more DGs are DG18:1 / 18:2.

[0021] In some embodiments, the levels of at least one or more FSLMs increase in subjects after treatment with FXN replacement therapy. In some embodiments, one or more FSLMs are selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-20:0 / 22:6), PC(O-20: 1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2 , PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7, PCO-46.8, PC(17:1 / 20:4), PC(1 8:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE16:0 and CE20:5.

[0022] In some embodiments, the amount of at least one or more FSLMs is reduced in subjects after treatment with FXN replacement therapy. In some embodiments, one or more FSLMs are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5 , TG54:4, TG54:5, TG54:6, TG54:7, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 2 2.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, DG18:1 / 18:2 and CE14:1.

[0023] In some embodiments, determining an FXN lipid profile for one or more FSLMs includes determining the amount of one or more FSLMs. In some embodiments, comparing a subject's FXN alternative lipid profile with a baseline FXN(-) lipid profile includes comparing the amount of one or more FSLMs in the FXN alternative lipid profile with the corresponding amount of one or more FSLMs in the baseline FXN(-) lipid profile.

[0024] In some embodiments, FXN replacement therapy is determined to be effective when the amount of one or more FSLMs in the FXN replacement lipid profile increases compared to the baseline FXN(-) lipid profile, wherein the one or more FSLMs are selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:4). 6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O -22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO -36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7, PCO-46.8, PC(17:1 / 20: 4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE16:0 and CE20:5.

[0025] In some embodiments, FXN replacement therapy is determined to be effective when the amount of one or more FSLMs in the FXN-replaced lipid profile is reduced compared to the baseline FXN(-) lipid profile, wherein the one or more FSLMs are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52: 6. TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC (15:0 / 20 :3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18: 1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, DG18:1 / 18:2 and CE14:1.

[0026] In some embodiments, determining an FXN lipid profile for one or more FSLMs includes determining FXN lipid feature vectors that indicate the values ​​of lipids in the one or more FSLMs. In some embodiments, determining the efficacy of an FXN replacement therapy includes determining a first FXN lipid feature vector for a subject's FXN replacement lipid profile and a second FXN lipid feature vector for a baseline FXN(-) lipid profile, and determining the distance between the first feature vector and the second lipid feature vector. In some embodiments, determining the distance between the lipid feature vectors includes determining the scalar product of the first feature vector and the second lipid feature vector.

[0027] In some embodiments, determining an FXN lipid profile for one or more FSLMs further includes determining a third lipid eigenvector of a normal FXN lipid profile for a healthy subject. In some embodiments, determining an FXN lipid profile for one or more FSLMs further includes determining the distance between a second lipid eigenvector and a third lipid eigenvector. In some embodiments, determining an FXN lipid profile for one or more FSLMs further includes determining the distance between a first lipid eigenvector and a third lipid eigenvector, and normalizing the distance between the first and third lipid eigenvectors to the distance between the second and third lipid eigenvectors. In some embodiments, determining an FXN lipid profile for one or more FSLMs further includes using the normalized distance to determine the effectiveness of FXN replacement therapy.

[0028] In some embodiments, the FXN lipid profile is determined by mass spectrometry.

[0029] In some embodiments, the method disclosed herein further includes recommending modifications to treatment using FXN alternative therapies to a healthcare provider based on the determination of efficacy of the FXN alternative therapies.

[0030] In some embodiments, the subjects had Friedreich ataxia (FRDA).

[0031] In some embodiments, the method of this disclosure further includes obtaining a sample from a subject lacking FXN. In some embodiments, the sample is selected from the group consisting of: cheek sample, skin sample, hair follicle sample, or blood-derived sample. In some embodiments, the sample is a blood-derived sample. In some embodiments, the blood-derived sample is a plasma sample.

[0032] In some aspects, this disclosure also provides a method for monitoring treatment of a subject with FXN (FXN) replacement therapy, the method comprising: (a) determining a first FXN replacement lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in a first sample, the first sample being obtained from an FXN-deficient subject at a first time point following administration of FXN replacement therapy to the subject; (b) determining a second FXN replacement lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in a second sample, the second sample being obtained from the subject at a second time point later than the first time point; and (c) comparing the second FXN replacement lipid profile with the first FXN replacement profile; thereby monitoring treatment of the subject with FXN replacement therapy; wherein the one or more FSLMs are selected from the group consisting of one or more of the following: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations; ether phospholipids; phosphatidylcholine (PC); cholesterol esters (CE); and diglycerides (DG).

[0033] In some embodiments, the method further includes making a decision on maintaining, increasing, or decreasing the dose or frequency of administration of FXN replacement therapy based on the comparison in step (c).

[0034] In some embodiments, at least one dose of FXN replacement therapy is administered to the subject between obtaining the first time point and the second time point. In some embodiments, FXN replacement therapy is not administered to the subject between obtaining the first time point and the second time point.

[0035] In some embodiments, one or more FSLMs are selected from the group consisting of one or more triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation. In some embodiments, one or more FSLMs are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0036] In some embodiments, one or more FSLMs are selected from one or more ether phospholipids. In some embodiments, one or more ether phospholipids comprise one or more ether diacylglycerol phosphorylcholine (PCO-). In some embodiments, one or more PCO- are selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC (O-(20:0 / 22:6), PC(O-20:1 / 22:6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, and PCO-44:7 and PCO-46.8. In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0037] In some embodiments, one or more FSLMs are selected from one or more phosphatidylcholine (PC) lines. In some embodiments, one or more PCs are selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), and PC(20:4 / 20:0).

[0038] In some embodiments, one or more FSLMs are selected from one or more cholesterol esters (CEs). In some embodiments, one or more CEs are selected from the group consisting of CE14:1, CE16:0, and CE20:5.

[0039] In some embodiments, one or more FSLMs are selected from one or more diglycerides (DG). In some embodiments, one or more DGs are DG18:1 / 18:2.

[0040] In some aspects, this disclosure also provides a method for treating FXN deficiency, the method comprising: (a) determining an FXN lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in a sample obtained from a subject lacking FXN; (b) comparing the FXN lipid profile of the sample with at least one other lipid profile selected from the group consisting of a normal FXN lipid profile for one or more FSLMs, a baseline FXN(-) lipid profile for one or more FSLMs, and an FXN alternative lipid profile for one or more FSLMs; (c) classifying the FXN lipid profile determined in step (a) as corresponding to a normal FXN lipid profile, a baseline FXN(-) lipid profile, or an FXN alternative lipid profile; and (d) initiating or modulating FXN replacement therapy based on the classification of the FXN lipid profile of the sample.

[0041] In some embodiments, adjusting FXN replacement therapy includes increasing the dose of FXN replacement therapy, decreasing the dose of FXN replacement therapy, increasing the frequency of FXN replacement therapy administration, or decreasing the frequency of FXN replacement therapy administration. In some embodiments, subjects lacking FXN suffer from Friedreich ataxia (FRDA).

[0042] In some aspects, this disclosure also provides a method for treating FXN deficiency in a subject, the method comprising: (a) determining an FXN lipid profile against one or more FSLMs in a sample from a subject lacking FXN; and (b) recommending to a healthcare provider, based on the subject's FXN lipid profile determined in step (a), the administration of an FXN replacement therapy to the subject.

[0043] In some aspects, this disclosure also provides a method for treating FXN deficiency in a subject, the method comprising: (a) obtaining an FXN lipid profile against one or more FSLMs in a sample obtained from a subject lacking FXN; and (b) administering an FXN replacement therapy to the subject based on the subject's FXN lipid profile.

[0044] In some embodiments, the method disclosed herein further includes obtaining samples from subjects lacking FXN for use in determining FXN lipid profiles for one or more FSLMs.

[0045] In some aspects, this disclosure also provides a method for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in a sample from a subject lacking coagulin (FXN), the method comprising contacting the sample or a portion thereof with one or more reagents specific for detecting the level of each of the one or more FSLMs.

[0046] In some aspects, this disclosure also provides a method for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in a sample from a subject lacking coagulin (FXN), the method comprising analyzing the sample or a portion thereof by mass spectrometry.

[0047] In some embodiments, subjects are being treated with or are planned to be treated with FXN replacement therapy. In some embodiments, the method of this disclosure further includes obtaining samples from subjects lacking FXN.

[0048] In some embodiments, one or more FSLMs are selected from the group consisting of: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation; ether phospholipids; phosphatidylcholine (PC); cholesterol esters (CE); and diglycerides (DG).

[0049] In some embodiments, one or more FSLMs are selected from the group consisting of one or more triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation. In some embodiments, one or more FSLMs are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0050] In some embodiments, one or more FSLMs are selected from one or more ether phospholipids. In some embodiments, one or more ether phospholipids comprise one or more ether diacylglycerol phosphorylcholine (PCO-). In some embodiments, one or more PCO- are selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC (O-(20:0 / 22:6), PC(O-20:1 / 22:6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, and PCO-44:7 and PCO-46.8. In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0051] In some embodiments, one or more FSLMs are selected from one or more phosphatidylcholine (PC) lines. In some embodiments, one or more PCs are selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), and PC(20:4 / 20:0).

[0052] In some embodiments, one or more FSLMs are selected from one or more cholesterol esters (CEs). In some embodiments, one or more CEs are selected from the group consisting of CE14:1, CE16:0, and CE20:5.

[0053] In some embodiments, one or more FSLMs are selected from one or more diglycerides (DG). In some embodiments, one or more DGs are DG18:1 / 18:2.

[0054] In some embodiments, the FXN lipid profile is determined by mass spectrometry.

[0055] In some embodiments, the subjects had Friedreich ataxia (FRDA).

[0056] In some embodiments, the method of this disclosure further includes obtaining a sample from a subject lacking FXN. In some embodiments, the sample is selected from the group consisting of: cheek sample, skin sample, hair follicle sample, or blood-derived sample. In some embodiments, the sample is a blood-derived sample. In some embodiments, the blood-derived sample is a plasma sample.

[0057] In some embodiments, FXN replacement therapy includes administration of an FXN fusion protein. In some embodiments, the FXN fusion protein comprises or consists of the amino acid sequence shown in SEQ ID NO:12.

[0058] In some aspects, this disclosure also provides a kit for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in samples obtained from subjects lacking coagulin (FXN), comprising one or more isotopically labeled lipids used as internal standards in mass spectrometry-based analyses for detecting one or more FSLMs in a sample, and a set of instructions for detecting the levels of one or more FSLMs in samples from subjects by mass spectrometry.

[0059] In some embodiments of the methods provided in this disclosure, the subject is a human being.

[0060] In some aspects, this disclosure provides a method for evaluating the efficacy of atamin (FXN) replacement therapy, the method comprising: (a) determining a baseline FSLM(-) lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy; (b) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (c) comparing the FXN-substituted lipid profile determined in step (b) with the baseline FXN(-) lipid profile determined in step (a); and (d) determining the efficacy of the FXN replacement therapy based on the comparison in step (c); wherein the one or more FSLMs are selected from the group consisting of one or more triglycerides.

[0061] In some embodiments, the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms.

[0062] In some embodiments, the three acyl groups in each triglyceride molecule contain a total of 56 or more carbon atoms.

[0063] In some embodiments, the three acyl groups in each triglyceride molecule contain seven or fewer degrees of unsaturation.

[0064] In some embodiments, the three acyl groups in each triglyceride molecule contain more than 7 degrees of unsaturation, or 6 or more degrees of unsaturation.

[0065] In some aspects, this disclosure provides a method for evaluating the efficacy of ataminin (FXN) replacement therapy, the method comprising: (a) determining a baseline FSLM(-) lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy; (b) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (c) comparing the FXN-substituted lipid profile determined in step (b) with the baseline FXN(-) lipid profile determined in step (a); and (d) determining the efficacy of the FXN replacement therapy based on the comparison in step (c); wherein the one or more FSLMs are selected from the group consisting of one or more cholesterol esters (CEs).

[0066] In some aspects, this disclosure provides a method for evaluating the efficacy of acoagulant (FXN) replacement therapy, the method comprising: (a) determining a baseline FSLM(-) lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy; (b) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (c) comparing the FXN-substituted lipid profile determined in step (b) with the baseline FXN(-) lipid profile determined in step (a); and (d) determining the efficacy of the FXN replacement therapy based on the comparison in step (c); wherein the one or more FSLMs are selected from the group consisting of one or more ether phospholipids.

[0067] In some embodiments, one or more ether phospholipids include one or more ether diacylglycerol phosphoric acid choline (PCO-).

[0068] In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0069] In some aspects, this disclosure provides a method for evaluating the efficacy of atamin (FXN) replacement therapy, the method comprising: (a) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from a subject lacking FXN after administration of FXN replacement therapy; (b) comparing the subject's FXN-substituted lipid profile determined in step (a) with a reference FXN lipid profile for one or more FSLMs; and (c) determining the efficacy of the FXN replacement therapy based on the comparison in step (b); wherein the one or more FSLMs are selected from the group consisting of one or more triglycerides.

[0070] In some embodiments, the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms.

[0071] In some embodiments, the three acyl groups in each triglyceride molecule contain a total of 56 or more carbon atoms.

[0072] In some embodiments, the three acyl groups in each triglyceride molecule contain seven or fewer degrees of unsaturation.

[0073] In some embodiments, the three acyl groups in each triglyceride molecule contain more than 7 degrees of unsaturation, or 6 or more degrees of unsaturation.

[0074] In some aspects, this disclosure provides a method for evaluating the efficacy of acoagulant (FXN) replacement therapy, the method comprising: (a) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from a subject lacking FXN after administration of FXN replacement therapy; (b) comparing the subject's FXN-substituted lipid profile determined in step (a) with a reference FXN lipid profile for one or more FSLMs; and (c) determining the efficacy of the FXN replacement therapy based on the comparison in step (b); wherein the one or more FSLMs are selected from the group consisting of one or more cholesterol esters (CEs).

[0075] In some aspects, this disclosure provides a method for evaluating the efficacy of acoagulant (FXN) replacement therapy, the method comprising: (a) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from a subject lacking FXN after administration of FXN replacement therapy; (b) comparing the subject's FXN-substituted lipid profile determined in step (a) with a reference FXN lipid profile for one or more FSLMs; and (c) determining the efficacy of the FXN replacement therapy based on the comparison in step (b); wherein the one or more FSLMs are selected from the group consisting of ether phospholipids.

[0076] In some embodiments, one or more ether phospholipids include one or more ether diacylglycerol phosphoric acid choline (PCO-).

[0077] In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0078] In some embodiments, the reference FXN lipid profile is a baseline FXN(-) lipid profile for one or more FSLMs. In some embodiments, a baseline FXN(-) lipid profile for one or more FSLMs is determined from samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy. In some embodiments, the method further includes determining a baseline FXN(-) lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy.

[0079] In some embodiments, one or more FSLMs include one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, or TG54:7. In some embodiments, one or more FSLMs include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, or TG54:7.

[0080] In some embodiments, one or more FSLMs include one or more of TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:8, and TG58:11.

[0081] In some embodiments, one or more FSLMs comprise cholesterol ester 16:0 (CE 16:0) or cholesterol ester 20:5 (CE 20:5).

[0082] In some embodiments, one or more FSLMs include PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0083] In some embodiments, at least one or more FSLMs are upregulated after treatment with FXN replacement therapy. In some embodiments, the one or more FSLMs upregulated after treatment with FXN replacement therapy include one or more of TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:8, TG58:11, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0084] In some embodiments, at least one or more FSLMs are downregulated after treatment with FXN replacement therapy. In some embodiments, the one or more FSLMs downregulated after treatment with FXN replacement therapy include one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, or TG54:7.

[0085] In some embodiments, determining an FXN lipid profile for one or more FSLMs includes detecting the lipid levels of one or more FSLMs. In some embodiments, comparing a subject’s FXN alternative lipid profile with a baseline FXN(-) lipid profile includes comparing the lipid levels of one or more FSLMs in the FXN alternative lipid profile with the lipid levels of the corresponding one or more FSLMs in the baseline FXN(-) lipid profile.

[0086] In some embodiments, FXN replacement therapy is determined to be effective when the lipid levels of one or more of the following lipid profiles in the FXN replacement lipid profile increase compared to the baseline FXN(-) lipid profile: TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:8, TG58:11, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0087] In some embodiments, FXN replacement therapy is deemed effective when the lipid levels of one or more of the following lipid profiles in the FXN alternative lipid profile are reduced compared to the baseline FXN(-) lipid profile: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, or TG54:7.

[0088] In some embodiments, determining an FXN lipid profile for one or more FSLMs includes determining FXN lipid feature vectors that indicate the values ​​of lipids in the one or more FSLMs. In some embodiments, determining the efficacy of an FXN replacement therapy includes determining a first FXN lipid feature vector for a subject's FXN replacement lipid profile and a second FXN lipid feature vector for a baseline FXN(-) lipid profile, and determining the distance between the first feature vector and the second lipid feature vector. In some embodiments, determining the distance between the lipid feature vectors includes determining the scalar product of the first feature vector and the second lipid feature vector.

[0089] In some embodiments, the method of this disclosure further includes determining a third lipid eigenvector of a normal FXN lipid profile for a healthy subject's FSLM. In some embodiments, the method of this disclosure further includes determining the distance between a second lipid eigenvector and a third lipid eigenvector. In some embodiments, the method of this disclosure further includes determining the distance between a first lipid eigenvector and a third lipid eigenvector, and normalizing the distance between the first lipid eigenvector and the third lipid eigenvector to the distance between the second lipid eigenvector and the third lipid eigenvector. In some embodiments, the method of this disclosure further includes using the normalized distance to determine the effectiveness of FXN replacement therapy.

[0090] In some embodiments, the FXN lipid profile is determined by mass spectrometry.

[0091] In some embodiments, the method disclosed herein further includes recommending modifications to treatment using FXN alternative therapies to a healthcare provider based on the determination of efficacy of the FXN alternative therapies.

[0092] In some embodiments, the subjects had Friedreich ataxia (FRDA).

[0093] In some embodiments, the method of this disclosure further includes obtaining a sample from a subject lacking FXN. In some embodiments, the sample is selected from the group consisting of: cheek sample, skin sample, hair follicle sample, or blood-derived sample. In some embodiments, the sample is a blood-derived sample. In some embodiments, the blood-derived sample is a plasma sample.

[0094] In some aspects, this disclosure provides a method for monitoring treatment of a subject with FXN (FXN) replacement therapy, the method comprising: (a) determining a first FXN replacement lipid profile in a first sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the first sample being obtained from an FXN-deficient subject at a first time point following administration of FXN replacement therapy to the subject, wherein the one or more FSLMs are selected from the group consisting of one or more triglycerides; (b) determining a second FXN replacement lipid profile in a second sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the second sample being obtained from the subject at a second time point later than the first time point; and (c) comparing the second FXN replacement lipid profile with the first FXN replacement profile; thereby monitoring treatment of the subject with FXN replacement therapy.

[0095] In some embodiments, the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms.

[0096] In some embodiments, the three acyl groups in each triglyceride molecule contain a total of 56 or more carbon atoms.

[0097] In some embodiments, the three acyl groups in each triglyceride molecule contain seven or fewer degrees of unsaturation.

[0098] In some embodiments, the three acyl groups in each triglyceride molecule contain more than 7 degrees of unsaturation, or 6 or more degrees of unsaturation.

[0099] In some aspects, this disclosure provides a method for monitoring treatment of a subject with FXN (FXN) replacement therapy, the method comprising: (a) determining a first FXN replacement lipid profile in a first sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the first sample being obtained from an FXN-deficient subject at a first time point following administration of FXN replacement therapy to the subject, wherein the one or more FSLMs are selected from the group consisting of one or more cholesterol esters (CEs); (b) determining a second FXN replacement lipid profile in a second sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the second sample being obtained from the subject at a second time point later than the first time point; and (c) comparing the second FXN replacement lipid profile with the first FXN replacement profile; thereby monitoring treatment of the subject with FXN replacement therapy.

[0100] In some aspects, this disclosure provides a method for monitoring treatment of a subject with FXN (FXN) replacement therapy, the method comprising: (a) determining a first FXN replacement lipid profile in a first sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the first sample being obtained from an FXN-deficient subject at a first time point following administration of FXN replacement therapy to the subject, wherein the one or more FSLMs are selected from the group consisting of one or more ether phospholipids; (b) determining a second FXN replacement lipid profile in a second sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the second sample being obtained from the subject at a second time point later than the first time point; and (c) comparing the second FXN replacement lipid profile with the first FXN replacement profile; thereby monitoring treatment of the subject with FXN replacement therapy.

[0101] In some embodiments, one or more ether phospholipids include one or more ether diacylglycerol phosphoric acid choline (PCO-).

[0102] In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0103] In some embodiments, the method of this disclosure further includes making a decision on maintaining, increasing or decreasing the dose or frequency of administration of FXN replacement therapy based on the comparison in step (c).

[0104] In some embodiments, at least one dose of FXN replacement therapy is administered to the subject between a first time point and a second time point.

[0105] In some embodiments, FXN replacement therapy is not administered to the subject between the first and second time points.

[0106] In some aspects, this disclosure provides a method for treating FXN deficiency, the method comprising: (a) determining an FXN lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in a sample obtained from a subject lacking FXN; (b) comparing the FXN lipid profile of the sample with at least one other lipid profile selected from the group consisting of a normal FXN lipid profile for one or more FSLMs, a baseline FXN(-) lipid profile for one or more FSLMs, and an FXN alternative lipid profile for one or more FSLMs; (c) classifying the FXN lipid profile determined in step (a) into a profile corresponding to a normal FXN lipid profile, a baseline FXN(-) lipid profile, or an FXN alternative lipid profile; and (d) initiating or modulating an FXN replacement therapy based on the classification of the FXN lipid profile of the sample, wherein one or more FSLMs are selected from the group consisting of one or more triglycerides.

[0107] In some embodiments, the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms.

[0108] In some embodiments, the three acyl groups in each triglyceride molecule contain a total of 56 or more carbon atoms.

[0109] In some embodiments, the three acyl groups in each triglyceride molecule contain seven or fewer degrees of unsaturation.

[0110] In some embodiments, the three acyl groups in each triglyceride molecule contain more than 7 degrees of unsaturation, or 6 or more degrees of unsaturation.

[0111] In some aspects, this disclosure provides a method for treating FXN deficiency, the method comprising: (a) determining an FXN lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in a sample obtained from a subject lacking FXN; (b) comparing the FXN lipid profile of the sample with at least one other lipid profile selected from the group consisting of a normal FXN lipid profile for one or more FSLMs, a baseline FXN(-) lipid profile for one or more FSLMs, and an FXN alternative lipid profile for one or more FSLMs; (c) classifying the FXN lipid profile determined in step (a) into a profile corresponding to a normal FXN lipid profile, a baseline FXN(-) lipid profile, or an FXN alternative lipid profile; and (d) initiating or modulating an FXN replacement therapy based on the classification of the FXN lipid profile of the sample, wherein the one or more FSLMs are selected from the group consisting of one or more cholesterol esters (CEs).

[0112] In some aspects, this disclosure provides a method for treating FXN deficiency, the method comprising: (a) determining an FXN lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in a sample obtained from a subject lacking FXN; (b) comparing the FXN lipid profile of the sample with at least one other lipid profile selected from the group consisting of a normal FXN lipid profile for one or more FSLMs, a baseline FXN(-) lipid profile for one or more FSLMs, and an FXN alternative lipid profile for one or more FSLMs; (c) classifying the FXN lipid profile determined in step (a) into a profile corresponding to a normal FXN lipid profile, a baseline FXN(-) lipid profile, or an FXN alternative lipid profile; and (d) initiating or modulating an FXN replacement therapy based on the classification of the FXN lipid profile of the sample, wherein the one or more FSLMs are selected from the group consisting of one or more ether phospholipids.

[0113] In some embodiments, one or more ether phospholipids include one or more ether diacylglycerol phosphoric acid choline (PCO-).

[0114] In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0115] In some embodiments, adjusting the FXN replacement therapy includes increasing the dose of the FXN replacement therapy, decreasing the dose of the FXN replacement therapy, increasing the frequency of administration of the FXN replacement therapy, or decreasing the frequency of administration of the FXN replacement therapy.

[0116] In some embodiments, subjects lacking FXN are classified as Friedreich ataxia (FRDA).

[0117] In some aspects, this disclosure also provides a method for treating FXN deficiency in a subject, the method comprising: (a) determining an FXN lipid profile against one or more FSLMs in a sample from a subject lacking FXN; and (b) recommending to a healthcare provider, based on the subject's FXN lipid profile determined in step (a), the administration of an FXN replacement therapy to the subject.

[0118] In some aspects, this disclosure also provides a method for treating FXN deficiency in a subject, the method comprising: (a) obtaining an FXN lipid profile against one or more FSLMs in a sample obtained from a subject lacking FXN; and (b) administering an FXN replacement therapy to the subject based on the subject's FXN lipid profile.

[0119] In some embodiments, the method disclosed herein further includes obtaining samples from subjects lacking FXN for use in determining FXN lipid profiles for one or more FSLMs.

[0120] In some aspects, this disclosure also provides a method for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in a sample from a subject lacking coagulin (FXN), the method comprising contacting the sample or a portion thereof with one or more reagents specific for detecting the level of each of the one or more FSLMs, wherein the one or more FSLMs are selected from the group consisting of one or more triglycerides, thereby detecting the FSLMs in the sample.

[0121] In some embodiments, the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms.

[0122] In some embodiments, the three acyl groups in each triglyceride molecule contain seven or fewer degrees of unsaturation.

[0123] In some aspects, this disclosure provides a method for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in a sample from a subject lacking coagulin (FXN), the method comprising contacting the sample or a portion thereof with one or more reagents specific for detecting the level of each of the one or more FSLMs, wherein the one or more FSLMs are selected from the group consisting of one or more cholesterol esters (CEs), thereby detecting the FSLMs in the sample.

[0124] In some aspects, this disclosure provides a method for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in a sample from a subject lacking coagulin (FXN), the method comprising contacting the sample or a portion thereof with one or more reagents specific for detecting the level of each of the one or more FSLMs, wherein the one or more FSLMs are selected from the group consisting of one or more ether phospholipids.

[0125] In some embodiments, one or more ether phospholipids include one or more ether diacylglycerol phosphoric acid choline (PCO-).

[0126] In some embodiments, one or more ether phospholipids include one or more phosphatidylethanolamine ethers (PEO-).

[0127] In some embodiments, subjects are being treated with or are planned to be treated with FXN replacement therapy.

[0128] In some embodiments, the method disclosed herein further includes obtaining samples from subjects lacking FXN.

[0129] In some embodiments, one or more FSLMs include one or more of TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:8, and TG58:11.

[0130] In some embodiments, one or more FSLMs include one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, or TG54:7.

[0131] In some embodiments, one or more FSLMs comprise cholesterol ester 16:0 (CE 16:0) or cholesterol ester 20:5 (CE 20:5).

[0132] In some embodiments, one or more FSLMs include PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0133] In some embodiments, the FXN lipid profile is determined by mass spectrometry.

[0134] In some embodiments, the subjects had Friedreich ataxia (FRDA).

[0135] In some embodiments, the method of this disclosure further includes obtaining a sample from a subject lacking FXN. In some embodiments, the sample is selected from the group consisting of: cheek sample, skin sample, hair follicle sample, or blood-derived sample. In some embodiments, the sample is a blood-derived sample. In some embodiments, the blood-derived sample is a plasma sample.

[0136] In some embodiments, FXN replacement therapy includes administration of an FXN fusion protein. In some embodiments, the FXN fusion protein comprises or consists of the amino acid sequence shown in SEQ ID NO:12.

[0137] In some aspects, this disclosure also provides a kit for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in samples obtained from subjects lacking coagulin (FXN), comprising one or more isotopically labeled lipids used as internal standards in mass spectrometry-based analyses for detecting one or more FSLMs in a sample, wherein the one or more isotopically labeled lipids are selected from the group consisting of one or more isotopically labeled triglycerides, and a set of instructions for detecting the levels of one or more FSLMs in samples from subjects by mass spectrometry.

[0138] In some embodiments, the three acyl groups in each isotopically labeled triglyceride molecule contain fewer than 56 carbon atoms. In some embodiments, the three acyl groups in each isotopically labeled triglyceride molecule contain 7 or fewer degrees of unsaturation. In some embodiments, one or more isotopically labeled triglycerides are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, or TG54:7.

[0139] In some embodiments, the three acyl groups in each isotopically labeled triglyceride molecule contain a total of 56 or more carbon atoms. In some embodiments, the three acyl groups in each isotopically labeled triglyceride molecule contain more than 7 degrees of unsaturation, or 6 or more degrees of unsaturation. In some embodiments, one or more isotopically labeled triglycerides are selected from the group consisting of: isotopically labeled TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:8, and TG58:11.

[0140] In some aspects, this disclosure also provides a kit for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in samples obtained from subjects lacking coagulin (FXN), comprising one or more isotopically labeled lipids used as internal standards in mass spectrometry-based analyses for detecting one or more FSLMs in a sample, wherein the one or more isotopically labeled lipids are selected from the group consisting of one or more isotopically labeled cholesterol esters (CE), and a set of instructions for detecting the levels of one or more FSLMs in samples from subjects by mass spectrometry.

[0141] In some embodiments, one or more isotopically labeled cholesterol esters are selected from the group consisting of isotopically labeled cholesterol ester 16:0 (CE 16:0) and isotopically labeled cholesterol ester 20:5 (CE 20:5).

[0142] In some aspects, this disclosure provides a kit for detecting one or more coagulin-sensitive lipid biomarkers (FSLMs) in a sample obtained from a subject lacking coagulin (FXN), comprising one or more isotopically labeled lipids used as internal standards in a mass spectrometry-based analysis for detecting one or more FSLMs in a sample, wherein the one or more isotopically labeled lipids are selected from the group consisting of one or more isotopically labeled ether phospholipids, and a set of instructions for detecting the levels of one or more FSLMs in a sample from a subject by mass spectrometry.

[0143] In some embodiments, one or more isotopically labeled ether phospholipids include one or more isotopically labeled ether diacylglycerol phosphoric acid choline (PCO-).

[0144] In some embodiments, one or more isotopically labeled ether diacylglycerol phosphoric acid choline (PCO-) comprises PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0145] In some embodiments, one or more isotopically labeled ether phospholipids include one or more isotopically labeled phosphatidylethanolamine ethers (PEO-). Attached Figure Description

[0146] Figure 1 It is a scatter plot showing the principal component analysis (PCA) results of all MS signals from all analyzed human plasma samples, with different colors indicating FRDA subjects and healthy subjects.

[0147] Figure 2 It is a scatter plot showing the PCA results of all MS signals from all plasma samples from all subjects, with different colors indicating subjects of different sexes.

[0148] Figure 3This is a volcano plot, showing a comparison of human plasma samples from FRDA subjects with those from healthy controls. Different lipid subclasses are indicated by different colors. Gray dots represent unidentified lipids. The horizontal red line indicates a threshold p-value of 0.04, and the vertical red line indicates a fold change of 1.23.

[0149] Figure 4 It is a box plot showing the log2 fold change in the most significantly regulated lipid levels in human plasma samples obtained from FRDA subjects compared to healthy subjects.

[0150] Figure 5 Figure A is a PCA loading plot of 168 features used with color codes of PC1 and PC2 to distinguish FRDA subjects from healthy subjects using lipid subclasses (66 unique lipids) with 111 annotated features.

[0151] Figure 5 Figure B is a PCA loading map of 168 features distinguishing FRDA subjects from healthy subjects using color codes for PC1 and PC2 (Figure A) and PC1 and PC3 (Figure B), with lipid subclasses (66 unique lipids) having 111 annotated features. Compared to healthy subjects, increased lipids in human plasma samples from FRDA subjects are shown on the left, while decreased lipids are shown on the right.

[0152] Figure 6 This is a scatter plot showing the PCA results for all MS signals from all mouse plasma samples, with different colors indicating different conditions: WT mice treated with the medium (WTV), WT mice treated with FXN replacement therapy (WTTA), FXN-KO mice treated with the medium (MV), and FXN-KO mice treated with FXN replacement therapy (MTA). The shape of the dots indicates different sexes.

[0153] Figure 7 It is a scatter plot with all MS signals, showing the PCA results of all plasma samples from female mice, where different colors indicate different conditions: WTV, WTTA, MV, and MTA.

[0154] Figure 8 This is a volcano plot, showing a comparison between plasma samples obtained from female MTA mice and those obtained from female WTV mice. Different lipid subclasses are indicated by different colors, and gray dots represent unidentified lipids. Horizontal red lines indicate a threshold p-value of 0.05, and vertical red lines indicate a fold change of 1.35.

[0155] Figure 9This is a set of box plots showing the most significantly regulated lipids in plasma samples obtained from female MV mice compared to female WTV mice (p<0.01).

[0156] Figure 10 This is a volcano plot showing a comparison of plasma samples from female MTA mice and female WV mice. Different lipid subclasses are indicated by different colors, and gray dots represent unidentified lipids. The horizontal red line indicates a threshold p-value of 0.05, and the vertical red line indicates a fold change of 1.35.

[0157] Figure 11 Box plots showing 63 annotated lipids identified in plasma samples from female MTA mice compared to female MV mice.

[0158] Figure 12 This is a Venn diagram, where the red (left) circles represent 167 entities distinguishing plasma samples from MTA mice from MV mice, and the blue circles represent 356 entities distinguishing plasma samples from MV mice from WTV mice. The overlapping portion of the red and blue circles represents 36 entities that represent lipids regulated by the FXN-KO mutation and further regulated by FXN replacement therapy in FXN-KO mice.

[0159] Figure 13 It is a series of box plots representing a representative lipid or characteristic that is increased in FXN-KO mice (MV) and decreased after treatment with FXN replacement therapy (MTA) compared to WT mice (WTV).

[0160] Figure 14 Figure A shows a series of box plots of representative lipids, which were reduced in FXN-KO mice (MV) compared to WT mice (WTV) and further reduced after treatment with FXN replacement therapy (MTA).

[0161] Figure 14 Figure B is a series of box plots of representative lipids and characteristics. Compared with WT mice treated with the medium (WTV), these representative lipids and characteristics were increased in FXN-KO mice treated with the medium (MV), and further increased after treatment with FXN replacement therapy (MTA).

[0162] Figure 15Figure A is a dot plot showing the log2 fold change in the levels of various triglycerides (TGs) in FXN-KO mice (MV and WTV) treated with the TG compared to wild-type mice treated with the TG, relative to the number of carbons in their acyl chains. Circled dots represent increased TGs in FXN-KO mice compared to wild-type mice, thus indicating the effect of the mutation. Many of these TGs have acyl chain lengths >55. Some of the TGs increased in FXN-KO mice have acyl chain lengths ≤50 compared to wild-type mice where FXN replacement therapy did not reduce their levels.

[0163] Figure 15 Figure B is a scatter plot showing the log2 fold change in various TG levels in FXN-KO mice (MTA and MV) treated with FXN replacement therapy or mediators, compared to the number of carbons in their acyl chains. Circled dots represent TG levels that were reduced in FXN-KO mice compared to wild-type mice and increased after treatment with the FXN replacement therapy compound. These TGs have long chain lengths (<55).

[0164] Figure 16 Figure A is a scatter plot showing the log2 fold change in the levels of various phosphatidylcholine (PC) in FXN-KO mice (MV and WTV) treated with the medium, compared with wild-type mice treated with the medium, and the number of carbons in their acyl chains.

[0165] Figure 16 Figure B is a scatter plot showing the log2 fold change in various PC levels compared with their acyl chain lengths in FXN-KO mice (MTA and MV) treated with FXN replacement therapy or mediators. Circled dots represent the two PCs that decreased in FXN-KO mice and increased after FXN replacement therapy.

[0166] Figure 17 This is a scatter plot with MS signal, showing the principal component analysis (PCA) results of the ratio of day 15 to day -2 for all samples, colored by groups: Group 1, Group 2, and Group 3 (corresponding to subjects treated with the exemplary FXN replacement therapy compound at 25 mg, 50 mg, and 100 mg, respectively). The PCA analysis revealed a clear separation between Group 1 and Group 3.

[0167] Figure 18 This is a volcano plot, showing a comparison of healthy human subjects with those suffering from FRDA on day -2 (i.e., before treatment). Different lipid subclasses are indicated by different colors. Gray dots represent unidentified lipids. Horizontal lines indicate threshold p-values ​​of 0.03 and 0.05, and vertical red lines indicate fold changes of 0.8 and 1.25.

[0168] Figure 19 This is a volcano plot, showing a comparison between day 15 and day -2 for subjects treated with placebo. For subjects receiving placebo, 200 out of all 3328 features distinguished day 15 from day -2, with p-values ​​<0.03 and a fold change of 1.25. 93 of these 200 features were annotated as lipid IDs: between day 15 and day -2, in the placebo case, 44 features (22 annotated) increased and 156 features (71 annotated) decreased.

[0169] Figure 20 This is a volcano plot, presenting a comparison of day 15 versus day -2 for Group 1 subjects (administered with 25 mg of the exemplary FXN alternative treatment compound). Of all 3328 features, 237 features distinguished day 15 from day -2, with p-values ​​<0.03 and fold changes of 1.25. 73 of these 237 features were annotated as lipid IDs: compared to day -2, on day 15 following administration of the 25 mg exemplary FXN alternative treatment compound, 125 features (49 annotated) increased, and 112 features (24 annotated) decreased.

[0170] Figure 21 This is a volcano plot, showing a comparison of day 15 versus day -2 for group 2 subjects (administered with 50 mg of the exemplary FXN alternative treatment compound). Of all 3328 features, 169 features distinguished day 15 from day -2, with p-values ​​<0.03 and fold changes of 1.25. 59 of these 169 features were annotated as lipid IDs: compared to day -2, on day 15 following administration of the 50 mg exemplary FXN alternative treatment compound, 49 features (8 annotated) increased and 120 features (51 annotated) decreased.

[0171] Figure 22 This is a volcano plot, showing the comparison of day 15 versus day -2 for group 3 subjects (administered with 100 mg of the exemplary FXN replacement therapy compound). Of all 3328 features, 506 features distinguished day 15 from day -2, with p-values ​​<0.03 (Q-values ​​<0.05) and a fold change of 1.25. 166 features from these 506 features were annotated as lipid IDs: compared to day -2, on day 15 following administration of the 100 mg exemplary FXN replacement therapy compound, 218 features (51 annotated) increased and 288 features (115 annotated) decreased. The effect of FXN replacement therapy compound administration observed in group 3 (506 significant features) was more pronounced than that observed in groups 1, 2, and placebo (<250 significant features).

[0172] Figure 23 Figure A is a dot plot showing the log2 fold change in TG levels in samples from FRDA subjects on day -2 (before treatment) compared to the number of carbons in the acyl chain, compared to healthy control subjects.

[0173] Figure 23 Figure B is a series of dot plots showing the log2 fold change in TG levels on day 15 compared to day -2, comparing the number of carbons in their acyl chain to samples from subjects administered with placebo, 100 mg (Group 3), 50 mg (Group 2), and 25 mg (Group 1) of the exemplary FXN alternative treatment compound. The TGs plotted in the dot plots are 49 unique TGs selected based on the results of Group 3, where the p-value was <0.03, FC >1.25, or FC <0.8 on day 15 compared to day -2.

[0174] Figure 24 Figure A is a dot plot showing the log2 fold change in TG levels on day -2 (before treatment) in samples from FRDA subjects compared to healthy control subjects, as a comparison of the number of acyl chain unsaturations.

[0175] Figure 24 Figure B is a series of dot plots showing a log2 fold change in TG levels compared to the number of acyl chain unsaturations. The dot plot in the upper left quadrant shows a comparison of samples obtained from FRDA subjects with samples obtained from healthy controls who had never been treated (see Example 1). The remaining dot plots show a comparison of samples obtained on day 15 post-dosing from subjects treated with the exemplary FXN alternative therapy compound at 100 mg (Group 3), 50 mg (Group 2), and 25 mg (Group 1) with samples obtained from the same subject on day -2 before dosing. The TGs plotted in the dot plots are 49 unique TGs selected based on the results of Group 3, where the p-value was <0.03, FC >1.25, or FC <0.8 on day 15 compared to day -2.

[0176] Figure 25 Figure A is a dot plot showing the log2 fold change in TG levels versus the number of carbon atoms in the acyl chain in samples from representative patients treated with placebo. The number of unsaturations in each TG is presented using grayscale, where white dots represent 0 unsaturations and dark dots represent increasing numbers of unsaturations.

[0177] Figure 25Figure B is a dot plot showing the log2 fold change in TG levels versus the number of carbon atoms in the acyl chain in samples from representative patients treated with 100 mg of the exemplary FXN replacement therapy compound. The number of unsaturations in each TG is presented using grayscale, where white dots represent 0 unsaturations and dark dots represent increasing numbers of unsaturations.

[0178] Figure 26 This is a graphical summary of day 15 versus day -2 for 49 TGs treated with placebo, 25 mg (Group 1), 50 mg (Group 2), and 100 mg (Group 3) of the exemplary FXN replacement therapy compound. These 49 TGs were selected as the most significantly modulated TGs in Group 3. Dot intensity represents the log2 fold change from day 15 to day -2 in each group, where p < 0.05. Red dots indicate increases with treatment, while blue dots indicate decreases with treatment. Dot color intensity is proportional to the fold change value: the stronger the color intensity, the greater the fold change.

[0179] Figure 27 This is a graphical summary of the correlation between conazoline levels and the 49 selected TG levels that are most significantly regulated in group 3. The intensity of each point reflects the strength of the correlation between lipid levels and conazoline levels, where p-value < 0.2, blue dots indicate negative correlation, and red dots indicate positive correlation.

[0180] Figure 28 This is a graphical summary of the correlation between coagulant levels and cholesterol ester (CE) levels. Figure 28 The results presented showed that only CE16:0 and CE20:5 were positively correlated with coagulant levels from the skin (p < 0.2) and to a lesser extent with coagulant levels in platelets.

[0181] Figure 29 Figure A is a dot plot comparing the lipid level ratio on day 15 to day -2 and the coenzyme level ratio on day 15 to day -2 in representative TG samples with acyl chain length <56 carbons.

[0182] Figure 29 Figure B is a dot plot comparing the lipid level ratio on day 15 to day -2 and the coenzyme level ratio on day 15 to day -2 for representative TG with an acyl chain length ≥56 carbons.

[0183] Figure 29 Figure C is a dot plot comparing the lipid level ratio on day 15 to day -2 and the co-protein level ratio on day 15 to day -2 for CD16:0.

[0184] Figure 30Figure A is a volcano plot showing the effect (positive or negative) and the p-value for each feature. The chosen threshold was p = 0.05, which is more stringent than Pearson correlation analysis because the goal was to identify the most significant lipids associated with consortium levels in the skin, in addition to TG and CE.

[0185] Figure 30 Figure B is Figure 30 Figure A is a summary table of the data presented in the volcano map.

[0186] Figure 31 Figure A is a dot plot comparing the lipid level ratio on day 15 to day -2 and the coenzyme level ratio on day 15 to day -2 for representative PC ether PC (O-17:0 / 20:4).

[0187] Figure 31 Figure B is a dot plot comparing the lipid level ratio on day 15 to day -2 and the co-protein level ratio on day 15 to day -2 for representative LPC18:0.

[0188] Figure 31 Figure C is a dot plot comparing the lipid level ratio on day 15 to day -2 and the coenzyme level ratio on day 15 to day -2 in skin samples with a representative acylcarnitine ratio of 18:2.

[0189] Figure 32 This is a 2D display of the positive correlations between differentially expressed annotated lipids on day 15 and day -2 in subjects (Group 3) treated with 100 mg of the exemplary FXN replacement therapy compound, obtained using the Fruchterman-Reingold layout algorithm. Edges represent connections or correlations (R>0.6) between nodes (lipids). The width of the connection is proportional to the correlation.

[0190] Figure 33 This is a 2D display of the positive correlation between annotated lipids associated with consortin, obtained using the Fruchterman-Reingold layout algorithm.

[0191] Figure 34The volcano plot shows the log2 fold change in MS signal intensity for each lipid feature between FRDA subjects (day -2) and healthy volunteers (T0) on the x-axis, and the p-value (-log10) on the y-axis. Horizontal dashed lines correspond to p-values ​​of 0.05 and 0.03. Vertical dashed lines correspond to fold changes of 0.8 (1 / 1.25; left) and 1.25 (right). The number of annotated lipids for each subclass is shown in a table on the right side of the volcano plot. This table shows the lipid features that changed (upregulated or downregulated) and the number of unique lipids for each lipid subclass. Lipid features showing higher fold changes in MS signal intensity for FRDA subjects compared to healthy volunteers are on the right side of the plot, and those showing lower values ​​are on the left side.

[0192] Figure 35 This is a graph showing the log2 fold change in various TG species that are significantly different in untreated FRDA subjects compared to healthy volunteers.

[0193] Figure 36 This is a dot plot showing the log2 fold change in TG levels in samples from untreated FRDA subjects compared to healthy volunteers, in relation to the number of carbons in the acyl chain.

[0194] Figure 37 This is a dot plot showing the log2 fold change in TG levels in samples from untreated FRDA subjects compared to healthy volunteers, in relation to the number of acyl chain unsaturations.

[0195] Figure 38 This is a graph showing the log2 fold change of various PCO-species that are significantly different in untreated FRDA subjects compared to healthy volunteers.

[0196] Figure 39 This is a graph showing the log2 fold change in various PC species that are significantly different in untreated FRDA subjects compared to healthy volunteers.

[0197] Figure 40 This is a 2D display of the positive correlation between differentially expressed annotated lipids in untreated FRDA subjects and healthy volunteers, obtained using the Fruchterman-Reingold layout algorithm.

[0198] Figure 41 The forest plot represents a comparison of the log2 fold change in 29 unique lipids on day 15 versus day -2 in FRDA subjects administered 100 mg of the exemplary FXN alternative therapy compound, and a comparison of the log2 fold change in 29 unique lipids in FRDA subjects versus healthy volunteers.

[0199] Figure 42 Figure A shows a representative box plot of TG48:1, which shows the changes in disease (FRDA vs. healthy volunteers) and treatment (day 15 vs. day -2) in opposite directions in FRDA subjects treated with the exemplary FXN alternative therapy compound at doses of 25 mg (cohort 1), 50 mg (cohort 2), and 100 mg (cohort 3).

[0200] Figure 42 Figure B shows a representative box plot of TG49:4, which shows the changes in disease (FRDA vs. healthy volunteers) and treatment (day 15 vs. day -2) in opposite directions in FRDA subjects treated with the exemplary FXN alternative therapy compound at doses of 25 mg (cohort 1), 50 mg (cohort 2), and 100 mg (cohort 3).

[0201] Figure 42 Figure C shows a representative box plot of PC (O-18:1 / 18:2), which shows the changes in disease (FRDA vs. healthy volunteers) and treatment (day 15 vs. day -2) in opposite directions in FRDA subjects treated with exemplary FXN alternative therapy compounds at doses of 25 mg (cohort 1), 50 mg (cohort 2), and 100 mg (cohort 3). Detailed Implementation

[0202] Overview

[0203] In one aspect, this disclosure is based, at least in part, on providing a set of biomarkers, also referred to herein as FXN-sensitive lipid biomarkers (or FSLMs), the levels of which are positively or negatively correlated with the levels of the conamin (FXN) in cells. In some embodiments, the FSLMs of this disclosure are conversely regulated by FXN gene ablation or deficiency followed by FXN protein replacement. Thus, the FSLMs of this disclosure are associated with both FXN deficiency and conversely with FXN replacement in subjects. The FSLMs disclosed herein have been found to be sensitive to FXN and are considered biomarkers of FXN replacement. Therefore, these FSLMs can be used to determine and / or monitor the efficacy of FXN replacement therapy in subjects, as described herein.

[0204] In some embodiments, the FSLM comprises one or more triglycerides (triacylglycerols, TG). In some embodiments, the FSLM comprises one or more triglycerides, wherein the three acyl groups in each triglyceride molecule contain 45 to 55 carbons, for example, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54 or 55 carbons.

[0205] In some embodiments, FSLM comprises one or more triglycerides, wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons. In some embodiments, FSLM comprises one or more triglycerides, wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation. In some embodiments, FSLM comprises triacylglycerol 45:1 (TG45:1), triacylglycerol 46:1 (TG46:1), triacylglycerol 46:3 (TG46:3), triacylglycerol 47:1 (TG47:1), triacylglycerol 47:2 (TG47:2), triacylglycerol 48:0 (TG48:0), triacylglycerol 48:1 (TG48:1), triacylglycerol 48:2 (TG48:2), triacylglycerol 49:1 (TG49:1), triacylglycerol 49:2 (TG49:2), triacylglycerol 49:3 (TG49:3), triacylglycerol 49:4 (TG49:4), triacylglycerol 50:1 (TG50:1), and triacylglycerol 50:2 (TG50:1). :2) One or more of the following: triacylglycerol 50:3 (TG50:3), triacylglycerol 50:4 (TG50:4), triacylglycerol 51:1 (TG51:1), triacylglycerol 51:2 (TG51:2), triacylglycerol 51:3 (TG51:3), triacylglycerol 51:4 (TG51:4), triacylglycerol 52:3 (TG52:3), triacylglycerol 52:5 (TG52:5), triacylglycerol 53:2 (TG53:2), triacylglycerol 53:3 (TG53:3), triacylglycerol 53:4 (TG53:4), triacylglycerol 54:5 (TG54:5), triacylglycerol 54:6 (TG54:6), and triacylglycerol 54:7 (TG54:7). In some embodiments, the FSLM includes two or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7.In some embodiments, the FSLM includes three or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7. In some embodiments, the FSLM includes five or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7. In some embodiments, the FSLM includes ten or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7. In some embodiments, the FSLM includes fifteen or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7.In some embodiments, the FSLM includes twenty or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7. In some embodiments, the FSLM includes twenty-five or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7.

[0206] In some embodiments, the FSLM comprises one or more cholesterol esters (CE), such as 16:0 (CE16:0) and cholesterol ester 20:5 (CE20:5). In some embodiments, the FSLM comprises one or more ether phospholipids, for example, one or more ether diacylglycerol phosphocholine (PCO-), one or more phosphatidylethanolamine ethers (PEO-), or one or more phosphatidylcholine ethers, such as phosphatidylcholine ether PC (O-17:0 / 20:4). In some embodiments, the FSLM comprises one or more cholesterol esters CE16:0, CE20:5, and O-17:0 / 20:4. In some embodiments, the FSLM comprises two or more cholesterol esters CE16:0, CE20:5, and O-17:0 / 20:4. In some embodiments, the FSLM comprises cholesterol esters CE16:0, CE20:5, and O-17:0 / 20:4.

[0207] In some embodiments, the efficacy of FXN replacement therapy in subjects can be determined, evaluated, and / or monitored based on analysis of one or more FSLM lipid profiles before and after administration or initiation of FXN replacement therapy. Based on the results of FSLM lipid profile analysis, the subject's FXN replacement therapy can be adjusted, for example, to initiate, increase, decrease, or discontinue the subject's FXN replacement therapy.

[0208] definition

[0209] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure pertains. The following references (the entire contents of which are incorporated herein by reference) provide those skilled in the art with general definitions of many terms used in this disclosure (unless otherwise defined herein): Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd edition, 1994); The Cambridge Dictionary of Science and Technology (Walker, ed., 1988); The Glossary of Genetics, 5th edition, R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, Harper Collins Dictionary of Biology (1991). In general, the procedures, etc., of the molecular biology methods described herein or inherent in this work are common practices used in the art. Such standard techniques can be found in reference manuals, such as Sambrook et al. (2000, Molecular Cloning - A Laboratory Manual, 3rd Edition, Cold Spring Harbor Laboratories); and Ausubel et al. (1994, Current Protocols in Molecular Biology, John Wiley & Sons, New York).

[0210] Unless otherwise stated, the following terms may have the meanings assigned to them as follows. However, it should be understood that other meanings known or understood by those skilled in the art are also possible and are within the scope of this disclosure.

[0211] As used herein, unless the context clearly indicates otherwise, the singular forms “a / a kind,” “and,” and “the” include plural indicators. All technical and scientific terms used herein have the same meaning.

[0212] Unless specifically stated or obvious from the context, as used herein, the term “about” is understood to mean within the normal tolerance range in the field, such as within 2 standard deviations of the mean. “About” can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the specified value. Unless the context otherwise requires, all numerical values ​​provided herein may be modified by the term “about.”

[0213] As used herein, the term "marker" or "biomarker" is a biomolecule or group of biomolecules whose lipid levels are correlated (e.g., positively or negatively correlated with FXN levels). In some embodiments, a "marker" or "biomarker" is an expressed gene whose lipid levels can be measured by measuring the levels of the corresponding mRNA or protein.

[0214] As used herein, the markers or biomarkers of this disclosure that are positively or negatively correlated with the levels of FXN in cells or samples obtained from subjects are referred to as “FXN-sensitive lipid biomarkers” or “FSLMs”.

[0215] In some embodiments, FSLM is a marker or biomarker, such as a lipid, present in a different amount in a sample obtained from a healthy subject compared to a sample obtained from a subject lacking FXN (e.g., a subject with FRDA). In further embodiments, FSLM is modulated in the opposite way by FXN gene ablation or deficiency followed by FXN replacement therapy. For example, FSLM can be a lipid, such as a triglyceride, wherein the three acyl groups in the triglyceride molecule contain fewer than 56 carbon atoms, e.g., TG53:2, which is present at a higher level in a sample obtained from a subject lacking FXN compared to a sample obtained from a healthy subject, and whose level decreases in a sample from a subject lacking FXN after FXN replacement therapy. Alternatively, for example, FSLM can be PCO-, such as PC(-16:0 / 20:3), which is present at a lower level in a sample obtained from a subject lacking FXN compared to a sample obtained from a healthy subject, and whose level increases in a sample from a subject lacking FXN after FXN replacement therapy.

[0216] In some embodiments, the FSLM of this disclosure modulates FXN gene ablation or deficiency followed by FXN protein replacement in the opposite manner. Therefore, in some embodiments, the FSLM of this disclosure is associated with both FXN deficiency and, conversely, FXN replacement in a subject. The FSLM of this disclosure can be used to detect and / or monitor FXN levels in a sample (e.g., cell or tissue sample) (e.g., as a substitute for FXN levels). In some embodiments, the FSLM comprises one or more triglycerides (e.g., one or more triglycerides wherein the three acyl groups in each triglyceride molecule contain 45 to 58 carbons, or wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons, or wherein the three acyl groups in each triglyceride molecule contain 56 or more carbons), ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE); and diglycerides (DG).

[0217] As used herein, the term “control sample” or “control” refers to any clinically relevant comparative sample or comparative lipid profile, including, for example, samples from healthy FXN subjects (i.e., subjects with normal FXN levels), normal FXN lipid profiles, samples obtained from FXN-deficient subjects (i.e., subjects completely or partially lacking FXN lipids), baseline FXN(-) lipid profiles, or samples obtained from FXN-deficient subjects after administration of FXN replacement therapy, or FXN replacement lipid profiles. Control samples can also be samples from subjects at an earlier time point (e.g., before treatment with FXN replacement therapy). Control samples can be purified samples and / or lipids provided by a kit. Such control samples can be diluted, for example, in a dilution series to allow quantitative measurement of the level of an analyte (e.g., a biomarker) in the test sample. Control samples can include samples derived from one or more subjects. Control samples can also be samples collected from subjects to be evaluated at an earlier time point. For example, a control sample could be a sample collected from a subject to be evaluated before treatment with FXN replacement therapy. Control samples may also be samples from animal models, or samples from tissues or cell lines derived from animal models of mitochondrial diseases such as FRDA. The levels of one or more FSLMs (e.g., 1, 2, 3, 4, 5, 6, 7, 8, or 9 or more FSLMs) in the control sample consist of a set of measurements that may be determined, for example, based on any suitable statistical measure, such as, for example, a measure of central tendency, including the mean, median, or mode. In one embodiment, “different from control” is preferably statistically significantly different from the control.

[0218] As used herein, “change, alteration, increase, or decrease” is understood to mean a level of one or more FSLMs to be detected that is statistically different (e.g., increased or decreased) compared to a control sample or a predetermined threshold, such as a sample from FXN-healthy subjects (i.e., subjects with normal FXN levels) or from subjects lacking FXN (e.g., subjects completely or partially lacking FXN lipids or subjects with reduced levels of FXN lipids compared to normal control subjects). A change, alteration, increase, or decrease compared to a control or threshold may also include differences in the rate of change of one or more FSLM levels obtained from a series of at least two subject samples obtained over time. The determination of statistical significance is within the capabilities of those skilled in the art and may include any acceptable manner for determining and / or measuring statistical significance, such as, for example, the number of standard deviations from the mean constituting a positive or negative result, an increase in the detection level of FSLMs in the sample relative to the control, wherein the increase is above a certain threshold, or a decrease in the detection level of FSLMs in the sample relative to the control, wherein the decrease is below a certain threshold.

[0219] As used herein, “detecting,” “detection,” “determining,” etc., should be understood as referring to the identification of the presence and / or level of one or more FSLMs, such as one or more triglycerides (e.g., one or more triglycerides wherein the three acyl groups in each triglyceride molecule contain 45 to 55 carbons, or wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons), CE16:0, CE20:5, and PC (O-17:0 / 20:4).

[0220] As used herein, the terms “patients with FXN deficiency” or “subjects with FXN deficiency” are used interchangeably and refer to subjects who have been identified as having FXN deficiency, for example, subjects diagnosed with Friedreich ataxia (FRDA). In some embodiments, subjects with FXN deficiency have reduced levels of FXN lipids or activity compared to normal control subjects, for example, partial or complete lack of FXN expression or activity (e.g., having less than 70%, 60%, 50%, 40%, 30%, 20%, or 10% of the FXN expression or activity of normal control subjects). In some embodiments, subjects with FXN deficiency have not received FXN replacement therapy and are therefore untreated. In some embodiments, subjects with FXN deficiency are scheduled to receive FXN replacement therapy. In some embodiments, subjects with FXN deficiency are currently undergoing FXN replacement therapy. In some embodiments, subjects with FXN deficiency have already undergone FXN replacement therapy. In some embodiments, the FXN levels of subjects with FXN deficiency who are undergoing or have undergone FXN replacement therapy have partially or completely recovered to the FXN levels of healthy subjects.

[0221] Certain diseases can cause FXN deficiency in subjects, including mitochondrial diseases such as Friedreich ataxia (FRDA). As used herein, the term "FXN replacement therapy" refers to the replacement of a subject's coagulant protein, resulting in an increase in the level or activity of the coagulant protein in the subject. FXN replacement therapy can be performed by delivery of FXN protein or by delivery of nucleic acids encoding FXN to the subject. Delivery of FXN protein to the subject can include delivery of FXN protein or delivery of FXN fusion protein. As used herein, the term "FXN fusion protein" refers to a full-length FXN or an FXN fragment fused to a full-length or fragmented form of a different protein or to a peptide. In some embodiments, the FXN fusion protein comprises a full-length hFXN (SEQ ID NO:1) or a mature hFXN (SEQ ID NO:2), as described herein. In some embodiments, the FXN protein or a fragment thereof is fused to a cell-penetrating peptide (CPP). In some embodiments, the CPP is an HIV-TAT peptide. In some embodiments, FXN replacement therapy comprises administering to a subject lacking FXN an FXN fusion protein comprising or consisting of SEQ ID NO:12.

[0222] As used herein, the terms “disease,” “illness,” and “abnormal state” are used inclusively and refer to any deviation from the normal structure or function of any part, organ, or system (or any combination thereof) of the body. Specific diseases manifest as characteristic symptoms and signs, including biological, chemical, and physical changes, and are often associated with a variety of other factors, including but not limited to demographic, environmental, employment, genetic, and medical history factors. Early disease states include those where one or more physical symptoms have not yet been detected. Certain characteristic signs, symptoms, and associated factors can be quantified using various methods to produce important diagnostic information.

[0223] As used herein, the term "mitochondrial disease" refers to a disease caused by hereditary or spontaneous mutations in mtDNA or nDNA that result in altered function of proteins or RNA molecules normally present in mitochondria, impairing mitochondrial function to induce various types of diseases in, for example, the central nervous system, skeletal muscle, heart, eyes, liver, kidneys, large intestine (colon), small intestine, inner ear, and pancreas; as well as the blood, skin, and endocrine glands. In one non-limiting embodiment, mitochondrial disease is Friedreich ataxia (FRDA).

[0224] As used herein, a sample obtained at an “earlier time point” is a sample obtained over a sufficient period of time to allow clinically relevant information to be obtained from the sample at an earlier time point compared to a later time point. In some embodiments, an earlier time point is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, or 23 hours earlier, or 1, 2, 3, 4, 5, 6, or 7 days earlier. In some embodiments, an earlier time point is at least one week, two weeks, three weeks, or four weeks earlier. In some embodiments, an earlier time point is at least six weeks earlier. In some embodiments, an earlier time point is at least two months earlier. In some embodiments, an earlier time point is at least three months earlier. In some embodiments, an earlier time point is at least six months earlier. In some embodiments, an earlier time point is at least nine months earlier. In some embodiments, an earlier time point is at least one year earlier. Multiple subject samples (e.g., 3, 4, 5, 6, 7 or more) can be obtained at regular or irregular intervals over time, and the samples can be analyzed for trends in FSLM levels. Those skilled in the art can determine the appropriate intervals for testing a particular subject based on conventional considerations.

[0225] As used herein, the term "lipid profile" refers to a set of data obtained by measuring the levels of one or more lipids in a sample (e.g., a sample obtained from a subject), such lipids as one or more triglycerides (e.g., one or more triglycerides in which the three acyl groups in each triglyceride molecule contain 45 to 55 carbons or where the three acyl groups in each triglyceride molecule contain fewer than 56 carbons), ether phospholipids (such as PCO- or PEC, e.g., PC(O-17:0 / 20:4)), cholesterol esters (such as CE16:0, CE20:5, and CE14:1), and diglycerides (such as DE(18:1 / 18:2)). The term "lipid profile" may refer to raw data obtained from the results of LC / MS analysis, e.g., m / z values ​​and / or retention times, or to normalized lipid values. Lipid profiles can be determined by any convenient means for measuring lipid levels (such as LC / MS) and other techniques known to those skilled in the art or described herein. Lipid profiling enables the analysis of differential lipid levels between two or more samples, between a sample and a control, and between a sample and a threshold. Lipid profiling can also be determined by any method known to those skilled in the art or described herein for measuring lipid levels, such as mass spectrometry, including LC / MS.

[0226] As mentioned herein, the term "FXN lipid profile" includes any of the following three FXN lipid profiles: normal FXN lipid profile, baseline FXN(-) lipid profile, or FXN alternative lipid profile. In some embodiments, the baseline FXN(-) lipid profile may be used as a control. In some embodiments, the normal FXN lipid profile may be used as a control.

[0227] In some embodiments, the term "FXN lipid profile" used for one or more FSLMs refers to the lipid levels of one or more FSLMs or values ​​or a set of values ​​indicating the lipid levels of one or more FSLMs. In some embodiments, an FXN lipid profile includes a feature vector indicating the values ​​of one or more FSLMs. In some embodiments, "determining an FXN lipid profile for one or more FSLMs" includes detecting the levels of one or more FSLMs. In some embodiments, "determining an FXN lipid profile for one or more FSLMs" includes determining a lipid feature vector indicating the values ​​of one or more FSLMs.

[0228] As mentioned herein, the term "normal FXN lipid profile" refers to the lipid profile of one or more FSLMs in a sample obtained from a normal, healthy subject (i.e., a subject not lacking FXN). In some embodiments, "normal FXN lipid profile" also encompasses the average of multiple, such as two or more normal FXN lipid profiles (e.g., from two or more subjects). As mentioned herein, the term "baseline FXN(-) lipid profile" refers to the lipid profile of one or more FSLMs in a sample obtained from a subject lacking FXN prior to treatment with FXN replacement therapy. In some embodiments, the term "baseline FXN(-) lipid profile" encompasses the average of multiple, such as two or more baseline FXN(-) lipid profiles (e.g., from two or more subjects).

[0229] The average FXN lipid profile, such as the average normal FXN lipid profile or the average baseline FXN(-) lipid profile, can be determined by methods known in the art, for example by determining the levels of one or more FSLMs in samples obtained from each of two or more subjects (e.g., normal subjects or subjects lacking FXN), and then calculating the average lipid level of one or more FSLMs.

[0230] As mentioned herein, the term “reference FXN lipid profile” encompasses both “normal FXN lipid profile” and “baseline FXN(-) lipid profile”, that is, it can be either of the above. A reference lipid profile, such as a reference normal FXN lipid profile or a reference baseline FXN(-) lipid profile, can be used as a control, for example, to compare with an FXN alternative lipid profile to assess a subject’s response to FXN alternative therapy.

[0231] As mentioned in this article, the term “FXN alternative lipid profile” refers to the lipid profile of one or more FSLMs in a sample obtained from a subject lacking FXN after administration of at least one dose of FXN alternative therapy.

[0232] As used herein, the term “treated with FXN replacement therapy” means that the subject has been given at least one dose of FXN replacement therapy. As used herein, the terms “after treatment with FXN replacement therapy,” “after treatment with FXN replacement therapy,” “after administration of FXN replacement therapy,” or “after administration of FXN replacement therapy” mean at least 1 day, for example, at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40 days or more after administration of the dose of FXN replacement therapy.

[0233] As mentioned herein, the term “assessing a subject’s response to FXN replacement therapy” encompasses assessing the efficacy of FXN replacement therapy by: (a) determining the FXN replacement lipid profile in samples from subjects lacking FXN after treatment with FXN replacement therapy; (b) comparing the FXN replacement lipid profile with a reference FXN lipid profile; and (c) using the comparison in step (b) to assess or determine the efficacy of FXN replacement therapy.

[0234] In some embodiments, the reference FXN lipid profile is the baseline FXN(-) lipid profile, i.e., the lipid profile of one or more FSLMs in a sample obtained from a subject lacking FXN prior to treatment with FXN replacement therapy. In some embodiments, the difference between the FXN replacement lipid profile and the baseline FXN(-) lipid profile indicates the efficacy of the FXN replacement therapy or the response to the therapy.

[0235] In some embodiments, the reference FXN lipid profile is a normal FXN lipid profile, i.e., the lipid profile of one or more FSLMs in a sample obtained from a normal subject. In some embodiments, a comparison between an FXN alternative lipid profile and a normal FXN lipid profile, for example, the similarity between the two profiles, indicates the efficacy of the FXN alternative therapy or the response to the therapy.

[0236] "Higher lipid level", "higher lipid level", "higher level", "increased level", etc., of FSLM means that the lipid level in the test sample is greater than the standard error of the determination used to assess lipid level, and preferably is at least 25%, at least 50%, or at least 75% higher than the FSLM lipid level in the control sample, and is at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, or at least ten times higher than the FSLM lipid level in the control sample (e.g., a sample obtained from a healthy subject, a sample obtained from a subject lacking FXN, or a sample obtained from a subject after FXN replacement therapy), and preferably is the average lipid level of one or more FSLMs in several control samples.

[0237] As used herein, the term “including” refers to the phrase “including but not limited to” and is used interchangeably with that phrase.

[0238] As used in this article, “one or more” should be understood to encompass each of the following values: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and any value greater than 10.

[0239] The term “or” as used herein means “and / or” and may be used interchangeably with the term “and / or” unless the context clearly indicates otherwise.

[0240] As used herein, "patient" or "subject" may refer to a human or a non-human animal, preferably a mammal. "Subject" refers to any animal, including horses, dogs, cats, pigs, goats, rabbits, hamsters, monkeys, guinea pigs, rats, mice, lizards, snakes, sheep, cattle, fish, and birds. Human subjects may be referred to as patients.

[0241] As used herein, a “reference level” for FSLMs can be the absolute or relative amount or concentration of FSLMs, the presence or absence of FSLMs, a range of amounts or concentrations of FSLMs, the minimum and / or maximum amount or concentration of FSLMs, the average amount or concentration of FSLMs, and / or the median amount or concentration of FSLMs; and furthermore, a “reference level” for a combination of FSLMs can also be the ratio of the absolute or relative amounts or concentrations of two or more FSLMs to each other. Appropriate positive and negative reference levels for FSLMs specific to a particular disease state, phenotype, or its absence can be determined by measuring the desired FSLM levels in one or more appropriate subjects, and such reference levels can be tailored to a specific subject population (e.g., reference levels can be age-matched so that FSLM levels in samples from subjects of a certain age can be compared to reference levels for a specific disease state, phenotype, or its absence in an age group). Such reference levels can also be tailored to a specific technique (e.g., LC-MS, GC-MS, etc.) used to measure FSLM levels in biological samples, where FSLM levels may vary depending on the specific technique used.

[0242] As used herein, "sample" or "biological sample" includes a sample or culture obtained from any source. In some embodiments, a sample includes any sample or culture containing cells in which the FXN lipid profile can be analyzed. In some embodiments, a sample includes any sample or culture from a subject lacking FXN or a subject being treated with FXN replacement therapy. For example, a biological sample may be obtained from: a solid tissue sample, preferably a buccal sample, alternatively a skin biopsy sample, skin band, hair follicle, muscle biopsy sample, or a bodily fluid sample such as blood (including any blood products such as whole blood, plasma, serum, or a specific type of blood cell (e.g., platelets)), urine, saliva, or semen. In one embodiment, the biological sample is a buccal sample. In another embodiment, the biological sample is a skin sample, such as a skin biopsy sample or skin band. In one embodiment, the biological sample is a platelet sample. Alternatively, the sample may contain exogenous bodies that can be harvested to test for FSLM.

[0243] As used herein, the term “such as” refers to the phrase “such as but not limited to” and is used interchangeably with that phrase.

[0244] The term "triglyceride" may be used interchangeably with "triacylglycerol" in this document, referring to the molecule represented by formula I:

[0245]

[0246] Each of R1, R2, and R3 is independently a hydrocarbon chain that may contain one or more double bonds. As will be readily understood by those skilled in the art, terms used with respect to specific triglycerides, such as "TG50:4," refer to a triglyceride of formula I, wherein R1, R2, and R3 contain a total of 50 carbons and 4 double bonds. Similarly, the term "TG51:1" refers to a triglyceride of formula I, wherein R1, R2, and R3 contain a total of 51 carbons and 1 double bond, and so on. All other references to specific triglycerides listed below should be understood accordingly.

[0247] Those skilled in the art should also understand that each term used with respect to the specific triglycerides listed below may cover more than one triglyceride species. For example, the term "TG50:4" may cover more than one triglyceride species in which R1, R2, and R3 contain a total of 56 carbons and 6 double bonds, such as TG(18:3 / 16:0 / 16:1) and TG(18:2 / 18:2 / 14:0). Additionally, the term "TG(18:3 / 16:0 / 16:1)" covers triglycerides in which the positions of the double bonds in R1 and R3 can vary.

[0248] In some embodiments, the term "triglycerides" refers to a group of lipids that encompass TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51: 4. TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG5 4:7, TG56:4, TG56:5, TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:5, TG58:6, TG58:7, TG58:8, TG58:11. In some embodiments, the term "triglyceride" refers to a group of triglycerides in which the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or in which the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation, for example, TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2. TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7.

[0249] In some embodiments, the term "triglyceride" also covers epoxy-TG, i.e., triglycerides in which one or more double bonds (if present) have been oxidized to form epoxides.

[0250] As used herein, the term "degree of unsaturation" refers to the double bonds present in triglycerides. In some embodiments, the phrase "the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation" means that the three acyl groups in each triglyceride molecule contain a total of 7 or fewer double bonds. In some embodiments, the phrase "the three acyl groups in each triglyceride molecule contain more than 7 degrees of unsaturation" means that the three acyl groups in each triglyceride molecule contain more than 7 double bonds. In some embodiments, the phrase "the three acyl groups in each triglyceride molecule contain 6 or more degrees of unsaturation" means that the three acyl groups in each triglyceride molecule contain 6 or more double bonds.

[0251] As used herein, the term "ether phospholipid" refers to a group of lipids encompassing ether diacylglycerol phosphocholine (PCO-) and phosphatidylethanolamine ether (PEO-).

[0252] The term “ether diacylglycerol phosphocholine” is used interchangeably with the terms “PCO-”, “ether phosphatidylcholine”, “phosphatidylcholine ether”, or “PC ether”, and refers to the molecule represented by formula (II):

[0253]

[0254] Each of R1 and R2 is independently a hydrocarbon chain that may contain one or more double bonds. The term "ether diacylglycerol phosphocholine" encompasses, but is not limited to, LIPID. lipid classification system ( http: / / lipidmaps.orgThe term "ether diacylglycerol phosphocholine" also encompasses PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18: 1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22.2 / 2 0:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.8.

[0255] As will be readily understood by those skilled in the art, the term "PC(O-18:0 / 18:1)" refers, for example, to a molecule of formula (II), wherein R1 contains a total of 18 carbons and no double bonds, and R2 contains a total of 18 carbons and one double bond. It will also be readily understood by those skilled in the art that the term "PCO-40:6" refers, for example, to a molecule of formula (II), wherein R1 and R2 contain a total of 40 carbons and a total of 6 double bonds. All other references to the specific triglycerides listed above should be understood accordingly. It should also be understood by those skilled in the art that each term used with respect to PCO- as listed above may encompass more than one PCO- species. For example, the term "PCO-40:6" may encompass a PCO- species in which the number of carbons and the position of the double bonds in R1 and R2 vary. For example, the term PCO-(18:0 / 18:1) may encompass a PCO- species in which the position of the double bond in R2 varies.

[0256] The term "phosphatidylethanolamine ether" may be used interchangeably with the terms "ether phosphatidylethanolamine," "PEO-," or "PE ether," and refers to the molecule represented by formula (III):

[0257]

[0258] The term "phosphatidylethanolamine ether" encompasses the meaning of LIPID. lipid classification system ( http: / / lipidmaps.orgGP0202 is a 1-alkyl,2-acylglycerol phosphate ethanolamine. Exemplary PEO species include, for example, PEO-38:5, PEO-36:0, PEO-38:0, PEO-40:0, PEO-34:1, PEO-38:6, etc. Those skilled in the art will also understand that each term used with respect to the PEOs listed above may encompass more than one PEO species. For example, the term PEO-38:6 may encompass PEO species in which the number of carbons and the position of the double bonds in R1 and R2 vary.

[0259] The term "phosphatidylcholine" is used interchangeably with the term "PC" to cover lipids comprising a glycerol backbone covalently bonded to two fatty acids and a phosphatidylcholine molecule. The fatty acids can be variable-length, hydroxylated, and contain double bonds. In some embodiments, the term "phosphatidylcholine" encompasses the following species: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22:5), PC(17:0 / 20:5), PC(17:1 / 20:4), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:1 / 24:1), PC(18:2 / 18:2), PC(18:2 / 18:3), PC(18:2 / 20:5), PC(20:4 / 15:0), PC(20:4 / 20:0), PC(40:6), and PC(42:7).

[0260] As will be readily understood by those skilled in the art, the term "PC (18:1 / 20:3)" refers, for example, to phosphatidylcholine, in which one fatty acid contains a total of 18 carbons and 1 double bond, and the second fatty acid contains a total of 20 carbons and 3 double bonds. It will also be readily understood by those skilled in the art that the term "PC (42:7)" refers, for example, to phosphatidylcholine in which both fatty acids contain a total of 42 carbon atoms and a total of 7 double bonds. All other references to the specific PCs listed above should be understood accordingly. It should also be understood by those skilled in the art that each term used with respect to the PCs listed above may encompass more than one species of PC.

[0261] The term "cholesterol ester" is used interchangeably with the term "CE" to cover lipids comprising a structure containing cholesterol covalently bonded to a fatty acid via an ester bond. An ester bond is formed between the carboxyl group of the fatty acid and the hydroxyl group of the cholesterol. In some embodiments, the term "cholesterol ester" covers CE14:1, CE16:0, and CE20:5. As will be readily understood by those skilled in the art, the term "CE14:1" refers, for example, to a cholesterol ester containing 14 carbon atoms and one double bond in its fatty acid. All other references to the specific PCs listed above should be understood accordingly. Those skilled in the art should also understand that each term used with respect to the PCs listed above may cover more than one PC species. For example, the term "CE14:1" may cover species with variations in the position of the double bond in the fatty acid.

[0262] The term "diacylglycerol" is used interchangeably with the term "DG" to cover lipids comprising a structure containing two fatty acid chains covalently bonded to a glycerol molecule via ester bonds. The term "diacylglycerol" covers 1,2-diacylglycerol and 1,3-diacylglycerol. In some embodiments, the term "diacylglycerol" covers DG(18:1 / 18:2), where one fatty acid contains a total of 18 carbons and one double bond, and the second fatty acid contains a total of 18 carbons and two double bonds. Those skilled in the art will also understand that each term used with respect to DG (e.g., DG(18:1 / 18:2)) may cover more than one DG species. For example, the term "DG(18:1)" may cover a DG species in which one or more double bonds have different positions.

[0263] As used herein, the term “progression of FXN deficiency” refers to a deterioration in the condition of a subject lacking FXN over time. This term encompasses an increase in the severity and / or duration of existing symptoms of FXN deficiency and / or the appearance of one or more new symptoms of FXN deficiency in subjects lacking FXN.

[0264] As used herein, an "internal standard" is understood to be a chemical substance added directly to each sample containing an analyte in a known amount. The amount of analyte present is then determined relative to the internal standard, which serves as a calibrator. In some embodiments, the internal standard is an isotopically labeled internal standard, and is an isotopically labeled form of the analyte molecule. The mass spectrometry signal generated by the analyte differs from the mass spectrometry signal generated by the isotopically labeled standard, the difference depending on the type and number of isotopic atoms in the analyte incorporated into the isotopically labeled form. In some embodiments, TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, TG54:7 The isotopic labels of one or more of the following can serve as internal standards: TG56:6, TG56:7, TG56:8, TG56:9, TG56:10, TG58:8, TG58:11, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0265] As used herein, the term “mass spectrometry” or “MS” refers to an analytical technique that identifies a compound by its mass. MS refers to the method of filtering, detecting, and measuring ions based on their mass-to-charge ratio, or “m / z”. MS techniques generally involve (1) ionizing a compound to form a charged compound; and (2) detecting the molecular weight of the charged compound and calculating its mass-to-charge ratio. Compounds can be ionized and detected by any suitable method. A “mass spectrometer” typically includes an ionizer and an ion detector. Typically, one or more molecules of interest are ionized, and the ions are subsequently introduced into a mass spectrometer, where they follow a path in space that depends on their mass (“m”) and charge (“z”) due to a combination of magnetic and electric fields.

[0266] As used herein, the term "operating in negative ion mode" refers to mass spectrometry methods that generate and detect negative ions. Similarly, the term "operating in positive ion mode" refers to mass spectrometry methods that generate and detect positive ions.

[0267] As used herein, the term "ionization" or "ionization of" refers to the process of generating analyte ions with a net charge equal to or greater than one or more electron units. A negative ion is an ion with a net negative charge of one or more electron units, while a positive ion is an ion with a net positive charge of one or more electron units.

[0268] Any composition or method provided herein may be combined with one or more of any other compositions and methods provided herein.

[0269] The ranges provided in this document should be understood as shorthand notations of all values ​​within that range. For example, the range 1 to 50 should be understood as including any number, combination of numbers, or subrange of numbers in the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, and 50.

[0270] Reference will now be made in detail to exemplary embodiments of the present disclosure. While the present disclosure will be described in conjunction with exemplary embodiments, it should be understood that this is not intended to limit the present disclosure to these embodiments. Rather, it is intended to cover alternatives, modifications, and equivalents that may be included within the spirit and scope of the present disclosure as defined by the appended claims.

[0271] This FSLM disclosure

[0272] This disclosure provides a set of biomarkers, also referred to herein as FXN-sensitive lipid biomarkers (FSLMs), the levels of which are positively or negatively correlated with levels of FXN protein in cells or subjects (e.g., samples from subjects). In some embodiments, the FSLMs of this disclosure are conversely regulated by FXN gene ablation or deficiency followed by FXN protein replacement. Thus, the FSLMs of this disclosure are associated with both FXN deficiency and, conversely, FXN replacement in subjects. All FSLMs disclosed herein have been found to be sensitive to FXN levels and are considered biomarkers for FXN replacement therapy. Therefore, these FSLMs can be used to assess and / or monitor the progression of FXN deficiency in subjects, as described herein. These FSLMs can also be used to assess and / or monitor FXN replacement therapy in subjects, for example, to assess, monitor, or determine the efficacy of FXN replacement therapy in subjects, as described herein.

[0273] For example, in one aspect, this disclosure provides a method for determining, evaluating, and / or monitoring the effectiveness of FXN replacement therapy, the method comprising determining: (i) a baseline FXN(-) lipid profile against one or more FSLMs in samples from subjects lacking FXN prior to treatment with FXN replacement therapy; and (ii) a subject FXN replacement lipid profile against one or more FSLMs in samples from subjects lacking FXN who are undergoing FXN replacement therapy or after treatment with FXN replacement therapy; comparing the subject FXN replacement lipid profile with the baseline FXN(-) lipid profile; and using the comparison results to determine, evaluate, or monitor the effectiveness of FXN replacement therapy. Based on the results of the FSLM lipid profile analysis, the subject's FXN replacement therapy can be adjusted to, for example, initiate, increase (e.g., increase the dose and / or frequency of administration), decrease (e.g., decrease the dose and / or frequency of administration), or discontinue FXN replacement therapy in the subject.

[0274] Another aspect of this disclosure relates to providing a method for identifying one or more FSLMs, the FSLM being a biomarker whose level is sensitive to FXN levels in the cells of a subject (e.g., a subject lacking FXN). The method includes determining a lipid profile in a sample from a healthy subject with normal FXN levels, referred herein as a normal FXN lipid profile; determining a lipid profile in a sample from a subject with lacking FXN levels, referred herein as a baseline FXN(-) lipid profile; and comparing the normal FXN lipid profile with the baseline FXN(-) lipid profile; wherein a lipid biomarker whose level changes in the baseline FXN(-) lipid profile compared to the normal FXN lipid profile is identified as an FSLM. Alternatively or additionally, the method for determining an FSLM may include a comparison between a lipid profile (baseline FXN(-) lipid profile) obtained from a sample from a subject lacking FXN receiving FXN replacement therapy and a lipid profile obtained from a sample from a subject lacking FXN during or after receiving FXN replacement therapy. The lipid profile from a sample obtained from a subject lacking FXN during or after FXN replacement therapy is also referred herein as an FXN replacement lipid profile. In the examples, lipids whose levels changed in the FXN alternative lipid profile compared to the baseline FXN(-) lipid profile were identified as FSLMs.

[0275] In some embodiments, the FSLM of this disclosure comprises one or more TGs (e.g., one or more triglycerides, wherein the three acyl groups in each triglyceride molecule contain 45 to 55 carbons, or wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons, or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation), cholesterol esters (e.g., CE16:0 or CE20:5); and ether phospholipids (e.g., PCO- or PEO, including phosphatidylcholine ethers, such as PC (O-17:0 / 20:4), phosphatidylcholine (PC), and any combination of diglycerides (DG). In some embodiments, the FSLM of this disclosure comprises TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, and TG48:1. , TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, T G51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, TG54 7. Any combination of one or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7 and PC(O-17:0 / 20:4).In some embodiments, the FSLM of this disclosure includes TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, T G54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O- 18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6 ), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34 :2. PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), Any combination of one or more of PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, CE16:0, CE20:5, CE14:1, and DG18:1 / 18:2. In some embodiments of this disclosure, other biomarkers known in the art for measuring the efficacy of FXN lipids or FXN replacement therapy may be used in conjunction with the methods of this disclosure.

[0276] In some embodiments, one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) FSLMs are selected, for example, from TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51 ...4, TG50:5, TG51:1, TG51:2, TG51:3, TG50:4, TG50:4, TG50:5, TG51:4, TG50:4, TG50:4, TG50:5, TG51:4 51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O -16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18: 0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22 :6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4) , PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO -46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2.

[0277] In some embodiments, the term "one or more FSLMs" is intended to mean one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) FSLMs selected, for example, from the group consisting of: (a) triglycerides (TG) wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation; (b) ether phospholipids (e.g., PCO- and PEO-); (c) phosphatidylcholine (PC); (d) cholesterol esters (CE); and (e) diglycerides (DG).In some embodiments, one or more FSLMs may be selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5 , TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4 ), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20: 0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PC O-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22: 4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5) and PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5 and DG18:1 / 18:2.

[0278] The methods provided herein include any combination of, for example, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more FSLMs selected from one or more TGs (wherein the three acyl groups in each TG molecule contain fewer than 56 carbon atoms and / or where the three acyl groups in each TG molecule contain 7 or fewer degrees of unsaturation), cholesterol esters (e.g., CE16:0 or CE20:5), and ether phospholipids (e.g., PCO- or PEO, including phosphatidylcholine ethers, such as PC (O-17:0 / 20:4)).

[0279] In some embodiments, one or more FSLMs disclosed herein comprise one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) lipid markers selected from one or more TGs (e.g., one or more triglycerides, wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms, or wherein the three acyl groups in each TG molecule contain 7 or fewer degrees of unsaturation), cholesterol esters (e.g., CE16:0 or CE20:5), and ether phospholipids (e.g., PCO- or PEO, including phosphatidylcholine ethers, such as PC(O-17:0 / 20:4).

[0280] In some embodiments, one or more FSLMs comprise one or more TGs or any combination thereof, wherein the three acyl groups in each TG molecule contain fewer than 56 carbon atoms. In some embodiments, one or more FSLMs comprise one or more TGs or any combination thereof, wherein the three acyl groups in each TG molecule contain 7 or fewer degrees of unsaturation. In some embodiments, one or more FSLMs comprise one or any combination thereof of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs comprise one or more TGs or any combination thereof, wherein the three acyl groups in each TG molecule contain fewer than 56 carbon atoms, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs comprise one or more TGs (CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4)) or any combination thereof, wherein the three acyl groups in each TG molecule contain seven or fewer degrees of unsaturation.

[0281] In some embodiments, one or more FSLMs include one or any combination of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include one or any combination of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0282] In some embodiments, one or more FSLMs include TG45:1. In some embodiments, one or more FSLMs include TG46:1. In some embodiments, one or more FSLMs include TG46:3. In some embodiments, one or more FSLMs include TG47:1. In some embodiments, one or more FSLMs include TG47:2. In some embodiments, one or more FSLMs include TG48:0. In some embodiments, one or more FSLMs include TG48:1. In some embodiments, one or more FSLMs include TG48:2. In some embodiments, one or more FSLMs include TG48:1. In some embodiments, one or more FSLMs include TG48:3. In some embodiments, one or more FSLMs include TG49:1. In some embodiments, one or more FSLMs include TG49:2. In some embodiments, one or more FSLMs include TG49:3. In some embodiments, one or more FSLMs include TG49:4. In some embodiments, one or more FSLMs include TG50:1. In some embodiments, one or more FSLMs include TG50:2. In some embodiments, one or more FSLMs include TG50:3. In some embodiments, one or more FSLMs include TG50:4. In some embodiments, one or more FSLMs include TG50:5. In some embodiments, one or more FSLMs include TG51:1. In some embodiments, one or more FSLMs include TG51:2. In some embodiments, one or more FSLMs include TG51:3. In some embodiments, one or more FSLMs include TG51:4. In some embodiments, one or more FSLMs include TG52:2. In some embodiments, one or more FSLMs include TG52:3. In some embodiments, one or more FSLMs include TG52:4. In some embodiments, one or more FSLMs include TG52:5. In some embodiments, one or more FSLMs include TG52:6. In some embodiments, one or more FSLMs include TG53:2. In some embodiments, one or more FSLMs include TG53:3. In some embodiments, one or more FSLMs include TG53:4. In some embodiments, one or more FSLMs include TG53:5. In some embodiments, one or more FSLMs include TG54:4. In some embodiments, one or more FSLMs include TG54:5. In some embodiments, one or more FSLMs include TG54:6. In some embodiments, one or more FSLMs include TG54:7.

[0283] In some embodiments, one or more FSLMs include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG5 4:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC( O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO- 36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5) and PC(20:4 / 20:0), CE14:1, CE16:0 and CE20:5 and DG18:1 / 18:2 or any combination thereof.

[0284] In some embodiments, one or more FSLMs include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52: 4. TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16: 0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24) :1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7, PCO-46. 8. PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40 :6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5) and PC(20:4 / 20:0), CE14:1, CE16: 0 and any combination of two or more of CE20:5 and DG18:1 / 18:2, such as three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, twelve or more, thirteen or more, fourteen or more, fifteen or more, sixteen or more, seventeen or more, eighteen or more, nineteen or more, twenty or more, or twenty-five or more.

[0285] In some embodiments, one or more FSLMs include CE16:0. In some embodiments, one or more FSLMs include CE20:5. In some embodiments, one or more FSLMs include PC (O-16:0 / 18:2). In some embodiments, one or more FSLMs include PC (O-16:0 / 22:6). In some embodiments, one or more FSLMs include PC (O-18:0 / 18:2). In some embodiments, one or more FSLMs include PC (O-18:1 / 20:5). In some embodiments, one or more FSLMs include PCO-36:3. In some embodiments, one or more FSLMs include PCO-34:2. In some embodiments, one or more FSLMs include PCO-40:2. In some embodiments, one or more FSLMs include PCO-44:7. In some embodiments, one or more FSLMs include PC (O-17:0 / 20:4).

[0286] In some embodiments, one or more FSLMs include one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include two or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include three or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include four or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include five or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include six or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include seven or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include eight or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include nine or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include ten or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include eleven or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twelve or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include thirteen or more of the following: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include fourteen or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include fifteen or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include sixteen or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include seventeen or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include eighteen or more of the following: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include nineteen or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twenty or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twenty-one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include twenty-two or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twenty-three or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twenty-four or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include twenty-five or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twenty-six or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7. In some embodiments, one or more FSLMs include twenty-seven or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.In some embodiments, one or more FSLMs include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0287] In some embodiments, one or more FSLMs include one or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include two or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include three or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include four or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include five or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include six or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).In some embodiments, one or more FSLMs include seven or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include eight or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include nine or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include ten or more of CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0288] In some embodiments, one or more FSLMs include CE16:0. In some embodiments, one or more FSLMs include CE20:5. In some embodiments, one or more FSLMs include PC (O-16:0 / 18:2). In some embodiments, one or more FSLMs include PC (O-16:0 / 22:6). In some embodiments, one or more FSLMs include PC (O-18:0 / 18:2). In some embodiments, one or more FSLMs include PC (O-18:1 / 20:5). In some embodiments, one or more FSLMs include PCO-36:3. In some embodiments, one or more FSLMs include PCO-34:2. In some embodiments, one or more FSLMs include PCO-40:2. In some embodiments, one or more FSLMs include PCO-44:7. In some embodiments, one or more FSLMs include PC (O-17:0 / 20:4). In some embodiments, one or more FSLMs include CE16:0 and CE20:5. In some embodiments, one or more FSLMs include CE16:0 and PC (O-17:0 / 20:4). In some embodiments, one or more FSLMs comprise CE20:5 and PC (O-17:0 / 20:4). In some embodiments, one or more FSLMs comprise CE16:0, CE20:5, and PC (O-17:0 / 20:4).

[0289] For example, an FXN lipid profile can be determined by measuring lipid levels of at least one FSLM or any combination of more than one FSLM. In the following text, a lipid profile may also be referred to as a characteristic.

[0290] In one embodiment of this disclosure, the baseline FXN(-) lipid profile includes at least one FSLM or any combination of more than one FSLM with varying levels, such as one or more triglycerides (e.g., one or more triglycerides wherein the three acyl groups in each triglyceride molecule contain 45 to 55 carbons, or wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons), ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE), and diglycerides (DG), such as CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).

[0291] In one embodiment of this disclosure, the baseline FXN(-) lipid profile may include at least one or any combination of the following: CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). In one embodiment of this disclosure, the baseline FXN(-) lipid profile may include PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-20:0 / 22:6), PC(O-20:1 / 22:6), PC(O-20:2 / 20:4) with downregulated lipid levels. The efficacy of FXN replacement therapy can be measured by at least one of the following: PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46:8, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE16:0, and CE20:5.

[0292] In one embodiment of this disclosure, the baseline FXN(-) lipid profile may include at least one of or any combination of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, and TG54:7 with upregulated lipid levels. In one embodiment of this disclosure, the baseline FXN(-) lipid profile may include the following upregulated lipid levels: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5 At least one of the following: TG54:4, TG54:5, TG54:6, TG54:7, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, DG18:1 / 18:2, and CE14:1. The effectiveness of FXN replacement therapy can be indicated by the downregulation pattern of any one or more of these FSLMs.

[0293] In one embodiment, the FXN alternative lipid profile includes a baseline FXN(-) lipid profile that reverses lipid levels.

[0294] In another embodiment, the FXN replacement lipid profile used as an indicator of the effectiveness of FXN replacement therapy may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG... One or any combination of 52:5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, TG54:7, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7 and PC(O-17:0 / 20:4).In another embodiment, the FXN replacement lipid profile used as an indicator of the effectiveness of FXN replacement therapy may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG5 3:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20: 4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 1 8:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC (16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5 and DG18:1 / 18:2 or any combination thereof.

[0295] In some embodiments, the FXN replacement lipid profile is characterized by the inverse regulation of FSLMs, defined by any FSLM that is downregulated under FXN depletion conditions (e.g., in subjects with FRDA) and becomes upregulated after FXN replacement therapy; and conversely, any FSLM that is upregulated under FXN depletion conditions (e.g., in subjects with FRDA) becomes downregulated after FXN replacement therapy. Therefore, detecting altered lipids of one or more FSLMs in a sample after FXN replacement therapy allows for monitoring the efficacy of FXN replacement therapy in subjects. For example, in one embodiment, the absence of altered lipids of one or more FSLMs in a sample after FXN replacement therapy indicates that FXN replacement therapy may not have been successful and / or may require additional FXN replacement therapy. Similarly, in another embodiment, altered lipids of one or more FSLMs in a sample after FXN replacement therapy indicates that FXN replacement therapy is successful.

[0296] As mentioned in this article, a lipid eigenvector is a set of values ​​characterizing a lipid profile. A lipid eigenvector can include a set of n FSLMs, where n is the number of different lipids whose levels are measured in a sample. For example, n can be all triglycerides (e.g., one or more triglycerides where the three acyl groups in each triglyceride molecule contain 45 to 55 carbons, or where the three acyl groups in each triglyceride molecule contain fewer than 56 carbons; or where the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations), CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4). Alternatively, n can be at least one, two, three, four, five, six, or any number of triglycerides, wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms and / or 7 or fewer degrees of unsaturation (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, T G49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, T G52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7).

[0297] In one embodiment, a set of FSLMs may comprise at least one FSLM or any combination of more than one FSLM, such as triglycerides, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, and PC(O-17:0 / 20:4).In one embodiment, one or more FSLMs include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG5 4:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC( O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO- 36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5 and any combination of one or more of DG18:1 / 18:2.

[0298] In one embodiment, the method provided in this disclosure includes determining an FXN lipid profile for one or more of the above-described FSLMs. In one embodiment, one or more FSLMs comprise CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7, or PC(O-17:0 / 20:4).In one embodiment, one or more FSLMs include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG 54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18 :0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), P P CO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16 One or more of the following: PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5 and DG18:1 / 18:2.

[0299] For example, a normal FXN lipid profile obtained from a sample of a healthy subject can consist of lipid levels of a set of FSLMs and can be represented by a normal FXN lipid feature vector, referred to as the normal FXN lipid feature vector. As illustrated in the following example, when measured in an FXN-deficient sample (e.g., a sample from a subject with FRDA), the FSLMs can exhibit lipid levels different from those in the FSLMs of a healthy subject, and therefore can be represented by a deficient FXN lipid feature vector, referred to as the deficient FXN lipid feature vector. In one embodiment, the difference between the deficient FXN lipid feature vector and the normal FXN lipid feature vector can be detected and quantified by the distance between the two lipid feature vectors. Alternatively, the FSLM lipid levels in samples from FXN-deficient subjects (e.g., subjects with FRDA) can exhibit different lipid levels after FXN replacement therapy and can be represented by an FXN alternative lipid feature vector, referred to as the FXN alternative lipid feature vector. For the first two lipid feature vectors, the difference between the FXN substituted lipid feature vector and the normal FXN lipid feature vector or the FXN-deficient lipid feature vector can be detected and quantified by the distance between the substituted FXN lipid feature vector and the normal FXN lipid feature vector or the FXN-deficient lipid feature vector.

[0300] Therefore, having samples obtained from subjects lacking FXN before treatment and samples obtained after FXN replacement therapy, a first FXN lipid feature vector can be determined for an FXN replacement lipid profile, and a second FXN lipid feature vector can be determined for a baseline FXN(-) lipid profile; wherein determining the distance or scalar product between the first and second lipid feature vectors can be used to determine the effectiveness of the FXN replacement therapy. In embodiments of this disclosure, a third lipid feature vector can be determined for a normal FXN lipid profile, which is constructed for FSLMs from samples from healthy subjects. In one embodiment, the distance between the second (baseline FXN(-) lipid profile) and the third (normal FXN lipid profile) FXN lipid feature vectors can be determined. In another embodiment, the distance between the first (FXN replacement lipid profile) and the third (normal FXN lipid profile) FXN lipid feature vectors can be determined and used to determine the effectiveness of the FXN replacement therapy. In one embodiment, the distance between the first and third lipid feature vectors can be normalized for the distance between the second and third lipid feature vectors, and the resulting normalized distance can be used to determine the effectiveness of the FXN replacement therapy. In an embodiment, the resulting normalized distance can be a value ranging from 0 (zero) to 1 (one), where the smaller the value (closest to zero), the more effective the therapy.

[0301] The biomarkers disclosed herein are associated with subjects’ FXN levels, such as one or more triglycerides (e.g., one or more triglycerides (TG) wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations); ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE); and diglycerides (DG). Therefore, in one aspect, this disclosure provides methods for determining and / or monitoring a subject's FXN status or determining, assessing and / or monitoring a subject's FXN replacement therapy by using, measuring, detecting, quantifying, etc., one or more FSLMs, such as: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations; ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE); and diglycerides (DG).

[0302] On the other hand, this disclosure relates to the use, measurement, detection, quantification, etc. of one or more FSLMs as alternatives to measuring FXN expression levels, such FSLMs being one or more of the following: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations; ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE); and diglycerides (DG).

[0303] Furthermore, in another embodiment, the FSLM can be used in combination with one or more additional biomarkers of mitochondrial diseases (e.g., FRDA). Other biomarkers that can be used in combination with one or more FSLMs include one or more of the following: triglycerides (TG), wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations; ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE); and diglycerides (DG), including any measurable characteristic described herein that quantitatively or qualitatively reflects the physiological state of an organism, such as whether the organism has a mitochondrial disease, e.g., FRDA. The physiological state of an organism includes any disease or non-disease state, e.g., a subject with a mitochondrial disease (e.g., FRDA), or otherwise healthy subjects. The FSLMs of this disclosure that can be used in combination with one or more additional biomarkers include characteristics that can be objectively measured and assessed as indicators of normal processes, pathogenic processes, or pharmacological responses to therapeutic interventions. Such combined biomarkers can be clinical parameters (e.g., age, performance status), laboratory measurements (e.g., molecular markers), or genetic or other molecular determinants. In other embodiments, this disclosure also relates to the analysis and consideration of any clinical and / or subject-related health data, such as data obtained from electronic health records (e.g., collection of electronic health information related to various types of data about individual subjects or groups, such as demographics, medical history, medications and allergies, immunization status, laboratory test results, radiographic images, vital signs, personal statistics such as age and weight, and billing information).

[0304] This disclosure also contemplates the use of specific combinations of the FSLMs disclosed herein, such as any combination of one or more of the following: triglycerides (wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or where the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation), ether phospholipids, phosphatidylcholine (PC), cholesterol esters (CE), and diglycerides (DG) (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49...). :2. TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52 :6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-1 6:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-1 8:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-2 2:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, P C(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5 and DG18:1 / 18:2). In one embodiment, this disclosure covers an FSLM group having at least two (2) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2 , TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14: 0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC (O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC( O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any two of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure covers an FSLM group having at least three (3) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52: 2. TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14 :0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1) , PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), C(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC( O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any three of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure covers an FSLM group having at least four (4) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52: 2. TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14 :0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1) , PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), C(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC( O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any four of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure covers an FSLM group having at least five (5) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52: 2. TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14 :0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1) , PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), C(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC( O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any five of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure covers an FSLM group having at least six (6) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52: 2. TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14 :0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1) , PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), C(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC( O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any six of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure covers an FSLM group having at least seven (7) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52: 2. TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14 :0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1) , PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), C(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC( O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any seven of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure envisions an FSLM group having at least eight (8) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51 ...4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG50:5, TG51:5, TG51:2, TG51:3, TG51:4, TG50:5, TG51:5, TG51:2, TG51:3, TG51:4, TG50:5, TG51:5, TG51:2, TG51:3, TG51:4, TG51:5, TG51:5, TG51:5, TG51:5, TG51:5, TG51:5, TG51:5, TG51:5, TG51:5, TG51:5, TG 52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18: 1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC (O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any eight of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure envisions an FSLM group having at least nine (9) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG50:5, TG51:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG51:5 ... 52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18: 1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC (O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-4 6.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5) Any nine of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure envisions an FSLM group having at least ten (10) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51: 1. TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, T G54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20 :4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC( O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8. PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(1 6:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20: 3) Any ten of the following: PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure envisions an FSLM group having at least eleven (11) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG53 ...7, TG53:8 54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16: 0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20 :4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6)、PC(O-20:2 / 20:4)、PC(O-22:2 / 20:4)、PC(O-22:1 / 22:6)、PC(O-22:2 / 20:4)、PC(O-(24:1 / 22:6)、PC(O-24:2 / 20:4)、PCO-34:2、PCO-36:3、PCO-34:2、PCO-38:3、PCO-40:2、PCO-40:6、PCO-44:7、PCO-46.8、PC(15:0 / 20:3)、PC(15:0 / 22:6)、PC(16:0 / 14:0)、PC(16:0 / 22:4)、PC(16:1 / 16:0)、PC(16:1 / 20:4)、PC(16:1 / 22.5) Any eleven of the following: PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2. In another embodiment, this disclosure envisions an FSLM group having at least twelve (12) members, which may include TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51 :1. TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 2 0:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC (O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20: 1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6 ), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8. PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(1 6:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20: 3) Any twelve of the following: PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5, and DG18:1 / 18:2.

[0305] In other embodiments, this disclosure covers the FSLM group, which includes at least 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, and 116 of the FSLMs. The numbers 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, or 138, and the FSLM such as TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4 P C(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4) , PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2 ), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 2 2:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8. PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC( 16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3) , PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE16:0, CE20:5 and DG18:1 / 18:2. .

[0306] In some embodiments, the levels of one or more FSLMs increase after a subject is treated with FXN replacement therapy (e.g., a subject lacking FXN). In some embodiments, one or more FSLMs are selected from the group consisting of cholesterol esters, such as CE16:0 or CE20:5, and ether phospholipids, such as PCO-, PEO-, including phosphatidylcholine ethers, such as PC(O-17:0 / 20:4). In some embodiments, one or more FSLMs include PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), One or more of the following: PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, PCO-46.8, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE16:0, and CE20:5.

[0307] In some embodiments, the levels of one or more FSLMs decreased after treatment with FXN replacement in the subject (e.g., a subject lacking FXN). In some embodiments, one or more FSLMs are selected from the group consisting of triglycerides, wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbon atoms, for example, TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4 , TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3 , TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7. In some embodiments, the FSLM is selected from the group consisting of the following: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, T G54:4, TG54:5, TG54:6, TG54:7, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22 .5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, DG18:1 / 18:2 and CE14:1.

[0308] On the other hand, this disclosure provides for the identification of "diagnostic lipid profiles" or "diagnostic lipid characterization" related to FXN in biological samples based on the FSLM levels disclosed herein. "FSLM levels" can refer to the lipid levels of FSLM in the biological sample.

[0309] In some embodiments, diagnostic characteristics are obtained by: (1) detecting the levels of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more FSLMs in biological samples from subjects receiving FXN replacement therapy, such as TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4. TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O -17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20: 5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O- 22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44: 7. PCO-46.8, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC4 0:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE14:1, CE 16:0, CE20:5, and DG18:1 / 18:2; (2) comparing the levels of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more FSLMs to the levels of the same FSLMs from a control sample (e.g., baseline FXN(-) lipid profile); and (3) determining whether the levels of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more FSLMs detected in the biological sample are higher or lower than the levels of FSLMs in the control (e.g., baseline FXN(-) lipid profile). If at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more FSLMs are higher or lower than the control (e.g., baseline FXN(-) lipid profile), the diagnostic characteristics indicate the effectiveness of FXN replacement therapy.

[0310] According to various embodiments, algorithms can be employed to predict whether a biological sample from a subject contains FXN, or to assess or monitor whether a subject has effectively received FXN replacement therapy. Those skilled in the art will understand that an algorithm can be any calculation, formula, statistical survey, nomogram, lookup table, decision tree method, or computer program that processes a set of input variables (e.g., the number (n) of biomarkers detected at levels exceeding a certain threshold level, or the number (n) of biomarkers detected at levels below a certain threshold level) through a number of well-defined, sequential steps to ultimately produce a score or “output.” This document considers any suitable algorithm—whether computer-based or manual (e.g., lookup table).

[0311] This disclosure provides for the use of various combinations and sub-combinations of FSLMs. For example, one or more FSLMs, such as triglycerides, wherein the three acyl groups in each triglyceride molecule contain fewer than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50: 4. TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, TG54:7), may be used alone or in combination with the following: one or more of ether phospholipids (e.g., PCO- and PEO-), phosphatidylcholine (PC), cholesterol esters (CE); and any combination of diglycerides (DG). It should be understood that, unless otherwise expressly indicated, any single FSLM or combination of FSLMs provided herein may be used in this disclosure.

[0312] sample

[0313] This disclosure can be practiced with any suitable biological sample that may contain, express, or include detectable FSLMs. For example, biological samples may be obtained from: solid tissue samples, such as skin biopsy samples, muscle biopsy samples, preferably buccal samples, or bodily fluid samples, such as blood (including any blood products, such as whole blood, plasma, serum, or specific types of blood cells), urine, saliva, or semen.

[0314] In some embodiments, samples that can be used to measure FXN lipid profiles in the context of this disclosure may be selected from the group consisting of: buccal samples, skin samples, hair follicle and muscle biopsy samples. In one embodiment, the sample is a buccal sample. In another embodiment, the sample is a skin sample.

[0315] In some embodiments, samples that can be used to measure FXN lipid profiles in the context of this disclosure may be blood samples or blood-derived samples, such as whole plasma samples, serum samples, or platelet samples. In one embodiment, the sample is a plasma sample. In another embodiment, the sample is a platelet sample.

[0316] In some embodiments, samples that can be used to measure FXN lipid profiles can be obtained from FXN-deficient subjects before, during, or after administration of FXN replacement therapy. In some embodiments, samples can be obtained from FXN-deficient subjects at least 5 days after the last administration of FXN replacement therapy. In some embodiments, samples can be obtained from FXN-deficient subjects at least 10 days after the last administration of FXN replacement therapy. In some embodiments, samples can be obtained from FXN-deficient subjects at least 15 days after the last administration of FXN replacement therapy. In some embodiments, samples can be obtained from FXN-deficient subjects 5 to 25 days, 10 to 40 days, or 15 to 45 days after the last administration of FXN replacement therapy, for example, 5 to 15 days, 10 to 25 days, 15 to 20 days, 20 to 35 days, or 25 to 45 days after the last administration of FXN replacement therapy. In some embodiments, samples can be obtained from FXN-deficient subjects 20 to 25 days (e.g., 20, 21, 22, 23, or 25 days) after the last administration of FXN replacement therapy. In some embodiments, samples may be obtained from subjects lacking FXN at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 days after the last administration of FXN replacement therapy.

[0317] Consideration is given to any commercial apparatus or system for separating and / or obtaining tissues and / or blood or other biological products and / or for processing said materials prior to conducting a detection reaction.

[0318] Detection and / or measurement of FSLM

[0319] Various methods can be used to measure the distance between lipid eigenvectors. Once the data is normalized, the distance can be obtained, for example, by calculating the mean squared error, which can be extracted from the difference in the level of each gene measured in two different spectra (such as, for example, baseline FXN(-) and FXN alternative). Alternatively, the distance can be obtained by calculating the correlation coefficient or applying a t-test.

[0320] This disclosure considers any suitable means, techniques, and / or procedures for detecting and / or measuring the FSLMs disclosed herein. For example, liquid chromatography-mass spectrometry (LC-MS) can be used to measure FSLM levels in a sample; LC-MS is an analytical chemistry technique that combines the physical separation capabilities of liquid chromatography with the mass analysis capabilities of mass spectrometry. LC-MS is a powerful technique with very high sensitivity, making it suitable for separating, generally detecting, and potentially identifying specific quantities of chemicals in the presence of other chemicals (i.e., in complex mixtures). LC-MS includes targeted LC-MS and untargeted LC-MS. Targeted LC-MS can be performed when standards required for the quantification of the target analyte are available. Alternatively, if standards for the target analyte are not commercially available, alternative analytes can be used to facilitate the quantification of the target analyte. Examples of alternative analytes include, but are not limited to, stable isotope-labeled standards of target analytes, such as TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG51:1, TG51:2, TG51:3, TG51:4, TG52:3, TG52 :5, TG53:2, TG53:3, TG53:4, TG54:5, TG54:6, TG54:7, CE16:0, CE20:5, PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:5), PCO-36:3, PCO-34:2, PCO-40:2, PCO-44:7 or PC(O-17:0 / 20:4) stable isotope-labeled analogues.

[0321] Exemplary workflows that can be used in the context of this disclosure for detecting and measuring lipid levels are described, for example, in Forest et al., J. of Proteome Research 2018, 17(11):3657-3670 and Wu et al., Advanced Drug Delivery Reviews 2020, 159:294-307, the entire contents of which are hereby incorporated herein by reference.

[0322] Ataminant replacement therapy

[0323] In some aspects, the methods provided in this disclosure refer to determining a lipid profile associated with FXN replacement therapy. FXN replacement therapy involves administering to a subject in need a therapeutic compound, such as an FXN replacement agent, capable of increasing FXN levels in the subject. Various alternatives for delivering exogenous FXN are conceivable. FXN replacement agents can be delivered via FXN protein delivery or via delivery of nucleic acids (e.g., nucleic acids encoding FXN) capable of increasing FXN levels in a subject. FXN protein delivery can be the delivery of full-length FXN or the delivery of an FXN fusion protein.

[0324] In some embodiments, FXN replacement therapy comprises administering a nucleic acid to a subject in need of this treatment, which can increase FXN levels in the subject. In some embodiments, the nucleic acid may be a nucleic acid encoding FXN, such as FXN mRNA. In some embodiments, the nucleic acid may be an antisense oligonucleotide, such as an antisense oligonucleotide that activates FXN protein expression as described, for example, Li et al., Nucleic Acid Ther. 2018, 28(1):23–33 or Mikaeili et al., Scientific Reports 2018, 8:17217, the entire contents of which are hereby incorporated herein by reference. In some embodiments, the nucleic acid may be siRNA that can activate FXN protein expression, such as Shen et al., Bioorganic & Medicinal Chemistry Letters 2018, 28(17):2850-2855, the entire contents of which are hereby incorporated herein by reference.

[0325] In some embodiments, FXN replacement therapy includes administration of an FXN fusion protein. As used herein, the term "FXN fusion protein" refers to an FXN or FXN fragment fused to a full-length or fragmented form of a different protein or to a peptide. In some embodiments, the FXN fusion protein comprises a polypeptide containing FXN, such as full-length hFXN (SEQ ID NO:1) or mature hFXN (SEQ ID NO:2). The full-length hFXN protein (amino acids 1-210) has the amino acid sequence of SEQ ID NO:1.

[0326]

[0327] In the mitochondrial matrix, the full-length hFXN protein is cleaved at amino acid 81, resulting in the mature form of FXN with a predicted molecular weight of 130 aa and 14.2 kDa (SEQ ID NO:2).

[0328]

[0329] The full-length hFXN (SEQ ID NO:1) contains mature hFXN (SEQ ID NO:2) and a mitochondrial targeting sequence (MTS) with the amino acid sequence MWTLGRRAVAGLLASPSPAQAQTLTRVPRPAELAPLCGRRGLRTD IDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRK (SEQ ID NO:3).

[0330] In some embodiments, the FXN fusion protein further comprises a cell-penetrating peptide (CPP). As used herein, the term "cell-penetrating peptide" or "CPP" refers to a short peptide sequence, typically between 5 and 30 amino acids in length, that facilitates cellular uptake of various molecular cargoes, such as proteins. In the context of this disclosure, the presence of a CPP in the FXN fusion protein facilitates the delivery of the FXN fusion protein to cells, such as recipient cells. The CPP can be polycationic, i.e., its amino acid composition contains a relatively high abundance of positively charged amino acids, such as lysine or arginine. The CPP can also be amphiphilic, i.e., having a sequence containing alternating patterns of polar / charged amino acids and nonpolar hydrophobic amino acids. The CPP can also be hydrophobic, i.e., containing only nonpolar residues with a low net charge, or having hydrophobic amino acid groups essential for cellular uptake.

[0331] The CPPs that may be included in the FXN fusion protein can be any CPP known to those skilled in the art. For example, a CPP can be any CPP listed in the Cell Penetrating Peptide Database CPPsite 2.0, the entire contents of which are hereby incorporated by reference. For example, a CPP useful in the context of this disclosure can be a cell penetrating peptide derived from a protein selected from the group consisting of: transactivator of HIV transcription peptides (HIV-TAT), glycopropyl peptide, wasp venom, transporter, membrane-penetrating peptide, polyarginine, VP22, transporter, amphiphilic peptides such as MAP, KALA, ppTG20, proline-rich peptides, MPG-derived peptides, Pep-1 and oligomers, arginine-rich peptides, and calcitonin-derived peptides.

[0332] In some embodiments, the CPP of this disclosure comprises a TAT protein domain comprising amino acids 47 to 57 of the full-length HIV-TAT protein of 86 amino acids (this 11-amino acid peptide may also be referred to herein as "HIV-TAT"; SEQ ID NO:4). In one embodiment, the CPP consists of HIV-TAT (SEQ ID NO:4). In some embodiments, the CPP comprises amino acids 47 to 57 of the full-length HIV-TAT protein of 86 amino acids, with a methionine (12AA; "HIV-TAT+M") added at the amino terminus for initiation: MYGRKKRRQRRR (SEQ ID NO:5). Table 1 below lists the amino acid sequences of exemplary CPPs.

[0333] Table 1. Exemplary CPPs and Corresponding Sequences

[0334]

[0335]

[0336] In some embodiments, the CPP included in the FXN fusion protein is HIV-TAT (SEQ ID NO:4). In some embodiments, the CPP included in the FXN fusion protein is HIV-TAT+M (SEQ ID NO:5). In some embodiments, the FXN fusion protein includes full-length FXN (e.g., SEQ ID NO:1) and HIV-TAT (e.g., SEQ ID NO:4) as CPPs. In some embodiments, the FXN fusion protein includes full-length FXN (e.g., SEQ ID NO:1) and HIV-TAT+M (e.g., SEQ ID NO:5) as CPPs.

[0337] In some embodiments, in the FXN fusion proteins of this disclosure, the CPP can be fused to an FXN (e.g., a full-length FXN) via a linker to form a single polypeptide chain. Examples of FXN fusion proteins include TAT-FXN fusion proteins, wherein a TAT or a TAT fragment can be directly or indirectly (via a linker) linked to the N-terminus or C-terminus of the FXN. In one specific example, the linker may comprise the amino acid sequence GG.

[0338] In some respects, the CPP (e.g., HIV-TAT) present in the FXN fusion protein of this disclosure facilitates the delivery of the FXN fusion protein into cells (e.g., cells that may be present in vitro, outside the body, or in a subject). Once inside the cell, the FXN fusion protein can be processed by cellular machinery to remove the CPP, such as HIV-TAT, from the FXN.

[0339] A specific example of the TAT-FXN fusion protein is referred to as the Exemplary FXN fusion protein. The Exemplary FXN fusion protein is a 24.9 kDa fusion protein currently being investigated as an FXN replacement therapy to restore FXN functional levels in the mitochondria of subjects with FRDA. The Exemplary FXN fusion protein comprises an HIV-TAT peptide linked to the N-terminus of the full-length hFXN protein. The mechanism of action of the Exemplary FXN fusion protein relies on the cell-penetrating ability of the HIV-TAT peptide to deliver the Exemplary FXN fusion protein into cells and subsequently process it into mature hFXN after translocation to the mitochondria. The Exemplary FXN fusion protein is described, for example, in US2021 / 0047378, the entire contents of which are hereby incorporated herein by reference. An exemplary FXN fusion protein contains the following amino acid sequence (224 amino acids): MYGRKKRRQRRRGGMWTLGRRAVAGLLASPSPAQAQTLTRVPRPAELAPLCGRRGLRTDIDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGKDA (SEQ ID NO:12).

[0340] FXN replacement can also be delivered via viral gene replacement, which can utilize retroviruses, lentiviruses, adeno-associated virus vectors, and adenoviruses. Alternatively, FXN replacement therapy can be achieved by upregulating the endogenous mutant FXN gene, which is expressed at varying levels in carriers of mutant FXN alleles depending on the number of GAA repeats.

[0341] FSLM Applications

[0342] Methods for evaluating the efficacy of FXN replacement therapy

[0343] In some aspects, this disclosure provides methods for evaluating and / or monitoring the efficacy of FXN replacement therapy in subjects. This disclosure further provides methods for determining whether a subject requires FXN replacement therapy or changes in FXN replacement therapy, such as determining whether FXN replacement therapy should be initiated, increased, decreased, or discontinued in the subject. In some embodiments, the method is performed by the subject using a sample obtained from the same subject or as a field test, and the results may be assessed by the subject or by a physician.

[0344] In some embodiments, this disclosure provides a method for evaluating the efficacy of atamin replacement therapy, the method comprising: (a) determining a baseline FSLM(-) lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy; (b) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (c) comparing the FXN-substituted lipid profile determined in step (b) with the baseline FXN(-) lipid profile determined in step (a); and (d) determining the efficacy of FXN replacement therapy based on the comparison in step (c).

[0345] In some embodiments, comparing an FXN alternative lipid profile with a baseline FXN(-) lipid profile includes comparing the amount of one or more FSLMs in the FXN alternative lipid profile with the lipid mass of the corresponding one or more FSLMs in the baseline FXN(-) lipid profile.

[0346] In some embodiments, this disclosure also provides a method for evaluating the efficacy of ataxin (FXN) replacement therapy, the method comprising: (a) determining an FXN-substituted lipid profile for one or more FXN-sensitive lipid markers (FSLMs) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy; (b) comparing the subject FXN-substituted lipid profile determined in step (a) with a reference FXN lipid profile for one or more FSLMs; and (c) determining the efficacy of the FXN replacement therapy based on the comparison in step (b). In some embodiments, the reference FXN lipid profile is a baseline FXN(-) lipid profile for one or more FSLMs. In some embodiments, the baseline FXN(-) lipid profile for one or more FSLMs is determined in samples obtained from FXN-deficient subjects prior to administration of FXN replacement therapy.

[0347] In some embodiments, comparing an FXN alternative lipid profile with a reference FXN lipid profile includes comparing the amount of one or more FSLMs in the FXN alternative lipid profile with the lipid mass of the corresponding one or more FSLMs in the reference FXN lipid profile.

[0348] In some embodiments, one or more FSLMs comprise one or more of TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE, or any combination thereof, as described herein. For example, one or more FSLMs may contain one or more TGs, wherein the three acyl groups in each TG molecule contain fewer than 56 carbon atoms, such as one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0349] In some embodiments, a reduction in the amount of one or more TGs in an FXN-alternative lipid profile compared to a reference FXN lipid profile (e.g., a baseline FXN(-) lipid profile) indicates effectiveness of the FXN-alternative therapy, wherein the three acyl groups in each TG molecule contain fewer than 56 carbon atoms (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG46 ...8:2, TG48:3, TG49:1, TG46:2, TG48:2, TG48:3, TG49:1, TG46:2, TG48:2, TG48:2, TG48:2, TG48:2, TG48:2, TG48:2, TG48:2, TG49:2, TG48:2, TG48:2, TG48:2, TG48:2, TG49:2, TG48:2, TG48:2, TG48:2, TG49:2, TG48:2, TG48:2, TG49:2, TG48:2, TG49:2, TG48:2, TG49:2, TG49:2, TG49:2, TG49:2, TG49:2, TG49:2, TG49:2, TG49: 49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52: 2. TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0350] In some embodiments, a reduction in the amount of one or more TGs in a sample obtained from an FXN-deficient subject after administration of FXN replacement therapy, compared to the amount of one or more FSLMs in a reference sample (e.g., a sample obtained from an FXN-deficient subject before administration of FXN replacement therapy), indicates that the FXN replacement therapy is effective, wherein each TG molecule contains fewer than 56 carbon atoms in its three acyl groups (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, T...). G48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, T G51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0351] In some embodiments, a reduction in the amount of one or more TGs in an FXN-alternative lipid profile compared to a reference FXN lipid profile (e.g., a baseline FXN(-) lipid profile) indicates effectiveness of the FXN-alternative therapy, wherein the three acyl groups in each TG molecule contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, T...). G49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52 :2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0352] In some embodiments, a reduction in the amount of TG in a sample obtained from an FXN-deficient subject after administration of FXN replacement therapy, compared to the amount of one or more FSLMs in a reference sample (e.g., a sample obtained from an FXN-deficient subject before administration of FXN replacement therapy), indicates that the FXN replacement therapy is effective, wherein the three acyl groups in each TG molecule contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:1, TG46:2, TG47:2, TG48:0, TG48:1, TG46:2, TG47:1, TG47:2, TG48:0, TG48:1, TG47:2 ... 48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, T G51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0353] Specifically, in some embodiments, a reduction in the amount of TG45:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG45:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0354] Specifically, in some embodiments, a reduction in the amount of TG46:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG46:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0355] Specifically, in some embodiments, a reduction in the amount of TG46:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG46:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0356] Specifically, in some embodiments, a reduction in the amount of TG47:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG47:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0357] Specifically, in some embodiments, a reduction in the amount of TG47:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG47:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0358] Specifically, in some embodiments, a reduction in the amount of TG48:0 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG48:0 in samples obtained from subjects before administration of FXN replacement therapy.

[0359] Specifically, in some embodiments, a reduction in the amount of TG48:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG48:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0360] Specifically, in some embodiments, a reduction in the amount of TG48:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG48:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0361] Specifically, in some embodiments, a reduction in the amount of TG48:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG48:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0362] Specifically, in some embodiments, a reduction in the amount of TG49:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG49:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0363] Specifically, in some embodiments, a reduction in the amount of TG49:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG49:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0364] Specifically, in some embodiments, a reduction in the amount of TG49:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG49:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0365] Specifically, in some embodiments, a reduction in the amount of TG49:4 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG49:4 in samples obtained from subjects before administration of FXN replacement therapy.

[0366] Specifically, in some embodiments, a reduction in the amount of TG50:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG50:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0367] Specifically, in some embodiments, a reduction in the amount of TG50:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG50:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0368] Specifically, in some embodiments, a reduction in the amount of TG50:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG50:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0369] Specifically, in some embodiments, a reduction in the amount of TG50:4 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG50:4 in samples obtained from subjects before administration of FXN replacement therapy.

[0370] Specifically, in some embodiments, a reduction in the amount of TG50:5 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG50:5 in samples obtained from subjects before administration of FXN replacement therapy.

[0371] Specifically, in some embodiments, a reduction in the amount of TG51:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG51:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0372] Specifically, in some embodiments, a reduction in the amount of TG51:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG51:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0373] Specifically, in some embodiments, a reduction in the amount of TG51:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG51:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0374] Specifically, in some embodiments, a reduction in the amount of TG51:4 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG51:4 in samples obtained from subjects before administration of FXN replacement therapy.

[0375] Specifically, in some embodiments, a reduction in the amount of TG52:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG52:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0376] Specifically, in some embodiments, a reduction in the amount of TG52:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG52:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0377] Specifically, in some embodiments, a reduction in the amount of TG52:4 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG52:4 in samples obtained from subjects before administration of FXN replacement therapy.

[0378] Specifically, in some embodiments, a reduction in the amount of TG52:5 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG52:5 in samples obtained from subjects before administration of FXN replacement therapy.

[0379] Specifically, in some embodiments, a reduction in the amount of TG52:6 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG52:6 in samples obtained from subjects before administration of FXN replacement therapy.

[0380] Specifically, in some embodiments, a reduction in the amount of TG53:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG53:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0381] Specifically, in some embodiments, a reduction in the amount of TG53:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG53:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0382] Specifically, in some embodiments, a reduction in the amount of TG53:4 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG53:4 in samples obtained from subjects before administration of FXN replacement therapy.

[0383] Specifically, in some embodiments, a reduction in the amount of TG53:5 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG53:5 in samples obtained from subjects before administration of FXN replacement therapy.

[0384] Specifically, in some embodiments, a reduction in the amount of TG54:4 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG54:4 in samples obtained from subjects before administration of FXN replacement therapy.

[0385] Specifically, in some embodiments, a reduction in the amount of TG54:5 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG54:5 in samples obtained from subjects before administration of FXN replacement therapy.

[0386] Specifically, in some embodiments, a reduction in the amount of TG54:6 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG54:6 in samples obtained from subjects before administration of FXN replacement therapy.

[0387] Specifically, in some embodiments, a reduction in the amount of TG54:7 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of TG54:7 in samples obtained from subjects before administration of FXN replacement therapy.

[0388] In some embodiments, an increase in the amount of one or more PCO- in the FXN alternative lipid profile compared to a reference FXN lipid profile (e.g., a baseline FXN(-) lipid profile) indicates effectiveness of the FXN replacement therapy. These PCO- include, for example, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), and PC(O-18:1 / 18:2). One or more of the following: / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, and PCO-46.8.

[0389] In some embodiments, an increase in the amount of one or more PCO- in a sample obtained from a subject lacking FXN after administration of FXN replacement therapy, compared to the amount of one or more FSLMs in a reference sample (e.g., a sample obtained from a subject lacking FXN prior to administration of FXN replacement therapy), indicates effectiveness of FXN replacement therapy. These PCO- include, for example, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(... O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-( 20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PC One or more of O-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.8.

[0390] In some embodiments, an increase in the amount of PC (O-16:0 / 14:0) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-16:0 / 14:0) in samples obtained from subjects before administration of FXN replacement therapy.

[0391] In some embodiments, an increase in the amount of PC (O-16:0 / 18:2) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-16:0 / 18:2) in samples obtained from subjects before administration of FXN replacement therapy.

[0392] In some embodiments, an increase in the amount of PC (O-16:0 / 20:3) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-16:0 / 20:3) in samples obtained from subjects before administration of FXN replacement therapy.

[0393] In some embodiments, an increase in the amount of PC (O-16:0 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-16:0 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0394] In some embodiments, an increase in the amount of PC (O-16:0 / 22:6) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-16:0 / 22:6) in samples obtained from subjects before administration of FXN replacement therapy.

[0395] In some embodiments, an increase in the amount of PC (O-17:0 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-17:0 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0396] In some embodiments, an increase in the amount of PC (O-18:0 / 18:1) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy, compared to the amount of PC (O-18:0 / 18:2) in samples obtained from subjects before administration of FXN replacement therapy, indicates that FXN replacement therapy is effective.

[0397] In some embodiments, an increase in the amount of PC (O-18:0 / 18:2) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-18:0 / 18:2) in samples obtained from subjects before administration of FXN replacement therapy.

[0398] In some embodiments, an increase in the amount of PC (O-18:0 / 22:6) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-18:0 / 22:6) in samples obtained from subjects before administration of FXN replacement therapy.

[0399] In some embodiments, an increase in the amount of PC (O-18:1 / 18:2) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-18:1 / 18:2) in samples obtained from subjects before administration of FXN replacement therapy.

[0400] In some embodiments, an increase in the amount of PC (O-18:1 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-18:1 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0401] In some embodiments, an increase in the amount of PC (O-18:1 / 20:5) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-18:1 / 20:5) in samples obtained from subjects before administration of FXN replacement therapy.

[0402] In some embodiments, an increase in the amount of PC (O-18:1 / 22:6) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-18:1 / 22:6) in samples obtained from subjects before administration of FXN replacement therapy.

[0403] In some embodiments, an increase in the amount of PC(O-(20:0 / 22:6)) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that FXN replacement therapy is effective, compared to the amount of PC(O-(20:0 / 22:6)) in samples obtained from subjects before administration of FXN replacement therapy.

[0404] In some embodiments, an increase in the amount of PC (O-20:1 / 22.6) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-20:1 / 22.6) in samples obtained from subjects before administration of FXN replacement therapy.

[0405] In some embodiments, an increase in the amount of PC (O-20:2 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-20:2 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0406] In some embodiments, an increase in the amount of PC (O-22:2 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-22:2 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0407] In some embodiments, an increase in the amount of PC (O-22:1 / 22:6) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-22:1 / 22:6) in samples obtained from subjects before administration of FXN replacement therapy.

[0408] In some embodiments, an increase in the amount of PC (O-22:2 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-22:2 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0409] In some embodiments, an increase in the amount of PC(O-(24:1 / 22:6)) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC(O-(24:1 / 22:6)) in samples obtained from subjects before administration of FXN replacement therapy.

[0410] In some embodiments, an increase in the amount of PC (O-24:2 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (O-24:2 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0411] In some embodiments, an increase in the amount of PCO-34:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that FXN replacement therapy is effective, compared to the amount of PCO-34:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0412] In some embodiments, an increase in the amount of PCO-36:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that FXN replacement therapy is effective, compared to the amount of PCO-36:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0413] In some embodiments, an increase in the amount of PCO-34:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that FXN replacement therapy is effective, compared to the amount of PCO-34:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0414] In some embodiments, an increase in the amount of PCO-38:3 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PCO-38:3 in samples obtained from subjects before administration of FXN replacement therapy.

[0415] In some embodiments, an increase in the amount of PCO-40:2 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PCO-40:2 in samples obtained from subjects before administration of FXN replacement therapy.

[0416] In some embodiments, an increase in the amount of PCO-40:6 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PCO-40:6 in samples obtained from subjects before administration of FXN replacement therapy.

[0417] In some embodiments, an increase in the amount of PCO-44:7 in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy, compared to the amount of PCO-44:7 in samples obtained from subjects before administration of FXN replacement therapy, indicates that FXN replacement therapy is effective.

[0418] In some embodiments, an increase in the amount of PCO-46.8 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PCO-46.8 in samples obtained from subjects before administration of FXN replacement therapy.

[0419] In some embodiments, a reduction in the amount of one or more PCs in an FXN alternative lipid profile compared to a reference FXN lipid profile (e.g., a baseline FXN(-) lipid profile) indicates that the FXN alternative therapy is effective. The PCs are selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, and PC42:7.

[0420] In some embodiments, a reduction in the amount of one or more PCs in a sample obtained from a subject lacking FXN after administration of FXN replacement therapy, compared to the amount of one or more FSLMs in a reference sample (e.g., a sample obtained from a subject lacking FXN prior to administration of FXN replacement therapy), indicates that the FXN replacement therapy is effective. The PCs are selected from the group consisting of: PC (15:0 / 20:3), PC (15:0 / 22:6), PC (16:0 / 14:0), PC (16:0 / 22:4), PC (16:1 / 16:0), PC (16:1 / 20:4), PC (16:1 / 22.5), PC (17:0 / 20:5), PC (18:0 / 20:3), PC (18:0 / 22:4), PC (18:1 / 20:3), PC (18:2 / 18:2), PC (20:4 / 15:0), PC40:6, PC42:7.

[0421] In some embodiments, a reduction in the amount of PC (15:0 / 20:3) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (15:0 / 20:3) in samples obtained from subjects before administration of FXN replacement therapy.

[0422] In some embodiments, a reduction in the amount of PC (15:0 / 22:6) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (15:0 / 22:6) in samples obtained from subjects before administration of FXN replacement therapy.

[0423] In some embodiments, a reduction in the amount of PC (16:0 / 14:0) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (16:0 / 14:0) in samples obtained from subjects before administration of FXN replacement therapy.

[0424] In some embodiments, a reduction in the amount of PC (16:0 / 22:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (16:0 / 22:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0425] In some embodiments, a reduction in the amount of PC (16:1 / 16:0) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (16:1 / 16:0) in samples obtained from subjects before administration of FXN replacement therapy.

[0426] In some embodiments, a reduction in the amount of PC (16:1 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (16:1 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0427] In some embodiments, a reduction in the amount of PC (16:1 / 22.5) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (16:1 / 22.5) in samples obtained from subjects before administration of FXN replacement therapy.

[0428] In some embodiments, a reduction in the amount of PC (17:0 / 20:5) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (17:0 / 20:5) in samples obtained from subjects before administration of FXN replacement therapy.

[0429] In some embodiments, a reduction in the amount of PC (18:0 / 20:3) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:0 / 20:3) in samples obtained from subjects before administration of FXN replacement therapy.

[0430] In some embodiments, a reduction in the amount of PC (18:0 / 22:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:0 / 22:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0431] In some embodiments, a reduction in the amount of PC (18:1 / 20:3) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:1 / 20:3) in samples obtained from subjects before administration of FXN replacement therapy.

[0432] In some embodiments, a reduction in the amount of PC (18:2 / 18:2) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:2 / 18:2) in samples obtained from subjects before administration of FXN replacement therapy.

[0433] In some embodiments, a reduction in the amount of PC (20:4 / 15:0) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (20:4 / 15:0) in samples obtained from subjects before administration of FXN replacement therapy.

[0434] In some embodiments, a reduction in the amount of PC40:6 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that FXN replacement therapy is effective, compared to the amount of PC40:6 in samples obtained from subjects before administration of FXN replacement therapy.

[0435] In some embodiments, a reduction in the amount of PC42:7 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that FXN replacement therapy is effective, compared to the amount of PC42:7 in samples obtained from subjects before administration of FXN replacement therapy.

[0436] In some embodiments, an increase in the amount of one or more PCs in an FXN alternative lipid profile compared to a reference FXN lipid profile (e.g., a baseline FXN(-) lipid profile) indicates that the FXN alternative therapy is effective. The PCs are selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0437] In some embodiments, an increase in the amount of one or more PCs in a sample obtained from a subject lacking FXN after administration of FXN replacement therapy, compared to the amount of one or more FSLMs in a reference sample (e.g., a sample obtained from a subject lacking FXN prior to administration of FXN replacement therapy), indicates that the FXN replacement therapy is effective. The PCs are selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0438] In some embodiments, an increase in the amount of PC (17:1 / 20:4) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (17:1 / 20:4) in samples obtained from subjects before administration of FXN replacement therapy.

[0439] In some embodiments, an increase in the amount of PC (18:2 / 18:3) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:2 / 18:3) in samples obtained from subjects before administration of FXN replacement therapy.

[0440] In some embodiments, an increase in the amount of PC (18:1 / 24:1) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:1 / 24:1) in samples obtained from subjects before administration of FXN replacement therapy.

[0441] In some embodiments, an increase in the amount of PC (18:2 / 20:5) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (18:2 / 20:5) in samples obtained from subjects before administration of FXN replacement therapy.

[0442] In some embodiments, an increase in the amount of PC (20:4 / 20:0) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of PC (20:4 / 20:0) in samples obtained from subjects before administration of FXN replacement therapy.

[0443] In some embodiments, a reduction in the amount of DG (18:1 / 18:2) in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of DG (18:1 / 18:2) in samples obtained from subjects before administration of FXN replacement therapy.

[0444] In some embodiments, a decrease in the amount of CE14:1 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of CE14:1 in samples obtained from subjects before administration of FXN replacement therapy.

[0445] In some embodiments, an increase in the amount of CE16:0 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of CE16:0 in samples obtained from subjects before administration of FXN replacement therapy.

[0446] In some embodiments, an increase in the amount of CE20:5 in samples obtained from subjects lacking FXN after administration of FXN replacement therapy indicates that the FXN replacement therapy is effective, compared to the amount of CE20:5 in samples obtained from subjects before administration of FXN replacement therapy.

[0447] In some embodiments of the methods provided herein, the absence of an increase or decrease in the amount of one or more FSLMs (e.g., one or more TGs, ether phospholipids (e.g., PCO- or PEO-), PCs, DGs, or CEs, or any combination thereof, as described herein, in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy compared to the amount of one or more FSLMs in a control sample (e.g., a sample from a subject lacking FXN replacement therapy prior to administration of FXN replacement therapy) indicates that the FXN replacement therapy is ineffective (e.g., ineffective at the current dose) and should be modified. For example, the FXN replacement therapy can be modified by increasing the dose and / or frequency of administration.

[0448] In some embodiments, the methods provided herein may further include monitoring a subject receiving FXN replacement therapy. In some embodiments, the detection of one or more FSLMs (e.g., one or more TGs, ether phospholipids (e.g., PCO- or PEO-), PCs, DGs, or CEs, or any combination thereof) in a second sample obtained from the subject after FXN replacement therapy administration, compared to the amount of one or more FSLMs in a first sample obtained from the subject before FXN replacement therapy administration, does not increase or decrease, indicating that FXN replacement therapy is ineffective and / or the subject is not responding to FXN replacement therapy. The method may further include the step of adjusting the FXN replacement therapy, for example, by increasing the dose and / or frequency of administration of the FXN replacement therapy.

[0449] In other embodiments, an increase or decrease in the lipid mass of one or more FSLMs (e.g., one or more TGs, ether phospholipids (e.g., PCO- or PEO-), PCs, DGs, or CEs, or any combination thereof) in a second sample obtained from the subject after administration of FXN replacement therapy, compared to the amount of one or more FSLMs in a first sample obtained from the subject before administration of FXN replacement therapy, indicates that FXN replacement therapy is effective and / or that the subject has responded to FXN replacement therapy. The method may further include the step of adjusting the FXN replacement therapy, for example, by reducing the dose and / or frequency of administration of the FXN replacement therapy or by discontinuing the therapy.

[0450] quantity

[0451] In some embodiments, after FXN replacement therapy, the amount of one or more TGs in subjects lacking FXN is reduced, wherein each TG molecule contains fewer than 56 carbon atoms or has 7 or fewer unsaturations. In some embodiments, one or more TGs are selected from the group consisting of: TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0452] In some embodiments, the amount of TG45:1 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG46:1 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG46:3 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG47:1 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG47:2 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG48:0 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG48:1 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG48:2 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG48:3 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG49:1 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG49:2 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG49:3 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG49:4 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG50:1 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG50:2 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG50:3 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG50:4 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG50:5 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG51:1 decreases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG51:2 decreases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG51:3 decreases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG51:4 decreases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG52:2 decreases after treatment with FXN-deficient subjects using FXN replacement therapy.In some embodiments, the amount of TG52:3 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG52:4 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG52:5 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG52:6 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG53:2 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG53:3 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG53:4 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG53:5 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG54:4 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG54:5 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG54:6 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of TG54:7 decreased after treatment with FXN-deficient subjects using FXN replacement therapy.

[0453] In some embodiments, following treatment with FXN replacement therapy, the levels of one or more PCO- groups increase in subjects lacking FXN. In some embodiments, one or more PCO- groups are selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5). , PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20 :4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7 and PCO-46.8.

[0454] In some embodiments, the level of PC (O-16:0 / 14:0) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-16:0 / 18:2) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-16:0 / 20:3) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-16:0 / 20:4) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-16:0 / 22:6) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-17:0 / 20:4) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-18:0 / 18:1) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (O-18:0 / 22:6) increases after subjects lacking FXN are treated with FXN replacement therapy. In some embodiments, the level of PC (O-18:0 / 18:2) increases after subjects lacking FXN are treated with FXN replacement therapy. In some embodiments, the level of PC (O-18:1 / 18:2) increases after subjects lacking FXN are treated with FXN replacement therapy. In some embodiments, the level of PC (O-18:1 / 20:4) increases after subjects lacking FXN are treated with FXN replacement therapy. In some embodiments, the level of PC (O-18:1 / 20:5) increases after subjects lacking FXN are treated with FXN replacement therapy. In some embodiments, the level of PC (O-18:1 / 22:6) increases after subjects lacking FXN are treated with FXN replacement therapy. In some embodiments, the amount of PC(O-(20:0 / 22:6) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC(O-20:1 / 22.6) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC(O-20:2 / 20:4) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC(O-22:2 / 20:4) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC(O-22:1 / 22:6) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC(O-22:2 / 20:4) increases after treatment with FXN-deficient subjects using FXN replacement therapy.In some embodiments, the amount of PC(O-(24:1 / 22:6) increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PCO-34:2 increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PCO-36:3 increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PCO-34:2 increases after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC(O-(24:1 / 22:6) increases after treatment with FXN-deficient subjects using FXN replacement therapy. Following treatment of subjects lacking FXN, the level of PCO-38:3 increased. In some embodiments, the level of PCO-40:2 increased after treatment of subjects lacking FXN with FXN replacement therapy. In some embodiments, the level of PCO-40:6 increased after treatment of subjects lacking FXN with FXN replacement therapy. In some embodiments, the level of PCO-44:7 increased after treatment of subjects lacking FXN with FXN replacement therapy. In some embodiments, the level of PCO-46:8 increased after treatment of subjects lacking FXN with FXN replacement therapy.

[0455] In some embodiments, following FXN replacement therapy, the amount of one or more PCs in subjects lacking FXN is reduced, the PCs being selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7.

[0456] In some embodiments, the amount of PC (15:0 / 20:3) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (15:0 / 22:6) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (16:0 / 14:0) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (16:0 / 22:4) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (16:1 / 16:0) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (16:1 / 20:4) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (16:1 / 22.5) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (17:0 / 20:5) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (18:0 / 20:3) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (18:0 / 22:4) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (18:1 / 20:3) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (18:2 / 18:2) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC (20:4 / 15:0) decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC40:6 decreased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the amount of PC42:7 decreased after treatment with FXN-deficient subjects using FXN replacement therapy.

[0457] In some embodiments, after FXN replacement therapy, the amount of one or more PCs in subjects lacking FXN increases, the PCs being selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0458] In some embodiments, the level of PC (17:1 / 20:4) increased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (18:2 / 18:3) increased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (18:1 / 24:1) increased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (18:2 / 20:5) increased after treatment with FXN-deficient subjects using FXN replacement therapy. In some embodiments, the level of PC (20:4 / 20:0) increased after treatment with FXN-deficient subjects using FXN replacement therapy.

[0459] In some embodiments, the amount of DG (18:1 / 18:2) was reduced after subjects lacking FXN were treated with FXN replacement therapy.

[0460] In some embodiments, the amount of CE14:1 is reduced after subjects lacking FXN are treated with FXN replacement therapy.

[0461] In some embodiments, the amount of CE16:0 increases after subjects lacking FXN are treated with FXN replacement therapy.

[0462] In some embodiments, the amount of CE20:5 increases after subjects lacking FXN are treated with FXN replacement therapy.

[0463] Methods for monitoring FXN replacement therapy

[0464] In some aspects, this disclosure also provides a method for monitoring treatment of a subject with FXN replacement therapy, the method comprising: (a) determining a first FXN replacement lipid profile in a first sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the first sample being obtained from an FXN-deficient subject at a first time point following administration of FXN replacement therapy to the subject; (b) determining a second FXN replacement lipid profile in a second sample for one or more FXN-sensitive lipid biomarkers (FSLMs), the second sample being obtained from the subject at a second time point later than the first time point; and (c) comparing the second FXN replacement lipid profile with the first FXN replacement lipid profile; thereby monitoring treatment of the subject with FXN replacement therapy.

[0465] In some embodiments, comparing the second FXN-substituted lipid profile with the first FXN-substituted lipid profile includes comparing the amounts of one or more FSLMs in the second FXN-substituted lipid profile with the amounts of the corresponding one or more FSLMs in the first FXN-substituted lipid profile.

[0466] In some embodiments, one or more FSLMs comprise one or more of TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE, or any combination thereof, as described herein. For example, one or more FSLMs may contain one or more TGs, wherein the three acyl groups in each TG molecule contain fewer than 56 carbon atoms, such as one or more of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:7.

[0467] In some embodiments, a reduction in the amount of one or more TGs in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates effectiveness of the FXN-alternative therapy, wherein each TG molecule contains fewer than 56 carbon atoms in its three acyl groups (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, T...). G49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, T G52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0468] In some embodiments, a reduction in the amount of one or more TGs in a second FXN-substituted lipid profile compared to a first FXN-substituted lipid profile indicates effectiveness of the FXN-substituted therapy, wherein each TG molecule contains 7 or fewer unsaturated acyl groups (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2). TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7). In some embodiments, the absence of a reduction in the amount of one or more TGs in a second FXN-substituted lipid profile compared to a first FXN-substituted lipid profile indicates ineffectiveness of the FXN-substituted therapy, wherein the three acyl groups in each TG molecule contain seven or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2). , TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0469] In some embodiments, an increase in the amount of one or more PCOs in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates effectiveness of the FXN-alternative therapy. These PCOs include, for example, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), and PC(O-18:1 / 20:4). PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22: In In some embodiments, the absence of an increase in the amount of one or more PCO- in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates ineffectiveness of the FXN-alternative therapy. These PCO- include, for example, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), and PC(O-18:1 / 20:4). , PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22 :2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.8.

[0470] In some embodiments, a reduction in the amount of one or more PCs in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates effectiveness of the FXN-alternative therapy. The PCs are selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, and PC42:7. In some embodiments, the absence of a reduction in the amount of one or more PCs in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates ineffectiveness of the FXN-alternative therapy. The PCs are selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, and PC42:7.

[0471] In some embodiments, an increase in the amount of one or more PCs in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates effectiveness of the FXN-alternative therapy. The PCs are selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0). In some embodiments, no increase in the amount of one or more PCs in a second FXN-alternative lipid profile compared to a first FXN-alternative lipid profile indicates ineffectiveness of the FXN-alternative therapy. The PCs are selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0472] In some embodiments, a reduction in the amount of DG (18:1 / 18:2) in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is effective. In some embodiments, no reduction in the amount of DG (18:1 / 18:2) in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is ineffective.

[0473] In some embodiments, a reduction in the amount of CE14:1 in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is effective. In some embodiments, no reduction in the amount of CE14:1 in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is ineffective.

[0474] In some embodiments, an increase in the amount of CE16:0 in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is effective. In some embodiments, no increase in the amount of CE16:0 in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is ineffective.

[0475] In some embodiments, an increase in the amount of CE20:5 in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is effective. In some embodiments, no increase in the amount of CE20:5 in the second FXN-substituted lipid profile compared to the first FXN-substituted lipid profile indicates that the FXN-substituted therapy is ineffective.

[0476] In some embodiments, the method for monitoring FXN replacement therapy further includes making a decision to maintain the FXN replacement therapy regimen based on the comparison in step (c) or recommending to a healthcare provider that the FXN replacement therapy regimen be maintained. In some embodiments, the method further includes making a decision to change the FXN replacement therapy regimen based on the comparison in step (c) or recommending to a healthcare provider that the FXN replacement therapy regimen be changed. In some embodiments, the method further includes making a decision to maintain the dose and / or frequency of FXN replacement therapy, increase the dose and / or frequency of FXN replacement therapy, or decrease the dose and / or frequency of FXN replacement therapy based on the comparison in step (c). In some embodiments, the method further includes, for example, recommending to a healthcare provider to maintain the dose and / or frequency of FXN replacement therapy, increase the dose and / or frequency of FXN replacement therapy, or decrease the dose and / or frequency of FXN replacement therapy based on the comparison in step (c).

[0477] For example, in some embodiments, the method includes continuing to administer an FXN alternative therapy regimen to the subject based on the comparison in step (c) (e.g., without changing the regimen, such as maintaining the dose and / or frequency of administration). In some embodiments, the method further includes changing the FXN alternative therapy regimen based on the comparison in step (c). In some embodiments, the method further includes administering the changed FXN alternative therapy regimen based on the comparison in step (c). In some embodiments, administering the changed FXN alternative therapy regimen includes administering an increased dose and / or frequency of FXN alternative therapy, or administering a decreased dose and / or frequency of FXN alternative therapy.

[0478] For example, a method for monitoring treatment of a subject with FXN replacement therapy may further include the step of: if the FXN replacement therapy is determined to be effective, continuing to administer the FXN replacement therapy to the subject without adjusting or reducing the dose and / or frequency of administration of the FXN replacement therapy. In other embodiments, a method for monitoring treatment of a subject with FXN replacement therapy may further include the step of: if the FXN replacement therapy is determined to be ineffective, adjusting the FXN replacement therapy by increasing the dose and / or frequency of administration of the FXN replacement therapy.

[0479] It should be understood that after administering FXN replacement therapy to subjects lacking FXN, the achieved FXN levels in the subjects may reach the desired or target levels of FXN, for example, similar to the FXN levels present in normal healthy subjects, or similar to the FXN levels present in hFXN heterozygotes. In this case, maintaining the dose and / or frequency of FXN replacement therapy is beneficial. Furthermore, maintaining the dose and / or frequency of FXN replacement therapy is beneficial when such desired FXN levels are achieved in the subjects and remain constant over time. It should also be understood that after administering FXN replacement therapy to subjects lacking FXN, the achieved FXN levels in the subjects may exceed the desired or target levels of FXN, for example, exceeding the FXN levels present in normal healthy subjects, or exceeding the FXN levels present in hFXN heterozygotes. In this case, reducing the dose and / or frequency of FXN replacement therapy is advantageous. Alternatively, the FXN levels achieved in subjects may be lower than the expected or target levels of FXN, for example, lower than the FXN levels present in normal healthy subjects, or lower than the FXN levels present in hFXN heterozygotes. In this case, increasing the dose and / or frequency of FXN replacement therapy is beneficial.

[0480] Therefore, a reduction in the amount of one or more TGs in the second FXN-alternative lipid profile compared to the first FXN-alternative lipid profile indicates that the dosage and / or administration schedule of FXN-alternative therapy should be maintained or reduced, wherein the three acyl groups in each TG molecule contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, T...). G49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52 :2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0481] In some embodiments, the amount of one or more TGs in a second FXN-alternative lipid profile that is not reduced compared to a first FXN-alternative lipid profile indicates that the dose and / or administration schedule of the FXN-alternative therapy should be maintained or increased, wherein each TG molecule contains three acyl groups with 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49 ... 1. TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG5 2:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0482] In some embodiments, an increase in the amount of one or more PCOs indicates that the dosage and / or administration schedule of the FXN replacement therapy should be maintained or reduced. These PCOs include, for example, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 18:2), PC(O-18:1 / 20:4 ... -18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.8.

[0483] In some embodiments, the amount of one or more PCOs does not increase, indicating that the dose and / or administration schedule of FXN replacement therapy should be maintained or increased. These PCOs include, for example, PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(... O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.8.

[0484] In some embodiments, a reduction in the amount of one or more PCs indicates that the dosage and / or administration schedule of the FXN replacement therapy should be maintained or reduced, the PC being selected from the group consisting of: PC (15:0 / 20:3), PC (15:0 / 22:6), PC (16:0 / 14:0), PC (16:0 / 22:4), PC (16:1 / 16:0), PC (16:1 / 20:4), PC (16:1 / 22.5), PC (17:0 / 20:5), PC (18:0 / 20:3), PC (18:0 / 22:4), PC (18:1 / 20:3), PC (18:2 / 18:2), PC (20:4 / 15:0), PC40:6, PC42:7.

[0485] In some embodiments, the amount of one or more PCs does not decrease, indicating that the dose and / or administration schedule of the FXN replacement therapy should be maintained or increased. The PCs are selected from the group consisting of: PC (15:0 / 20:3), PC (15:0 / 22:6), PC (16:0 / 14:0), PC (16:0 / 22:4), PC (16:1 / 16:0), PC (16:1 / 20:4), PC (16:1 / 22.5), PC (17:0 / 20:5), PC (18:0 / 20:3), PC (18:0 / 22:4), PC (18:1 / 20:3), PC (18:2 / 18:2), PC (20:4 / 15:0), PC40:6, PC42:7.

[0486] In some embodiments, an increase in the amount of one or more PCs in a second FXN alternative lipid profile compared to a first FXN alternative lipid profile indicates that the dose and / or administration schedule of the FXN alternative therapy should be maintained or reduced, wherein the PC is selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0487] In some embodiments, the absence of an increase in the amount of one or more PCs in a second FXN alternative lipid profile compared to a first FXN alternative lipid profile indicates that the dose and / or administration schedule of the FXN alternative therapy should be maintained or increased. The PCs are selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0488] In some embodiments, a reduction in the amount of DG (18:1 / 18:2) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy, compared to the amount of DG (18:1 / 18:2) in the first FXN replacement lipid profile and compared to the amount of DG (18:1 / 18:2) in the second FXN replacement lipid profile, indicates that the dose and / or administration schedule of FXN replacement therapy should be maintained or reduced.

[0489] In some embodiments, the amount of DG (18:1 / 18:2) in samples obtained from FXN-deficient subjects after administration of FXN replacement therapy is not reduced compared to the amount of DG (18:1 / 18:2) in the first FXN replacement lipid profile and compared to the amount of DG (18:1 / 18:2) in the second FXN replacement lipid profile, indicating that the dose and / or administration schedule of FXN replacement therapy should be maintained or increased.

[0490] In some embodiments, a reduction in the amount of CE14:1 in samples in a second FXN alternative lipid profile compared to a first FXN alternative lipid profile indicates that the dosage and / or administration schedule of the FXN alternative therapy should be maintained or reduced.

[0491] In some embodiments, the amount of CE14:1 in the second FXN alternative lipid profile is not reduced compared to the first FXN alternative lipid profile, indicating that the dose and / or administration schedule of the FXN alternative therapy should be maintained or increased.

[0492] In some embodiments, an increase in the amount of CE16:0 in the second FXN alternative lipid profile compared to the first FXN alternative lipid profile indicates that the dose and / or administration schedule of the FXN alternative therapy should be maintained or reduced.

[0493] In some embodiments, the fact that the amount of CE16:0 in the second FXN alternative lipid profile is not increased compared to the first FXN alternative lipid profile indicates that the dose and / or administration schedule of the FXN alternative therapy should be maintained or increased.

[0494] In some embodiments, an increase in the amount of CE20:5 in the second FXN alternative lipid profile compared to the first FXN alternative lipid profile indicates that the dose and / or administration schedule of the FXN alternative therapy should be maintained or reduced.

[0495] In some embodiments, the fact that the amount of CE20:5 in the second FXN alternative lipid profile is not increased compared to the first FXN alternative lipid profile indicates that the dose and / or administration schedule of the FXN alternative therapy should be maintained or increased.

[0496] The methods disclosed herein for evaluating the efficacy of coagulant replacement therapy or for detecting and / or measuring one or more FSLMs (e.g., TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE) involve the detection and / or quantification of one or more FSLMs using mass spectrometry (MS). During analysis using MS, FSLMs can be ionized and thereby converted into ionized FSLMs (e.g., positively charged ionized FSLMs or negatively charged ionized FSLMs). The ionization of FSLMs makes it possible to detect ionized FSLMs by identifying their corresponding m / z values ​​using MS. In some embodiments, tandem mass spectrometry (MS / MS) can be used to detect and / or quantify one or more FSLMs. During analysis using MS / MS, FSLMs can be ionized and subsequently fragmented in the mass spectrometer, thereby forming ionized FSLM fragments (e.g., positively charged ionized FSLM fragments or negatively charged ionized FSLM fragments). The ionization and fragmentation of FSLMs enable the detection and identification of ionized FSLMs by identifying the m / z of FSLM fragments using MS / MS. Therefore, the methods of this disclosure convert the FSLMs of this disclosure (e.g., TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE) into ionized FSLMs or ionized FSLM fragments. The formation of ionized FSLMs or ionized FSLM fragments is necessary to identify, detect, and / or quantify the presence of the FSLM of interest, and necessarily alters the physical characteristics and properties of the FSLM of interest due to the methods of this disclosure.

[0497] Exemplary methods for detecting the presence or absence of lipids in a biological sample or determining the amount of lipids (e.g., FSLM) in a biological sample involve obtaining a biological sample from a subject and performing liquid chromatography-mass spectrometry (LC / MS) on the biological sample. It should be understood that the methods provided herein for detecting lipids in a biological sample or determining the amount of lipids in a biological sample include the step of performing a determination.

[0498] In some embodiments, the same method is used to detect all FSLMs. In some embodiments, the same biological sample (e.g., the same bodily fluid or tissue) is used to detect all FSLMs. In some embodiments, various methods are used to detect different FSLMs. In some embodiments, FSLMs are detected in different biological samples. In some embodiments, the biological sample is a solid tissue sample, preferably a buccal sample, which may alternatively be a skin biopsy sample, skin band, hair follicle, muscle biopsy sample, or bodily fluid sample such as blood (including any blood product, such as whole blood, plasma, serum, or a specific type of blood cells), urine, saliva, or semen. In one embodiment, the biological sample is a skin sample. In one embodiment, the biological sample is a buccal sample. In one embodiment, the biological sample is a blood-derived sample, such as a plasma sample or a platelet sample.

[0499] FSLM levels can be detected based on absolute, normalized, or relative levels. Detection of absolute FSLM levels may be preferred when monitoring a subject's treatment or determining whether there are changes in the subject's FXN status. For example, the levels of one or more FSLMs can be monitored in subjects undergoing FXN replacement therapy at regular intervals, such as monthly. The regulation of the levels of one or more FSLMs over time can be monitored to observe trends in FSLM level changes. The FSLM levels disclosed herein may be higher than those in normal samples, but lower than previous levels, thereby indicating a lack of efficacy of FXN replacement therapy in the subject. Changes in FSLM levels may be more relevant to a subject's treatment decisions than the FSLM levels present in the population. Rapid changes in FSLM levels in subjects can indicate abnormal FXN levels, even if FSLM levels are within the normal range for the population.

[0500] As an alternative to making decisions based on absolute FSLM levels, decisions can be based on normalized FSLM levels. FSLM levels are normalized by correcting for absolute FSLM levels by comparing them to levels of non-FSLM lipids (e.g., lipids insensitive to FXN levels). This normalization allows comparisons of FSLM levels in one sample (e.g., from a subject lacking FXN) with FSLM levels in another sample (e.g., a normal sample), or between FSLM levels from samples from different sources.

[0501] Any of the FXN lipid profiles described herein may be part of one or more algorithms that can be used to analyze the FXN lipid profile of a sample and determine whether the sample represents a sample from a normal subject, a sample from a subject prior to FXN replacement therapy, or a sample from a subject after FXN replacement therapy. One or more algorithms may be used to analyze samples from subjects treated with FXN replacement therapy and determine whether the subject has responded effectively to the treatment and, therefore, whether they express spectral features of the FXN replacement lipid profile. Thus, the algorithm used to analyze the lipid profile of a sample may use any of the following: baseline FXN(-) lipid profile, FXN replacement lipid profile, or normal FXN lipid profile, or a combination of profiles. A sample with an FXN-characteristic lipid profile consistent with the baseline FXN(-) lipid profile represents the lack of effectiveness of FXN replacement therapy; a sample with an FXN lipid profile consistent with the FXN replacement lipid profile and / or normal FXN lipid profile represents the effectiveness of FXN replacement therapy. In one embodiment, a classifier may be applied to the FXN lipid profile obtained from a subject sample to obtain information about the sample, such as characterizing the state of the FXN lipid profile or defining whether FXN replacement therapy has been administered to the subject. Alternatively or additionally, a classifier may be applied to assess whether the FXN lipid profile of a subject's sample reaches a certain threshold required for FXN replacement therapy to be considered effective.

[0502] Methods for treating FXN deficiency

[0503] This disclosure also provides a method for treating a subject with a mitochondrial disease characterized by FXN deficiency, the method comprising determining an FXN lipid profile in a sample from the subject, and comparing the FXN lipid profile obtained from the sample with at least one of a normal FXN lipid profile, a baseline FXN(-) lipid profile, or an FXN replacement lipid profile. The sample may be further classified as having a normal FXN, a baseline FXN(-), or an FXN replacement profile. Using the comparison results of the sample FXN profile with the FXN profile described herein, a treatment regimen using FXN replacement therapy may be initiated, paused, or discontinued. Alternatively, the FXN replacement therapy dosage regimen may be modified (e.g., increased or decreased). In one embodiment, the method further comprises obtaining or providing a sample from a subject (e.g., a subject lacking FXN, such as a subject with FRDA).

[0504] In some embodiments, this disclosure provides a method for treating FXN deficiency, the method comprising: (a) determining an FXN lipid profile for one or more FXN-sensitive lipid biomarkers (FSLMs) in a sample obtained from a subject lacking FXN; (b) comparing the FXN lipid profile of the sample with at least one other lipid profile selected from the group consisting of a normal FXN lipid profile for one or more FSLMs, a baseline FXN(-) lipid profile for one or more FSLMs, and an FXN alternative lipid profile for one or more FSLMs; (c) classifying the FXN lipid profile determined in step (a) as corresponding to a normal FXN lipid profile, a baseline FXN(-) lipid profile, or an FXN alternative lipid profile; and (d) maintaining, initiating, or modulating FXN replacement therapy based on the classification of the FXN lipid profile of the sample.

[0505] In some embodiments, adjusting the FXN replacement therapy includes increasing the dose of the FXN replacement therapy, decreasing the dose of the FXN replacement therapy, increasing the frequency of administration of the FXN replacement therapy, decreasing the frequency of administration of the FXN replacement therapy, or any combination thereof.

[0506] In some embodiments, one or more FSLMs comprise one or more of TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE, or any combination thereof, as described herein.

[0507] In some embodiments, when the amount of one or more TGs in a sample obtained from an FXN-deficient subject increases compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to a baseline FXN(-) lipid profile in which the three acyl groups in each TG molecule contain fewer than 56 carbon atoms or contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2). , TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG5 1:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0508] In some embodiments, when compared with the amount in the normal FXN lipid profile, one or more PCO- (e.g., PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 20:5), PC(O-18:1 / 20:5), PC(O-18:1 / 20:6), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 20:6 ... When the amounts of / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22:6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.8 decrease, the FXN lipid profile determined in step (a) is classified as corresponding to the baseline FXN(-) lipid profile.

[0509] In some embodiments, when the amount of one or more PCs in a sample obtained from a subject lacking FXN increases compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to a baseline FXN(-) lipid profile, wherein the PC is selected from the group consisting of: PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7.

[0510] In some embodiments, when the amount of one or more PCs in a sample obtained from a subject lacking FXN is reduced compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to a baseline FXN(-) lipid profile, wherein the PC is selected from the group consisting of: PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5), and PC (20:4 / 20:0).

[0511] In some embodiments, when the amount of DG (18:1 / 18:2) in a sample obtained from a subject lacking FXN increases compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to the baseline FXN(-) lipid profile.

[0512] In some embodiments, when the amount of CE14:1 in a sample obtained from a subject lacking FXN increases compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to the baseline FXN(-) lipid profile.

[0513] In some embodiments, when the amount of CE16:0 in a sample obtained from a subject lacking FXN is reduced compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to the baseline FXN(-) lipid profile.

[0514] In some embodiments, when the amount of CE20:5 in a sample obtained from a subject lacking FXN is reduced compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to the baseline FXN(-) lipid profile.

[0515] In some embodiments, when the FXN lipid profile in the sample is classified as a baseline FXN(-) lipid profile, administration of FXN replacement therapy is initiated in subjects lacking FXN. In some embodiments, when the FXN lipid profile in the sample is classified as a baseline FXN(-) lipid profile and subjects lacking FXN are already receiving FXN replacement therapy, the FXN replacement therapy regimen is changed, for example, by increasing the dose and / or frequency of administration of the FXN replacement therapy.

[0516] In some embodiments, when the amount of any of the following in a sample obtained from a subject lacking FXN, such as TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE, as described herein, is unchanged compared to the amount in a normal FXN lipid profile, the FXN lipid profile determined in step (a) is classified as corresponding to a normal FXN lipid profile.

[0517] In some embodiments, when the FXN lipid profile in a sample is classified as a normal FXN lipid profile, administration of FXN replacement therapy is not initiated in subjects lacking FXN. In some embodiments, when the FXN lipid profile in a sample is classified as a normal FXN lipid profile and subjects lacking FXN have already received FXN replacement therapy, the FXN replacement therapy regimen is maintained (i.e., not changed), for example, maintaining the dose and / or frequency of FXN replacement therapy.

[0518] In some aspects, this disclosure also provides a method for treating FXN deficiency in a subject, the method comprising: (a) determining an FXN lipid profile against one or more FSLMs in a sample from an FXN-deficient subject; and (b) recommending, based on the subject's FXN lipid profile determined in step (a), to a healthcare provider the administration of an FXN replacement therapy to the subject. In some aspects, this disclosure also provides a method for treating FXN deficiency in a subject, the method comprising: (a) obtaining an FXN lipid profile against one or more FSLMs in a sample obtained from an FXN-deficient subject; and (b) administering an FXN replacement therapy to the subject based on the subject's FXN lipid profile.

[0519] In some embodiments, the method further includes comparing an FXN lipid profile of a sample against one or more FSGMs with at least one other lipid profile selected from the group consisting of a normal FXN lipid profile against one or more FSGMs, a baseline FXN(-) lipid profile against one or more FSGMs, and an FXN alternative lipid profile against one or more FSGMs. In some embodiments, the method further includes classifying the FXN lipid profile of a sample against one or more FSGMs into a profile corresponding to a normal FXN lipid profile against one or more FSGMs, a baseline FXN(-) lipid profile against one or more FSGMs, or an FXN alternative lipid profile against one or more FSGMs. In some embodiments, one or more FSLMs comprise one or more of TG, ether phospholipids (e.g., PCO- or PEO-), PC, DG, or CE, or any combination thereof, as described herein.

[0520] In some embodiments, when the amount of one or more TGs in a sample obtained from an FXN-deficient subject is increased compared to the amount in a normal FXN lipid profile, FXN replacement therapy is administered to the FXN-deficient subject, or a recommendation is made to a healthcare provider to administer FXN replacement therapy to an FXN-deficient subject, wherein each TG molecule contains three acyl groups with fewer than 56 carbon atoms or with 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG46:3, TG47:1, TG47:2, TG48:0, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG46:1, TG46:2, TG47:1, TG47:2, TG47:3 ... 48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51: 3. TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7). In some embodiments, when the amount of one or more TGs in a sample obtained from an FXN-deficient subject is increased compared to the amount in a normal FXN lipid profile, and the FXN-deficient subject is undergoing FXN replacement therapy, the FXN replacement therapy regimen is changed (e.g., the dose and / or frequency of administration is increased), or a recommendation is made to a healthcare provider to change the FXN replacement therapy regimen in a TG in which the three acyl groups in each TG molecule contain fewer than 56 carbon atoms or contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:3, TG47:46:46, TG46:46, TG47 ... 2. TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2 , TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0521] In some embodiments, FXN replacement therapy is not administered to FXN-deficient subjects when the amount of one or more TGs in a sample obtained from an FXN-deficient subject is not increased compared to the amount in a normal FXN lipid profile, or a recommendation is made to the healthcare provider not to administer FXN replacement therapy to FXN-deficient subjects in which the three acyl groups in each TG molecule contain fewer than 56 carbon atoms or contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0). TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51 :3,TG51:4,TG52:2,TG52:3,TG52:4,TG52:5,TG52:6,TG53:2,TG53:3,TG53:4,TG53:5,TG54:4,TG54:5,TG54:6 and TG54:7). In some embodiments, when the amount of one or more TGs in a sample obtained from an FXN-deficient subject is not increased compared to the amount in a normal FXN lipid profile, and the FXN-deficient subject is undergoing FXN replacement therapy, the FXN replacement therapy regimen is maintained (i.e., not changed), or a recommendation is made to a healthcare provider to maintain the FXN replacement therapy regimen in which the three acyl groups in each TG molecule contain fewer than 56 carbon atoms or contain 7 or fewer unsaturations (e.g., TG45:1, TG46:1, TG46:3, TG47:1, TG47:2). TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6 and TG54:7).

[0522] In some embodiments, when compared with the amount in the normal FXN lipid profile, one or more PCO- (e.g., PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-18:1 / 22:6), PC(O-18:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 22:6), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-18:1 / 22:6), PC(O-18:0 / 14:0), PC(O-16:0 / 18:2), PC(O-18:0 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 22:6), PC(O-18:0 / 18:2), PC(O-18:0 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-18:0 / 18:2), PC(O-1 When the amounts of -(20:0 / 22:6), PC(O-20:1 / 22:6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, and PCO-46.8 are reduced, FXN replacement therapy is administered to subjects lacking FXN, or a recommendation is made to a healthcare provider to administer FXN replacement therapy to subjects lacking FXN.In some embodiments, when compared to the amount in the normal FXN lipid profile, one or more PCO- (e.g., PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-20:0 / 22:6)) in samples obtained from subjects lacking FXN are present. If the amount of PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7, and PCO-46.8 is reduced, and the subject lacking FXN is undergoing FXN replacement therapy, then the FXN replacement therapy regimen should be changed (e.g., the dose and / or frequency of administration should be increased), or a recommendation to a healthcare provider to change the FXN replacement therapy regimen should be made.

[0523] In some embodiments, when compared with the amount in the normal FXN lipid profile, one or more PCO- (e.g., PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O...

Claims

1. A method for evaluating the efficacy of FXN replacement therapy, the method comprising: (a) determining a baseline FSLM(-) lipid profile for one or more FXN sensitive lipid markers (FSLM) in a sample obtained from a subject deficient in FXN prior to administration of said FXN replacement therapy; (b) determining a FXN replacement lipid profile for said one or more FXN sensitive lipid markers (FSLM) in a sample obtained from said FXN-deficient subject after administration of said FXN replacement therapy; (c) comparing the FXN replacement lipid profile determined in step (b) with the baseline FXN(-) lipid profile determined in step (a); and (d) determining the efficacy of the FXN replacement therapy based on the comparison in step (c); wherein the one or more FSLMs are selected from the group consisting of: triglycerides (TG) wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation; Ether phospholipids; Phosphatidylcholine (PC); Cholesteryl ester (CE); and Diacylceride (DG).

2. A method for evaluating the efficacy of FXN replacement therapy, the method comprising: (a) determining a FXN replacement lipid profile for one or more FXN sensitive lipid markers (FSLM) in a sample obtained from a subject deficient in FXN following administration of FXN replacement therapy; (b) comparing the subject's FXN surrogate lipid profile determined in step (a) to a reference FXN lipid profile for said one or more FSLMs; and (c) determining the efficacy of the FXN replacement therapy based on the comparison in step (b); wherein the one or more FSLMs are selected from the group consisting of one or more of the following: triglycerides (TG) wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation; Ether phospholipids; Phosphatidylcholine (PC); Cholesteryl ester (CE); and Diacylceride (DG).

3. The method of claim 2, wherein the reference FXN lipid profile is a baseline FXN(-) lipid profile for the one or more FSLMs.

4. The method of claim 3, wherein the baseline FXN(-) lipid profile for the one or more FSLMs is determined in a sample obtained from a subject deficient in FXN prior to administration of FXN replacement therapy.

5. The method of claim 4, further comprising determining a baseline FXN(-) lipid profile for the one or more FXN sensitive lipid markers (FSLM) in a sample obtained from the FXN-deficient subject prior to administration of the FXN replacement therapy.

6. The method of any one of claims 1 to 5, wherein the one or more FSLMs are selected from the group consisting of: one or more triglycerides (TGs), wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations.

7. The method of claim 6, wherein the one or more FSLMs are selected from the group consisting of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:

7.

8. The method of claim 7, wherein the one or more FSLMs are selected from the group consisting of TG48:1, TG48:2, TG49:1, TG49:2, TG49:4, TG50:1, TG50:3, TG51:1, TG51:2, TG51:3, TG52:3, TG53:2, and TG56:

8.

9. The method according to any one of claims 1 to 5, wherein the one or more FSLMs are selected from one or more ether phospholipids.

10. The method of claim 9, wherein the one or more ether phospholipids comprise one or more ether diacylglycerophosphocholine (PCO-).

11. The method of claim 10, wherein the one or more PCO- is selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.

8.

12. The method of claim 11, wherein the one or more PCO-s are selected from the group consisting of PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-18:1 / 18:2), PC(O-22:2 / 20:4) and PC(O-24:2 / 20:4).

13. The method of claim 9, wherein the one or more ether phospholipids comprise one or more phosphatidylethanolamine ethers (PEO-).

14. The method according to any one of claims 1 to 5, wherein the one or more FSLMs are selected from one or more phosphatidylcholines (PC).

15. The method of claim 14, wherein the one or more PCs are selected from the group consisting of PC (15:0 / 20:3), PC (15:0 / 22:6), PC (16:0 / 14:0), PC (16:0 / 22:4), PC (16:1 / 16:0), PC (16:1 / 20:4), PC (16:1 / 22.5), PC (17:0 / 20:5), PC (18:0 / 20:3), PC (18:0 / 22:4), PC (18:1 / 20:3), PC (18:2 / 18:2), PC (20:4 / 15:0), PC40:6 and PC42:

7.

16. The method of claim 15, wherein the one or more PCs are selected from the group consisting of: PC (15:0 / 22:6) and PC (16:0 / 14:0).

17. The method of claim 14, wherein the one or more PCs are selected from the group consisting of PC (17:1 / 20:4), PC (18:2 / 18:3), PC (18:1 / 24:1), PC (18:2 / 20:5) and PC (20:4 / 20:0). The method according to claim 17 , wherein the one or more PCs are PC(18:2 / 18:3).

19. The method according to any one of claims 1 to 5, wherein the one or more FSLMs are selected from one or more cholesteryl esters (CE).

20. The method of claim 19, wherein the one or more CEs are selected from the group consisting of: CE16:0 and CE20:

5.

21. The method of claim 19, wherein the one or more CEs are CE14:

1.

22. The method of any one of claims 1 to 5, wherein the one or more FSLMs are selected from one or more diglycerides (DG).

23. The method of claim 22, wherein the one or more DGs are DG18:1 / 18:

2.

24. The method of any one of claims 1 to 5, 9 to 14, and 17 to 20, wherein the amount of at least one or more FSLM in the subject is increased following treatment with FXN replacement therapy.

25. The method of claim 24, wherein the one or more FSLMs are selected from the group consisting of PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 22:6). (O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O- 22:2 / 20:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-3 4:2, PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7, PCO-46.8, PC(17:1 / 20:4), PC( 18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE16:0 and CE20:

5.

26. The method of any one of claims 1 to 8, 15 to 16, and 21 to 23, wherein the amount of at least one or more FSLM in the subject is reduced following treatment with FXN replacement therapy.

27. The method of claim 26, wherein the one or more FSLMs are selected from the group consisting of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4 , TG53:5, TG54:4, TG54:5, TG54:6, TG54:7, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16 :1 / 22.5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, DG18:1 / 18:2 and CE14:

1.

28. The method of any one of claims 1 to 27, wherein determining the lipid profile of FXN for one or more FSLM comprises determining the amount of the one or more FSLM.

29. The method of claim 28, wherein comparing the subject's FXN replacement lipid profile to the baseline FXN(-) lipid profile comprises comparing the amount of one or more FSLMs in the FXN replacement lipid profile to the corresponding amount of one or more FSLMs in the baseline FXN(-) lipid profile.

30. The method of claim 29, wherein the FXN replacement therapy is determined to be effective when the amount of one or more FSLMs in the FXN replacement lipid profile is increased compared to the baseline FXN(-) lipid profile, wherein the one or more FSLMs are selected from the group consisting of PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-20:0 / 22:6), PC(O-20:1 / 22:6). 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 2 0:4), PC(O-(24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6 and PCO-44:7, PCO-46.8, PC(17:1 / 20:4), PC(18 :2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5), PC(20:4 / 20:0), CE16:0 and CE20:

5.

31. The method of claim 29, wherein the FXN replacement therapy is determined to be effective when the amount of one or more FSLMs in the FXN replacement lipid profile is reduced compared to the baseline FXN(-) lipid profile, wherein the one or more FSLMs are selected from the group consisting of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG53:6 G54:4, TG54:5, TG54:6, TG54:7, PC(15:0 / 20:3), PC(15:0 / 22:6), PC(16:0 / 14:0), PC(16:0 / 22:4), PC(16:1 / 16:0), PC(16:1 / 20:4), PC(16:1 / 22 .5), PC(17:0 / 20:5), PC(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, DG18:1 / 18:2 and CE14:

1.

32. The method of any one of claims 1 to 31, wherein determining the FXN lipid profile for one or more FSLMs comprises determining a FXN lipid feature vector indicative of values ​​of lipids of the one or more FSLMs.

33. The method of claim 32, wherein determining the efficacy of the FXN replacement therapy comprises determining a first FXN lipid feature vector for the subject's FXN replacement lipid profile and a second FXN lipid feature vector for the baseline FXN(-) lipid profile, and determining a distance between the first lipid feature vector and the second lipid feature vector.

34. The method of claim 33, wherein determining the distance between the lipid feature vectors comprises determining a scalar product of the first lipid feature vector and the second lipid feature vector.

35. The method of any one of claims 33 to 34, further comprising determining a third lipid feature vector of a normal FXN lipid profile of the FSLM for healthy subjects.

36. The method of claim 35, further comprising determining a distance between the second lipid feature vector and the third lipid feature vector.

37. The method of claim 36, further comprising determining a distance between the first lipid characteristic vector and the third lipid characteristic vector, and normalizing the distance between the first lipid characteristic vector and the third lipid characteristic vector to the distance between the second lipid characteristic vector and the third lipid characteristic vector.

38. The method of claim 37, further comprising using the normalized distance to determine the effectiveness of the FXN replacement therapy.

39. The method of any one of claims 1 to 38, wherein the FXN lipid profile is determined by mass spectrometry.

40. The method of any one of claims 1 to 39, further comprising recommending to a healthcare provider to modify treatment with the FXN replacement therapy based on the determination of efficacy of the FXN replacement therapy.

41. The method of any one of claims 1 to 40, wherein the subject has Friedreich's ataxia (FRDA).

42. The method of any one of claims 1 to 41, further comprising obtaining a sample from the subject deficient in FXN.

43. The method of claim 45, wherein the sample is selected from the group consisting of a cheek sample, a skin sample, a hair follicle, or a blood-derived sample.

44. The method of claim 43, wherein the sample is a blood-derived sample.

45. The method of claim 44, wherein the blood-derived sample is a plasma sample.

46. ​​A method of monitoring treatment of a subject with FXN replacement therapy, the method comprising: (a) determining a first FXN replacement lipid profile for one or more FXN sensitivity lipid markers (FSLM) in a first sample obtained from a subject deficient in FXN at a first time point after administration of a FXN replacement therapy to the subject, (b) determining a second FXN surrogate lipid profile for the one or more FXN sensitivity lipid markers (FSLM) in a second sample obtained from the subject at a second time point later than the first time point; (c) comparing the second FXN replacement lipid profile to the first FXN replacement profile; thereby monitoring treatment of the subject with the FXN replacement therapy; wherein the one or more FSLMs are selected from the group consisting of one or more of the following: triglycerides (TG) wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation; Ether phospholipids; Phosphatidylcholine (PC); Cholesteryl ester (CE); and Diacylceride (DG).

47. The method of claim 46, further comprising making a decision to maintain, increase, or decrease the dosage or frequency of administration of the FXN replacement therapy based on the comparison in step (c).

48. The method of claim 46 or 47, wherein at least one dose of the FXN replacement therapy is administered to the subject between obtaining the first time point and the second time point.

49. The method of any one of claims 46 to 48, wherein the FXN replacement therapy is not administered to the subject between obtaining the first time point and the second time point.

50. The method of any one of claims 46 to 49, wherein the one or more FSLMs are selected from the group consisting of: one or more triglycerides (TGs), wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer unsaturations.

51. The method of claim 50, wherein the one or more FSLMs are selected from the group consisting of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:

7.

52. The method of any one of claims 46 to 49, wherein the one or more FSLMs are selected from one or more ether phospholipids.

53. The method of claim 52, wherein the one or more ether phospholipids comprise one or more ether diacylglycerophosphocholine (PCO-).

54. The method of claim 53, wherein the one or more PCO- is selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.

8.

55. The method of claim 52, wherein the one or more ether phospholipids comprise one or more phosphatidylethanolamine ethers (PEO-).

56. The method of any one of claims 46 to 49, wherein the one or more FSLMs are selected from one or more phosphatidylcholines (PC).

57. The method of claim 56, wherein the one or more PCs are selected from the group consisting of PC (15:0 / 20:3), PC (15:0 / 22:6), PC (16:0 / 14:0), PC (16:0 / 22:4), PC (16:1 / 16:0), PC (16:1 / 20:4), PC (16:1 / 22.5), PC (17:0 / 20: ...4), PC (17:0 / 20:5), PC (17:0 / 20:5), PC (17:0 / 20:4), PC (17:0 / 20:4), PC C(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5) and PC(20:4 / 20:0).

58. The method of any one of claims 46 to 49, wherein the one or more FSLMs are selected from one or more cholesteryl esters (CE).

59. The method of claim 58, wherein the one or more CEs are selected from the group consisting of: CE14:1, CE16:0, and CE20:

5.

60. The method of any one of claims 46 to 49, wherein the one or more FSLMs are selected from one or more diglycerides (DG).

61. The method of claim 60, wherein the one or more DGs are DG 18:1 / 18:

2.

62. A method for treating FXN deficiency, the method comprising: (a) determining the FXN lipid profile for one or more FXN sensitive lipid markers (FSLM) in a sample obtained from a subject deficient in FXN, (b) comparing the FXN lipid profile of the sample to at least one other lipid profile selected from the group consisting of a normal FXN lipid profile for the one or more FSLMs, a baseline FXN(-) lipid profile for the one or more FSLMs, and a FXN surrogate lipid profile for the one or more FSLMs, (c) classifying the FXN lipid profile determined in step (a) as corresponding to a normal FXN lipid profile, a baseline FXN(-) lipid profile, or a FXN replacement lipid profile, and (d) initiating or regulating FXN replacement therapy based on said classification of said FXN lipid profile of said sample.

63. The method of claim 62, wherein adjusting the FXN replacement therapy comprises increasing the dosage of the FXN replacement therapy, decreasing the dosage of the FXN replacement therapy, increasing the frequency of administration of the FXN replacement therapy, or decreasing the frequency of administration of the FXN replacement therapy.

64. The method of claim 62 or 63, wherein the subject lacking FXN suffers from Friedreich's ataxia (FRDA).

65. A method of treating FXN deficiency in a subject, the method comprising: (a) determining the FXN lipid profile for one or more FSLMs in a sample from a subject deficient in FXN; as well as (b) recommending to a healthcare provider that FXN replacement therapy be administered to the subject based on the subject's FXN lipid profile determined in step (a).

66. A method of treating FXN deficiency in a subject, the method comprising: (a) obtaining a FXN lipid profile for one or more FSLMs in a sample obtained from a subject deficient in FXN; as well as (b) administering a FXN replacement therapy to the subject based on the subject's FXN lipid profile.

67. The method of claim 65 or 66, further comprising obtaining the sample from the FXN-deficient subject for use in determining the FXN lipid profile for the one or more FSLMs.

68. A method for detecting one or more fraxin-sensitive lipid markers (FSLM) in a sample from a subject lacking fraxin (FXN), the method comprising The sample, or a portion thereof, is contacted with one or more reagents specific for detecting the level of each of the one or more FSLMs.

69. A method for detecting one or more fraxin-sensitive lipid markers (FSLM) in a sample from a subject lacking fraxin (FXN), the method comprising The sample or a portion thereof is analyzed by mass spectrometry.

70. The method of claim 68 or 69, wherein the subject is being treated with FXN replacement therapy or is planned to be treated with FXN replacement therapy.

71. The method of any one of claims 68 to 70, further comprising obtaining the sample from the subject deficient in FXN.

72. The method of any one of claims 62 to 71, wherein the one or more FSLMs are selected from the group consisting of: triglycerides (TG) wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation; Ether phospholipids; Phosphatidylcholine (PC); Cholesteryl ester (CE); and Diacylceride (DG).

73. The method of claim 72, wherein the one or more FSLMs are selected from the group consisting of: one or more triglycerides (TGs), wherein the three acyl groups in each triglyceride molecule contain less than 56 carbons and / or wherein the three acyl groups in each triglyceride molecule contain 7 or fewer degrees of unsaturation.

74. The method of claim 73, wherein the one or more FSLMs are selected from the group consisting of TG45:1, TG46:1, TG46:3, TG47:1, TG47:2, TG48:0, TG48:1, TG48:2, TG48:3, TG49:1, TG49:2, TG49:3, TG49:4, TG50:1, TG50:2, TG50:3, TG50:4, TG50:5, TG51:1, TG51:2, TG51:3, TG51:4, TG52:2, TG52:3, TG52:4, TG52:5, TG52:6, TG53:2, TG53:3, TG53:4, TG53:5, TG54:4, TG54:5, TG54:6, and TG54:

7.

75. The method of claim 72, wherein the one or more FSLMs are selected from one or more ether phospholipids.

76. The method of claim 75, wherein the one or more ether phospholipids comprise one or more ether diacylglycerophosphocholine (PCO-).

77. The method of claim 76, wherein the one or more PCO- is selected from the group consisting of: PC(O-16:0 / 14:0), PC(O-16:0 / 18:2), PC(O-16:0 / 20:3), PC(O-16:0 / 20:4), PC(O-16:0 / 22:6), PC(O-17:0 / 20:4), PC(O-18:0 / 18:1), PC(O-18:0 / 22:6), PC(O-18:0 / 18:2), PC(O-18:1 / 18:2), PC(O-18:1 / 20:4), PC(O-18:1 / 20:5), PC(O-18:1 / 22:6), PC(O-(20:0 / 22:6), PC(O-20:1 / 22.6), PC(O-20:2 / 20:4), PC(O-22:2 / 20:4), PC(O-22:1 / 22:6), PC(O-22:2 / 20:4), PC(O-24:1 / 22:6), PC(O-24:2 / 20:4), PCO-34:2, PCO-36:3, PCO-34:2, PCO-38:3, PCO-40:2, PCO-40:6, PCO-44:7 and PCO-46.

8.

78. The method of claim 75, wherein the one or more ether phospholipids comprise one or more phosphatidylethanolamine ethers (PEO-).

79. The method of claim 72, wherein the one or more FSLMs are selected from one or more phosphatidylcholines (PCs).

80. The method of claim 79, wherein the one or more PCs are selected from the group consisting of PC (15:0 / 20:3), PC (15:0 / 22:6), PC (16:0 / 14:0), PC (16:0 / 22:4), PC (16:1 / 16:0), PC (16:1 / 20:4), PC (16:1 / 22.5), PC (17:0 / 20:5), PC (18:0 / 20:6), PC (19:0 / 20:7), PC (21:0 / 20:8), PC (22:0 / 20:9), PC (23:0 / 20:10), PC (24:0 / 20:11), PC (25:0 / 20:12), PC (26:0 / 20:13), PC (27:0 / 20:14), PC (28:0 / 20:15), PC (29:0 / C(18:0 / 20:3), PC(18:0 / 22:4), PC(18:1 / 20:3), PC(18:2 / 18:2), PC(20:4 / 15:0), PC40:6, PC42:7, PC(17:1 / 20:4), PC(18:2 / 18:3), PC(18:1 / 24:1), PC(18:2 / 20:5) and PC(20:4 / 20:0).

81. The method of claim 72, wherein the one or more FSLMs are selected from one or more cholesteryl esters (CE).

82. The method of claim 81, wherein the one or more CEs are selected from the group consisting of: CE14:1, CE16:0, and CE20:

5.

83. The method of claim 72, wherein the one or more FSLMs are selected from one or more diglycerides (DG).

84. The method of claim 83, wherein the one or more DGs are DG 18:1 / 18:

2.

85. The method of any one of claims 46 to 84, wherein the FXN lipid profile is determined by mass spectrometry.

86. The method of any one of claims 46 to 85, wherein the subject suffers from Friedreich's ataxia (FRDA).

87. The method of any one of claims 46 to 86, further comprising obtaining a sample from the subject deficient in FXN.

88. The method of claim 87, wherein the sample is selected from the group consisting of a cheek sample, a skin sample, a hair follicle, or a blood-derived sample.

89. The method of claim 88, wherein the sample is a blood-derived sample.

90. The method of claim 89, wherein the blood-derived sample is a plasma sample.

91. The method of any one of claims 1 to 67 and 72 to 90, wherein the FXN replacement therapy comprises administering a FXN fusion protein.

92. The method of claim 91, wherein the FXN fusion protein comprises or consists of the amino acid sequence shown in SEQ ID NO:

12.

93. A kit for detecting one or more fraxin-sensitive lipid markers (FSLM) in a sample obtained from a subject lacking fraxin (FXN), the kit comprising one or more isotopically labeled lipids for use as internal standards in a mass spectrometry-based analysis for detecting one or more FSLMs in said sample, and A set of instructions for detecting the level of said one or more FSLMs in said sample from said subject by mass spectrometry.

94. The method of any one of claims 1 to 93, wherein the subject is a human.

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