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Title:
IMPROVING QUALITY OF MITOCHONDRIAL DNA MEASUREMENTS FOR USE IN ASSESSING MITOCHONDRIAL DYSFUNCTIONS
Document Type and Number:
WIPO Patent Application WO/2017/062992
Kind Code:
A1
Abstract:
A method for enhancing mitochondrial DNA data is described. The method includes providing data representing raw mitochondrial DNA (mtDNA) levels in a subject, either as an absolute value or a ratio to nuclear DNA (nuDNA); modifying the raw mtDNA data based on based on at least two of the following factors selected from the group consisting of: exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease-specific mutations, and reference values specific to that subject; and generating user-readable output reflective of the modified data.

Inventors:
CANTOR CHARLES (US)
DE JAGER ROBERT (US)
SANO TAKESHI (US)
PHILLIPS ANGELICA (US)
GIRTON BRUCE (US)
Application Number:
PCT/US2016/056473
Publication Date:
April 13, 2017
Filing Date:
October 11, 2016
Export Citation:
Click for automatic bibliography generation   Help
Assignee:
RETROTOPE INC (US)
International Classes:
A61B5/00; A61K31/12; A61P3/00; C07H21/00; C12Q1/68; G06F19/18
Foreign References:
US20100168051A12010-07-01
US20090181367A12009-07-16
US20140044692A12014-02-13
US20110144051A12011-06-16
US20140099648A12014-04-10
Other References:
KNEZ ET AL.: "1A.04: CORRELATES OF PERIPHERAL BLOOD MITOCHONDRIAL DNA COPY NUMBER IN A GENERAL POPULATION", J HYPERTENS., vol. 33, no. 1, June 2015 (2015-06-01), pages e2
PUENTE-MAESTU ET AL.: "Effects of exercise on mitochondrial DNA content in skeletal muscle of patients with COPD", THORAX., vol. 66, 20 November 2010 (2010-11-20), pages 121 - 127, XP055374611
Attorney, Agent or Firm:
DELANEY, Karoline (Martens Olson & Bear LLP,2040 Main Street 14th Floo, Irvine CA, US)
Download PDF:
Claims:
WHAT IS CLAIMED IS:

1 . A method for enhancing mitochondrial DNA data, comprising:

(a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject, either as an absolute value or a ratio to nuclear DNA (nuDNA);

(b) modifying the raw mtDNA data based on at least two factors selected from the group consisting of exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease-specific mutations, and reference values specific to that subject; and

(c) generating user-readable output reflective of the modified data.

2. The method of Claim 1 , wherein the subject has a mitochondrial deficiency disease and the modifying step further comprises comparing the data to one or more reference values for subjects not having mitochondrial deficiency disease.

3. The method of Claim 1 or 2, wherein the subject has a mitochondrial deficiency disease and the modifying step further comprises comparing the data to one or more reference values for subjects having the same mitochondrial deficiency disease.

4. The method of any one of claims 1-3, wherein the reference values for subjects not having mitochondrial deficiency disease is substantially greater than the reference values for subjects having the mitochondrial deficiency disease.

5. The method of any one of claims 1 -4, wherein the raw mtDNA data is from a subject who has undergone aerobic exercise within the previous 1 , 2, 3, 4, 5, 6, or 7 days.

6. The method of any one of claims 1 -4, wherein the raw mtDNA data is from a subject who has undergone anaerobic exercise to fatigue within the previous 1, 2, 3, 4, 5, 6, or 7 days.

7. The method of any one of claims 1-4, wherein the raw mtDNA data is from a subject who has not undergone anaerobic exercise to fatigue.

8. The method of any one of claims 1 -4, wherein the raw mtDNA data is from a subject who has not undergone anaerobic exercise to fatigue within the previous 1 , 2, 3, 4, 5, 6, or 7 days.

9. The method of any one of claims 1 -8, further comprising repeating steps (a) and (b) at least 2, 3, 4, 5, or more additional times and reflecting the data generated in step (b) for such repetitions in step (c).

10. The method of any one of claims 1-9, comprising including in the user- readable output of step (c) data reflecting change of mtDNA levels in the subject over time, adjusted for exercise status.

1 1 . The method of Claim 10, in which the data reflecting change of mtDNA levels in the subject over time data reflective of multiple time points while the subject was receiving a therapeutic agent to treat mitochondrial deficiency disease.

12. A method for assessing mitochondrial status, comprising:

determining the level of mitochondrial DNA (mtDNA) in a first sample from a subject who has or is at risk of mitochondrial dysfunction, either as a quantitative mtDNA value or as a ratio to a level of another component in the sample;

subjecting the subject to a treatment or a stress;

determining the level of mtDNA in a second sample of blood or serum from the subject, wherein the first sample was taken before the treatment or stress and the second sample was taken after the treatment or stress;

normalizing the first and second values modifying the raw mtDNA data based on at least two factors selected from the group consisting of exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease- specific mutations, and reference values specific to that subject; and

comparing the normalized first and second values to determine whether the treatment or stress caused an increase in cell death as reflected in an increase in mtDNA levels, or a decrease in cell death as reflected in a decrease in mtDNA levels.

13. The method of Claim 12, wherein the sample is selected from plasma, blood cell, serum, tissue, saliva, mucus, buffy coat, buccal swab, and any other bodily fluid.

14. The method of Claim 12 or 13, wherein the treatment or stress is exercise to fatigue.

15. The method of Claim 12 or 13, wherein the treatment or stress is administration of a therapeutic agent for mitochondrial dysfunction.

16. The method of any one of claims 12-15, wherein the mitochondrial status is Friedreich's Ataxia, Parkinson's Disease, Alzheimer's Disease, ischemic heart disease, dementia, Huntington's disease, Amyotrophic lateral sclerosis, cytochrome c oxidase deficiency, autosomal dominant progressive external ophthalmoplegia, Leber's Hereditary Optic Neuropathy, mitochondrial myopathy, diabetes mellitus and deafness, leigh syndrome, myoneurogenic gastrointestinal encephalopathy, myoclonic epilepsy with ragged red fibers, and mitochondrial neurogastrointestinal encephalomyopathy.

17. The method of any one of claims 12 - 16, comprising determining the ratio of mtDNA to nuclear DNA (nuDNA).

18. The method of any one of claims 12- 16, comprising determining the absolute level of the mtDNA.

19. The method of Claim 17 or 18, wherein the absolute level of mtDNA or the ratio of mtDNA to nuDNA is determined using mass spectrometry, PCR, or a combination thereof.

20. The method of any one of claims 12 -19, further comprising characterizing the mitochondrial status of the subject as deficient when the ratio of mtDNA to nuclear DNA(nuDNA) measured prior to treatment or stress is at least 20% greater than the ratio measured after the treatment or stress.

21 . The method of any one of claims 12-19, further comprising characterizing the mitochondrial status of the subject as deficient when the ratio of mtDNA to nuclear DNA(nuDNA) measured prior to treatment or stress is at least 20% less than the ratio measured after the treatment or stress.

22. The method of any one of claims 12-19, further comprising characterizing the mitochondrial status of the subject as deficient when the absolute level of mtDNA measured prior to treatment or stress is at least 20% greater than the absolute level of mtDNA measured after the treatment or stress.

23. The method of any one of claims 12-19, further comprising characterizing the mitochondrial status of the subject as deficient when the ratio of mtDNA/nuDNA measured after the treatment or stress is substantially greater than the ratio of mtDNA/nuDNA measured prior to treatment or stress.

24. The method of any one of claims 12-19, further comprising characterizing the treatment or stress as effective when the ratio of mtDNA/nuDNA measured after treatment or stress is substantially greater than the ratio of mtDNA/nuDNA measured prior to the treatment or stress.

25. The method of any one of claims 12-24, wherein the treatment comprises: administering an effective amount of a polyunsaturated substance to a patient having an impaired energy processing disorder or mitochondrial deficiency and in need of treatment, wherein the polyunsaturated substance is chemically modified such that one or more bonds is stabilized against oxidation;

wherein the polyunsaturated substance or a polyunsaturated metabolite thereof comprising said one or more stabilized bonds is incorporated into the patient's body following administration

26. The method of Claim 12, wherein the polyunsaturated substance is selected from the group consisting of a fatty acid, fatty acid ester, fatty acid thioester, fatty acid amide, fatty acid mimetic, and fatty acid prodrug, each isotopically modified at one or more positions..

27. A method for treating a patient having or at risk of mitochondrial dysfunction, comprising:

administering a therapeutic agent to the patient for mitochondrial dysfunction; determining the effect of such administration on levels of mitochondrial DNA (mtDNA) or the ratio of mtDNA to nuclear DNA in the blood or serum of the patient by comparing said levels after said administration to said levels before said administration; and tailoring therapy delivered to the patient to decrease levels of mtDNA or increase in the ratio of mtDNA/nuDNA in the blood or serum of the patient, by increasing or terminating administration of the therapeutic agent where suitable decrease in levels of mtDNA or increase in the ratio of mtDNA/nuDNA is not achieved; continuing administration of the therapeutic agent where suitable decrease in levels of mtDNA or increase in the ratio of mtDNA/nuDNA is achieved; or reducing the administration of the therapeutic agent to the patient where the decrease in levels of mtDNA or increase in the ratio of mtDNA/nuDNA achieved supports such reduction.

28. The method of claim 27, wherein a substantial increase in the ratio of mtDNA/nuDNA after the treatment or stress with the treatment or stress is indicative that the therapeutic agent is effective.

29. The method of claim 27, comprising continuing or increasing the administration of the therapeutic agent to the patient when a substantial increase in the ratio of mtDNA/nuDNA is observed after the administration.

30. A method of assessing status of mitochondrial deficiency disease in a subject, comprising:

(a) providing data representing raw mitochondrial DNA (mtDNA) levels either as an absolute value or a ratio to nuclear DNA (nuDNA) in a subject;

(b) normalizing the raw mtDNA data based on at least two of the following factors selected from the group consisting of: exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease-specific mutations, and reference values specific to that subject to provide a normalized mtDNA value; and

(c) deducing the status of the mitochondrial deficiency disease in the subject based on the normalized mtDNA value.

31. The method of claim 30, further comprising: performing step (a) and step (b) on one or more healthy subject having no mitochondrial deficiency disease;

establishing a reference range based on the normalized mtDNA values obtained from the one or more healthy subject.

32. The method of claim 30, wherein the deducing step further comprises comprising the normalized mtDNA value with the reference range.

33. The method of claim 32, further comprising determining that the subject has no mitochondrial deficiency disease when the normalized mtDNA value falls within the reference range.

34. The method of claim 32, further comprising determining the severity and progression of the mitochondrial deficiency disease in the subject based on the difference between the normalized mtDNA value of the subject and the reference range.

35. A method for treating a mitochondrial deficiency disease in a subject comprising:

ascertaining whether the subject has a mitochondrial DNA level that is substantially lower than the mitochondrial DNA level in a healthy subject; and if so administering a polyunsaturated substance to the subject.

36. The method of claim 35, wherein the ascertaining step comprises requesting a test providing the results of an analysis to determine the mitochondrial DNA level in the subject.

37. The method of claim 36, wherein the level of the mitochondrial DNA is ascertained as a ratio of the mitochondrial DNA to nuclear DNA.

38. The method of claim 36, wherein the level of the mitochondrial DNA is ascertained as the absolute amount of the mitochondrial DNA.

39. The method of any one of claims 35-38, wherein the polyunsaturated substance is selected from the group consisting of a fatty acid, fatty acid ester, fatty acid thioester, fatty acid amide, fatty acid mimetic, and fatty acid prodrug, each isotopically modified at one or more positions.

40. The method of any one of claims 35-39, wherein the mitochondrial deficiency disease is ataxia.

41 . The method of any one of claims 35-40, wherein the mitochondrial DNA level increases over time after the administration of the polyunsaturated substance to the subject.

42. The method of any one of claims 35-41 , further comprising continuing or increasing the administration of the polyunsaturated substance to the subject after an increase in mitochondrial DNA level is observed over a one-month period.

43. The method of any one of claims 35-41, further comprising terminating the administration of the polyunsaturated substance to the subject after no increase in mitochondrial DNA level is observed over a one-month period.

44. The method of any one of claims 35-40, wherein the mitochondrial DNA level decreases over time after the administration of the polyunsaturated substance to the subject.

45. The method of any one of claims 35-41 , further comprising continuing or increasing the administration of the polyunsaturated substance to the subject after an decrease in mitochondrial DNA level is observed over a one-month period.

46. The method of any one of claims 35-41, further comprising terminating the administration of the polyunsaturated substance to the subject after no decrease in mitochondrial DNA level is observed over a one-month period.

Description:
IMPROVING QUALITY OF MITOCHONDRIAL DNA MEASUREMENTS FOR USE IN ASSESSING MITOCHONDRIAL DYSFUNCTIONS

INCORPORATION BY REFERENCE TO ANY PRIORITY APPLICATIONS

[0001] Any and all priority claims identified in the Application Data Sheet, or any correction thereto, are hereby incorporated by reference. This application claims the benefit of U.S. Provisional Application No. 62/239156, filed October 8, 2015. The aforementioned application is incorporated by reference herein in its entirety, and is hereby expressly made a part of this specification.

BACKGROUND

Field

[0002] The present disclosure relates generally to methods for improving the quality of mitochondrial DNA measurements in connection with screening, prognosis, and monitoring treatment of diseases or disorders associated with a deficiency in mitochondrial function.

Description of the Related Art

[0003] Mitochondrial DNA (mtDNA) is found in eukaryotes and differs from nuclear DNA (nuDNA) in its location, its sequence, its quantity in the cell, and its mode of inheritance. The essential role of mitochondria is the generation of the cellular fuel, adenosine triphosphate (ATP), which fires cellular metabolism. Significantly, mitochondria are dependent on seventy nuclear-encoded proteins to accomplish the oxidation and reduction reactions necessary to this vital function, in addition to the thirteen polypeptides encoded in the mitochondrial genome. Different tissues and organs depend on oxidative phosphorylation to a varied extent. Moreover, mutations in the mitochondrial genome are associated with a variety of chronic, degenerative diseases. Diseases related to defective oxidative phosphorylation (OXPHOS) appear to be closely linked to mtDNA mutations. Consequently as OXPHOS diminishes due to increased severity of mtDNA mutations, organ-specific energetic thresholds are exceeded which give rise to a variety of clinical phenotypes.

[0004] Diagnosis of mitochondrial dysfunction has so far been based on the following detection systems. Various DNA-based detection/screening methods are commonly used for mutations in nuclear and mitochondrial DNAs. There are methods to determine enzymatic activities of mitochondrial proteins, such as enzymatic activities of the respiratory chain or FiFo-ATP synthase and various histological methods allowing staining of enzymes of the respiratory chain complexes. Evaluation of the ultrastructure of mitochondria is done by electron microscopy. These methods are very laborious, difficult to automate, too specialized (for only single defects), not robust, not easy to perform, or require large amounts and difficult to get tissue samples. Methods employed in the art mostly determine isolated mitochondrial activities and do not allow a simple and general evaluation of the functionality of mitochondria. Mostly a variety of methods have to be performed and evaluated in a combined fashion to give a general diagnostic overview of mitochondrial function. There is currently no clinically predictive known biomarker for mitochondrial diseases. There is currently no treatment that will cure or delay progression of these mitochondrial diseases. Thus, there is a need to find disease markers that can help diagnose the disease, follow its progression, and monitor the effects of treatment.

SUMMARY

[0005] Some embodiments relate to a method for enhancing mitochondrial DNA data, comprising: (a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject, either as an absolute value or a ratio to nuclear DNA (nuDNA); (b) modifying the raw mtDNA data based on at least two factors selected from the group consisting of exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease-specific mutations, and reference values specific to that subject; and (c) generating user-readable output reflective of the modified data.

[0006] Some embodiments relate to a method for enhancing mitochondrial DNA data, comprising: (a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject, either as an absolute value or a ratio to nuclear DNA (nuDNA); and (b) generating user-readable output reflective of the modified data. [0007] Some embodiments relate to a method for assessing mitochondrial status, comprising:

determining the level of mitochondrial D A (mtDNA) in a first sample from a subject who has or is at risk of mitochondrial dysfunction, either as a quantitative mtDNA value or as a ratio to a level of another component in the sample;

subjecting the subject to a treatment or a stress;

determining the level of mtDNA in a second sample of blood or serum from the subject, wherein the first sample was taken before the treatment or stress and the second sample was taken after the treatment or stress;

normalizing the first and second values modifying the raw mtDNA data based on at least two factors selected from the group consisting of exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease- specific mutations, and reference values specific to that subject; and

comparing the normalized first and second values to determine whether the treatment or stress caused an increase in cell death as reflected in an increase in mtDNA levels, or a decrease in cell death as reflected in a decrease in mtDNA levels.

[0008] Some embodiments relate to a method for assessing mitochondrial status, comprising:

determining the level of mitochondrial DNA (mtDNA) in a first sample from a subject who has or is at risk of mitochondrial dysfunction, either as a quantitative mtDNA value or as a ratio to a level of another component in the sample;

subjecting the subject to a treatment or a stress;

determining the level of mtDNA in a second sample of blood or serum from the subject, wherein the first sample was taken before the treatment or stress and the second sample was taken after the treatment or stress; and

comparing the first and second values to determine whether the treatment or stress caused an increase in cell death as reflected in an increase in mtDNA levels, or a decrease in cell death as reflected in a decrease in mtDNA levels. [0009] Some embodiments relate to A method for treating a patient having or at risk of mitochondrial dysfunction, comprising:

administering a therapeutic agent to the patient for mitochondrial dysfunction; determining the effect of such administration on levels of mitochondrial DNA (mtDNA) in the blood or serum of the patient by comparing said levels after said administration to said levels before said administration; and

tailoring therapy delivered to the patient to reduce levels of mtDNA in the blood or serum of the patient, by increasing or terminating administration of the therapeutic agent where suitable reduction of mtDNA was not achieved; continuing administration of the therapeutic agent where suitable reduction of mtDNA was achieved; or reducing the administration of the therapeutic agent to the patient where the reduction of mtDNA achieved supports such reduction.

[0010] Some embodiments relate to a method of assessing status of mitochondrial deficiency disease in a subject, comprising: (a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject; (b) normalizing the raw mtDNA data based on at least two of the following factors selected from the group consisting of: exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease-specific mutations, and reference values specific to that subject to provide a normalized mtDNA value; and (c) deducing the status of the mitochondrial deficiency disease in the subject based on the normalized mtDNA value.

[0011] Some embodiments relate to a method of assessing status of mitochondrial deficiency disease in a subject, comprising: (a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject; and (b) deducing the status of the mitochondrial deficiency disease in the subject based on the mtDNA value.

[0012] Some embodiments relate to a method for treating a patient having or at risk of mitochondrial dysfunction, comprising:

administering a therapeutic agent to the patient for mitochondrial dysfunction; determining the effect of such administration on levels of mitochondrial DNA (mtDNA) or the ratio of mtDNA to nuclear DNA in the blood or serum of the patient by comparing said levels after said administration to said levels before said administration; and

tailoring therapy delivered to the patient to decrease levels of mtDNA or increase in the ratio of mtDNA/nuDNA in the blood or serum of the patient, by increasing or terminating administration of the therapeutic agent where suitable decrease in levels of mtDNA or increase in the ratio of mtDNA/nuDNA is not achieved; continuing administration of the therapeutic agent where suitable decrease in levels of mtDNA or increase in the ratio of mtDNA/nuDNA is achieved; or reducing the administration of the therapeutic agent to the patient where the decrease in levels of mtDNA or increase in the ratio of mtDNA/nuDNA achieved supports such reduction.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

[0013] Diagnosing or evaluating mitochondrial deficiency diseases (including mitochondrial myopathies) is a time consuming process. These may include functional studies are performed, including reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease-specific mutations. For example, Friedreich's Ataxia is assessed using the Friedreich's Ataxia Rating Scale (FARS), which includes neurological signs that specifically reflect neural substrates affected in FRDA. Based on a neurological examination bulbar, upper limb, lower limb, peripheral nerve, and upright stability/gait functions are assessed. Further, a functional staging and activities of daily living (ADL) assessment are incorporated. The scales are supplemented by quantitative performance measures including 8m walk at maximum speed (8MW), the 9-hole peg test (9HPT), PATA rate and low-contrast letter acuity.

[0014] For many of these mitochondrial diseases, no satisfactory biomarker exists. It would be desirable to be able to determine whether the subject had a disease or to assess disease status based on a simple bodily-fluid test rather than the much more time- intensive assessments that are currently required. The measurements of mtDNA described herein can be done with a simple blood test or test of other bodily fluid, including CSF, saliva, and other DNA-containing samples. The measured absolute levels of mtDNA or ratio of mtDNA to nuDNA can then be normalized as described herein, and compared to normalized disease and non-disease values to provide a powerful biomarker analysis for objectively assessing disease state or disease status. Note that the absolute mtDNA numbers or ratios from a patient do not, without more, provide full biomarker functionality. It is only with the benefit of the normalization and/or evaluation against standardized normal or disease values disclosed herein that a crude and general correlation is converted into a relatively precise and informative measurement of disease state or status.

[0015] Biomarkers useful for assessing impaired energy processing disorders and mitochondrial deficiency have been discovered. Significantly, it has been discovered that changes in the absolute level of mtDNA and ratio of mtDNA to nuDNA at a control state (e.g. resting) and at a stress or treatment state (e.g. exercise or administration of a pharmaceutical agent) can be used to assess impaired energy processing disorders and mitochondrial deficiency or for monitoring disease progression or response to therapy.

[0016] There are many variables that can affect absolute or ratio-based mtDNA measurements. For example, exercise (especially hypoxic exercise or exercise to fatigue, with accumulation of lactic acid) leads to apoptosis and autophagy, which in turn causes the release of both mtDNA and nuDNA into the serum as cells damaged by the exercise are replaced. This process, in a normal individual, generally results in increased levels of both mtDNA and nuDNA for about a week, but with a lower ratio of mtDNA to nuDNA (presumably due to oxidative damage to the mitochondria). Other variables include sex, age, treatment status, other oxidative stress (chemical, physiological, and external stresses) and mitochondrial disease status, with oxidative stress and mitochondrial deficiency diseases generally correlating with lower total mtDNA and lower ratios of mtDNA to nuDNA in the serum. Due to the variability of mtDNA measurements, correcting the measured data for the various other factors affecting that data can greatly enhance the value of the mtDNA measurements. In some embodiments, longitudinally following or monitoring the changes in mtDNA to nuDNA ratio can be used to assess mitochondrial deficiency disease status, disease progression and predicting or selecting suitable therapeutic treatment. [0017] Some embodiments relate to methods of using the quantitative value of mtDNA or the ratio of mtDNA to nuDNA as biomarkers to indicate mitochondria stress in patients with mitochondria deficiency disorders.

[0018] Some embodiments relate to methods of quantifying the level of plasma cell free nucleic acid and use it in monitoring or prognosis of mitochondria deficiency disorders.

[0019] Some embodiments relate to methods of measuring the absolute levels of mtDNA or the ratios of mtDNA to nuDNA in a control state (e.g. resting state) and in a treatment or stress state (e.g. exercise or treatment with a pharmaceutical agent) comparing the values measured in the two states for use in monitoring or prognosis of mitochondria deficiency disorders.

[0020] Some embodiments relate to methods of measuring the absolute levels of mtDNA or the ratios of mtDNA to nuDNA in the control group of healthy human and in the group of patients with mitochondria deficiency disorders in a control state and in a treatment or stress state and comparing the values measured in the two groups in different states for use in monitoring or prognosis of mitochondria deficiency disorders.

[0021] Some embodiments relate to a method for enhancing or modulating mitochondrial DNA data, the method comprising:

(a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject, either as an absolute value or a ratio to nuclear DNA (nuDNA);

(b) modifying the raw mtDNA data based on exercise status of the subject and/or at least two of the following factors: age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, mitochondria increase, and reference values specific to that subject; and

(c) generating user-readable output reflective of the modified data.

[0022] Some embodiments relate to a method for assessing mitochondrial status, the method including:

determining the level of mitochondrial DNA (mtDNA) in a first sample of blood or serum from a subject who has or is at risk of mitochondrial dysfunction, either as a quantitative mtDNA value or as a ratio to a level of another component in the sample;

subjecting the subject to a treatment or a stress;

determining the level of mtDNA in a second sample of blood or serum from the subject, wherein the first sample was taken before the treatment or stress and the second sample was taken after the treatment or stress; and

[0023] comparing the first and second values to determine whether the treatment or stress caused a change (increase or decrease) in cell death as reflected in a change (increase or decrease) in mtDNA levels, or a change (increase or decrease) in cell death as reflected in a change (increase or decrease) in mtDNA levels.

[0024] Some embodiments relate to a method for treating a patient having or at risk of mitochondrial dysfunction, the method comprising:

administering a therapeutic agent to the patient for mitochondrial dysfunction; determining the effect of such administration on levels of mitochondrial DNA (mtDNA) in the blood or serum of the patient by comparing said levels after said administration to said levels before said administration; and

tailoring therapy delivered to the patient to reduce levels of mtDNA in the blood or serum of the patient, by increasing or terminating administration of the therapeutic agent where suitable change (reduction or increase) of mtDNA was not achieved; continuing administration of the therapeutic agent where suitable change (reduction or increase) of mtDNA was achieved; or reducing the administration of the therapeutic agent to the patient where the change (reduction or increase) of mtDNA achieved supports such change.

[0025] Some embodiments relate to a method for treating a patient having or at risk of mitochondrial dysfunction, the method comprising:

administering a therapeutic agent to the patient for mitochondrial dysfunction; determining the effect of such administration on levels of mitochondrial DNA (mtDNA) in the blood or serum of the patient by comparing said levels after said administration to said levels before said administration; and tailoring therapy delivered to the patient to reduce levels of mtDNA in the blood or serum of the patient, by increasing or terminating administration of the therapeutic agent where suitable change (reduction or increase) of mtDNA was achieved; continuing administration of the therapeutic agent where suitable change (reduction or increase) of mtDNA was not achieved; or reducing the administration of the therapeutic agent to the patient where the change (reduction or increase) of mtDNA achieved supports such reduction.

[0026] In some embodiments, mtDNA to nuDNA ratio changes are measured in the spinal cord and compared to reference ratio range of the control, and the ratio can be restored following treatment, indicating that a disease process and treatment can alter and restore the mtDNA expression level in a mitochondrial deficiency disease affected subject.

Polyunsaturated Lipid

[0027] As used herein, abbreviations are defined as follows:

ALA Alpha-linolenic acid

LIN Linoleate

LNN Linolenate

ARA Arachidonate

cap caprolactamate

D " Negatively charged deuterium ion

T " Negatively charged tritium ion

DHA Docosahexaenoic acid

DNA Deoxyribonucleic acid

EPA Eicosapentaenoic acid

HPLC High performance liquid chromatography

IR Infrared

LA Linoleic acid

LC/MS Liquid Chromatography / Mass Spectrometry

mg milligram

mmol millimole

NMR Nuclear magnetic resonance

PUFAs Polyunsaturated fatty acids

Rf Retention factor

ROS Reactive oxygen species

TBHP feri-butylhydroperoxide

TLC Thin layer chromatography

uv Ultraviolet

Cp Cyclopentadienyl [0028] The term "polyunsaturated lipid," as used herein, refers to a lipid that contains one or more unsaturated bonds, such as a double or a triple bond, in its hydrophobic tail. The polyunsaturated lipid here can be a polyunsaturated fatty acid, polyunsaturated fatty acid ester, polyunsaturated fatty acid thioester, polyunsaturated fatty acid amide, polyunsaturated fatty acid mimetic, or polyunsaturated fatty acid prodrug.

[0029] The term "mono-allylic site", as used herein, refers to the position of the polyunsaturated lipid, such as polyunsaturated fatty acid or ester thereof, that corresponds to a methylene group attached to only one vinyl group and is not adjacent to two or more vinyl group. For example, the mono-allylic site in a (9Z, 12Z)-9, 12-Octadecadienoic acid (linoleic acid) include the methylene groups at carbon 8 and carbon 14 positions.

[0030] The term "bis-allylic site," as used herein, refers to the position of the polyunsaturated lipid, such as polyunsaturated fatty acid or ester thereof, that corresponds to the methylene groups of 1,4-diene systems. Examples of polyunsaturated lipid having deuterium at one or more bis-allylic positions include but are not limited to 1 1, 1 1-dideutero- cis,cis-9, 12-Octadecadienoic acid (1 1, 1 l-dideutero-(9Z, 12Z)-9, 12-octadecadienoic acid; D2- LA); and 1 1 , 1 1 , 14, 14-tetradeutero-cis,cis,cis-9, 12, 15-octadecatrienoic acid (1 1 , 1 1 , 14, 14- tetradeutero-(9Z, 12Z, 15Z)-9, 12, 15-octadecatrienoic acid; D4-ALA).

[0031] The term "pro-bis-allylic position," as used herein, refers to the methylene group that becomes the bis-allylic position upon desaturation. Some sites which are not bis- allylic in the precursor PUFAs will become bis-allylic upon biochemical transformation. The pro-bis-allylic positions, in addition to deuteration, can be further reinforced by carbon- 13, each at levels of isotope abundance above the naturally-occurring abundance level. For example, the pro-bis-allylic positions, in addition to existing bis-allylic positions, can be reinforced by isotope substitution as shown below in Formula (2), wherein R 1 is alkyl, cation, or H; m = 1 -10; n = 1 -5; and p = 1 -10. In Formula (2), the position of the X atom represents the pro-bis-allylic position, while the position of the Y atom represents the bis-allylic

1 2 1 2

position, and one or more of X , X , Y , or Y atoms can be deuterium atoms.

R = H, C 3 H 7; R 1 = H, alkyl, or cation;

Y 1 and Y 2 = H or D; X 1 and X 2 = H or D

Another example of a compound having bis-allylic and pro-bis-allylic positions is shown in Formula (3), wherein any of the pairs of Υ'-Υ η and/or X^X™ represent the bis-allylic and pro- bis-allylic positions of PUFAs respectively and these positions may contain deuterium atoms.

R = H, C 3 H 7; R ' = H, alkyl, or cation; Y to Y = H or D;

X 1 to X m = H or D; m =1 -10; n=1 -6; and p =1 -10

[0032] It is understood that, in any compound described herein having one or more chiral centers, if an absolute stereochemistry is not expressly indicated, then each center may independently be of R-configuration or S-configuration or a mixture thereof. Thus, the compounds provided herein may be enantiomerically pure, enantiomerically enriched, or may be stereoisomeric mixtures, and include all diastereomeric, and enantiomeric forms. In addition it is understood that, in any compound described herein having one or more double bond(s) generating geometrical isomers that can be defined as E or Z, each double bond may independently be E or Z a mixture thereof. Stereoisomers are obtained, if desired, by methods such as, stereoselective synthesis and/or the separation of stereoisomers by chiral chromatographic columns.

[0033] Likewise, it is understood that, in any compound described, all tautomeric forms are also intended to be included.

[0034] As used herein, the term "thioester" refers to a structure in which a carboxylic acid and a thiol group are linked by an ester linkage or where a carbonyl carbon forms a covalent bond with a sulfur atom -COSR, wherein R may include hydrogen, C 1-30 alkyl (branched or straight) and optionally substituted C 6-10 aryl, heteroaryl, cyclic, or heterocyclic structure. "Polyunsaturated fatty acid thioester" refers to a structure P-COS , wherein P is a polyunsaturated fatty acid described herein.

[0035] As used herein, the term "amide" refers to compounds or moieties that contain a nitrogen atom bound to the carbon of a carbonyl or a thiocarbonyl group such as

1 2 1 2 1 2

compounds containing -C(0)NR R or -S(0)N NR R , and R and R can independently be Ci_3o alkyl (branched or straight), optionally substituted C 6- i 0 aryl, heteroaryl, cyclic, heterocyclic, or Ci-20 hydroalkyl. "Polyunsaturated fatty acid amide" refers to a structure wherein the amide group is attached to the polyunsaturated fatty acid described herein through the carbon of the carbonyl moiety.

[0036] As used herein the term "prodrug" refers to a precursor compound that will undergo metabolic activation in vivo to produce the active drug. It is well-known that carboxylic acids may be converted to esters and various other functional groups to enhance pharmacokinetics such as absorption, distribution, metabolism, and excretion. Esters are a well-known pro-drug form of carboxylic acids formed by the condensation of an alcohol (or its chemical equivalent) with a carboxylic acid (or its chemical equivalent). In some embodiments, alcohols (or their chemical equivalent) for incorporation into pro-drugs of PUFAs include pharmaceutically acceptable alcohols or chemicals that upon metabolism yield pharmaceutically acceptable alcohols. Such alcohols include, but are not limited to, propylene glycol, ethanol, isopropanol, 2-(2-ethoxyethoxy)ethanol (Transcutol®, Gattefosse, Westwood, N.J. 07675), benzyl alcohol, glycerol, polyethylene glycol 200, polyethylene glycol 300, or polyethylene glycol 400; polyoxyethylene castor oil derivatives (for example, polyoxyethyleneglyceroltriricinoleate or polyoxyl 35 castor oil (Cremophor®EL, BASF Corp.), polyoxyethyleneglycerol oxystearate (Cremophor®RH 40 (polyethyleneglycol 40 hydrogenated castor oil) or Cremophor®RH 60 (polyethyleneglycol 60 hydrogenated castor oil), BASF Corp.)); saturated polyglycolized glycerides (for example, Gelucire® 35/10, Gelucire® 44/14, Gelucire® 46/07, Gelucire® 50/13 or Gelucire® 53/10, available from Gattefosse, Westwood, N.J. 07675); polyoxyethylene alkyl ethers (for example, cetomacrogol 1000); polyoxyethylene stearates (for example, PEG-6 stearate, PEG-8 stearate, polyoxyl 40 stearate NF, polyoxyethyl 50 stearate NF, PEG- 12 stearate, PEG-20 stearate, PEG- 100 stearate, PEG- 12 distearate, PEG-32 distearate, or PEG-150 distearate); ethyl oleate, isopropyl palmitate, isopropyl myristate; dimethyl isosorbide; N-methylpyrrolidinone; paraffin; cholesterol; lecithin; suppository bases; pharmaceutically acceptable waxes (for example, carnauba wax, yellow wax, white wax, microcrystalline wax, or emulsifying wax); pharmaceutically acceptable silicon fluids; sorbitan fatty acid esters (including sorbitan laurate, sorbitan oleate, sorbitan palmitate, or sorbitan stearate); pharmaceutically acceptable saturated fats or pharmaceutically acceptable saturated oils (for example, hydrogenated castor oil (glyceryl-tris-12-hydroxystearate), cetyl esters wax (a mixture of primarily C14-C 18 saturated esters of C 14-C18 saturated fatty acids having a melting range of about 43°-47° C), or glyceryl monostearate).

[0037] In some embodiments, the fatty acid pro-drug is represented by the ester P— B, wherein the radical P is a PUFA and the radical B is a biologically acceptable molecule. Thus, cleavage of the ester P— B affords a PUFA and a biologically acceptable molecule. Such cleavage may be induced by acids, bases, oxidizing agents, and/or reducing agents. Examples of biologically acceptable molecules include, but are not limited to, nutritional materials, peptides, amino acids, proteins, carbohydrates (including monosaccharides, disaccharides, polysaccharides, glycosaminoglycans, and oligosaccharides), nucleotides, nucleosides, lipids (including mono-, di- and tri-substituted glycerols, glycerophospholipids, sphingolipids, and steroids). In some embodiments, alcohols (or their chemical equivalent) for incorporation into pro-drugs of PUFAs include polyalcohols such as diols, triols, tetra-ols, penta-ols, etc. Examples of alcohol include methyl, ethyl, iso-propyl, and other alkyl alcohol. Examples of polyalcohols include ethylene glycol, propylene glycol, 1,3-butylene glycol, polyethylene glycol, methylpropanediol, ethoxydiglycol, hexylene glycol, dipropylene glycol glycerol, and carbohydrates. Esters formed from polyalcohols and PUFAs may be mono-esters, di-esters, tri-esters, etc. In some embodiments, multiply esterified polyalcohols are esterified with the same PUFAs. In other embodiments, multiply esterified polyalcohols are esterified with different PUFAs. In some embodiments, the different PUFAs are stabilized in the same manner. In other embodiments, the different PUFAs are stabilized in different manners (such as deuterium substitution in one PUFA and 13 C substitution in another PUFA). In some embodiments, the one or more PUFAs is an omega-3 fatty acid and the one or more PUFAs is an omega-6 fatty acid. In some embodiments, the ester is an ethyl ester. In some embodiments, the ester is a mono-, di- or triglyceride.

[0038] It is also contemplated that it may be useful to formulate PUFAs and/or PUFA mimetics and/or PUFA pro-drugs as salts for use in the embodiments. For example, the use of salt formation as a means of tailoring the properties of pharmaceutical compounds is well known. See Stahl et al., Handbook of pharmaceutical salts: Properties, selection and use (2002) Weinheim/Zurich: Wiley- VCH/VHCA; Gould, Salt selection for basic drugs, Int. J. Pharm. (1986), 33 :201-217. Salt formation can be used to increase or decrease solubility, to improve stability or toxicity, and to reduce hygroscopicity of a drug product.

[0039] Formulation of PUFAs and/or PUFA esters and/or PUFA mimetics and/or PUFA pro-drugs as salts can include any PUFA salt described herein.

[0040] The term "polyunsaturated fatty acid mimetic," as used herein, refers to compounds that are structurally similar to naturally occurring polyunsaturated fatty acid but are non-isotopically modified to prevent hydrogen abstraction at the bis-allylic position. Various methods can be used to non-isotopically modify the polyunsaturated fatty acid to produce the polyunsaturated fatty acid mimetic, and examples include but are not limited to moving unsaturated bonds to eliminate one or more bis-allylic positions, replacing at least one carbon atom at the bis-allylic position with an oxygen or sulfur, replacing at least one hydrogen atom at the bis-allylic position with an alkyl group, replacing the hydrogen atoms at the bis-allylic position with a cycloalkyl group, and replacing at least one double bond with a cycloalkyl group.

[0041] In some embodiments, the non-isotopic modification is achieved by moving unsaturated bonds to eliminate one or more bis-allylic positions. The polyunsaturated fatty acid can have the structure of Formula I):

wherein R is H or C M 0 alkyl, R 1 is H or C M 0 alkyl, n is 1 to 4, and m is 1 to 12. In some embodiments, R 1 can be -C3H7. Examples of the polyunsaturated fatty acid mimetic include but are not limited to:

Octadeca-8, 12-dienoic acid ^ Octadeca-7,1 1 ,15-trienoic acid

[0042] In some embodiments, the non-isotopic modification is achieved by replacing at least one carbon atom at the bis-allylic position with an oxygen or sulfur. The polyunsaturated fatty acid can have the structure of Formula (II):

(I D

wherein R is H or CM 0 alkyl, R 1 is H or CM 0 alkyl, X is O or S, n is 1 to 4, and m is 1 to 12. In some embodiments, R 1 can be -C 3 H 7 . Examples of the polyunsaturated fatty acid mimetic include but are not limited to:

X = S: 10-Hept-1 -enylsulfanyl-dec-9-enoic acid X = S: 10-(2-But-1 -enylsulfanyl-vinylsulfanyl)-dec-9-enoic acid

X = 0: 10-Hept-1 -enyloxy-dec-9-enoic acid j X = 0:10-(2-But-1-enyloxy-vinyloxy)-dec-9-enoic acid

[0043] In some embodiments, the non-isotopic modification is achieved by replacing at least one hydrogen atom at the bis-allylic position with an alkyl group. The polyunsaturated fatty acid can have the structure of Formula (III)

wherein is H or CM 0 alkyl, R is H or Ci_i 0 alkyl, X is O or S, n is 1 to 4, and m is 1 to 12. In some embodiments, R 1 can be -C3H7. Examples of the polyunsaturated fatty acid mimetic include but are not limited to:

1 1 , 1 1 -Dimethyl-octadeca-9, 12-dienoic acid an( j l l ,l l ,l4,14-Tetramethyl-octadeca-9,12,15-trienoic acid

[0044] In some embodiments, the non-isotopic modification is achieved by replacing the hydrogen atoms at the bis-allylic position with a cycloalkyl group. The polyunsaturated fatty acid can have the structure of Formula (IV):

(IV) wherein R is H or Ci_i 0 alkyl, R 1 is H or CM 0 alkyl, n is 1 to 5, and m is 1 to 12. In some embodiments, R 1 can be -C3H7. Examples of the polyunsaturated fatty acid mimetic include but are not limited to:

10-{1 -[2-(1 -But-1 -enyl-cyclopropyl)-vinyl]-cyclopropyl}-dec-9- 10-(1-Hept-1-enyl-cyclopropyl)-dec-9-enoic acid anc j enoic acid

[0045] In some embodiments, the non-isotopic modification is achieved by replacing at least one double bond with a cycloalkyl group. The polyunsaturated fatty acid can have the structure of Formula (V), (VI), or (VII)

(V) (VI) (VII)

wherein R is H or CM 0 alkyl, R is H or C M 0 alkyl, n is 1 to 5, and m is 1 to 12. In some embodiments, R 1 can be -C 3 H 7 . Examples of the polyunsaturated fatty acid mimetic include but are not limited to:

-[3-(3-Pentyl-cyclobutylmethyl)- 8-{3-[3-(3-Ethyl-cyclobutylmethyl)-cyclobutylmethyl]- cyclobutyl]-octanoic acid cyclobutylj-octanoic acid

-[2-(2-Pentyl-cyclobutylmethyl)-cyclobutyl]- 8-{2-[2-(2-Ethyl-cyclobutylmethyl)- octanoic acid cyclobutylmethyl]-cyclobutyl}-octanoic acid

8-[2-(2-Pentyl-cyclopropylmethyl)-cyclopropyl]- 8-{2-[2-(2-Ethyl-cyclopropylmethyl)- octanoic acid cyclopropylmethyl]-cyclopropyl}-octanoic acid

[0046] As used herein, "substantially greater" refers to about 20% or greater. In one embodiment, substantially greater refers to greater than about 10%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 250%, 300%), 350%, 400%, 450%), or 500%. In one embodiment, substantially greater refers to about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100%. In one embodiment, substantially greater refers to about 50%-98%, 55%-98%, 60%-98%, 70%- 98%, 50%-95%, 55%-95%, 60%-95%, or 70%-95%. In one embodiment, substantially greater refers to six times greater, five times greater, four times greater, three times greater, or two times greater.

[0047] As used herein, the term "substantial increase" refers to about 20% or greater increase. In one embodiment, substantial increase refers to an increase of about 10%, 20%, 30%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%), 200%), 250%), 300%, 350%, 400%, 450%, or 500%. In one embodiment, substantial increase refers to about an increase of about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100%. In one embodiment, substantial increase refers to an increase of about 50%-98%, 55%-98%, 60%-98%, 70%-98%, 50%-95%, 55%-95%, 60%-95%, or 70%-95%. In some embodiments, substantial increase refers to an increase of about five times, four times, three times, or two times.

[0048] "Subject" as used herein, means a human or a non-human mammal, e.g., a dog, a cat, a mouse, a rat, a cow, a sheep, a pig, a goat, a non-human primate or a bird, e.g., a chicken, as well as any other vertebrate or invertebrate.

[0049] The term "healthy " " refers to a subject possessing good health and free of mitochondrial deficiency disease such as ataxia, Parkinson's Disease, Alzheimer's Disease, ischemic heart disease, dementia, Huntington's disease, Amyotrophic lateral sclerosis, cytochrome c oxidase deficiency, autosomal dominant progressive external ophthalmoplegia, Leber's Hereditary Optic Neuropathy, mitochondrial myopathy, diabetes mellitus and deafness, leigh syndrome, myoneurogenic gastrointestinal encephalopathy, myoclonic epilepsy with ragged red fibers, and mitochondrial neurogastrointestinal encephalomyopathy. A healthy subject is one with normal or good mitochondrial function.

[0050] The term "mammal" is used in its usual biological sense. Thus, it specifically includes, but is not limited to, primates, including simians (chimpanzees, apes, monkeys) and humans, cattle, horses, sheep, goats, swine, rabbits, dogs, cats, rodents, rats, mice guinea pigs, or the like.

[0051] An "effective amount" or a "therapeutically effective amount" as used herein refers to an amount of a therapeutic agent that is effective to relieve, to some extent, or to reduce the likelihood of onset of, one or more of the symptoms of a disease or condition, and includes curing a disease or condition. "Curing" means that the symptoms of a disease or condition are eliminated; however, certain long-term or permanent effects may exist even after a cure is obtained (such as extensive tissue damage).

[0052] "Treat," "treatment," or "treating," as used herein refers to administering a compound or pharmaceutical composition to a subject for prophylactic and/or therapeutic purposes. The term "prophylactic treatment" refers to treating a subject who does not yet exhibit symptoms of a disease or condition, but who is susceptible to, or otherwise at risk of, a particular disease or condition, whereby the treatment reduces the likelihood that the patient will develop the disease or condition. The term "therapeutic treatment" refers to administering treatment to a subject already suffering from a disease or condition.

[0053] The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.

1 2 3

[0054] As used herein, any "R" group(s) such as, without limitation, R , R , R , R 4 , R 5 , and R' represent substituents that can be attached to the indicated atom. An R group may be substituted or unsubstituted.

[0055] As used herein, "C a to C b " in which "a" and "b" are integers refer to the number of carbon atoms in an alkyl, alkenyl or alkynyl group, or the number of carbon atoms in the ring of a cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl or heteroalicyclyl group. That is, the alkyl, alkenyl, alkynyl, ring of the cycloalkyl, ring of the cycloalkenyl, ring of the cycloalkynyl, ring of the aryl, ring of the heteroaryl or ring of the heteroalicyclyl can contain from "a" to "b", inclusive, carbon atoms. Thus, for example, a "Ci to C 4 alkyl" group refers to all alkyl groups having from 1 to 4 carbons, that is, CH 3 -, CH 3 CH 2 -, CH 3 CH 2 CH 2 -, (CH 3 ) 2 CH-, CH 3 CH 2 CH 2 CH 2 -, CH 3 CH 2 CH(CH 3 )- and (CH 3 ) 3 C-. If no "a" and "b" are designated with regard to an alkyl, alkenyl, alkynyl, cycloalkyl cycloalkenyl, cycloalkynyl, aryl, heteroaryl or heteroalicyclyl group, the broadest range described in these definitions is to be assumed.

[0056] As used herein, "alkyl" refers to a straight or branched hydrocarbon chain that comprises a fully saturated (no double or triple bonds) hydrocarbon group. The alkyl group may have 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as " 1 to 20" refers to each integer in the given range; e.g., "1 to 20 carbon atoms" means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc. , up to and including 20 carbon atoms, although the present definition also covers the occurrence of the term "alkyl" where no numerical range is designated). The alkyl group may also be a medium size alkyl having 1 to 10 carbon atoms. The alkyl group could also be a lower alkyl having 1 to 6 carbon atoms. The alkyl group of the compounds may be designated as "C1-C4 alkyl" or similar designations. By way of example only, "C1 -C4 alkyl" indicates that there are one to four carbon atoms in the alkyl chain, i.e. , the alkyl chain is selected from methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl, and hexyls. The alkyl group may be substituted or unsubstituted.

[0057] As used herein, "alkenyl" refers to an alkyl group that contains in the straight or branched hydrocarbon chain one or more double bonds. The alkenyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term "alkenyl" where no numerical range is designated. The alkenyl group may also be a medium size alkenyl having 2 to 9 carbon atoms. The alkenyl group could also be a lower alkenyl having 2 to 4 carbon atoms. The alkenyl group of the compounds may be designated as "C2-4 alkenyl" or similar designations. By way of example only, "C2-4 alkenyl" indicates that there are two to four carbon atoms in the alkenyl chain, i.e., the alkenyl chain is selected from the group consisting of ethenyl, propen-l-yl, propen-2-yl, propen-3-yl, buten-l-yl, buten-2-yl, buten-3-yl, buten-4-yl, 1-methyl-propen- l-yl, 2-methyl-propen-l-yl, 1-ethyl- ethen-l-yl, 2-methyl-propen-3-yl, buta-l ,3-dienyl, buta-l,2,-dienyl, and buta- l,2-dien-4-yl. Typical alkenyl groups include, but are in no way limited to, ethenyl, propenyl, butenyl, pentenyl, and hexenyl, and the like. An alkenyl group may be unsubstituted or substituted.

[0058] As used herein, "alkynyl" refers to an alkyl group that contains in the straight or branched hydrocarbon chain one or more triple bonds. The alkynyl group may have 2 to 20 carbon atoms, although the present definition also covers the occurrence of the term "alkynyl" where no numerical range is designated. The alkynyl group may also be a medium size alkynyl having 2 to 9 carbon atoms. The alkynyl group could also be a lower alkynyl having 2 to 4 carbon atoms. The alkynyl group of the compounds may be designated as "C2-4 alkynyl" or similar designations. By way of example only, "C 2 - 4 alkynyl" indicates that there are two to four carbon atoms in the alkynyl chain, i.e., the alkynyl chain is selected from the group consisting of ethynyl, propyn-l -yl, propyn-2-yl, butyn-l -yl, butyn-3-yl, butyn- 4-yl, and 2-butynyl. Typical alkynyl groups include, but are in no way limited to, ethynyl, propynyl, butynyl, pentynyl, and hexynyl, and the like. An alkynyl group may be unsubstituted or substituted.

[0059] As used herein, "cycloalkyl" refers to a completely saturated (no double or triple bonds) mono- or multi- cyclic hydrocarbon ring system. When composed of two or more rings, the rings may be joined together in a fused fashion. Cycloalkyl groups can contain 3 to 10 atoms in the ring(s) or 3 to 8 atoms in the ring(s). A cycloalkyl group may be unsubstituted or substituted. Typical cycloalkyl groups include, but are in no way limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. A cycloalkyl group may be unsubstituted or substituted.

[0060] As used herein, "cycloalkenyl" refers to a mono- or multi- cyclic hydrocarbon ring system that contains one or more double bonds in at least one ring; although, if there is more than one, the double bonds cannot form a fully delocalized pi- electron system throughout all the rings (otherwise the group would be "aryl," as defined herein). When composed of two or more rings, the rings may be connected together in a fused fashion. A cycloalkenyl group may be unsubstituted or substituted.

[0061] As used herein, "cycloalkynyl" refers to a mono- or multi- cyclic hydrocarbon ring system that contains one or more triple bonds in at least one ring. If there is more than one triple bond, the triple bonds cannot form a fully delocalized pi-electron system throughout all the rings. When composed of two or more rings, the rings may be joined together in a fused fashion. A cycloalkynyl group may be unsubstituted or substituted.

[0062] As used herein, "carbocyclyl" refers to all carbon ring systems. Such systems can be unsaturated, can include some unsaturation, or can contain some aromatic portion, or be all aromatic. A carbocyclyl group may be unsubstituted or substituted.

[0063] As used herein, "aryl" refers to a carbocyclic (all carbon) monocyclic or multicyclic aromatic ring system (including, e.g., fused, bridged, or spiro ring systems where two carbocyclic rings share a chemical bond, e.g., one or more aryl rings with one or more aryl or non-aryl rings) that has a fully delocalized pi-electron system throughout at least one of the rings. The number of carbon atoms in an aryl group can vary. For example, the aryl group can be a C 6 -Ci4 aryl group, a C 6 -Cio aryl group, or a C 6 aryl group. Examples of aryl groups include, but are not limited to, benzene, naphthalene, and azulene. An aryl group may be substituted or unsubstituted.

[0064] As used herein, "heterocyclyl" refers to ring systems including at least one heteroatom (e.g., O, N, S). Such systems can be unsaturated, can include some unsaturation, or can contain some aromatic portion, or be all aromatic. A heterocyclyl group may be unsubstituted or substituted.

[0065] As used herein, "heteroaryl" refers to a monocyclic or multicyclic aromatic ring system (a ring system having a least one ring with a fully delocalized pi-electron system) that contain(s) one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen, and sulfur, and at least one aromatic ring. The number of atoms in the ring(s) of a heteroaryl group can vary. For example, the heteroaryl group can contain 4 to 14 atoms in the ring(s), 5 to 10 atoms in the ring(s) or 5 to 6 atoms in the ring(s). Furthermore, the term "heteroaryl" includes fused ring systems where two rings, such as at least one aryl ring and at least one heteroaryl ring, or at least two heteroaryl rings, share at least one chemical bond. Examples of heteroaryl rings include, but are not limited to, furan, furazan, thiophene, benzothiophene, phthalazine, pyrrole, oxazole, benzoxazole, 1 ,2,3- oxadiazole, 1 ,2,4-oxadiazole, thiazole, 1 ,2,3-thiadiazole, 1 ,2,4-thiadiazole, benzothiazole, imidazole, benzimidazole, indole, indazole, pyrazole, benzopyrazole, isoxazole, benzoisoxazole, isothiazole, triazole, benzotriazole, thiadiazole, tetrazole, pyridine, pyridazine, pyrimidine, pyrazine, purine, pteridine, quinoline, isoquinoline, quinazoline, quinoxaline, cinnoline, and triazine. A heteroaryl group may be substituted or unsubstituted.

[0066] As used herein, "heteroalicyclic" or "heteroalicyclyl" refers to three-, four- , five-, six-, seven-, eight-, nine-, ten-, up to 18-membered monocyclic, bicyclic, and tricyclic ring system wherein carbon atoms together with from 1 to 5 heteroatoms constitute said ring system. A heterocycle may optionally contain one or more unsaturated bonds situated in such a way, however, that a fully delocalized pi-electron system does not occur throughout all the rings. The heteroatoms are independently selected from oxygen, sulfur, and nitrogen. A heterocycle may further contain one or more carbonyl or thiocarbonyl functionalities, so as to make the definition include oxo-systems and thio-systems such as lactams, lactones, cyclic imides, cyclic thioimides, and cyclic carbamates. When composed of two or more rings, the rings may be joined together in a fused fashion. Additionally, any nitrogens in a heteroalicyclic may be quaternized. Heteroalicyclyl or heteroalicyclic groups may be unsubstituted or substituted. Examples of such "heteroalicyclic" or "heteroalicyclyl" groups include but are not limited to, 1,3-dioxin, 1,3-dioxane, 1,4-dioxane, 1 ,2-dioxolane, 1 ,3- dioxolane, 1,4-dioxolane, 1 ,3-oxathiane, 1,4-oxathiin, 1 ,3-oxathiolane, 1,3-dithiole, 1 ,3- dithiolane, 1,4-oxathiane, tetrahydro-l ,4-thiazine, 2H-l,2-oxazine, maleimide, succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine, hydantoin, dihydrouracil, trioxane, hexahydro-l ,3,5-triazine, imidazoline, imidazolidine, isoxazoline, isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline, thiazolidine, morpholine, oxirane, piperidine N- Oxide, piperidine, piperazine, pyrrolidine, pyrrolidone, pyrrolidione, 4-piperidone, pyrazoline, pyrazolidine, 2-oxopyrrolidine, tetrahydropyran, 4H-pyran, tetrahydrothiopyran, thiamorpholine, thiamorpholine sulfoxide, thiamorpholine sulfone, and their benzo-fused analogs (e.g., benzimidazolidinone, tetrahydroquinoline, 3,4-methylenedioxyphenyl).

[0067] As used herein, "aralkyl" and "aryl(alkyl)" refer to an aryl group connected, as a substituent, via a lower alkylene group. The lower alkylene and aryl group of an aralkyl may be substituted or unsubstituted. Examples include but are not limited to benzyl, 2-phenylalkyl, 3-phenylalkyl, and naphthylalkyl.

[0068] As used herein, "heteroaralkyl" and "heteroaryl(alkyl)" refer to a heteroaryl group connected, as a substituent, via a lower alkylene group. The lower alkylene and heteroaryl group of heteroaralkyl may be substituted or unsubstituted. Examples include but are not limited to 2-thienylalkyl, 3-thienylalkyl, furylalkyl, thienylalkyl, pyrrolylalkyl, pyridylalkyl, isoxazolylalkyl, and imidazolylalkyl, and their benzo-fused analogs.

[0069] A "(heteroalicyclyl)alkyl" is a heterocyclic or a heteroalicyclyl ic group connected, as a substituent, via a lower alkylene group. The lower alkylene and heterocyclic or a heterocyclyl of a (heteroalicyclyl)alkyl may be substituted or unsubstituted. Examples include but are not limited tetrahydro-2H-pyran-4-yl)methyl, (piperidin-4-yl)ethyl, (piperidin- 4-yl)propyl, (tetrahydro-2H-thiopyran-4-yl)methyl, and (l ,3-thiazinan-4-yl)methyl. [0070] "Lower alkylene groups" are straight-chained -CH 2 - tethering groups, forming bonds to connect molecular fragments via their terminal carbon atoms. Examples include but are not limited to methylene (-CH 2 -), ethylene (-CH 2 CH 2 -), propylene (- CH 2 CH 2 CH 2 -), and butylene (-CH 2 CH 2 CH 2 CH 2 -). A lower alkylene group can be substituted by replacing one or more hydrogen of the lower alkylene group with a substituent(s) listed under the definition of "substituted."

[0071] As used herein, a substituted group is derived from the unsubstituted parent group in which there has been an exchange of one or more hydrogen atoms for another atom or group. Unless otherwise indicated, when a group is deemed to be "substituted," it is meant that the group is substituted with one or more substituents independently selected from Ci-C 6 alkyl, Ci-C 6 alkenyl, Ci-C 6 alkynyl, Ci-C 6 heteroalkyl, C 3 -C 7 carbocyclyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), C 3 - C7-carbocyclyl-Ci-C 6 -alkyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Q- C 6 haloalkyl, and Ci -C 6 haloalkoxy), 5-10 membered heterocyclyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), 5-10 membered heterocyclyl-Ci-Ce-alkyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), aryl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), aryl(Ci-C 6 )alkyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), 5- 10 membered heteroaryl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), 5-10 membered heteroaryl(Ci-C 6 )alkyl (optionally substituted with halo, Ci-C 6 alkyl, Ci-C 6 alkoxy, Ci-C 6 haloalkyl, and Ci-C 6 haloalkoxy), halo, cyano, hydroxy, Ci-C 6 alkoxy, Ci-C 6 alkoxy(C]-C 6 )alkyl (i.e., ether), aryloxy, sulfhydryl (mercapto), halo(Ci-C 6 )alkyl (e.g., -CF 3 ), halo(Ci-C 6 )alkoxy (e.g., -OCF 3 ), Ci-C 6 alkylthio, arylthio, amino, amino(Ci-C 6 )alkyl, nitro, O-carbamyl, N-carbamyl, O- thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C- carboxy, O-carboxy, acyl, cyanato, isocyanato, thiocyanato, isothiocyanato, sulfinyl, sulfonyl, and oxo (=0). Wherever a group is described as "substituted" that group can be substituted with the above substituents. [0072] In some embodiments, substituted group(s) is (are) substituted with one or more substituent(s) individually and independently selected from C1 -C4 alkyl, amino, hydroxy, and halogen.

[0073] It is to be understood that certain radical naming conventions can include either a mono-radical or a di-radical, depending on the context. For example, where a substituent requires two points of attachment to the rest of the molecule, it is understood that the substituent is a di-radical. For example, a substituent identified as alkyl that requires two points of attachment includes di-radicals such as -CH 2 - -CH2CH2-, -CH 2 CH(CH 3 )CH 2 - and the like. Other radical naming conventions clearly indicate that the radical is a di-radical such as "alkylene" or "alkenylene."

Impaired Energy Processing Disorders and Mitochondrial Deficiency

[0074] Mitochondrial disorders can be caused by genetic mutations (both in mitochondrial and nuclear DNA) as well as by environmental factors. Mitochondrial deficiency or mitochondrial respiration deficiency diseases include diseases and disorders caused by oxidation of mitochondrial membrane elements, such as mitochondrial respiration deficiency, which occurs in the mitochondrial membrane. Membrane functionality is important to overall mitochondrial function. Oxidative phosphorylation (Ox-Phos) pathways are located in the inner mitochondrial membrane which is rich in linoleic acid-containing phospholipid cardiolipin. Any imbalance in ROS processing may thus result in increased autoxidation of this and other membrane polyunsaturated fatty acids (PUFAs), giving rise to increased levels of reactive carbonyl compounds. Some of these can initiate, up-, and down- regulate numerous cellular processes such as activation/deactivation of uncoupling protein-2 (UCP-2), apoptosis, etc. A substantial number of diseases are linked to mitochondrial dysfunction. These diseases include, but are not limited to: Co-enzyme Q deficiency; Diabetes mellitus and deafness (DAD), Alzheimer's disease; Maternally Inherited Diabetes and Deafness (MIDD); Friedreich's ataxia (FA); Leber's congenital amaurosis; Leber's hereditary optic neuropathy (LHON); Leigh syndrome; Mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke (MELAS) syndrome; Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE); Myoclonus Epilepsy Associated with Ragged-Red Fibers (MERRF) syndrome; Myoneurogenetic gastrointestinal encephalopathy (MNGIE) and neuropathy; Neuropathy, ataxia, retinitis pigmentosa, and ptosis (NA P); optic neuropathies and opthalmoplegias; Wolff-Parkinson- White syndrome and other cardiomyopathies; X-linked Adrenoleukodystrophy (X-ALD), as well as diseases of musculoskeletal system (lipid myopathies, chronic fatigue, fibromyalgia syndrome); kidney (Fanconi's syndrome and glomerulonephropathies); blood (Pearson's syndrome), and brain (migraines, seizures, and strokes). See Santos et al. Antioxidants & Redox Signaling (2010), 13:5, 651-690; Meier et al. J. Neurol. (201 1) PMID: 21779958; Marobbio et al. Mitochondrion (201 1) PMID: 21782979; Orsucci et al. Curr. Med. Chem. (201 1) 18:26, 4053-64; Lynch et al. Arch. Neurol. (2010) 67:8, 941 -947; Schultz et al. J. Neurol. (2009) 256 Suppl. 1 :42-5; Drinkard et al. Arch. Phys. Med. Rehabil. (2010) 91 :7, 1044-1050; Berger et al. Brain Pathol. (2010) 20:4, 845-856; Singh et al. Brain Pathol. (2010) 20:4, 838-844; Lopez-Erauskin et al. Ann Neurol. (201 1) 70, 84-92. These and other mitochondrial diseases have increased ROS levels and as a corollary, sustain increased damage to cellular components such as lipids (McKenzie M et al, Neurochem Res 2004;29:589-600). For example, early oxidative damage in spinal cord and other tissues has been observed using lipid and amino acid peroxidation biomarkers underlying neurodegeneration in X-ALD (Fourcade S. et al., Human Mol Genetics 2008; 77: 1762-1773).

[0075] More specifically, Coenzyme Q deficiency is associated with many diseases, including nervous system diseases (dyskinesias, ataxias); musculoskeletal diseases (muscle weakness, neuromuscular diseases); metabolic diseases etc. Coenzyme Q 10 plays an important role in controlling the oxidative stress. Q10- has been shown to be linked to increased PUFA toxicity, through PUFA peroxidation and toxicity of the formed products (Do TQ et al, PNAS USA 1996;93:7534-7539). Numerous diagnostic tests are known in the art to identify subjects having a Coenzyme Q10 deficiency. In FA, the deficiency in a mitochondrial protein frataxin leads to iron accumulation within the mitochondria and a consequent increase in oxidative stress, through both Haber-Weiss - Fenton-type processes and a breakdown in the respiratory chain. (Bradley JL et al, Hum. Mol. Genet. 2000;9:275- 282). Lipid peroxidation is increased in FA, and reducing the level of this peroxidation has a strong protective effect (Navarro JA et al, Hum. Mol. Genet. 2010;79:2828-2840). DAD and MIDD are characterised by a substantially elevated oxidative stress level (Aladaq I et al, J. Laryngol. Otol. 2009;723:957-963). These, and many other mitochondrial diseases, are often characterised by accumulation of both mitochondria and lipid droplets, leading to increased lipid peroxidation (Narbonne H et al, Diabetes Metab. 2004;30:61 -66). Conditions like LHON and Leber's syndrome result from the mutations in a gene encoding for a subunit of the mitochondrial NADH dehydrogenase, compromising the performance of Complex I and leading to increased ROS generation (Wallace DC Science 1999;253: 1482-1488). MERRF is associated with both elevated oxidative stress level and abnormal lipid storage (Wu SB et al, Mol. Neurobiol. 2010;47:256-266). MNGIE and NARP are another two similar examples (Wallace DC Science 1999;253: 1482-1488). X-ALD, which can be slowed by a combination of Lorenzo's oil and a low fat diet, is linked to both overproduction of ROS and a deficit in ROS scavenging (Al-Omar MA. J. Herb. Pharmacother. 2006;6: 125-134).

[0076] In some embodiments, the mitochondrial dysfunction is associated with Friedreich's Ataxia, Parkinson's Disease, Alzheimer's Disease, ischemic heart disease, dementia, Huntington's disease, Amyotrophic lateral sclerosis, cytochrome c oxidase deficiency, autosomal dominant progressive external ophthalmoplegia, Leber's Hereditary Optic Neuropathy, mitochondrial myopathy, diabetes mellitus and deafness, leigh syndrome, myoneurogenic gastrointestinal encephalopathy, myoclonic epilepsy with ragged red fibers, or mitochondrial neurogastrointestinal encephalomyopathy.

Methods of Determining mtDNA Level and ratio of mtDNA to nuDNA

[0077] Various suitable methods can be used for quantification of mtDNA level and measuring the ratio of mtDNA to nuDNA. Examples of the methods include but are not limited to Northern-blot hybridization, Southern-blot hybridization, ribonuclease protection assay, reverse transcriptase polymerase chain reaction, real time PCR based methods, and mass spectrometry, and any combinations thereof.

[0078] In some embodiments, quantification of mtDNA absolute level or the ratio mtDNA to nuDNA can be achieved by adding a known concentration of a nucleic acid standard to the biological specimen, wherein the standard is designed to have one base difference with the target mtDNA or nuDNA; amplifying a sample with the target and standard nucleic acids, for example, using a polymerase chain reaction, removing the excessive dNTPs, for example by treating the amplified sample with a phosphatase (e.g. Shrimp alkaline phosphatase), and consequently enhancing the nucleic acid difference between the standard and the target mtDNA, for example, by extending the differing base in the target and the standard nucleic acid samples. The standard and the target mtDNA produce two different products, typically having one to two bases difference, and are subsequently quantified. The concentration of the target mtDNA can be calculated based upon the amount of standard present in the amplified sample.

[0079] In some embodiments, the sample is selected from plasma, blood cell, serum, tissue, saliva, mucus, and any other bodily fluid. In some embodiments, the sample is a blood sample. In some embodiments, the sample is a plasma sample. In some embodiments, the sample is a buffy coat. In some embodiments, the sample is a buccal swab.

[0080] In one preferred embodiment, the quantification is performed based upon the different mass of the "enhanced" target and standard nucleic acid products using MALDI- TOF mass spectrometry as described in US 20120028838, which is incorporated by reference in its entirety. The ratio of the peaks in the mass spectrum is used to calculate the ratio of the standard and the target nucleic acid. The concentration of a target DNA can be calculated based upon the initial amount of standard used/added in the sample before amplification. In one preferred embodiment, the enhancement of the nucleic acid difference between the standard and the target nucleic acid is performed using primer extension methods.

[0081] In another embodiment, the enhancement of the nucleic acid difference in the target and the standard after the PCR is performed using fluorescence tagged dNTP/ddNTP for base extension. In yet another embodiment, the enhancement of the nucleic acid difference in the target and the standard after the PCR is performed using different dye- labeled ddNTPs which are differentially incorporated into the target and standard nucleic acids in a primer extension reaction. In one embodiment, the enhancement of the nucleic acid difference in the target and the standard after the PCR, is performed using real time PCR. In another embodiment, the enhancement of the nucleic acid difference in the target and the standard after the PCR is performed using hybridization based techniques wherein two oligonucleotides specific to either the target or the standard are designed for hybridization. In another embodiment, the enhancement of the nucleic acid difference in the target and the standard after the PCR is performed using pyrosequencing technology. In another embodiment, the enhancement of the nucleic acid difference in the target and the standard after the PCR is performed using a third wave invader assay using an artificial single nucleotide polymorphism (SNP) as an internal reference. In an alternative embodiment, when using pyrosequencing, no pre-amplification is needed.

[0082] A DNA standard with known concentration is added to the DNA sample. The DNA sample is then amplified by PCR. The standard is designed to have one base mutation difference compared with the gene of interest, i.e. the target nucleic acid. Thus, the standard and the target nucleic acid are amplified with same efficiency in PCR. And these two can be identified, using, for example a base extension reaction carried right at the mutation site. The amount of the PCR products is consequently measured by any of a variety of means, preferably by Mass Spectrometry (MALDI-TOF, or Matrix Assisted Laser Desorption Ionization— Time of Flight). The peak area ratio between the products from the standard and the target nucleic acid represents the ratio of the standard and the target nucleic acid. Since the concentration of the standard is known, the concentration of target nucleic acid can be calculated.

[0083] In some embodiments, quantification of mtDNA absolute level or the ratio mtDNA to nuDNA can be achieved using a mtDNA Monitoring Primer Set, which is designed to quantify the relative number of copies of human mitochondrial DNA (mtDNA) using nuclear DNA (nDNA) content as a standard by real-time PCR. This kit contains one or more primer pairs for the amplification of selected regions: one or more primer pairs for detecting mtDNA and one or more primer pairs for detecting nDNA. These primers will not amplify pseudogenes. As the primers are human-specific, human mtDNA content can be monitored.

[0084] In some embodiments, quantification of mtDNA level or the ratio mtDNA to nuDNA can be achieved using real time quantitative PCR. In some embodiments, quantification of mtDNA level or the ratio mtDNA to nuDNA includes using a DNA standard (e.g. natural or synthetic DNA standard) to determine the actual copy numbers of a target sequence in a sample via qPCR. In some embodiments, the standard contains a DNA sequence, which is different from, but associated with or linked to, the sequence to be analyzed. In some embodiments, human mtDNA analysis involves the non-coding hypervariable regions (HV s) where most variation in mtDNA is found. In some embodiments, quantification of mtDNA level or the ratio mtDNA to nuDNA includes generating a standard dilution curve using the DNA standards and determining the mtDNA level or the ratio mtDNA to nuDNA by comparing the measurements with the standard dilution curve.

[0085] In some embodiments, quantification of mtDNA level or the ratio mtDNA to nuDNA can include selecting one or more target nucleotide sequences in the mtDNA and nuDNA and analyzing the one or more one or more target nucleotide sequences by mass spectrometry. In some embodiments, the selected one or more one or more target nucleotide sequences include mass-distinguishable products that can be analyzed using mass spectrometry. In some embodiments, the mass-distinguishable products result from (a) annealing an oligonucleotide primer to a target nucleic acid; (b) annealing a detector oligonucleotide to the same target nucleic acid; and (c) contacting the target nucleic acid with an enzyme that extends the oligonucleotide primer in the direction of the detector oligonucleotide, wherein: the detector oligonucleotide or portion thereof is complementary to the target nucleic acid sequence, and the enzyme cleaves and thereby releases at least a portion of the detector oligonucleotide, thereby producing one or more mass-distinguishable products; whereby the target nucleic acid sequence is detected by identifying the mass- distinguishable products by mass spectrometry. In certain embodiments, a second oligonucleotide is introduced that binds to the synthesis product of the first oligonucleotide, whereby exponential amplification can subsequently occur.

[0086] In some embodiments, quantification comprises analyzing the one or more selected target nucleotide sequences containing mass-distinguishable products by mass spectrometry, wherein the mass-distinguishable products result from (a) contacting a target biomolecule with a detectable probe containing an oligonucleotide that serves as a template nucleic acid under conditions in which the detectable probe specifically binds to the target biomolecule; (b) annealing an oligonucleotide primer to the template nucleic acid; (c) annealing a detector oligonucleotide to the same template nucleic acid; and (d) contacting the template nucleic acid with an enzyme that extends the oligonucleotide primer in the direction of the detector oligonucleotide, wherein: the detector oligonucleotide or portion thereof is complementary to the target nucleic acid sequence, and the enzyme cleaves and thereby releases at least a portion of the detector oligonucleotide, thereby producing one or more mass-distinguishable products; whereby the target nucleic acid sequence is detected by identifying the mass-distinguishable products by mass spectrometry. In certain embodiments, a second oligonucleotide is introduced that binds to the synthesis product of the first oligonucleotide, whereby exponential amplification can subsequently occur.

[0087] In some embodiments, methods of detecting and quantifying biomolecules, such as target nucleic acids, wherein the generation of PCR product is monitored by detection of mass-distinguishable product (MDP). In one embodiment, the detection is done in real-time. In some embodiments, the detection in real-time is performed with an electrospray mass spectrometer or LC-MS. In another embodiment, the one or more MDP's are spotted at specific locations on a mass spectrometry-related medium that corresponds to a specific time during the amplification process. An example of a mass spectrometry-related medium is a matrix suitable for MALDI-TOF MS. In another embodiment, a competitor template nucleic acid is introduced, wherein the template nucleic acid serves as an internal control. In yet another embodiment, the number of amplification cycles is determined to obtain a quantitative result. The amount of starting target nucleic acid present in the reaction mixture may be quantified by cycle threshold (Ct), by comparing with a standard dilution curve or a standard efficiency curve prepared using a reference sample, or any other method known in the art.

[0088] In typical applications, the amount of mass-distinguishable product generated during the reaction is determined based on cycle threshold (Ct) value, which represents the number of cycles required to generate a detectable amount of nucleic acid. Determination of Ct values is well known in the art. Briefly, during PCR, as the amount of formed amplicon increases, the signal intensity increases to a measurable level and reaches a plateau in later cycles when the reaction enters into a non-logarithmic phase. By plotting signal intensity versus the cycle number during the logarithmic phase of the reaction, the specific cycle at which a measurable signal is obtained can be deduced and used to calculate the quantity of the target before the start of the PCR. Exemplary methods of determining Ct are described in, e.g., Heid et al. Genome Methods 6:986-94, 1996, with reference to hydrolysis probes.

[0089] For quantification, one may choose to use controls, which provide a signal in relation to the amount of the target that is present or is introduced. A control to allow conversion of relative mass signals into absolute quantities is accomplished by addition of a known quantity of a mass tag or mass label to each sample before detection of the mass- distinguishable products. See for example, Ding and Cantor Proc Natl Acad Sci USA. 2003 Mar. 18; 100(6):3059-64, who describes a method for quantitative gene expression analysis, wherein the control nucleotide contains an artificial single nucleotide polymorphism to distinguish it from the gene of interest. Any mass tag that does not interfere with detection of the MDP's can be used for normalizing the mass signal. Such standards preferably have separation properties that are different from those of any of the molecular tags in the sample, and could have the same or different mass signatures. In some embodiments, the ratio of mtDNA to nuDNA can be determined by comparing the relative mass signals of the selected MDPs on the two types of DNA.

Methods of Using mtDNA Level or ratio of mtDNA to nuDNA as Biomarkers

[0090] In some embodiments, the mtDNA level or ratio of mtDNA to nuDNA can be used as a biomarker to access the mitochondrial status and impaired energy processing disorders and mitochondrial deficiency.

[0091] In some embodiments, the methods described herein can include creating a reference baseline using the mtDNA levels or ratios of mtDNA to nuDNA obtained from one or more measurements of healthy people at a control state and/or a stress or treatment state during a pre-defined time period. In some embodiments, the methods described herein can include creating a baseline using the mtDNA levels or ratios of mtDNA to nuDNA obtained from one or more measurements of the subject at a control state. In some embodiments, the methods described herein can include creating a baseline using the mtDNA levels or ratios of mtDNA to nuDNA obtained from one or more measurements of the subject at a stress or treatment state.

[0092] In some embodiments, the methods described herein can include repeated measurements of mtDNA levels and/or ratios of mtDNA to nuDNA for the subject at a control state and/or a stress or treatment state during a pre-defined time period. In some embodiments, the pre-defined period can be 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, or more than 5 weeks. In some embodiments, the repeated measurements can include measurement of mtDNA levels and/or ratios of mtDNA to nuDNA on day 1, followed by repeated measurements at a control state and a stress state after an interval of 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, or 1 week.

[0093] It is desirable to take sufficient measurements to generate a profile applicable to a given subject. This profile can include, for example, one or more of the following types of measurements: one or preferably multiple measurements over time when the subject has not been under mitochondrial stress, one or preferably multiple measurements over time when the subject has been under mitochondrial stress (such as by exercise to fatigue), and comparison of the subject's measurements to a standard value, such as baseline values for normal (non-mitochondrial deficiency disease) individuals, with or without the effects of mitochondrial stress.

[0094] In some embodiments, the methods described herein can include comparing the changes of mtDNA levels and/or ratios of mtDNA to nuDNA for the subject with the baseline, determining the difference between the baseline and a measurement for the subject, and correlating the difference between the baseline and the measurement of the subject with the mitochondria status of the subject.

[0095] In some embodiments, the methods described herein can include characterizing the mitochondria status of the subject as deficient when the difference between the baseline level and the measurement for the subject is greater than 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% of the baseline level.

[0096] In some embodiments, the methods described herein can include characterizing the mitochondria status of the subject as deficient when the absolute DNA level or the ratio of mtDNA to nuclear DNA(nuDNA) measured prior to treatment or stress is at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% greater than the absolute level or the ratio measured after the treatment or stress.

[0097] In some embodiments, the methods described herein can include characterizing the mitochondria status of the subject as deficient when the absolute DNA level or the ratio of mtDNA to nuclear DNA(nuDNA) measured prior to treatment or stress is at least 1 %, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%less than the absolute level or the ratio measured after the treatment or stress.

[0098] In some embodiments, the raw measurement data for mtDNA level and ratio of mtDNA to nuDNA are modified based on one or more factors selected from the exercise status, sex, age, health condition (e.g. mitochondrial deficiency disease status). In some embodiments, the raw mtDNA data are adjusted based on exercise status of the subject and at least two of the following factors: age; sex; other oxidative or mitochondrial stress conditions; mitochondrial deficiency disease status; and reference values specific to that subject or generalized from other similarly-situated or normal individuals.

[0099] In some embodiments, the subject has a mitochondrial deficiency disease and the modifying step further comprises comparing the data to one or more reference values for subjects not having mitochondrial deficiency disease.

[0100] In some embodiments, the subject has a mitochondrial deficiency disease and the modifying step further comprises comparing the data to one or more reference values for subjects having the same mitochondrial deficiency disease.

[0101] In some embodiments, the raw mtDNA data is from a subject who has undergone aerobic exercise within the previous 1 , 2, 3, 4, 5, 6, or 7 days.

[0102] In some embodiments, the raw mtDNA data is from a subject who has undergone anaerobic exercise to fatigue within the previous 1, 2, 3, 4, 5, 6, or 7 days.

[0103] In some embodiments, the raw mtDNA data is from a subject who has not undergone anaerobic exercise to fatigue within the previous 1, 2, 3, 4, 5, 6, or 7 days.

[0104] In some embodiments, the methods described herein further include repeating the providing data step and the modifying step at least 2, 3, 4, 5, or more additional times and reflecting the data generated in the modifying step for such repetitions in the step of generating user-readable output reflective of the modified data.

[0105] In some embodiments, the methods described herein further include in the user-readable output of step of generating user-readable output reflective of the modified data reflecting change of mtDNA levels in the subject over time, adjusted for exercise status. [0106] In some embodiments, the data reflecting change of mtDNA levels in the subject over time data reflective of multiple time points while the subject was receiving a therapeutic agent to treat mitochondrial deficiency disease.

[0107] For subjects having or at risk for a mitochondrial deficiency disease, it is desirable to generate a subject-specific data profile using one or more of the foregoing techniques to allow comparison of the subject's values to those of other subject who have or do not have the disease (cross-sectional analysis). In addition, the subject-specific data profile can permit tracking of the patient's mtDNA values over time (longitudinal analysis) in order to assess disease progression and/or response to therapy (such as deuterated PUFA therapy).

[0108] One aspect of the disclosure includes combining therapy for a mitochondrial deficiency disease with any of the foregoing techniques or measurements. For example, after generating subject-specific baseline data, optionally including data reflective of mtDNA values in both unstressed and stressed conditions, a therapy for mitochondrial deficiency disease can be administered to the subject. One or more additional measurements of mtDNA values can then be obtained reflective of mtDNA values from a stressed or unstressed state, or both. After optionally adjusting or annotating the data thus obtained (as described elsewhere herein), improvements in mtDNA values (or reduction in rate of deterioration of mtDNA values) can be used to indicate response to therapy, after which therapy is continued or the amount of drug administered can be increased if response is too low or decreased if response is sufficient to warrant a decrease. Alternatively, if no positive response is seen, the amount of therapeutic is either increased or the administration of that particular therapeutic is discontinued.

[0109] In some embodiments, the method described herein further comprises modifying the raw mtDNA data based on at least two factors selected from the group consisting of exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease- specific mutations, and reference values specific to that subject. [0110] In some embodiments, the method described herein further comprises comparing the data representing mitochondrial DNA (mtDNA) levels in the subject with a reference data representing mitochondrial DNA (mtDNA) levels in a healthy subject having no mitochondrial deficiency disease.

[0111] In some embodiments, the reference values for subjects not having mitochondrial deficiency disease is substantially greater than the reference values for subjects having the same mitochondrial disease.

[0112] In some embodiments, the method described herein further comprises characterizing the mitochondrial status of the subject as deficient when the ratio of mtDNA/nuDNA measured after the treatment or stress is substantially greater than the ratio of mtDNA/nuDNA measured prior to treatment or stress.

[0113] In some embodiments, the method described herein further comprises characterizing the treatment or stress as effective when the ratio of mtDNA/nuDNA measured after treatment or stress is substantially greater than the ratio of mtDNA/nuDNA measured prior to the treatment or stress.

[0114] Some embodiments relate to a method of assessing status of mitochondrial deficiency disease in a subject, comprising:

(a) providing data representing raw mitochondrial DNA (mtDNA) levels in a subject;

(b) normalizing the raw mtDNA data based on exercise status of the subject and at least two of the following factors selected from the group consisting of: age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, mitochondrial increase, and reference values specific to that subject to provide a normalized mtDNA value; and

(c) deducing the status of the mitochondrial deficiency disease in the subject based on the normalized mtDNA value.

[0115] In some embodiments, the method described herein further includes performing step (a) and step (b) on one or more healthy subject having no mitochondrial deficiency disease; and establishing a reference range based on the normalized mtDNA values obtained from the one or more healthy subject. [0116] In some embodiments, the deducing step further comprises comprising the normalized mtDNA value with the reference range.

[0117] In some embodiments, the method described herein can further include determining that the subject has no mitochondrial deficiency disease when the normalized mtDNA value falls within the reference range.

[0118] In some embodiments, the method described herein can further include determining the severity and progression of the mitochondrial deficiency disease in the subject based on the difference between the normalized mtDNA value of the subject and the reference range.

[0119] In some embodiments, the reference values specific to the subject can include cognitive test, tremor level, self-assessment, performance measure (e.g., timed walks, dexterity test, vision test), skill of daily living, disease rating scale (e.g. Friedreich Ataxia Rating Scale).

[0120] In some embodiments, the methods described herein can include administering a therapeutic treatment and determining whether the therapeutic treatment is effective by comparing the normalized mtDNA values measured prior treatment with the normalized mtDNA values measured post treatment.

[0121] In some embodiments, the methods described herein can include adjusting the therapeutic treatment based on the difference between the normalized mtDNA values measured prior treatment and the normalized mtDNA values measured post treatment.

[0122] In some embodiments, the therapeutic treatment is effective when the normalized mtDNA value prior to treatment is at least 1%, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%), 70%, 80%), 90%, 100% greater than value post treatment.

[0123] In some embodiments, the therapeutic treatment is effective when the normalized mtDNA value prior to treatment is at least 1 %, 5%, 10%, 15%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% less than the value post treatment.

[0124] In some embodiments, the therapeutic treatment is effective when the mtDNA/nuDNA ratio after treatment is at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%), 90%, 100%, 150%, 200%, or 300%> greater than value measured prior to treatment. In some embodiments, the ratio after treatment is measured 1 day, 2 days, 3days, 5 days, 7 days, 2 weeks, 3 weeks, 4 weeks, 1 month, 5 weeks, 6 weeks, 7 weeks after the first day that the subject receives the treatment. In some embodiments, the ratio prior to treatment is measured one week, 5 days, or one day before the patient receives the treatment.

[0125] Some embodiments relate to the method for treating a mitochondrial deficiency disease in a subject comprising ascertaining whether the subject has a mitochondrial DNA level that is substantially lower than the mitochondrial DNA level in a healthy subject; and if so, administering a polyunsaturated substance to the subject.

[0126] In some embodiments, the ascertaining step comprises requesting a test providing the results of an analysis to determine the mitochondrial DNA level in the subject.

[0127] In some embodiments, the level of the mitochondrial DNA is ascertained as a ratio of the mitochondrial DNA to nuclear DNA.

[0128] In some embodiments, the polyunsaturated substance is selected from the group consisting of a fatty acid, fatty acid ester, fatty acid thioester, fatty acid amide, fatty acid mimetic, and fatty acid prodrug, each isotopically modified at one or more positions.

[0129] In some embodiments, the mitochondrial deficiency disease is ataxia.

[0130] In some embodiments, the mitochondrial DNA level increases over time after the administration of the polyunsaturated substance to the subject.

[0131] In some embodiments, the method described herein further comprises continuing or increasing the administration of the polyunsaturated substance to the subject after an increase in mitochondrial DNA level is observed over a one-month period. In some embodiments, the method described herein further comprises continuing or increasing the administration of the polyunsaturated substance to the subject after an increase in mitochondrial DNA level is observed over a 3 days, 5 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, or 6 months period.

[0132] In some embodiments, the method described herein further comprises terminating the the administration of the polyunsaturated substance to the subject after no increase in mitochondrial DNA level is observed over a one-month period. In some embodiments, the method described herein further comprises terminating the the administration of the polyunsaturated substance to the subject after no increase in mitochondrial DNA level is observed over a 3 days, 5 days, 1 week, 2 weeks, 3 weeks, 4 weeks, 5 weeks, 6 weeks, 7 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, or 6 months period.

[0133] In some embodiments, the method described herein further comprises obtaining a biological sample from a subject, and processing the biological sample to separate cell free DNA from the rest of the sample.

[0134] Some embodiments relate to a method for enhancing mitochondrial DNA data, comprising:

obtaining a biological sample from a subject;

processing the biological sample to separate cell free DNA from the rest of the sample;

analyzing the cell free DNA to provide data representing mitochondrial DNA (mtDNA) levels in the subject, either as an absolute value or a ratio to nuclear DNA (nuDNA); and

generating user-readable output reflective of the modified data.

[0135] In some embodiments, the method described herein further comprises modifying the raw mtDNA data based on at least two factors selected from the group consisting of exercise status, age; sex; mitochondrial deficiency disease status, mitochondrial turnover rate, reflexes, trembling, strength testing, endurance, daily living skills, disease rating scales, electromyography, nerve conduction velocities, and genetic testing for disease- specific mutations, and reference values specific to that subject.

[0136] In some embodiments, the method described herein further comprises comparing the data representing mitochondrial DNA (mtDNA) levels in the subject with a reference data representing mitochondrial DNA (mtDNA) levels in a healthy subject having no mitochondrial deficiency disease.

[0137] In some embodiments, the processing step comprises undergoing one or more centrifugations to remove extracellular fractions. In some embodiments, centrifugation of the sample is performed at a speed of about 18,000 g or a range of 15000 to 20000 to isolate the extracellular fractions from the plasma fraction. In some embodiments, the plasma fraction is centrifugated at a speed of about 7000-17000 g. In some embodiments, centrifugation is performed at a speed of about 10,000-20,000 g.

[0138] In some embodiments, the processing step comprises separating plasma fraction from the sample. In some embodiments, the processing step comprises extracting DNA from the plasma fraction.

Treatment of impaired energy processing disorder and mitochondrial deficiency

[0139] In some embodiments, the treatment of impaired energy processing disorder and mitochondrial deficiency can include administering a pharmaceutical agent or therapy to the subject in need thereof.

[0140] In some embodiments, the pharmaceutical agent or therapy can be an isotopically modified polyunsaturated fatty acid or ester refers to a compound haying structural similarity to a naturally occurring PUFA that is stabilized chemically or by reinforcement with one or more isotopes, for example 13 C and/or deuterium. Generally, if deuterium is used for reinforcement, one or both hydrogens on a methylene group may be reinforced. Isotopically modified polyunsaturated fatty acid or ester includes those isotopically modified compounds described in US 2014/0044692, which is incorporated herein by reference in its entirety. In some embodiments, the pharmaceutical agent or therapy can be 9-cis, \2-cis-\ 1 , 1 l-D2-linoleic acid ethyl ester.

[0141] In some embodiments, the pharmaceutical agent or therapy can be vitamins {e.g., riboflavin), cofactors {e.g., coenzyme Q), amino acid {e.g. , carnitine), antioxidants, and any other suitable supplements. In some embodiments, the pharmaceutical agent or therapy can include CoQI O (5 - 15 mg/kg/day), Levo-carnitine (Variable, starting dose of 30 mg/kg/day, typical maximum of 100 mg/kg/day), Riboflavin (B2) (100 - 400 mg a day). In some embodiments, the pharmaceutical agent or therapy can include Acetyl-L- Carnitine (250 - 1000 mg per day), Thiamine (B l) (50 - 100 mg a day), Niacin (B3) (50 - 100 mg a day), Vitamin E (200 - 400 IU; 1 - 3 times a day), Vitamin C (100 - 500 mg; 1 - 3 times a day), Lipoic Acid (a -lipoate) (60 - 200 mg; 3 times a day), Selenium (25 - 50 micrograms a day), β -carotene (10,000 IU; every other day to daily), Biotin (2.5 - 10 mg a day), Folic Acid (1 - 10 mg a day). In some embodiments, the pharmaceutical agent or therapy can includey Calcium, Magnesium, Phosphorus, Succinate, Creatine, Uridine, Citrates, Prednisone, and Vitamin 3.

[0142] In some embodiments, the pharmaceutical agent or therapy can be coenzyme Q10, along with other antioxidants, as described in Parikh S. et al., Curr Treat Options Neurol. (2009) 1 1(6): 414^-30, which is incorporated herein by reference.

[0143] In some embodiments, the pharmaceutical agent or therapy can include adjusting the amount of fat (e.g., medium length triglyceride) or carbohydrate that is in the subject's diet.

[0144] In some embodiments, the pharmaceutical agent or therapy can include limit or reduce the amount of iron intake.

[0145] In some embodiments, the pharmaceutical agent or therapy can include additional supportive therapies such as physical therapy, speech therapy, respiratory therapy, or any other suitable therapy that may preserve or even improve the patient's existing functioning, mobility and strength.

[0146] In some embodiments, the pharmaceutical agent or therapy can include avoid or reduce the alcohol or cigarette use.

[0147] In some embodiments, the pharmaceutical agent or therapy can include avoid any intake of monosodium glutamate.

[0148] In some embodiments, the pharmaceutical agent or therapy can include avoiding or lowering physiologic stress. In some embodiments, the pharmaceutical agent or therapy can include avoiding or lowering physiologic stress from cold, heat, or starvation, or lack of sleep.

[0149] In some embodiments, the pharmaceutical agent or therapy can include administering an inhibitor of a Pumilio-like protein and/or an inhibitor of an S protein as described in WO 2014/105751 , which is incorporated herein by reference.

[0150] In some embodiments, the pharmaceutical agent or therapy can be 5- Hydroxytryptophan. In some embodiments, the pharmaceutical agent or therapy can be Idebenone. In some embodiments, the pharmaceutical agent or therapy can be in vivo treatment with interferon-gamma. In some embodiments, the pharmaceutical agent or therapy can be deferiprone. In some embodiments, the pharmaceutical agent or therapy can include near infrared muscle spectroscopy to monitor the biochemical and functional features of the subject.

[0151] In some embodiments, the treatment includes administering a polyunsaturated substance. In some embodiments, the polyunsaturated substance is a polyunsaturated lipid.

[0152] In some embodiments, the polyunsaturated lipid is selected from the group consisting of a fatty acid, fatty acid ester, fatty acid thioester, fatty acid amide, fatty acid mimetic, and fatty acid prodrug. In some embodiments, the polyunsaturated lipid is selected from the group consisting of a fatty acid, fatty acid ester, fatty acid thioester and fatty acid amide. In some embodiments, the polyunsaturated lipid is a fatty acid or fatty acid ester.

[0153] Polyunsaturated lipid having multiple double bonds can be isotopically modified using the methods described herein. In some embodiments, the polyunsaturated lipid has two or more carbon-carbon double bonds. In some embodiments, the polyunsaturated lipid has three or more carbon-carbon double bonds.

[0154] In some embodiments, the polyunsaturated fatty acid has a structure according to Formula (IA):

1 is selected from the group consisting of H and Ci_io alkyl;

R 2 is selected from the group consisting of -OH, -OR 3 , -SR 3 , phosphate, and -

N(R 3 ) 2 ;

each R is independently selected from the group consisting of C 1-10 alkyl, C 2- io alkene, C 2- i 0 alkyne, C 3 _io cycloalkyl, C 6- i 0 aryl, 4-10 membered heteroaryl, and 3- 10 membered heterocyclic ring, wherein each R is substituted or unsubstituted;

n is an integer of from 1 to 10; and

p is an integer of from 1 to 10.

[0155] In some embodiments, the polyunsaturated lipid is selected from the group consisting of omega-3 fatty acid, omega-6 fatty acid, and omega-9 fatty acid. In some embodiments, the polyunsaturated lipid is an omega-3 fatty acid. In some embodiments, the polyunsaturated lipid is an omega-6 fatty acid. In some embodiments, the polyunsaturated lipid is an omega-9 fatty acid.

[0156] In some embodiments, the polyunsaturated lipid is selected from the group consisting of linoleic acid and linolenic acid. In some embodiments, the polyunsaturated lipid is a linoleic acid. In some embodiments, the polyunsaturated lipid is a linolenic acid.

[0157] In some embodiments, the polyunsaturated lipid is selected from the group consisting of gamma linolenic acid, dihomo gamma linolenic acid, arachidonic acid, and docosatetraenoic acid.

[0158] In some embodiments, the polyunsaturated fatty acid ester is selected from the group consisting of a triglyceride, a diglyceride, and a monoglyceride.

[0159] In some embodiments, the fatty acid ester is an ethyl ester.

[0160] In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having deuterium at one or more bis-allylic sites.

[0161] In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having deuterium at all bis-allylic sites.

[0162] In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having deuterium at one or more mono-allylic sites.

[0163] In some embodiments, the polyunsaturated lipid have at least one 1 ,4- diene moiety. In some embodiments, the polyunsaturated lipid have two or more 1 ,4-diene moieties.

[0164] In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of more than 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 92%, 95%, 96%, 97%, 98%, or 99% at bis-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of more than 50% at bis-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of more than 90% at bis-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of more than 95% at bis-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree in the range of about 50% to about 95% at bis-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree in the range of about 80% to about 95% at bis-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree in the range of about 80% to about 99% at bis-allylic sites.

[0165] In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 80%, 70%, 60%, 50%, 45%, 40%, 35%, 30%, 20%, or 10% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 60% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 50% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 45% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 40% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 35% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of lower than 30% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of in the range of about 50% to about 20% at mono-allylic sites. In some embodiments, the isotopically-modified polyunsaturated lipid is a deuterated polyunsaturated lipid having a deuteration degree of in the range of about 60% to about 20% at mono-allylic sites.

EXAMPLES

Example 1 . mtDNA and nuDNA biomarker assessment in healthy volunteers at resting and after exercise stress [0166] This study can identify the absolute number and the ratio of mitochondrial DNA (mtDNA) to nuclear DNA (nuDNA) that are found in the plasma of healthy volunteers. The experiment protocol is combined with exercise testing, directly related to mitochondrial energetics with the possibly most sensitive and specific mitochondrial function biomarker.

[0167] 20 healthy volunteers participate in the test. Peak energy consumption is measured on the recumbent static bicycle for each volunteer with baseline and 2 hours post exercise plasma (mtDNA)/nuDNA) ratio.

[0168] The test can establish the levels of mitochondrial and nuclear DNA in healthy volunteers at rest, undergoing exercise stress conditions and following (9-cis, \ 2-cis- 1 1 , 1 l -D2-linoleic acid ethyl ester (D2-LA) 5.4 g (6 capsules of 900 mg) dosing. The test evaluates the acute pharmacokinetics (P ), and mitochondrial DNA/nuclear DNA (PD) in volunteers after being orally administered 6 capsules of study drug (D2-LA, 5.4g) and subjected to bike exercise to fatigue. The test follows the following protocol provided in Table 1.

Table 1. Measurement Protocol for Healthy Volunteer group

Day 4: PD blood sample (48 hours post- exercise Day 2)

[0169] Blood samples are collected for P and PD. P blood samples are collected in EDTA tubes, plasma separated and stored at -80 ° C. PD blood samples are collected in Streck tubes and the plasma is separated and stored at -80 ° C.

[0170] At baseline over time and under conditions of peak exercise effort, there are relatively small changes in the plasma mtDNA/nuDNA ratio and in the absolute level of mtDNA in healthy individuals. It is possible that D2-LA may blunt that response to effort compared to H2-LA.

[0171] It is possible that exercise may modify the mitochondrial lifespan in a differential way between FRDA patients and normal individuals as well as between FRDA patients with and without exposure to Deuterated Linoleic acid.

Example 2. mtDNA and nuDNA biomarker assessment in Patients with Mitochondrial

Deficiency Disease

[0172] This study can identify the absolute number and the ratio of mtDNA to nuDNA in the plasma of patients with mitochondrial deficiency. The experiment protocol is combined with exercise testing, directly related to mitochondrial energetics with the possibly most sensitive and specific mitochondrial function biomarker.

[0173] 20 patients are selected to participate in the test. Peak energy consumption is measured on the recumbent static bicycle for each patient with baseline and 2 hours post exercise plasma (mtDNA)/nuDNA) ratio.

[0174] The test measures the levels of mitochondrial and nuclear DNA in patients at rest, undergoing exercise stress conditions and following D2-LA 5.4 g (6 capsules of 900 mg) dosing. The test evaluates the acute pharmacokinetics (PK), and mitochondrial DNA/nuclear DNA (PD) in patients after being orally administered 6 capsules of study drug (D2-LA, 5.4g) and subjected to bike exercise. Exercise will be to fatigue. The test follows the following protocol provided in Table 2.

Table 2. Test Protocol for patient group

Time Procedures Day 1 : Pre-exercise PD blood sample, Exercise on bike 20 minutes sustained lipid/hematology/serum chemistry panel exercise (around 2 PM)

PD blood sample post-exercise: 0, l hr

Day 2: D2-LA administered in the morning Blood sample for lipid/hematology/serum chemistry panel;

PK blood sample profile: pre-dose, 0.5, 1,

1.5, 2, 4, 6, 8, 12 and 16 hours;

Pre-exercise PD blood sample (this sample is also 24 hours post-exercise Day 1 );

Exercise on bike 20 minutes sustained exercise (around 2 PM);

PD blood sample post-exercise: 0, l hr

Day 3 : PD blood sample (24 hours post- exercise Day 2)

Day 4: PD blood sample (48 hours post- exercise Day 2)

[0175] Blood samples are collected for PK and PD. PK blood samples are collected in EDTA tubes, plasma separated and stored at -80 ° C. PD blood samples are collected in Streck tubes and shipped to Biostorage where plasma is separated and stored at - 80 °C.

[0176] At baseline over time and under conditions of peak exercise effort, there are variations over time and after peak exercise effort for the patients. When compared with the measurement obtained from the healthy volunteer group in Example 1 , the variations for the overtime measurement and after peak exercise effort measured for the patients are significantly greater.

[0177] An increase in the ratio of mtDNA/nuDNA may be observed for the patient group administered with the isotopically modified polyunsaturated lipid, indicating the effectiveness of the isotopically modified polyunsaturated lipid in treating or inhibiting the progression of the mitochondrial deficiency such as Fredrick's Ataxia, Alzheimer, or Parkinson's Disease.

Example 3. Prognosis and Monitoring of Ataxia

[0178] Example 1 provides data necessary to establish the baseline in healthy volunteers the ratio of mitochondrial and nuclear DNA. The next step will be to use this method to determine the absolute number and the ratio of mitochondrial and nuclear DNA in patients with mitochondrial disease. The studies will consider patients with variants of the disease, and healthy normal volunteers to determine differences in the protein that might serve as a disease marker. An increase in the ratio of mtDNA/nuDNA over time can be indicative that the treatment is effective in treating or inhibiting the progression of the Ataxia disease.

Example 4. Sample Preparation

[0179] Collection and transport of blood samples: The blood samples of healthy individuals or patients were collected into Streck Cell-free DNA BCT (approximately 10 ml per subject). The BCTs were inverted 10 times and kept at room temperature. The BCTs were labeled with appropriate labels. Each BCT were uniquely identified and labeled. The BCTs were stored at 18 - 24 °C.

[0180] Preparation and storage of plasma: Blood were centrifuged at 1 ,600 x g for 15 min at room temperature (15 - 25 °C). Plasma (top layer; 4.5 - 5 ml) were transferred to a fresh tube. Care was taken not to disturb the buffy coat layer (white middle layer above the erythrocyte layer; approximately 100 μΐ). Buffy coat were collected and dispensed into one or more 2-ml tubes, depending on volume. All remaining RBCs were collected and dispensed into one or more 2ml tubes, depending on volume remaining. The second centrifugation, which involved ONLY the plasma tube, was done at 2,500 x g for 10 min at room temperature. Plasma (approximately 4 ml) was collected. A residual amount of plasma (approximately 0.5 ml) was left in the bottom of the centrifuge tube to avoid contamination with cells. The collected plasma were aliquoted into two cryovials (2 x approximately 2 ml) and stored frozen at - 70 °C or lower along with the buffy coat and RBC aliquots.

[0181] Preparation of cell-free DNA from plasma using a Qiagen kit and its storage: Preparation of cell-free DNA from plasma was carried out by using a QIAamp DSP Circulating NA Kit (catalog number 61504; Qiagen). A QIAvac 24 Plus vacuum manifold (catalog number 19413; Qiagen), along with a QIAvac Connecting System (catalog number 19413; Qiagen) and an appropriate vacuum pump, were used to process, in parallel, up to 24 QIAamp Mini columns of the QIAamp DSP Circulating NA Kit.

[0182] Plasma was prepared from whole blood and stored frozen in 2-ml aliquots. Preparation of cell-free DNA were performed by using a plasma volume of either 2 ml or 4 ml (i.e., two 2-ml aliquots from a single blood sample are combined). Plasma samples, which have been stored frozen at - 70 °C or lower, were thawed at room temperature and subjected immediately to the preparation of cell-free DNA.

[0183] The preparation of plasma from the whole blood can be adjusted by increasing the centrifugation speed. For example, blood sample can be centrifuged at 7,000- 17,000 x g for 15 min at room temperature (15 - 25 °C). The second centrifugation, which involved only the plasma tube, can be done at 18,000 x g for 10 min at room temperature.

[0184] Prior to the initiation of the preparation of cell-free DNA from plasma, the following buffers in the QIAamp DSP Circulating NA Kit were prepared. Buffer ACB - Add 200 ml of isopropyl alcohol (100%; also called incorrectly "isopropanol") to the Buffer ACB concentrate (300 ml) and mix well. Buffer ACW 1 - Add 25 ml of ethanol (96 - 100%) to the Buffer ACW 1 concentrate (13 ml) and mix well. Buffer ACW2 - Add 30 ml of ethanol (96 - 100%) to the Buffer ACW2 concentrate (13 ml) and mix well. Carrier RNA - Add 1 ,550 μΐ of Buffer AVE to the tube containing 310 μg of lyophilized carrier RNA. The carrier RNA was dissolved by thorough mixing, aliquoted, and store frozen at - 15°C or lower. Repeated freeze-thaw cycles were avoided. Buffer ACL - Add Buffer AVE containing carrier RNA, prepared above, to Buffer ACL.

[0185] Preparation of cell-free DNA from 2 ml of plasma: When the volume of each plasma sample was smaller than 2 ml, phosphate-buffered saline (PBS) was added to adjust the final volume to 2 ml. The proteinase K solution (200 μΐ each) in the QIAamp DSP Circulating NA Kit was dispensed into 50-ml centrifuge tubes. Each plasma sample (2 ml), which was thawed as above and equilibrated at room temperature, was added to the 50-ml centrifuge tube containing proteinase K. Buffer ACL containing carrier RNA, prepared as above, (1.6 ml each) was added to the 50-ml centrifuge tube, mixed thoroughly by pulse-vortexing for 30 sec, and incubated at 60°C for 60 min. The resulting mixture was termed "a lysate". Buffer ACB (3.6 ml each) was added to each lysate in a 50-ml tube, mixed thoroughly by pulse-vortexing for 15 - 30 sec, and incubate on ice for 5 min. QIAamp Mini columns in the QIAamp DSP Circulating NA Kit was placed into a QIAvac 24 Plus vacuum manifold with the VacConnector. Each lysate prepared above was applied into the column extender of a QIAamp Mini column. Pressure was applied to each column by a vacuum pump, which was connected to the QIAvac 24 Plus vacuum manifold. When all lysates were drawn through the QIAamp Mini columns, the vacuum pump was turned off, and the applied pressure was released. The column extenders were removed and discarded.

[0186] Buffer ACW 1 (600 μΐ each) was applied to the QIAamp Mini columns. As in step described above pressure was applied to each QIAamp Mini column by the vacuum pump, which was turned off when applied. Buffer ACW 1 was drawn through the QIAamp Mini columns. The QIAamp Mini columns will be washed with Buffer ACW2 (750 μΐ each) in the same manner as in the step above. The QIAamp Mini columns were washed with ethanol (96 - 100%; 750 μΐ each) in the same manner as in Steps 7 - 9 above. The lid of each QIAamp Mini column was closed, followed by the removal of the columns from the QIAvac 24 Plus vacuum manifold. Each QIAamp Mini column was placed in a clean 2-ml wash tube and centrifuged at full speed (20,000 x g) for 3 min. Then, each QIAamp Mini column was placed in a new 2-ml wash tube. Each QIAamp Mini column was incubated at 56 °C for 10 min after its lid has been opened. During the incubation, the membrane of the column was dried completely. Each QIAamp Mini column was placed in a clean 1 .5-ml elution tube in the QIAamp DSP Circulating NA Kit. Buffer AVE was applied to the center of the membrane of each QIAamp Mini column. The lid of each column was closed, followed by incubation at room temperature (15 - 25 °C ) for 3 min. Each 1.5-ml elution tube containing a QIAamp Mini column was centrifuged at full speed (20,000 x g) for 1 min. Eluted nucleic acids in the 1.5-ml elution tube was stored frozen at - 20 °C or lower.

[0187] Preparation of cell-free DNA from 4 ml of plasma: When the volume of each plasma sample was smaller than 4 ml, phosphate-bufferd saline (PBS) was added to adjust the final volume to 4 ml. The proteinase K solution (400 μΐ each) in the QIAamp DSP Circulating NA Kit was dispensed into 50-ml centrifuge tubes. Each plasma sample (4 ml), which has been thawed as above and equilibrated at room temperature, was added to the 50- ml centrifuge tube containing proteinase . Buffer ACL containing carrier NA, prepared as above, (1 .6 ml each) was added to the 50-ml centrifuge tube, mixed thoroughly by pulse- vortexing for 30 sec, and incubated at 60 °C for 60 min. The resulting mixture was termed "a lysate"._Buffer ACB (7.2 ml each) was added to each lysate in a 50-ml tube, mixed thoroughly by pulse-vortexing for 15 - 30 sec, and incubate on ice for 5 min. QIAamp Mini columns in the QIAamp DSP Circulating NA Kit was placed into a QIAvac 24 Plus vacuum manifold with the VacConnector._Each lysate was applied into the column extender of a QIAamp Mini column. Pressure was applied to each column by a vacuum pump, which was connected to the QIAvac 24 Plus vacuum manifold. When all lysates have been drawn through the QIAamp Mini columns, the vacuum pump was turned off, and the applied pressure was released. The column extenders was removed and discarded. Buffer ACW 1 (600 μΐ each) was applied to the QIAamp Mini columns. As in Step 7 above pressure was applied to each QIAamp Mini column by the vacuum pump, which was turned off when applied Buffer ACW1 has been drawn through the QIAamp Mini columns. The QIAamp Mini columns was washed with Buffer ACW2 (750 μΐ each) in the same manner as in the step described above. The QIAamp Mini columns was washed with ethanol (96 - 100%; 750 μΐ each) in the same manner as in the steps described above._The lid of each QIAamp Mini column was closed, followed by the removal of the columns from the QIAvac 24 Plus vacuum manifold. Each QIAamp Mini column was placed in a clean 2-ml wash tube and centrifuged at full speed (20,000 x g) for 3 min. Then, each QIAamp Mini column was placed in a new 2-ml wash tube. Each QIAamp Mini column was incubated at 56 °C for 10 min after its lid has been opened. During the incubation, the membrane of the column should be dried completely._E ac h QIAamp Mini column was placed in a clean 1.5-ml elution tube in the QIAamp DSP Circulating NA Kit. Buffer AVE (55 μΐ each; this volume will need to be confirmed) was applied to the center of the membrane of each QIAamp Mini column. The lid of each column was closed, followed by incubation at room temperature (15 - 25 °C) for 3 min. Each 1 .5-ml elution tube containing a QIAamp Mini column was centrifuged at full speed (20,000 x g) for 1 min. Eluted nucleic acids in the 1 .5-ml elution tube was stored frozen at - 20 °C or lower.

Example 5.Analysis of Samples from healthy individuals [0188] Circulating cell-free DNA samples from multiple healthy volunteers were analyzed. The cell-free DNA samples extracted from plasma were prepared using the procedures described in Example 4. Quantifications of the total nuclear cfDNA and mitochondrial cfDNA were based on the amplification of sequences using digital PCR and measurement using a benchtop mass spectrometer system. The results are shown in Table 1.

Table 1

Example 6.Analysis of Samples from healthy individuals and patients

[0189] Analysis of Circulating cell-free DNA samples from healthy volunteers and patients with Fredrick's ataxia was conducted. The cell-free DNA samples from plasma were prepared using the procedures described in Example 4. Quantifications of the total nuclear cfDNA and mitochondrial cfDNA were based on the amplification of sequences using digital PCR and measurement using a benchtop mass spectrometer system. The results are shown in Table 2.

Table 2

Patient #2 nuDNA 1 8.5 4 4 34

Healthy #1 mtDNA 25 2457 20 500 1228500 9307

Healthy #1 nuDNA 1 33 4 4 132

Healthy #2 mtDNA 25 2016 20 500 1008000 15652

Healthy #2 nuDNA 1 16.1 4 4 64

Healthy #3 mtDNA 25 3350 20 500 1675000 6374

Healthy #3 nuDNA 1 65.7 4 4 263

[0190] As shown in Table 2, the mtDNA/nuDNA ratio for healthy volunteers was higher than the ratio for patients with Fredrick's ataxia.

Example 7. Sample Preparation

[0191] Biological samples collected form the subject are processed to first separate into vesicular and soluble fractions. Two centrifugation steps are performed in this step to isolate the vesicular fractions. The first centrifugation involves centrifuging the sample at 18,000 x g for 15 min at room temperature (15 - 25 °C). After the plasma is transferred to a fresh tube, the plasma tube is centrifuged at 7000-17000 x g for 10 min at room temperature. DNA extraction is performed from the plasma fraction and is later used to conduct analysis of the mitochondrial DNA level and/or the ratio of mitochondrial DNA to nuclear DNA.