Mass Spectrometry Methods for Cancer Diagnosis

Claims

1. A method for detecting the presence, level and / or length of a lipid of at least one ganglioside and / or at least one lipoform of a ganglioside, comprising detecting said ganglioside and / or at least one lipoform of a ganglioside in a sample using mass spectrometry, optionally wherein the sample is obtained from a subject suffering from cancer, a subject suspected of having cancer or a subject not suffering from cancer.

2. The method of claim 1, wherein the mass spectrometry is selected from LC-ESI-MS / MS, LC-ESI-DIS-MS / MS, nanodiameter LC-ESI-MS and nanodiameter LC-ESI-MS / MS.

3. A method for diagnosing cancer in a subject, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject using the mass spectrometry of paragraph 1 or 2; and b) comparing said level of at least one ganglioside and / or at least one lipoform of ganglioside with the level in a control sample, wherein a significantly higher level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to a control sample indicates that the subject has cancer.

4. A method for determining the extent of cancer, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject using the mass spectrometry of paragraph 1 or 2; and b) comparing said level of at least one ganglioside and / or at least one lipoform of ganglioside with the level in a control sample, wherein at least 100% and no more than 200% increase in the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control sample indicates that the subject has low grade cancer; and / or wherein at least a 200% increase in the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control sample indicates that the subject has high grade cancer.

5. A method for determining the tumor load of cancer, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject using the mass spectrometry of paragraph 1 or 2; and b) comparing said level of at least one ganglioside and / or at least one lipoform of ganglioside with the level in a control sample, wherein at least 100% and no more than 200% increase in the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control sample indicates that the subject has a low tumor burden; and / or wherein at least a 200% increase in the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control sample indicates that the subject has a high tumor burden.

6. A method for detecting a recurrence of cancer in a subject, wherein the method comprises: (a) obtaining or providing a sample from a subject whose cancer has regressed following anti-cancer treatment; b) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and c) comparing the said level of at least one ganglioside and / or at least one lipoform of ganglioside with the level in a control sample, wherein a significantly higher level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control sample indicates a recurrence of cancer in the subject.

7. A method for detecting minimal residual disease in a subject, wherein the method comprises: a) obtaining or providing a sample from a subject in remission; b) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and c) comparing the said level of at least one ganglioside and / or at least one lipoform of ganglioside with the level in a control sample, wherein a significantly higher level of at least one ganglioside and / or at least one lipoform of ganglioside in a subject sample compared to the level in a control sample indicates that the subject has minimal residual disease.

8. A method for classifying a subject suffering from cancer depending on the benefit from anti-cancer therapy, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample from a subject to whom an anti-cancer therapy is administered, using the mass spectrometry of paragraph 1 or 2; b) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in the control; and c) comparing the level of at least one ganglioside and / or at least one lipoform of ganglioside detected in steps a) and b); wherein the absence of a significant change or a decrease in the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control is an indication that the subject suffering from cancer will benefit from anti-cancer therapy.

9. A method for determining the likelihood of a subject suffering from cancer responding to anti-cancer therapy, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample from a subject to whom an anti-cancer therapy is administered, using the mass spectrometry of paragraph 1 or 2; b) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in the control; and c) comparing the level of at least one ganglioside and / or at least one lipoform of ganglioside detected in steps a) and b); wherein a significantly higher level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to a level in a control is an indication that the subject suffering from cancer will not respond to anti-cancer therapy; and / or wherein the absence of a significant change or a decrease in the level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control is an indication that the subject suffering from cancer will respond to anti-cancer therapy.

10. A method for predicting a clinical outcome in a subject suffering from cancer, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in a test sample using mass spectrometry according to claim 1 or 2; b) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside in the control; and c) comparing the level of at least one ganglioside and / or at least one lipoform of ganglioside determined in steps a) and b); wherein a significantly higher level of at least one ganglioside and / or at least one lipoform of ganglioside in a sample of a subject compared to the level in a control is an indication that the subject has a poor clinical outcome.

11. A method for monitoring the progression of cancer in a subject, wherein the method comprises: a) determining in a sample of the subject at a first point in time the level of at least one ganglioside and / or at least one lipoform of ganglioside using mass spectrometry according to paragraph 1 or 2; b) repeating stage a) at a subsequent point in time; and c) comparing the level of at least one ganglioside and / or at least one lipoform of ganglioside detected in stages a) and b) to monitor the progression of cancer in the subject, optionally where the subject is at risk of developing cancer.

12. The method of claim 11, wherein between the first time point and the subsequent time point the subject has received anti-cancer therapy.

13. A method for assessing the effectiveness of anticancer therapy in a subject suffering from cancer, wherein the method comprises: a) determining the level of at least one ganglioside and / or at least one lipoform of ganglioside using mass spectrometry according to claim 1 or 2 in a first sample obtained from the subject; b) repeating step a) at least one subsequent time point after administration of anticancer therapy; and c) comparing the level of at least one ganglioside and / or at least one lipoform of ganglioside detected in steps a) and b), wherein a significantly lower level of at least one ganglioside and / or at least one lipoform of ganglioside in at least one subsequent sample compared to the first sample is an indication that the therapy is effective in treating cancer in the subject.

14. The method according to any one of claims 11-13, wherein the first and / or at least one subsequent sample is a portion of a single sample or pooled samples obtained from the subject.

15. A method for diagnosing cancer in a subject, wherein the method comprises: a) determining the lipid length of at least one ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and b) comparing the indicated lipid length of at least one ganglioside with that of a control sample, wherein a significant change in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample indicates that the subject has cancer.

16. A method for determining the extent of cancer, wherein the method comprises: a) determining the lipid length of at least one ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and b) comparing the indicated lipid length of at least one ganglioside with that of a control sample, wherein at least 100% and no more than 200% change (e.g., increase or decrease) in lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample indicates that the subject has low grade cancer; and / or wherein at least a 200% change (e.g., increase or decrease) in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample indicates that the subject has high grade cancer.

17. A method for determining the tumor load of cancer, wherein the method comprises: a) determining the lipid length of at least one ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and b) comparing the indicated lipid length of at least one ganglioside with that of a control sample, wherein at least 100% and no more than 200% change (e.g., increase or decrease) in lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample indicates that the subject has a low tumor burden; and / or wherein at least a 200% change (e.g., increase or decrease) in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to that in a control sample indicates that the subject has a high tumor burden.

18. A method for detecting recurrence of cancer in a subject, wherein the method comprises: (a) obtaining or providing a sample from a subject whose cancer has regressed after receiving anti-cancer treatment; b) determining the lipid length of at least one ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and c) comparing the indicated lipid length of at least one ganglioside with that of a control sample, wherein a significant change in the lipid length heterogeneity of at least one ganglioside in a test sample compared to a control sample indicates a recurrence of cancer in the subject.

19. A method for detecting minimal residual disease in a subject, wherein the method comprises: a) obtaining or providing a sample from a subject in remission; b) determining the lipid length of at least one ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; and c) comparing the indicated lipid length of at least one ganglioside with that of a control sample, wherein a significant change in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to that in a control sample indicates that the subject has minimal residual disease.

20. A method for classifying a subject suffering from cancer depending on the benefit from an anti-cancer therapy (e.g., immunotherapy), wherein the method comprises: a) determining the lipid length of at least one ganglioside in a sample from a subject administered an anti-cancer therapy using the mass spectrometry of claim 1 or 2; b) determining the lipid length of at least one ganglioside in the control; and c) comparing the lipid length of at least one ganglioside detected in steps a) and b); wherein the absence of a significant change in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample is an indication that the subject suffering from cancer will benefit from the anti-cancer therapy.

21. A method for determining the likelihood of a response of a subject suffering from cancer to an anti-cancer therapy (e.g., immunotherapy), wherein the method comprises: a) determining the lipid length of at least one ganglioside in a sample from a subject administered an anti-cancer therapy using the mass spectrometry of claim 1 or 2; b) determining the lipid length of at least one ganglioside in the control; and c) comparing the lipid length of at least one ganglioside detected in steps a) and b); wherein a significant change in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample is an indication that the subject having cancer will not respond to anti-cancer therapy; and / or wherein the absence of a significant change in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample is an indication that the subject having cancer will respond to anti-cancer therapy.

22. A method for predicting a clinical outcome in a subject suffering from cancer, wherein the method comprises: a) determining the lipid length of at least one ganglioside in the test sample using mass spectrometry according to paragraph 1 or 2; b) determining the lipid length of at least one ganglioside in the control; and c) comparing the lipid length of at least one ganglioside determined in steps a) and b); wherein a significant change in the lipid length heterogeneity of at least one ganglioside in a subject sample compared to a control sample is an indication that the subject has a poor clinical outcome.

23. A method for monitoring the progression of cancer in a subject, wherein the method comprises: a) determining in a sample of the subject at a first time point the length of the lipid of at least one ganglioside using the mass spectrometry of paragraph 1 or 2; b) repeating stage a) at a subsequent point in time; and c) comparing the lipid length heterogeneity of at least one ganglioside detected in steps a) and b) to monitor the progression of cancer in the subject, if necessary, if the subject is at risk of developing cancer.

24. The method of claim 23, wherein between the first time point and the subsequent time point the subject has received anti-cancer therapy.

25. A method for assessing the effectiveness of anticancer therapy in a subject suffering from cancer, wherein the method comprises: a) determining the lipid length of at least one ganglioside using mass spectrometry according to claim 1 or 2 in a first sample obtained from the subject; b) repeating step a) at least one subsequent time point after administration of anticancer therapy; and wherein a significant change in the lipid length heterogeneity of at least one ganglioside in the second sample compared to the first sample is an indication that the therapy is effective in treating cancer in the subject.

26. The method according to any one of claims 23-25, wherein the first and / or at least one subsequent sample is a portion of a single sample or pooled samples obtained from the subject.

27. The method of any one of claims 3-26, further comprising treating the subject with an anti-cancer therapy (e.g., recommending, prescribing, and / or administering to the subject an anti-cancer therapy).

28. The method according to any one of claims 8, 9, 12-14, 20, 21 and 24-27, wherein the anti-cancer therapy is surgery, chemotherapy, anti-cancer vaccines, chimeric antigen receptors, radiation therapy, immunotherapy, a modulator of the expression of proteins or ligands that inhibit immune checkpoints, or any combination thereof.

29. The method of claim 28, wherein the immunotherapy is immune checkpoint inhibition therapy.

30. The method according to any one of claims 8, 9, 12-14, 20, 21 and 24-29, wherein the anti-cancer therapy is avelumab, durvalumab, atezolizumab, a BRAF / MEK inhibitor, pembrolizumab, nivolumab, ipilimumab or a combination thereof.

31. The method according to any one of claims 1-30, wherein at least one ganglioside and / or at least one lipoform of a ganglioside is a tumor-associated ganglioside and / or a lipoform of a tumor-associated ganglioside.

32. The method according to any one of claims 1-31, wherein the ganglioside comprises GD2, GD3, GD1b, GT1b, fucosyl-GM1, GloboH, polysialic acid (PSA), GM2, GM3, sialyl-Lewis X , sialyl-Lewis Y , sialyl-Lewis A , sialyl-Lewis B , Lewis Y , any part of them, any lipoform of them, or any combination of them.

33. The method according to any one of claims 1-32, wherein at least one ganglioside and / or at least one lipoform of ganglioside comprises GM2, GD3, GD2, GD1b, any lipoform thereof, or any combination thereof.

34. The method according to any one of claims 1-33, wherein at least one ganglioside and / or at least one lipoform of ganglioside comprises a combination of two or more selected from GM2, GD3, GD2, GD1b and any lipoform thereof.

35. The method according to any one of claims 1-34, wherein at least one ganglioside and / or at least one lipoform of a ganglioside comprises GD3(d18:1 / 16:0), GD3(d18:1 / 23:0), GD3(d18:1 / 24:1), GD2(d18:1 / 16:0), GD1b(d18:1 / 16:0), GD1b(d18:1 / 24:1), GD1b(d18:1 / 18:1) or any combination of two or more of them.

36. The method according to any one of claims 1-35, wherein at least one ganglioside and / or at least one lipoform of ganglioside comprises GD3(d18:1 / 23:0) and / or GD3(d18:1 / 24:1).

37. The method according to any one of claims 1-36, wherein at least one ganglioside and / or at least one lipoform of ganglioside comprises GD3(d18:1 / 23:0).

38. The method according to any one of claims 1-36, wherein at least one ganglioside and / or at least one lipoform of ganglioside comprises a 24:1 acyl chain.

39. The method of claim 38, wherein the 24:1 acyl chain is present in GD3 and / or GD1b.

40. The method according to any one of claims 1-39, wherein the cancer or tumor is selected from the group consisting of neuroblastoma, lymphoma, leukemia, melanoma, glioma, small cell lung cancer, breast carcinoma, ovarian cancer, soft tissue sarcomas, osteosarcoma, Ewing's sarcoma, desmoplastic round cell tumor, rhabdomyosarcoma, retinoblastoma, non-small cell lung cancer, renal cell carcinoma, Wilms' tumor, prostate cancer, gastric cancer, endometrial cancer, pancreatic cancer and colon cancer.

41. The method according to any one of claims 1-40, wherein the cancer or tumor is ovarian cancer, melanoma, kidney cancer or lung cancer, optionally wherein the cancer or tumor is ovarian cancer.

42. The method according to any one of claims 1-41, wherein the cancer is a borderline tumor.

43. The method of any one of claims 1-42, wherein the sample comprises cells, serum, blood, peritumoral tissue and / or intratumoral tissue obtained from a subject.

44. The method according to any one of claims 1 to 43, wherein the sample comprises serum or blood.

45. The method of any one of claims 3-44, wherein said significantly higher level of at least one ganglioside comprises at least a twenty percent increase in the level of at least one ganglioside.

46. The method of any one of claims 3-45, wherein the significantly lower level of at least one ganglioside comprises at least a twenty percent reduction in the level of at least one ganglioside.

47. The method of any one of claims 3-46, wherein the control sample is a sample from a subject not suffering from cancer.

48. The method of any one of claims 3-47, wherein the control sample is a sample from a subject (e.g., a first sample collected from a subject during longitudinal collections to assess changes over time in the level of at least one ganglioside).

49. The method of any one of claims 3-48, wherein the subject is a mammal (e.g., suffering from cancer, e.g., an asymptomatic subject).

50. The method according to any one of paragraphs 3-49, wherein the subject is an animal model of cancer, a dog, a cat or a human.

51. The method according to any of paragraphs 3-50, wherein the subject is a human.