COMPANION DIAGNOSTICS FOR MITOCHONDRIAL INHIBITORS

Abstract

The present disclosure relates to methods of identifying patients that may be responsive to mitochondrial inhibitor therapies to target and eradicate cancer stem cells. Also described are diagnostic kits that may be used to identify patients responsive to mitochondrial inhibitor therapies.

Claims

1. A method for identifying a breast cancer patient for anti-mitochondrial therapy, the method comprising: obtaining a breast tumor sample obtained from the patient; determining a level of at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence selected from: at least one prognostic mitochondrial chaperone protein or mRNA selected from HSPD1, HSPA9, FXN, and TRAP1; at least one prognostic mitochondrial membrane protein or mRNA selected from VDAC2, AKAP1, IMMT, TOMM70A, TIMM44, TIMM13, TIMM17A, TIMM17A, TIMM17B; at least one prognostic mitochondrial carrier family protein or mRNA selected from SLC25A38, SLC25A1, SLC25A5, SLC25A32; the prognostic mitochondrial antioxidant protein or mRNA SOD2; at least one prognostic mitochondrial creatine kinase selected from CKMT2 and CKMT1A; at least one prognostic large mitochondrial ribosomal subunit protein or mRNA selected from MRPL15, MRPL18, MRPL46, MRPL24, MRPL13, MRPL48, MRPL3, MRPL23, MRPL4, MRPL17, MRPL42, and MRPL44; at least one prognostic small mitochondrial ribosomal subunit protein or mRNA selected from MRPS12, MRPS11, MRPS28, MRPL42, MRPS22, and MRPS33; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFA8, NDUFA6, NDUFS1, NDUFS3, NDUFB6, NDUFV1, NDUFS6, and NDUFA1; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from UQCRB, UQCR6, UQCR4, and UQCRC2; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX17, COX5B, COX4I1, COX6A1, COX4NB, and COX7A2; and at least one OXPHOS complex V subunit selected from ATP5J, ATP5J2, ATP5C1, ATP5C1, ATP5C1, PPA1, ATP50, ATP5E, and ATP5G3; classifying the patient as a candidate for therapy with an anti-mitochondrial therapy, wherein a patient is classified as a candidate for therapy with an anti-mitochondrial therapy if the sample is determined to have an increased level of the at least one mitochondrial marker relative to a threshold level; and if the patient is classified as a candidate for anti-mitochondrial therapy, administering at least one mitochondrial inhibitor.

2. The method of claim 1, wherein the mitochondrial inhibitor inhibits the propagation of breast cancer stem cells.

3. The method of claim 2, wherein the breast cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

4. The method of claim 1, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

5. The method of claim 1, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

6. The method of claim 1, wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises at least one of HSPD1, UQCRB, MRPL15, and COX17.

7. The method of claim 1, wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises at least two prognostic markers selected from HSPD1, UQCRB, MRPL15, and COX17.

8. The method of claim 1, wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises the combination of HSPD1, UQCRB, MRPL15, and COX17.

9. The method of claim 1, wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises the combination of VDAC2 and HSPD1.

10. The method of claim 1, further comprising determining a level of at least two mitochondrial marker having prognostic value for breast cancer metastasis and recurrence.

11. The method of claim 1, further comprising determining a level of at least three mitochondrial markers having prognostic value for breast cancer metastasis and recurrence.

12. A method for identifying a lung cancer patient for anti-mitochondrial therapy, the method comprising: obtaining a lung tumor sample obtained from the patient; determining a level of at least one mitochondrial marker having prognostic value for lung cancer metastasis and recurrence selected from: at least one prognostic mitochondrial heat shock protein or mRNA or mitochondrial membrane protein or mRNA selected from HSPD1, TIMM23, TIMM8B, TIMM17B, TIMM44, TIMM10B, TIMM9, TIMM17A, TIMM13, TJMM23, TIMM10, TOMM40, TOMM22, TOMM34, TOMM7, TOMM70A, TOMM20, VDAC1, VDAC3, VDAC2, AKAP1, and SLC25A5; at least one prognostic mitochondrial creatine kinase selected from CKMT1A and CKMT2; at least one prognostic mitochondrial genome maintenance protein or mRNA selected from PRKDC, PRKDC, and PRKDC; at least one prognostic large mitochondrial ribosomal subunit protein or mRNA selected from MRPL48, MRPL23, MRPL11, MRPL52, MRPL34, MRPL12, MRPL2, MRPL42, MRPL24, MRPL4, MRPL44, MRPL17, MRPL35, MRPL28, MRPL20, MRPL49, MRPL13, MRPL16, MRPL40, MRPL15, and MRPL33; at least one prognostic small mitochondrial ribosomal subunit protein or mRNA selected from MRPS12, MRPS12, MRPS12, MRPS12, MRPS7, MRPS2, MRPS4, MRPS11, MRPS34, MRPS31, MRPS28, MRPS35, MRPS15, MRPS27, MRPS30, MRPS33, and MRPS14; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFB3, NDUFS8, NDUFS8, NDUFS4, NDUFA4L2, NDUFB4, NDUFA13, NDUFV2, NDUFS3, NDUFA10, NDUFA3, NDUFB8, NDUFB2, NDUFA5, NDUFA7, NDUFA1, NDUFS2, NDUFB7, NDUFS5, NDUFA2, NDUFA9, NDUFS7, NDUFB6, NDUFA2, NDUFB11, NDUFB2, and NDUFV1; at least one prognostic OXPHOS complex II subunit protein or mRNA selected from SDHC and SDHB; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from UQCR7, UQCR6, UQCR8, UQCRFS1, UQCR4/CYCI, BCS1L, and UQCR; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX5B, COX6A, COX8A, COX17, COX6C, COX7A2, COX6B, COX6A2, COX10, COX7B, COX10, COX15, COX5A, COX4NB, COX7A, and COX4I1; at least one prognostic OXPHOS complex V subunit protein or mRNA selected from ATP5J2, ATP5G3, ATP5H, ATP5I, ATP5D, ATP5G2, ATP5E, ATPSL, ATP5B, ATP5S, ATP5G, ATP5O, and ATP5C; classifying the patient as a candidate for therapy with an anti-mitochondrial therapy, wherein a patient is classified as a candidate for therapy with an anti-mitochondrial therapy if the sample is determined to have an increased level of the at least one mitochondrial marker relative to a threshold level; and if the patient is classified as a candidate for anti-mitochondrial therapy, administering at least one mitochondrial inhibitor.

13. The method of claim 12, wherein the mitochondrial inhibitor inhibits the propagation of lung cancer stem cells.

14. The method of claim 13, wherein the lung cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

15. The method of claim 12, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

16. The method of claim 12, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

17. The method of claim 12, further comprising determining a level of at least two mitochondrial marker having prognostic value for lung cancer metastasis and recurrence.

18. The method of claim 12, further comprising determining a level of at least three mitochondrial markers having prognostic value for lung cancer metastasis and recurrence.

19. A method for identifying a gastric cancer patient for anti-mitochondrial therapy, the method comprising: obtaining a gastric tumor sample obtained from the patient; determining a level of at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence selected from: at least one prognostic heat shock protein or mRNA or mitochondrial chaperone protein or mRNA selected from HSPD1, HSPA9, and FXN; at least one prognostic mitochondrial membrane protein or mRNA selected from VDAC3, VDAC2, IMMT, TIMM23, TIMM10, TTMM8B, TIMM17A, TOMM34, and TOMM40; a prognostic mitochondrial antioxidant protein or mRNA comprising SOD2; a prognostic mitochondrial genome maintenance protein or mRNA comprising PRKDC; at least one prognostic large mitochondrial ribosomal subunit protein or mRNA selected from MRPL28, MRPL52, MRPL17, MRPL20, MRPL18, MRPL2, MRPL12, MRPL3, MRPL42, MRPL13, MRPL48, and MRPL23; at least one prognostic small mitochondrial ribosomal subunit protein or mRNA selected from MRPS11, MRPS12, MRPS14, MRPS22, MRPS28, and MRPS34; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFS5, NDUFA5, NDUFA9, NDUFS6, NDUFB8, NDUFB3, NDUFB4, NDUFA6, NDUFA8, NDUFA7, and NDUFA3; a prognostic OXPHOS complex II subunit protein or mRNA comprising SDHB; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from BCS1L and UQCR8; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX5B, COX4NB, COX6C, COX6B1, COX6A1, COX17, COX5A, COX7B, COX7A2, and COX10; at least one prognostic OXPHOS complex V subunit protein or mRNA selected from ATP5O, ATP5G2, ATP5I, ATP5E, ATP5G1, ATP5H, ATP5J2, ATP5L, ATP5C, ATP5S, and ATP5C1; classifying the patient as a candidate for therapy with an anti-mitochondrial therapy, wherein a patient is classified as a candidate for therapy with an anti-mitochondrial therapy if the sample is determined to have an increased level of the at least one mitochondrial marker relative to a threshold level; and if the patient is classified as a candidate for anti-mitochondrial therapy, administering at least one mitochondrial inhibitor.

20. The method of claim 19, wherein the mitochondrial inhibitor inhibits the propagation of gastric cancer stem cells.

21. The method of claim 20, wherein the gastric cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

22. The method of claim 19, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

23. The method of claim 19, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

24. The method of claim 19, further comprising determining a level of at least two mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence.

25. The method of claim 19, further comprising determining a level of at least three mitochondrial markers having prognostic value for gastric cancer metastasis and recurrence.

26. The method of claim 19, wherein the at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence comprises at least one of NDUFS5, VDAC3, ATP5O, IMMT, MRPL28, COX5B, MRPL52, and PRKDC.

27. The method of claim 19, wherein the at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence comprises at least two of NDUFS5, VDAC3, ATP5O, IMMT, MRPL28, COX5B, MRPL52, and PRKDC.

28. The method of claim 19, wherein the at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence comprises the combination of NDUFSS, VDAC3, ATP5O, IMMT, MRPL28, COX5B, MRPL52, and PRKDC.

29. A method for identifying a ovarian cancer patient for anti-mitochondrial therapy, the method comprising: obtaining a ovarian tumor sample obtained from the patient; determining a level of at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence selected from: a prognostic mitochondrial heat shock protein or mRNA comprising HSPA9; at least one prognostic mitochondrial membrane protein or mRNA selected from IMMT, TIMM10, TIMM17A, TIMMIOB, TIMM23, TOMM70A, VDAC2, VDAC3, SLC25A5, and SLC25A32; at least one prognostic mitochondrial antioxidant protein or mRNA selected from NQO1 and SOD2; a prognostic mitochondrial creatine kinase comprising CKMT2; at least one prognostic mitochondrial large ribosomal subunit protein or mRNA selected from MRPL49, MRPL34, MRPL35, MRPL23, MRPL18, MRPL48, MRPL17, MRPL16, MRPL11, and MRPL4; at least one prognostic mitochondrial small ribosomal subunit protein or mRNA selected from MRPS14, MRPS12, MRPS4, MRPS28, MRPS2, MRPS22, MRPS33, MRPS35, MRPS31, and MRPS15; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFA3, NDUFB11, NDUFS3, NDUFB2, NDUFB3, NDUFS8, NDUFB2, NDUFB6, NDUFA7, NDUFA13, NDUFS4, NDUFA8, NDUFSS, NDUFV2, NDUFV1, NDUFA2, NDUFS7, NDUFA10, NDUFA1, NDUFA9, and NDUFS2; at least one prognostic OXPHOS complex II subunit protein or mRNA selected from SDHC and SDHB; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from UQCRFS1, UQCR7, UQCR6, UQCR, and UQCR2; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX6B, COX17, COX10, COX5B, COX7B, COX4NB, COX4I1, COX8A, and COX7A; at least one prognostic OXPHOS complex V subunit protein or mRNA selected from ATP5C, ATP5L, ATP5G, ATP5G3, ATP5J2, PPA1, and ATP5J; classifying the patient as a candidate for therapy with an anti-mitochondrial therapy, wherein a patient is classified as a candidate for therapy with an anti-mitochondrial therapy if the sample is determined to have an increased level of the at least one mitochondrial marker relative to a threshold level; and if the patient is classified as a candidate for anti-mitochondrial therapy, administering at least one mitochondrial inhibitor.

30. The method of claim 29, wherein the mitochondrial inhibitor inhibits the propagation of ovarian cancer stem cells.

31. The method of claim 30, wherein the ovarian cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

32. The method of claim 29, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

33. The method of claim 29, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

34. The method of claim 29, further comprising determining a level of at least two mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence.

35. The method of claim 29, further comprising determining a level of at least three mitochondrial markers having prognostic value for ovarian cancer metastasis and recurrence.

36. The method of claim 29, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence comprises at least one of UQCRFS1 and MRPL49.

37. The method of claim 29, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence comprises the combination of UQCRFS1 and MRPL49.

38. The method of claim 29, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence comprises the combination of UQCRFS1 and NDUFA3.

39. The method of claim 38, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence further comprises PCNA.

40. A method for treating breast cancer with an anti-mitochondrial therapy, the method comprising: administering at least one mitochondrial inhibitor if a breast cancer sample level of at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence exceeds a threshold level; wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises: at least one prognostic mitochondrial chaperone protein or mRNA selected from HSPD1, HSPA9, FXN, and TRAP1; at least one prognostic mitochondrial membrane protein or mRNA selected from VDAC2, AKAP1, IMMT, TOMM70A, TIMM44, TIMM13, TIMM17A, TIMM17A, TIMM17B; at least one prognostic mitochondrial carrier family protein or mRNA selected from SLC25A38, SLC25A1, SLC25A5, SLC25A32; the prognostic mitochondrial antioxidant protein or mRNA SOD2; at least one prognostic mitochondrial creatine kinase selected from CKMT2 and CKMT1A; at least one prognostic large mitochondrial ribosomal subunit protein or mRNA selected from MRPL15, MRPL18, MRPL46, MRPL24, MRPL13, MRPL48, MRPL3, MRPL23, MRPL4, MRPL17, MRPL42, and MRPL44; at least one prognostic small mitochondrial ribosomal subunit protein or mRNA selected from MRPS12, MRPS11, MRPS28, MRPL42, MRPS22, and MRPS33; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFA8, NDUFA6, NDUFS1, NDUFS3, NDUFB6, NDUFV1, NDUFS6, and NDUFA1; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from UQCRB, UQCR6, UQCR4, and UQCRC2; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX17, COXSB, COX4I1, COX6A1, COX4NB, and COX7A2; and at least one OXPHOS complex V subunit selected from ATP5J, ATP5J2, ATP5C1, ATP5C1, ATP5C1, PPA1, ATP5O, ATP5E, and ATP5G3.

41. The method of claim 40, wherein the mitochondrial inhibitor inhibits the propagation of breast cancer stem cells.

42. The method of claim 41, wherein the breast cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

43. The method of claim 40, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

44. The method of claim 40, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

45. The method of claim 40, wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises the combination of HSPD1, UQCRB, MRPL15, and COX17.

46. The method of claim 40, wherein the at least one mitochondrial marker having prognostic value for breast cancer metastasis and recurrence comprises the combination of VDAC2 and HSPD1.

47. A method for treating lung cancer with an anti-mitochondrial therapy, the method comprising: administering at least one mitochondrial inhibitor if a lung cancer sample level of at least one mitochondrial marker having prognostic value for lung cancer metastasis and recurrence exceeds a threshold level; wherein the at least one mitochondrial marker having prognostic value for lung cancer metastasis and recurrence comprises: at least one prognostic mitochondrial heat shock protein or mRNA or mitochondrial membrane protein or mRNA selected from HSPD1, TIMM23, TIMM8B, TIMM17B, TIMM44, TIMM10B, TIMM9, TIMM17A, TIMM13, TIMM23, TIMM10, TOMM40, TOMM22, TOMM34, TOMM7, TOMM70A, TOMM20, VDAC1, VDAC3, VDAC2, AKAP1, and SLC25A5; at least one prognostic mitochondrial creatine kinase selected from CKMT1A and CKMT2; at least one prognostic mitochondrial genome maintenance protein or mRNA selected from PRKDC, PRKDC, and PRKDC; at least one prognostic large mitochondrial ribosomal subunit protein or mRNA selected from MRPL48, MRPL23, MRPL11, MRPL52, MRPL34, MRPL12, MRPL2, MRPL42, MRPL24, MRPL4, MRPL44, MRPL17, MRPL35, MRPL28, MRPL20, MRPL49, MRPL13, MRPL16, MRPL40, MRPL15, and MRPL33; at least one prognostic small mitochondrial ribosomal subunit protein or mRNA selected from MRPS12, MRPS12, MRPS12, MRPS12, MRPS7, MRPS2, MRPS4, MRPS11, MRPS34, MRPS31, MRPS28, MRPS35, MRPS15, MRPS27, MRPS30, MRPS33, and MRPS14; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFB3, NDUFS8, NDUFS8, NDUFS4, NDUFA4L2, NDUFB4, NDUFA13, NDUFV2, NDUFS3, NDUFA10, NDUFA3, NDUFB8, NDUFB2, NDUFA5, NDUFA7, NDUFA1, NDUFS2, NDUFB7, NDUFS5, NDUFA2, NDUFA9, NDUFS7, NDUFB6, NDUFA2, NDUFB11, NDUFB2, and NDUFV1; at least one prognostic OXPHOS complex II subunit protein or mRNA selected from SDHC and SDHB; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from UQCR7, UQCR6, UQCR8, UQCRFS1, UQCR4/CYC1, BCS1L, and UQCR; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX5B, COX6A, COX8A, COX17, COX6C, COX7A2, COX6B, COX6A2, COX10, COX7B, COX10, COX15, COX5A, COX4NB, COX7A, and COX4I1; at least one prognostic OXPHOS complex V subunit protein or mRNA selected from ATP5J2, ATP5G3, ATP5H, ATP5I, ATP5D, ATP5G2, ATP5E, ATP5L, ATP5B, ATP5S, ATP5G, ATP5O, and ATP5C.

48. The method of claim 47, wherein the mitochondrial inhibitor inhibits the propagation of lung cancer stem cells.

49. The method of claim 48, wherein the lung cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

50. The method of claim 47, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

51. The method of claim 47, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

52. A method for treating gastric cancer with an anti-mitochondrial therapy, the method comprising: administering at least one mitochondrial inhibitor if a gastric cancer sample level of at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence exceeds a threshold level; wherein the at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence comprises: at least one prognostic heat shock protein or mRNA or mitochondrial chaperone protein or mRNA selected from HSPD1, HSPA9, and FXN; at least one prognostic mitochondrial membrane protein or mRNA selected from VDAC3, VDAC2, IMMT, TIMM23, TIMM10, TIMM8B, TIMMI7A, TOMM34, and TOMM40; a prognostic mitochondrial antioxidant protein or mRNA comprising SOD2; a prognostic mitochondrial genome maintenance protein or mRNA comprising PRKDC; at least one prognostic large mitochondrial ribosomal subunit protein or mRNA selected from MRPL28, MRPL52, MRPL17, MRPL20, MRPL18, MRPL2, MRPL12, MRPL3, MRPL42, MRPL13, MRPL48, and MRPL23; at least one prognostic small mitochondrial ribosomal subunit protein or mRNA selected from MRPS11, MRPS12, MRPS14, MRPS22, MRPS28, and MRPS34; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFS5, NDUFA5, NDUFA9, NDUFS6, NDUFB8, NDUFB3, NDUFB4, NDUFA6, NDUFA8, NDUFA7, and NDUFA3; a prognostic OXPHOS complex H subunit protein or mRNA comprising SDHB; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from BCS1L and UQCR8; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX5B, COX4NB, COX6C, COX6B1, COX6A1, COX17, COXSA, COX7B, COX7A2, and COX10; and at least one prognostic OXPHOS complex V subunit protein or mRNA selected from ATP5O, ATP5G2, ATP5I, ATP5E, ATP5G1, ATP5H, ATP5J2, ATP5L, ATP5C, ATP5S, and ATP5C1.

53. The method of claim 52, wherein the mitochondrial inhibitor inhibits the propagation of gastric cancer stem cells.

54. The method of claim 53, wherein the gastric cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

55. The method of claim 52 wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

56. The method of claim 52, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

57. The method of claim 52, wherein the at least one mitochondrial marker having prognostic value for gastric cancer metastasis and recurrence comprises at least two or more of NDUFS5, VDAC3, ATPSO, IMMT, MRPL28, COXSB, MRPL52, and PRKDC.

58. A method for treating ovarian cancer with an anti-mitochondrial therapy, the method comprising: administering at least one mitochondrial inhibitor if a ovarian cancer sample level of at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence exceeds a threshold level; wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence comprises: a prognostic mitochondrial heat shock protein or mRNA comprising HSPA9; at least one prognostic mitochondrial membrane protein or mRNA selected from IMMT, TIMM10, TIMM17A, TIMM10B, TIMM23, TOMM70A, VDAC2, VDAC3, SLC25A5, and SLC25A32; at least one prognostic mitochondrial antioxidant protein or mRNA selected from NQO1 and SOD2; a prognostic mitochondrial creatine kinase comprising CKMT2; at least one prognostic mitochondrial large ribosomal subunit protein or mRNA selected from MRPL49, MRPL34, MRPL35, MRPL23, MRPL18, MRPL48, MRPL17, MRPL16, MRPL11, and MRPL4; at least one prognostic mitochondrial small ribosomal subunit protein or mRNA selected from MRPS14, MRPS12, MRPS4, MRPS28, MRPS2, MRPS22, MRPS33, MRPS35, MRPS31, and MRPS15; at least one prognostic OXPHOS complex I subunit protein or mRNA selected from NDUFA3, NDUFB11, NDUFS3, NDUFB2, NDUFB3, NDUFS8, NDUFB2, NDUFB6, NDUFA7, NDUFA13, NDUFS4, NDUFA8, NDUFS8, NDUFV2, NDUFV1, NDUFA2, NDUFS7, NDUFA10, NDUFA1, NDUFA9, and NDUFS2; at least one prognostic OXPHOS complex II subunit protein or mRNA selected from SDHC and SDHB; at least one prognostic OXPHOS complex III subunit protein or mRNA selected from UQCRFS1, UQCR7, UQCR6, UQCR, and UQCR2; at least one prognostic OXPHOS complex IV subunit protein or mRNA selected from COX6B, COX17, COX10, COX5B, COX7B, COX4NB, COX4I1, COX8A, and COX7A; and at least one prognostic OXPHOS complex V subunit protein or mRNA selected from ATP5C, ATP5L, ATP5G, ATP5G3, ATP5J2, PPA1, and ATP5J.

59. The method of claim 58, wherein the mitochondrial inhibitor inhibits the propagation of ovarian cancer stem cells.

60. The method of claim 59, wherein the ovarian cancer stem cells comprise drug-resistant stem cells, and further comprising administering at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

61. The method of claim 58, wherein the at least one mitochondrial inhibitor comprises at least one mitochondrial biogenesis inhibitor and at least one of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.

62. The method of claim 58, wherein the mitochondrial inhibitor is at least one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, a tetracycline family member, a erythromycin family member, atovaquone, bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.

63. The method of claim 58, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence comprises the combination of UQCRFS1 and MRPL49.

64. The method of claim 58, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence comprises the combination of UQCRFS1 and NDUFA3.

65. The method of claim 67, wherein the at least one mitochondrial marker having prognostic value for ovarian cancer metastasis and recurrence further comprises PCNA.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0012] FIGS. 1A-E illustrate the structures of antibiotics that may be used inhibit the propagation of cancer stem cells (CSCs).

[0013] FIGS. 2A-D illustrate the structures of naturally occurring compounds that may be used to inhibit the propagation of CSCs.

[0014] FIGS. 3A-C illustrate the structures of experimental compounds that may be used to inhibit the propagation of CSCs.

[0015] FIGS. 4A-D illustrate the structure of exemplary mitoriboscins.

[0016] FIG. 5 illustrates an exemplary pharmacophore for a mitoketoscin.

[0017] FIG. 6A shows a docking image of Compound 2 docking at a succinyl-CoA binding site of 3-oxoacid CoA-transferase 1 (OXCT1). FIG. 6B shows a docking image of Compound 8 docking at a CoA binding site of human acetyl-CoA acetyltransferase (ACAT1).

[0018] FIG. 7 shows the structures of diphenyleneiodium chloride (DPI) and 2-butene-1,4-bis-triphenylphosphonium (TPP).

[0019] FIGS. 8A-C show the structures of brutieridin, melitidin, and mDIVI1, respectively.

[0020] FIG. 9 provides a summary for personalized cancer diagnosis and treatment based on mitochondrial-based diagnostics.

[0021] FIGS. 10A-B show the probability of recurrence and distant metastasis, respectively, of patients having specific Mito-Signatures.

[0022] FIGS. 11A-B show the probability of overall survival in patients having a specific Mito-Signature and undergoing platin or taxol treatment, respectively.

[0023] FIG. 12 shows the basic components of a mitochondrial-based oncology platform.

DESCRIPTION

[0024] The following description illustrates embodiments of the present approach in sufficient detail to enable practice of the present approach. Although the present approach is described with reference to these specific embodiments, it should be appreciated that the present approach can be embodied in different forms, and this description should not be construed as limiting any appended claims to the specific embodiments set forth herein. Rather, these embodiments are provided so that this disclosure will be thorough and complete, and will fully convey the scope of the present approach to those skilled in the art.

[0025] Tumors and their microenvironment are heterogeneous structures that behave like metabolic ecosystems. It is well accepted that more than a single type of cancer cell exists. For example, within a given epithelial cancer cell line (such as MCF7 cells), there are bulk cancer cells (85-95%; the majority of the population), as well as various types of progenitor cells (less than 5%), and cancer stem cells (CSCs; less than 1%). CSCs and progenitor cells are thought to be the most dangerous as they behave as tumor-initiating cells (TICs) in vivo and can undergo metastasis. In contrast, bulk cancer cells are largely non-tumorigenic.

[0026] Because CSCs are relatively rare, little is known about their metabolic properties. The inventors previously showed that cells may be functionally enriched for CSCs by trypsinizing the entire cell population and seeding it as a single-cell suspension onto low-attachment plates. Under such conditions, the majority (more than 90%) of bulk cancer cells die via apoptosis, while only the CSCs survive and propagate, ultimately resulting in the formation of 3D spheroid structures after about 5 days. Each 3D spheroid is clonally formed from a single CSC. For breast CSCs, these 3D spheroids are also known as tumor-spheres or mammospheres. The generation of these 3D spheroids is thought to mimic the process of tumor formation and/or metastasis, thus providing a model for drug discovery and functional validation.

[0027] To understand the metabolic differences between bulk cancer cells and CSCs, the inventors previously compared cultured breast cancer cells grown either as monolayers or 3D spheroids. These cells were subjected to profiling via unbiased label-free proteomics analysis. The inventors found that over 60 nuclear-encoded mitochondrial proteins were specifically up-regulated in 3D spheroid structures relative to monolayer cells processed in parallel. Virtually identical results were obtained with two distinct ER(+) breast cancer cell lines (MCF7 and T47D; more than 40 overlapping mitochondrial proteins). Informatics analysis of the list of up-regulated mitochondrial proteins was consistent with an increase in mitochondrial mass, due either to i) increased mitochondrial biogenesis or ii) a shut down in mitophagy, or both. These results indicate that high mitochondrial mass is a characteristic feature of the CSC phenotype. These results also suggest that CSCs are dependent on OXPHOS and/or new mitochondrial biogenesis (protein translation) for survival and propagation. While testing this hypothesis, inventors showed that 3D spheroid formation is effectively blocked using specific mitochondrial inhibitors, such as oligomycin, which targets mitochondrial Complex V and shuts off ATP synthesis. However, oligomycin is toxic and cannot be used as an anti-cancer therapeutic. Thus, these results highlight the need for compounds that can target mitochondria in CSCs without inducing deleterious side effects in normal cells.

[0028] To further validate the functional relationship between high mitochondrial mass and stemness, inventors employed staining with MitoTracker to metabolically fractionate an MCF7 cell line into Mito-high and Mito-low cell sub-populations. MitoTracker is a non-toxic fluorescent probe that can be used to directly measure mitochondrial mass in live cells by flow cytometry. As predicted, the Mito-high cell population, with increased mitochondrial mass, showed the greatest capacity for i) 3D spheroid formation and ii) tumor initiation in a pre-clinical animal model in vivo. Therefore, mitochondrial mass may be a critical determinant of stemness in cancer cells. Similarly, elevated telomerase activity (hTERT), a functional marker of proliferation and immortality in CSCs, was also specifically associated with high mitochondrial mass. The inventors hypothesized that a targeted reduction in mitochondrial mass or OXPHOS may be used to eradicate CSCs.

[0029] The inventors have recently focused efforts on the identification and repurposing of FDA-approved drugs that may be used to inhibit the propagation of CSCs. These antibiotics include members of the tetracycline family (doxycycline/tigecycline), the erythromycin family (azithromycin), anti-parasitic drugs (pyrvinium pamoate and atovaquone), and antimicrobials targeting drug-resistant mycobacterium (bedaquiline; TB, tuberculosis). FIG. 1 provides exemplary structures of these antibiotics (FIGS. 1A-E show the structures of doxycycline, azithromycin, pyrvinium (pamoate salt; not shown), atovaquone, and bedaquiline, respectively). Table 1 lists exemplary antibiotics and shows which mitochondrial structure or process is targeted. For example, doxycycline and azithromycin inhibit mitochondrial protein translation, thereby inhibiting mitochondrial biogenesis as an off-target side effect. Pyrvinium pamoate and atovaquone inhibit OXPHOS (related to mitochondrial complex II/III) as a side effect. Bedaquiline inhibits ATP-synthase (mitochondrial complex V). Each of these antibiotics has been shown to inhibit anchorage-independent propagation of CSCs by targeting mitochondrial function.

TABLE-US-00001 TABLE 1 Exemplary FDA-approved drugs that may be used to eradicate CSCs. Drug Name Inhibition of FDA-approved Doxycycline Mito Biogenesis Yes Tigecycline Mito Biogenesis Yes Azithromycin Mito Biogenesis Yes Pyrvinium pamoate OXPHOS/Complex II Yes Atovaquone OXPHOS/Complex III Yes Bedaquiline Complex V Yes Palbociclib CDK4/6 Yes

[0030] Inventors have also previously identified experimental and natural compounds that target CSCs, including glycolysis inhibitors (Vitamin C and Silibinin), mitochondrial inhibitors (Actinonin; CAPE, from Honey bee propolis), and inhibitors of protein synthesis (puromycin) and NAD(+) recycling (FK-866). As CSCs appear to be highly proliferative, due to their over-expression of telomerase (hTERT), they are sensitive to Palbociclib, an FDA-approved CDK4/6 inhibitor, with an IC-50 of 100 nM. Therefore, inhibition of CSC proliferation is an alternative or could be used in conjunction with other cancer therapies.

[0031] Doxycycline shows many other anti-cancer properties that may be further explored. For example, Doxycycline behaves as a radio-sensitizer, making CSCs approximately 3 to 5 times more sensitive to radiation treatment. In addition, Doxycycline effectively targets hypoxic CSCs and overcomes Paclitaxel-resistance under conditions of hypoxia; this may have important implications for achieving more effective anti-angiogenic therapy. Doxycycline appears to be effective as a mutation-independent approach for targeting CSCs as it inhibits both activated H-Ras (G12V) and c-Myc oncogenes as well as other environmental oncogenic stimuli (mitochondrial oxidative stress/ROS), via the specific targeting of mitochondrial biogenesis.

[0032] One concern with doxycycline therapy is the potential for the development of drug-resistance in CSCs. To investigate this issue, the inventors developed and characterized the phenotypic behavior of Doxy-resistant (DoxyR)-MCF7 cells. The inventors found that DoxyR-CSCs show a significant shift towards aerobic glycolysis due to a loss of mitochondrial function, which ultimately results in metabolic inflexibility. (DoxyR)-MCF7 cells showed an up to 35-fold loss of mitochondrial-DNA encoded proteins (mt-DNA) that are required for OXPHOS activity, such as MT-ND3, MT-0O2, MT-ATP6 and MT-ATP8. DoxyR-CSCs appeared to be more quiescent, with greater than 50% reductions in proliferation and cell migration, as well as a significantly impaired ability to form 3D spheroids. The inventors showed that DoxyR-CSCs are sensitive to other metabolic therapies, including inhibitors of i) OXPHOS (Atovaquone, Irinotecan, Sorafenib, Niclosamide), ii) glycolysis (Vitamin C and Stiripentol) and iii) autophagy (Chloroquine). A listing of these drugs and their targets is provided in Table 2. Therefore, the efficacy of doxycycline treatment may be improved by developing combination therapies with other metabolic inhibitors, based on the concepts of metabolic inflexibility and synthetic lethality in cancer cells.

TABLE-US-00002 TABLE 2 Exemplary drugs used in conjugation with doxycycline to eradicate CSCs. Drug Name Target FDA-approved Atovaquone OXPHOS Yes Irinotecan OXPHOS Yes Sorafenib OXPHOS Yes Niclosamide OXPHOS Yes Berberine OXPHOS Natural supplement 2-deoxy-glucose (2-DG) Glycolysis Experimental Vitamin C Glycolysis Natural supplement Stiripentol Glycolysis Clinically-approved (EU/CA/JP) Chloroquine Autophagy Yes

[0033] The inventors have also focused efforts on the development of therapeutics that focus on specific mitochondrial targets. Exemplary therapeutics are listed in Table 3.

TABLE-US-00003 TABLE 3 Exemplary therapeutics that focus on mitochondrial targets. Metabolic Process/ Drug Name Target Mechanism Mitoriboscins Mitochondrial Mitochondrial Protein Ribosome Synthesis Mitoketoscins OXCT1/ACAT1 Mitochondrial Ketone Metabolism Mitoflavoscins Mito Complex VII Flavin-containing proteins (Vit-B2) Tri-phenyl- Mitochondria Mitochondrial-targeting- phosphonium (TPP) signal (MTS)

[0034] One family of therapeutics, coined mitoriboscins, are mito-ribosome inhibitors that inhibit mitochondrial protein synthesis. FIG. 4A-D illustrates examples of mitoriboscins. The inventors identified these compounds by combining computational chemistry (in silico drug design in which the target used was the 3D structure of the large mitochondrial ribosome, as determined by cryo-electron microscopy) with phenotypic library screening to detect ATP depletion.

[0035] By targeting the mitochondrial enzymes OXCT1 and ACAT1, inventors also developed mitochondrial inhibitors that interfere with ketone metabolism (these compounds mimic the structure of CoA). These compounds are known as mitoketoscins. FIG. 5 illustrates a pharmacophore for a mitoketoscin. FIG. 6A illustrates the docking of Compound 2 (a hit for an OXCT1 screen) at the succinyl-CoA binding site of OXCT1. FIG. 6B illustrates the docking of Compound 8 (a hit for an ACAT1 screen) at the CoA binding site of human ACAT1.

[0036] Inventors also identified compounds named mitoflavoscins, compounds that bind to flavin-containing enzymes and inhibit mitochondrial function. Such compounds may be designed to target and deplete FMN, FAD, and/or riboflavin. The inventors identified an approach to acutely induce a Vitamin B2 (riboflavin) deficiency that potently inhibits CSC propagation, with an IC-50 of 3 nM. This drug is approximately 30 times more potent than Palbociclib for targeting CSCs. FIG. 7 illustrates the structure of DPI, one embodiment of a mitoflavoscin.

[0037] Inventors also identified the use of tri-phenyl-phosphonium (TPP) to eradicate CSCs. TPP behaves as a mitochondrial targeting signal. FIG. 7 illustrates the structure of TPP. TPP compounds appear to be able to metabolically distinguish between normal cell mitochondria and malignant mitochondria of bulk cancer cells and CSCs, as the TPP compounds are non-toxic in normal human fibroblasts and yet block CSC propagation.

[0038] Inventors also investigated naturally-occurring mitochondrial inhibitors that may be used to more effectively target CSCs. A list of exemplary naturally-occurring mitochondrial inhibitors is provided in Table 4. The inventors found that brutieridin and melitidin, two compounds found in bergamot, act as statin-like drugs and inhibit mevolonate metabolism as well as CSC propagation. FIGS. 8A-B illustrate the structures of brutieridin and melitidin, respectively. FIG. 8C illustrates the structure of mDIVI1 for comparison. Interference with the normal process of mitochondrial fission-fusion cycles, such as by targeting the DRP1 protein, may represent a viable strategy for eradicating CSCs.

TABLE-US-00004 TABLE 4 Naturally-occurring mitochondrial inhibitors that target CSCs. Drug Name Target Metabolic Process Inhibited mDIVI1 DRP1* Mitochondrial Fission/Fusion Brutieridin HMGR** Mevalonate Metabolism Melitidin HMGR** Mevalonate Metabolism *Dynamin-related protein 1 **3-hydroxy-3-methylglutaryl-CoA-reductase.

[0039] The identification and design of new mitochondrial inhibitors may have other medical applications and benefits such as the development of new anti-bacterial and anti-fungal agents and combating antibiotic-resistance. According to the ndo-symbiotic Theory of Mitochondrial Evolution, mitochondria first originated historically from the engulfment of aerobic bacteria, an event that occurred 1.45 billion years ago. As a result, mitochondria share strong structural and functional similarities with bacteria, explaining the off-target effects of antibiotics, which often show manageable mitochondrial side-effects. Conversely, it would be predicted that mitochondrial inhibitors may also show some moderate anti-bacterial and anti-fungal side effects.

[0040] To directly test this hypothesis, the inventors evaluated the anti-bacterial and anti-fungal activity of exemplary mitoriboscins. Several mitoriboscins showed anti-bacterial activity towards both gram-positive and gram-negative organism(s), pathogenic yeast (Candida albicans) and Methicillin-resistant Staphylococcus aureus (MRSA). Therefore, using cancer cells for initial drug screening may also be useful for developing new antibiotics to combat drug-resistant micro-organisms.

[0041] Over one thousand mitochondrial proteins are encoded by the nuclear genome. The inventors have begun to assess their potential prognostic value as biomarkers and companion diagnostics. The inventors hypothesize that the over-expression of a given mitochondrial protein in cancer cells and CSCs may be associated with tumor recurrence and metastasis, due to the emergence of drug resistance, and ultimately resulting in treatment failure. To test this hypothesis, the inventors used an online survival-analysis tool to perform Kaplan-Meier (K-M) studies on more than 400 nuclear mitochondrial gene transcripts to interrogate publicly available microarray data from patients with four distinct epithelial cancer types: i) breast, ii) ovarian, iii) lung and iv) gastric. In all four anatomic cancer types, the inventors observed that the over-expression of mitochondrial gene transcripts is associated with poor clinical outcome. For example, this approach effectively predicted tamoxifen-resistance in ER(+) breast cancer patients (represented as recurrence and distant metastasis in FIGS. 10A-B, respectively), as well as Taxol and Platin resistance in ovarian cancer patients (represented as overall survival in FIGS. 11A-B, respectively). These results are functionally supported by further experimental observations demonstrating that Tamoxifen-resistant MCF7 cells (TAMR) show a significant increase in mitochondrial oxygen consumption and ATP production.

[0042] The present disclosure therefore relates to methods of predicting the sensitivity of neoplastic cell growth to anti-mitochondrial agents. The methods may include obtaining a sample of a neoplasm from a patient, determining the level of mitochondrial markers in the sample and comparing the level of mitochondrial markers to a control, and predicting the sensitivity of the neoplastic cell growth to inhibition by an anti-mitochondrial agent based on relative marker levels. High expression levels of mitochondrial markers correlate with high sensitivity to inhibition by an anti-mitochondrial agent. Mitochondrial markers may be obtained from tumor biopsy samples and/or by isolating circulating tumor cells from serum, plasma, and/or blood samples. Mitochondrial markers may include mitochondrial RNAs, proteins, and/or mitochondrial DNA. In some embodiments, mitochondrial DNA may be obtained from body fluids (e.g., blood, serum, plasma, saliva, sputum, milk, tears, urine, ascites, cyst fluid, pleural fluid, and/or cerebral spinal fluid). Mitochondrial marker levels may be measured by any number of ways known in the art, including quantitative PCR and/or RT-PCR, microarrays, Northern blots, Western blots, etc.

[0043] In some embodiments, mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA that are associated with or regulate beta-oxidation and/or ketone metabolism, such as HSD17B10, BDH1, ACAT1, ACADVL, ACACA, ACLY, HADHB, SUCLG2, ACAD9, HADHA, ECHS1, ACADSB. In some embodiments, mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA that are involved in: mitochondrial biogenesis, such as HSPA9, TIMM8A, GFM1, MRPL45, MRPL17, HSPD1(HSP60), TSFM, TUFM; electron transport, such as NDUFB10, COX6B1, PMPCA, COX5B, SDHA, UQCRC1; metabolism, such as CHCHD2, ATP synthesis, such as ATP5B, ATPIF1, ATP5A1, ATP5F1, ATP5H, ATP5O; ADP/ATP exchange/transport, such as SLC25A5; CoQ synthesis, such as COQ9; ROS production, such as GPD2; and/or suppression of glycolysis, autophagy and mitophagy, such as SOGA1 and LRPPRC. In some embodiments, the mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA related to the enzymes ACAT1/2 and/or OXCT1/2.

[0044] In some embodiments, the mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA that are upregulated or increased in certain cancer types. For example, Table 5, adapted from U.S. Provisional Application No. 62/508,799, the contents of which is incorporated by reference in its entirety, shows exemplary proteins that may be used as mitochondrial biomarkers in gastric cancers. As is shown in Table 5, mitochondrial biomarkers may include mitochondrial proteins, RNA, and/or DNA associated with heat shock proteins and chaperones, membrane proteins, mitochondrial antioxidants, mitochondrial genome maintenance, large and/or small ribosomal subunits, and OXPHOS complexes. In some embodiments, two or more mitochondrial biomarkers may be used to create a Mito-Signature, a predictor for clinical outcomes. An exemplary Mito-Signature for gastric cancer is shown in Table 6.

TABLE-US-00005 TABLE 5 Prognostic value of mitochondrial markers in gastric cancers. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Heat Shock Proteins and Chaperones (4 probes) 200807_s_at HSPD1 1.83 1.9e06 200806_s_at HSPD1 1.56 0.003 200691_s_at HSPA9 1.61 0.0002 205565_s_at FXN 1.38 0.01 Membrane Proteins (9 probes) 208844_at VDAC3 2.22 1.4e09 211662_s_at VDAC2 1.51 0.002 200955_at IMMT 2.20 2.4e09 218118_s_at TIMM23 1.91 4.2e07 218408_at TIMM10 1.88 1.4e06 218357_s_at TIMM8B 1.49 0.002 201821_s_at TIMM17A 1.33 0.025 201870_at TOMM34 1.95 5.1e07 202264_s_at TOMM40 1.44 0.009 Mitochondrial Anti-Oxidants (2 probes) 215223_s_at SOD2 1.72 2.1e05 215078_at SOD2 1.70 2.9e05 Mitochondrial Genome Maintenance (3 probes) 208694_at PRKDC 2.05 1.2e07 210543_s_at PRKDC 1.78 6.9e06 215757_at PRKDC 1.47 0.003 Large Ribosomal Subunit (12 probes) 204599_s_at MRPL28 2.17 1.2e08 221997_s_at MRPL52 2.12 3.2e09 222216_s_at MRPL17 1.68 0.0001 220527_at MRPL20 1.67 0.0002 217907_at MRPL18 1.62 0.0004 218887_at MRPL2 1.60 0.0002 203931_s_at MRPL12 1.56 0.001 208787_at MRPL3 1.53 0.0007 217919_s_at MRPL42 1.52 0.002 218049_s_at MRPL13 1.47 0.008 218281_at MRPL48 1.40 0.009 213897_s_at MRPL23 1.29 0.049 Small Ribosomal Subunit (8 probes) 215919_s_at MRPS11 1.89 5.1e07 213840_s_at MRPS12 1.84 1.5e06 210008_s_at MRPS12 1.47 0.004 204330_s_at MRPS12 1.37 0.015 204331_s_at MRPS12 1.37 0.037 203800_s_at MRPS14 1.53 0.002 219220_x_at MRPS22 1.44 0.005 219819_s_at MRPS28 1.42 0.01 218112_at MRPS34 1.36 0.02 Complex I (11 probes) 201757_at NDUFS5 2.27 6e10 215850_s_at NDUFA5 1.93 2.1e07 208969_at NDUFA9 1.92 1.5e06 203606_at NDUFS6 1.74 7.9e05 214241_at NDUFB8 1.67 5.7e05 203371_s_at NDUFB3 1.51 0.002 218226_s_at NDUFB4 1.49 0.003 202001_s_at NDUFA6 1.37 0.02 218160_at NDUFA8 1.31 0.04 202785_at NDUFA7 1.31 0.04 218563_at NDUFA3 1.30 0.04 Complex II (1 probe) 214166_at SDHB 1.40 0.009 Complex III (2 probes) 207618_s_at BCS1L 1.76 7.1e06 202233_s_at UQCR8 1.51 0.001 Complex IV (10 probes) 213736_at COX5B 2.14 1.4e08 218057_x_at COX4NB 1.94 7.7e07 201754_at COX6C 1.74 7.1e05 201441_at COX6B1 1.67 0.0001 200925_at COX6A1 1.64 8.8e05 203880_at COX17 1.60 0.0003 217451_at COX5A 1.49 0.006 202110_at COX7B 1.42 0.01 217249_x_at COX7A2 1.33 0.035 216003_at COX10 1.33 0.046 Complex V (13 probes) 221677_s_at ATP5O 2.22 2.1e10 207552_at ATP5G2 1.90 7.5e06 207335_x_at ATP5I 1.84 8.4e06 217801_at ATP5E 1.64 0.0002 208972_s_at ATP5G1 1.51 0.002 210149_s_at ATP5H 1.49 0.003 202961_s_at ATP5J2 1.47 0.004 210453_x_at ATP5L 1.45 0.006 207573_x_at ATP5L 1.44 0.01 208746_x_at ATP5L 1.40 0.009 213366_x_at ATP5C 1.33 0.03 206993_at ATP5S 1.29 0.04 213366_x_at ATP5C1 1.33 0.03

TABLE-US-00006 TABLE 6 Exemplary compact gastric cancer Mito-Signature for predicting clinical outcome. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test 201757_at NDUFS5 2.27 .sup.6e10 208844_at VDAC3 2.22 1.4e09 221677_s_at ATP5O 2.22 2.1e10 200955_at IMMT 2.20 2.4e09 204599_s_at MRPL28 2.17 1.2e08 213736_at COX5B 2.14 1.4e08 221997_s_at MRPL52 2.12 3.2e09 208694_at PRKDC 2.05 1.2e07 Combined 2.77 1.4e14

[0045] In some embodiments, the mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA that are upregulated or increased in ovarian cancers. Table 7, adapted from U.S. Provisional Application No. 62/508,788, the contents of which is incorporated by reference in its entirety, shows exemplary proteins that may be used as mitochondrial biomarkers in ovarian cancers. As is shown in Table 7, mitochondrial biomarkers may include mitochondrial proteins, RNA, and/or DNA associated with heat shock proteins and chaperones, membrane proteins, mitochondrial antioxidants, mitochondrial creatine kinases, large and/or small ribosomal subunits, and OXPHOS complexes. Exemplary Mito-Signatures for ovarian cancer are shown in Table 8.

TABLE-US-00007 TABLE 7 Prognostic value of mitochondrial markers in ovarian cancers. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Chaperones/HSPs 200691_s_at HSPA9 1.77 0.047 Membrane Proteins 200955_at IMMT 2.61 0.002 218408_at TIMM10 2.63 0.0008 201821_s_at TIMM17A 2.46 0.003 217981_s_at TIMM10B 1.94 0.05 218118_s_at TIMM23 1.79 0.05 201519_at TOMM70A 2.28 0.005 211662_s_at VDAC2 2.32 0.01 208845_at VDAC3 2.07 0.01 208846_s_at VDAC3 1.96 0.048 200657_at SLC25A5 2.67 0.0008 221020_s_at SLC25A32 1.98 0.05 Anti-Oxidant Proteins 201468_s_at NQO1 3.48 0.001 210519_s_at NQO1 2.37 0.006 215223_s_at SOD2 1.82 0.048 Mitochondrial Creatine Kinase 205295_at CKMT2 2.27 0.0035 Large Ribosomal Subunit 201717_at MRPL49 3.56 4.3e05 221692_s_at MRPL34 2.99 0.001 218890_x_at MRPL35 2.48 0.002 213897_s_at MRPL23 2.48 0.01 217907_at MRPL18 2.36 0.006 218281_at MRPL48 2.29 0.007 222216_s_at MRPL17 2.17 0.007 217980_s_at MRPL16 2.17 0.008 219162_s_at MRPL11 2.14 0.02 218105_s_at MRPL4 1.90 0.03 Small Ribosomal Subunit 203800_s_at MRPS14 2.97 0.0002 204331_s_at MRPS12 2.90 9e04 210008_s_at MRPS12 2.46 0.0035 221688_s_at MRPS4 2.88 0.002 219819_s_at MRPS28 2.64 0.0008 218001_at MRPS2 2.15 0.01 219220_x_at MRPS22 2.13 0.025 218654_s_at MRPS33 2.05 0.02 217942_at MRPS35 2.05 0.03 212604_at MRPS31 2.02 0.02 221437_s_at MRPS15 1.88 0.05 Complex I 218563_at NDUFA3 3.55 2.3e05 218320_s_at NDUFB11 3.12 7e05 201740_at NDUFS3 2.93 0.001 218200_s_at NDUFB2 2.60 0.001 203371_s_at NDUFB3 2.56 0.0008 203189_s_at NDUFS8 2.43 0.002 218201_at NDUFB2 2.43 0.002 203613_s_at NDUFB6 2.43 0.008 202000_at NDUFA6 2.43 0.0015 202785_at NDUFA7 2.30 0.01 220864_s_at NDUFA13 2.25 0.006 209303_at NDUFS4 2.20 0.009 218160_at NDUFA8 2.16 0.008 203190_at NDUFS8 2.15 0.01 202941_at NDUFV2 2.13 0.02 208714_at NDUFV1 2.07 0.03 209224_s_at NDUFA2 2.03 0.044 211752_s_at NDUFS7 1.98 0.02 217860_at NDUFA10 1.95 0.037 202298_at NDUFA1 1.91 0.03 208969_at NDUFA9 1.89 0.26 201966_at NDUFS2 1.86 0.035 Complex II 210131_x_at SDHC 2.97 0.0005 202004_x_at SDHC 2.78 0.0005 202675_at SDHB 1.83 0.04 Complex III 208909_at UQCRFS1 3.68 9.8e05 201568_at UQCR7 2.28 0.004 209065_at UQCR6 2.12 0.04 202090_s_at UQCR 1.86 0.04 212600_s_at UQCR2 1.76 0.047 Complex IV 201441_at COX6B 2.64 0.0009 203880_at COX17 2.49 0.004 203858_s_at COX10 2.47 0.002 211025_x_at COX5B 2.34 0.004 202343_x_at COX5B 2.32 0.004 202110_at COX7B 2.30 0.02 218057_x_at COX4NB 2.08 0.01 202698_x_at COX4I1 1.89 0.03 201119_s_at COX8A 1.87 0.04 204570_at COX7A 1.76 0.05 Complex V 208870_x_at ATP5C 2.57 0.0008 213366_x_at ATP5C 2.44 0.002 205711_x_at ATP5C 2.08 0.01 207507_s_at ATP5G3 2.40 0.002 210453_x_at ATP5L 2.35 0.003 208746_x_at ATP5L 2.24 0.005 207573_x_at ATP5L 2.20 0.006 208972_s_at ATP5G 2.15 0.007 207508_at ATP5G3 2.12 0.01 202961_s_at ATP5J2 1.91 0.02 217848_s_at PPA1 1.89 0.03 202325_s_at ATP5J 1.78 0.05

TABLE-US-00008 TABLE 8 Exemplary compact ovarian cancer Mito-Signatures for predicting clinical outcome. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Mito-Signature 1 208909_at UQCRFS1 3.68 9.8e05 201717_at MRPL49 3.56 4.3e05 Combination 4.59 3.1e05 Mito-Signature 2 208909_at UQCRFS1 3.68 9.8e05 218563_at NDUFA3 3.55 2.3e05 Combination 5.03 1.2e05 Mito-Signature 3 208909_at UQCRFS1 3.68 9.8e05 218563_at NDUFA3 3.55 2.3e05 201202_at PCNA 2.85 0.0003 Combination 5.63 7.6e06

[0046] In some embodiments, the mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA that are upregulated or increased in breast cancers. Table 9, adapted from U.S. Provisional Application No. 62/508,750, the contents of which is incorporated by reference in its entirety, shows exemplary proteins that may be used as mitochondrial biomarkers in breast cancers. As is shown in Table 9, mitochondrial biomarkers may include mitochondrial proteins, RNA, and/or DNA associated mitochondrial chaperones, membrane proteins, mitochondrial carrier families, mitochondrial antioxidants, mitochondrial creatine kinases, large and/or small ribosomal subunits, and OXPHOS complexes. Exemplary Mito-Signatures for breast cancer are shown in Table 10.

TABLE-US-00009 TABLE 9 Prognostic value of mitochondrial markers in breast cancers. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Mito Chaperones 200807_s_at HSPD1 3.61 5.9e06 200806_s_at HSPD1 2.30 0.006 200691_s_at HSPA9 2.04 0.01 205565_s_at FXN 1.83 0.038 221235_s_at TRAP1 1.79 0.047 Mito Membrane Proteins 211662_s_at VDAC2 4.17 2.2e07 210626_at AKAP1 2.15 0.01 200955_at IMMT 1.81 0.04 201519_at TOMM70A 2.78 0.0003 201512_s_at TOMM70A 2.15 0.01 203093_s_at TIMM44 2.23 0.01 218188_s_at TIMM13 2.23 0.02 201822_at TIMM17A 2.01 0.01 215171_s_at TIMM17A 1.85 0.04 203342_at TIMM17B 1.78 0.04 Mito Carrier Family 217961_at SLC25A38 2.77 0.0003 210010_s_at SLC25A1 2.38 0.002 200657_at SLC25A5 2.04 0.01 221020_s_at SLC25A32 1.98 0.02 Mito Anti-Oxidants 215223_s_at SOD2 2.94 0.0001 215078_at SOD2 2.81 0.008 Mito Creatine Kinase 205295_at CKMT2 2.18 0.04 202712_s_at CKMT1A 2.03 0.02 Large Ribosomal Subunit 218027_at MRPL15 3.28 1.6e05 217907_at MRPL18 2.91 0.0001 219244_s_at MRPL46 2.89 0.02 218270_at MRPL24 2.38 0.002 218049_s_at MRPL13 2.14 0.01 218281_at MRPL48 2.11 0.01 208787_at MRPL3 2.07 0.03 213897_s_at MRPL23 2.02 0.04 218105_s_at MRPL4 1.99 0.02 222216_s_at MRPL17 1.97 0.02 217919_s_at MRPL42 1.88 0.05 218202_x_at MRPL44 1.78 0.04 Small Ribosomal Subunit 204330_s_at MRPS12 2.35 0.03 211595_s_at MRPS11 2.26 0.01 219819_s_at MRPS28 1.88 0.03 217919_s_at MRPL42 1.88 0.05 219220_x_at MRPS22 1.85 0.04 218654_s_at MRPS33 1.84 0.04 Complex I 218160_at NDUFA8 2.45 0.002 202000_at NDUFA6 2.41 0.002 202001_s_at NDUFA6 2.23 0.006 203039_s_at NDUFS1 2.40 0.003 201740_at NDUFS3 2.17 0.006 203613_s_at NDUFB6 1.99 0.02 208714_at NDUFV1 1.96 0.03 203606_at NDUFS6 1.92 0.04 202298_at NDUFA1 1.89 0.03 Complex III 209065_at UQCRB 3.42 1.9e05 209066_x_at UQCRB 2.12 0.01 205849_s_at UQCR6 2.53 0.002 201066_at UQCR4 1.96 0.02 212600_s_at UQCRC2 1.92 0.04 Complex IV 203880_at COX17 2.99 7.6e05 213735_s_at COX5B 2.51 0.001 202343_x_at COX5B 2.10 0.01 211025_x_at COX5B 2.08 0.01 202698_x_at COX4I1 2.36 0.02 200925_at COX6A1 2.14 0.01 218057_x_at COX4NB 1.99 0.04 217249_x_at COX7A2 1.90 0.03 Complex V 202325_s_at ATP5J 2.65 0.01 202961_s_at ATP5J2 2.44 0.035 213366_x_at ATP5C1 2.19 0.01 208870_x_at ATP5C1 2.08 0.01 205711_x_at ATP5C1 2.00 0.02 217848_s_at PPA1 2.07 0.01 221677_s_at ATP5O 2.03 0.02 217801_at ATP5E 1.99 0.02 207508_at ATP5G3 1.93 0.02

TABLE-US-00010 TABLE 10 Exemplary compact breast cancer Mito-Signatures for predicting clinical outcome. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Mito-Signature 1 200807_s_at HSPD1 3.61 5.9e06 209065_at UQCRB 3.42 1.9e05 218027_at MRPL15 3.28 1.6e05 203880_at COX17 2.99 7.6e05 Combined 5.34 1e09 Mito-Signature 2 211662_s_at VDAC2 4.17 2.2e07 200807_s_at HSPD1 3.61 5.9e06 Combined 5.19 6e09

[0047] In some embodiments, the mitochondrial markers may include mitochondrial proteins, RNA, and/or DNA that are upregulated or increased in lung cancers. Table 11, adapted from U.S. Provisional Application No. 62/508,769, the contents of which is incorporated by reference in its entirety, shows exemplary proteins that may be used as mitochondrial biomarkers in lung cancers. As is shown in Table 11, mitochondrial biomarkers may include mitochondrial proteins, RNA, and/or DNA associated with mitochondrial heat shock proteins and membrane proteins, mitochondrial creatine kinases, mitochondrial genome maintenance proteins, large and/or small ribosomal subunits, and OXPHOS complexes.

TABLE-US-00011 TABLE 11 Prognostic value of mitochondrial markers in lung cancers. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test HSPs and Membrane Proteins (28 probes in total) 200806_s_at HSPD1 4.89 <1.0e16 218119_at TIMM23 4.68 1.1e16 218357_s_at TIMM8B 4.26 7.8e16 203342_at TIMM17B 3.31 2.5e11 203093_s_at TIMM44 2.29 1.1e09 217981_s_at TIMM10B 2.15 1.2e06 218316_at TIMM9 2.06 4.3e08 201821_s_at TIMM17A 2.04 1.7e09 218188_s_at TIMM13 1.94 8.5e09 218118_s_at TIMM23 1.83 1.8e07 218408_at TIMM10 1.79 4e05 202264_s_at TOMM40 4.29 1.1e14 217960_s_at TOMM22 3.19 1.3e13 201870_at TOMM34 2.83 9.8e12 201812_s_at TOMM7 2.84 5.4e13 201512_s_at TOMM70A 1.90 3.1e08 212773_s_at TOMM20 1.54 0.0006 217139_at VDAC1 3.74 1.9e14 217140_s_at VDAC1 2.58 1.1e16 212038_s_at VDAC1 1.63 7.8e05 208844_at VDAC3 3.64 3.9e14 211662_s_at VDAC2 2.36 6e14 210625_s_at AKAP1 1.88 1.3e06 200657_at SLC25A5 1.54 0.0001 Mitochondrial Creatine Kinase (2 probes in total) 202712_s_at CKMT1A 2.88 7.8e10 205295_at CKMT2 1.51 0.0005 Mitochondrial Genome Maintenance (3 probes in total) 210543_s_at PRKDC 4.69 1.1e16 208694_at PRKDC 2.23 4.3e12 215757_at PRKDC 1.65 4.0e05 Large Ribosomal Subunit (21 probes in total) 218281_at MRPL48 4.36 1.9e15 213897_s_at MRPL23 3.55 5.4e13 219162_s_at MRPL11 3.29 2.5e13 221997_s_at MRPL52 3.20 3.6e14 221692_s_at MRPL34 3.08 1.6e11 203931_s_at MRPL12 2.82 3.3e12 218887_at MRPL2 2.81 4.4e11 217919_s_at MRPL42 2.54 1.6e13 218270_at MRPL24 2.35 1.8e09 218105_s_at MRPL4 2.32 1.6e09 218202_x_at MRPL44 2.19 2.5e10 222216_s_at MRPL17 2.02 1.4e08 218890_x_at MRPL35 1.96 5.7e09 204599_s_at MRPL28 1.91 1.4e07 220527_at MRPL20 1.84 9.1e05 201717_at MRPL49 1.68 8.7e06 218049_s_at MRPL13 1.68 8.1e06 217980_s_at MRPL16 1.66 1.5e05 203152_at MRPL40 1.62 0.0001 218027_at MRPL15 1.59 0.0001 203781_at MRPL33 1.47 0.001 Small Ribosomal Subunit (19 probes in total) 204331_s_at MRPS12 4.10 1.1e16 210008_s_at MRPS12 3.93 4.9e14 204330_s_at MRPS12 3.27 1e13 213840_s_at MRPS12 2.99 2.3e12 217932_at MRPS7 3.55 2.3e12 218001_at MRPS2 3.28 1e11 221688_s_at MRPS4 3.09 7.7e11 211595_s_at MRPS11 2.96 9.1e12 215919_s_at MRPS11 1.55 0.0002 218112_at MRPS34 2.43 7.6e08 212604_at MRPS31 2.29 2.7e07 219819_s_at MRPS28 1.74 2.7e06 217942_at MRPS35 1.70 8.4e06 221437_s_at MRPS15 1.59 0.0001 12145_at MRPS27 1.61 7.4e05 218398_at MRPS30 1.47 0.003 218654_s_at MRPS33 1.35 0.01 203800_s_at MRPS14 1.27 0.05 Complex I (27 probes in total) 203371_s_at NDUFB3 4.30 3.6e15 203189_s_at NDUFS8 4.15 4.4e16 203190_at NDUFS8 2.94 2.1e11 209303_at NDUFS4 3.83 1.1e15 218484_at NDUFA4L2 3.33 2.1e13 218226_s_at NDUFB4 3.21 1.8e14 220864_s_at NDUFA13 3.00 9.5e11 202941_at NDUFV2 3.00 1.3e13 201740_at NDUFS3 2.92 1.2e11 217860_at NDUFA10 2.77 3e14 218563_at NDUFA3 2.23 1.9e10 214241_at NDUFB8 2.23 1.5e09 218201_at NDUFB2 2.21 1.2e08 215850_s_at NDUFA5 1.83 3.6e07 202785_at NDUFA7 1.81 3e07 202298_at NDUFA1 1.72 3e06 201966_at NDUFS2 1.70 6.6e06 202839_s_at NDUFB7 1.64 0.0009 201757_at NDUFS5 1.64 4.3e05 209224_s_at NDUFA2 1.59 6.6e05 208969_at NDUFA9 1.56 0.0002 211752_s_at NDUFS7 1.50 0.0007 203613_s_at NDUFB6 1.49 0.0009 209223_at NDUFA2 1.49 0.0009 218320_s_at NDUFB11 1.48 0.001 218200_s_at NDUFB2 1.48 0.001 208714_at NDUFV1 1.44 0.002 Complex II (5 probes in total) 216591_s_at SDHC 4.27 7.8e16 202004_x_at SDHC 3.64 4e14 210131_x_at SDHC 3.45 4.2e14 202675_at SDHB 2.06 7.4e07 214166_at SDHB 1.94 2.5e08 Complex III (8 probes in total) 201568_at UQCR7 3.34 3.7e13 209066_x_at UQCR6 2.96 2.5e10 202233_s_at UQCR8 2.09 5.9e07 208909_at UQCRFS1 1.69 2.6e05 201066_at UQCR4/CYC1 1.54 0.0006 207618_s_at BCS1L 1.54 0.0003 205849_s_at UQCR6 1.48 0.0008 202090_s_at UQCR 1.45 0.004 Complex IV (19 probes in total) 211025_x_at COX5B 4.46 5.3e15 202343_x_at COX5B 3.97 1.1e16 213735_s_at COX5B 2.15 9.6e10 213736_at COX5B 1.51 0.0015 200925_at COX6A 3.94 1.1e16 201119_s_at COX8A 3.78 2.4e15 203880_at COX17 3.55 3.9e15 201754_at COX6C 3.24 1.8e14 217249_x_at COX7A2 3.05 3.3e13 201441_at COX6B 2.93 3.8e12 206353_at COX6A2 2.77 1.8e11 203858_s_at COX10 2.44 1.3e09 202110_at COX7B 2.29 2.5e12 216003_at COX10 2.18 1.8e07 221550_at COX15 2.09 1.5e10 217451_at COX5A 2.01 9e06 218057_x_at COX4NB 1.54 0.0008 204570_at COX7A 1.51 0.0015 202698_x_at COX4I1 1.39 0.01 Complex V (23 probes in total) 202961_s_at ATP5J2 4.38 1.3e14 207507_s_at ATP5G3 4.14 <1e17 207508_at ATP5G3 2.34 1.6e13 210149_s_at ATP5H 3.70 3.7e15 209492_x_at ATP5I 3.33 7.7e13 207335_x_at ATP5I 2.14 2e08 203926_x_at ATP5D 3.02 2.7e11 213041_s_at ATP5D 2.41 3.1e10 208764_s_at ATP5G2 2.75 2.9e10 207552_at ATP5G2 2.55 4.3e09 217368_at ATP5G2 1.85 4.9e07 217801_at ATP5E 2.62 2e09 210453_x_at ATP5L 2.56 1.8e11 207573_x_at ATP5L 2.25 1.9e10 208746_x_at ATP5L 2.10 7.4e10 201322_at ATP5B 1.88 1.5e07 206992_s_at ATP5S 1.88 2.9e07 206993_at ATP5S 1.85 2.1e07 208972_s_at ATP5G 1.87 5.4e08 221677_s_at ATP5O 1.71 6.8e06 208870_x_at ATP5C 1.54 0.0008 205711_x_at ATP5C 1.42 0.004 213366_x_at ATP5C 1.40 0.007

[0048] The present disclosure also relates to methods of treating a neoplastic disease in a patient. Such treatment may occur following the determination of increased expression levels of one or more mitochondrial markers. Methods may include obtaining a sample of a neoplasm from a neoplastic disease patient, determining the expression level of one or more mitochondrial markers in the CSCs (e.g., Mito-signature) of the neoplasm sample relative to a control sample, and, if the higher expression levels of one or more mitochondrial markers is detected, administering to the patient a therapeutically effective amount of an anti-mitochondrial agent. The anti-mitochondrial agent may include one or more mitoriboscins, mitoketoscins, and/or antimitoscins. The anti-mitochondrial agent may include compounds that inhibit mitochondrial function as an off-target effect, such as metformin, tetracycline family members (such as doxycycline), erythromycin family members (such as azithromycin), atovaquone, bedaquiline. In some embodiments, the anti-mitochondrial agent comprises a lactate transporter inhibitor or a glycolysis inhibitor. In some embodiments, the glycolysis inhibitor comprises an agent which inhibits triose-phosphate isomerase, fructose 1,6 bisphosphate aldolase, glycero-3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, enolase, pyruvate kinase, and/or lactate dehydrogenase.

[0049] In some embodiments, the neoplastic disease is a breast neoplasm subtype such as ER(+), PR(+), HER2(+), triple-negative (ER()/PR()/HER2()), ER(), PR(), any neoplasm and nodal stages, and any neoplasm grades. The neoplasm may include Luminal A, Luminal B, and Basal breast cancers. In some embodiments, wherein the neoplasm is a pre-malignant lesion such as a ductal carcinoma in situ (DCIS) of the breast or myelodysplastic syndrome of the bone marrow. In some embodiments, the neoplasm may be from a tissue including breast, skin, kidney, lung, pancreas, gastric, rectum and colon, prostate, ovarian, and bladder, and may include epithelial cells, non-epithelial cells, lymphomas, sarcomas, and melanomas.

[0050] In some embodiments, a patient may be treated with an anti-mitochondrial agent concurrently with an anti-angiogenic agent and/or an anti-neoplastic agent. For example, patients may be treated with an anti-mitochondrial agent in addition to treatment with a conventional cancer therapy, as is outline in FIG. 9. In some embodiments, one or more anti-neoplastic agents and/ or anti-angiogenic agents may be administered simultaneously to or sequentially with the anti-mitochondrial agent. Anti-angiogenic agents may include one or more of angiostatin, bevacizumab, arresten, canstatin, combretastatin, endostatin, NM-3, thrombospondin, tumstatin, 2-methoxyestradiol, Vitaxin, Getfitinib, ZD6474, erlotinib, CI1033, PKI1666, cetuximab, PTK787, SU6668, SU1 1248, trastuzumab, Marimastat, COL-3, Neovastat, 2-ME, SU6668, anti-VEGF antibody, Medi-522 (Vitaxin E), tumstatin, arrestin, recombinant EPO, troponin I, EMD121974, IFN- celecoxib, PD0332991, tamoxifen, paclitaxel (taxol) and thalidomide. Anti-neoplastic agents may include natural products such as vitamin C, caffeic acid phenyl ester (CAPE), and/or berberine. The anti-neoplastic agent may include one or more of 17-AAG, Apatinib, Ascomycin, Axitinib, Bexarotene, Bortezomib, Bosutinib, Bryostatin 1, Bryostatin 2, Canertinib, Carboplatin, Cediranib, Cisplatin, Cyclopamine, Dasatinib, 17-DMAG, Docetaxel, Doramapimod, Dovitinib, Erlotinib, Everolimus, Gefitinib, Geldanamycin, Gemcitabine, Imatinib, Imiquimod, Ingenol 3-Angelate, Ingenol 3-Angelate 20-Acetate, Irinotecan, Lapatinib, Lestaurtinib, Nedaplatin, Masitinib, Mubritinib, Nilotinib, NVP-BEZ235, OSU-03012, Oxaliplatin, Paclitaxel, Palbociclib (and other CDK4/6 inhibitors), Pazopanib, Picoplatin, Pimecrolimus, PKC412, Rapamycin, Satraplatin, Sorafenib, Sunitinib, Tandutinib, Tivozanib, Thalidomide, Temsirolimus, Tozasertib, Vandetanib, Vargatef, Vatalanib, Zotarolimus, ZSTK474, Bevacizumab (Avasti), Cetuximab, Herceptin, Rituximab, Tamoxifen, Trastuzumab, Apatinib, Axitinib, Bisindolylmaleimide I, Bisindolylmaleimide I, Bosutinib, Canertinib, Cediranib, Chelerythrine, CP690550, Dasatinib, Dovitinib, Erlotinib, Fasudil, Gefitinib, Genistein, Go 6976, H-89, HA-1077, Imatinib, K252a, K252c, Lapatinib, Di-p- Toluenesulfonate, Lestaurtinib, LY 294002, Masitinib, Mubritinib, Nilotinib, OSU-03012, Pazopanib, PD 98059, PKC412, Roscovitine, SB 202190, SB 203580, Sorafenib, SP600125, Staurosporine, Sunitinib, Tandutinib, Tivozanib, Tozasertib, Tyrphostin AG 490, Tyrphostin AG 1478, U0126, Vandetanib, Vargatef, Vatalanib, Wortmannin, ZSTK474, Cyclopamine, Carboplatin, Cisplatin, Eptaplatin, Nedaplatin, Oxaliplatin, Picoplatin, Satraplatin, Bortezomib (Velcade), Metformin, Halofuginone. Metformin, N-acetyl-cysteine (NAC), RTA 402 (Bardoxolone methyl), Auranofin, BMS-345541, IMD-0354, PS-1145, TPCA-I, Wedelolactone, Echinomycin, 2-deoxy-D-glucose (2-DG), 2-bromo-D-glucose, 2-fluoro-D-glucose, and 2-iodo- D-glucose, dichloro-acetate (DCA), 3-chloro-pyruvate, 3-Bromo-pyruvate (3-BrPA), 3-Bromo- 2-oxopropionate, Oxamate, LY 294002, NVP-BEZ235, Rapamycin, Wortmannin, Quercetin, Resveratrol, N-acetyl-cysteine (NAC), N-acetyl-cysteine amide (NACA), Ascomycin, CP690550, Cyclosporin A, Everolimus, Fingolimod, FK-506, Mycophenolic Acid, Pimecrolimus, Rapamycin, Temsirolimus, Zotarolimus, Roscovitine, PD 0332991 (CDK4/6 inhibitor), Chloroquine, BSI-201 , Olaparib, DR 2313, and NU 1025.

[0051] The present disclosure relates to diagnostic kits that may be used to assay a cancer sample for sensitivity to mitochondrial inhibitor therapy. In some embodiments, this kit or platform, known as MITO-ONC-RX, includes both therapeutic and diagnostic modalities (FIG. 12). In some embodiments, the present disclosure includes a kit for measuring one or more mitochondrial markers (companion diagnostics) to identify a high-risk cancer patient population that is most likely to benefit from anti-mitochondrial therapy. In some embodiments, the kit may include a component for measuring for measuring levels of mitochondrial marker RNA, DNA, and/or protein relative to a normal control. In some embodiments, the mitochondrial marker is measured by any number of ways known in the art for measuring RNA, DNA, and or protein, including quantitative PCR and/or RT-PCR kits, microarrays, Northern blots, and Western blots. In some embodiments, the kit may include an antibody specific to a mitochondrial marker. The antibody may be a monoclonal or a polyclonal antibody. In some embodiments, the kit may include a molecule that binds to at least one of a mitochondrial ribosomal protein (MRP), an OXPHOS complex, and a mitochondrial membrane protein/chaperone.

[0052] The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. As used in the description of the invention and the appended claims, the singular forms a, an and the are intended to include the plural forms as well, unless the context clearly indicates otherwise. The invention includes numerous alternatives, modifications, and equivalents as will become apparent from consideration of the following detailed description.

[0053] It will be understood that although the terms first, second, third, a), b), and c), etc. may be used herein to describe various elements of the invention should not be limited by these terms. These terms are only used to distinguish one element of the invention from another. Thus, a first element discussed below could be termed an element aspect, and similarly, a third without departing from the teachings of the present invention. Thus, the terms first, second, third, a), b), and c), etc. are not intended to necessarily convey a sequence or other hierarchy to the associated elements but are used for identification purposes only. The sequence of operations (or steps) is not limited to the order presented in the claims.

[0054] Unless otherwise defined, all terms (including technical and scientific terms) used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. It will be further understood that terms, such as those defined in commonly used dictionaries, should be interpreted as having a meaning that is consistent with their meaning in the context of the present application and relevant art and should not be interpreted in an idealized or overly formal sense unless expressly so defined herein. The terminology used in the description of the invention herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the invention. All publications, patent applications, patents and other references mentioned herein are incorporated by reference in their entirety. In case of a conflict in terminology, the present specification is controlling.

[0055] Also, as used herein, and/or refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative (or).

[0056] Unless the context indicates otherwise, it is specifically intended that the various features of the invention described herein can be used in any combination. Moreover, the present invention also contemplates that in some embodiments of the invention, any feature or combination of features set forth herein can be excluded or omitted. To illustrate, if the specification states that a complex comprises components A, B and C, it is specifically intended that any of A, B or C, or a combination thereof, can be omitted and disclaimed.

[0057] As used herein, the transitional phrase consisting essentially of (and grammatical variants) is to be interpreted as encompassing the recited materials or steps and those that do not materially affect the basic and novel characteristic(s) of the claimed invention. Thus, the term consisting essentially of as used herein should not be interpreted as equivalent to comprising.

[0058] The term about, as used herein when referring to a measurable value, such as, for example, an amount or concentration and the like, is meant to encompass variations of 20%, 10%, 5%, 1%, 0.5%, or even 0.1% of the specified amount. A range provided herein for a measurable value may include any other range and/or individual value therein.

[0059] Having thus described certain embodiments of the present invention, it is to be understood that the invention defined by the appended claims is not to be limited by particular details set forth in the above description as many apparent variations thereof are possible without departing from the spirit or scope thereof as hereinafter claimed.