Methods of treating cells containing fusion genes by genomic targeting

Patent metadata

Field	Value
Publication number	US-2019282708-A1
Application number	US-201916427212-A
Country	US
Kind code	A1
Filing date	May 30, 2019
Priority date	Dec 13, 2016
Publication date	Sep 19, 2019
Grant date	—

Abstract

The present invention relates to methods for treating patients having cancer or a premalignant or neoplastic condition. It is based, at least in part, on the discovery that a genome editing technique that specifically targets a fusion gene can induce cell death in a cancer cell other than a prostate cancer cell, e.g., a hepatocellular cancer cell, having the fusion gene. The present invention provides methods for treating cancer patients that include performing a genome editing technique targeting a fusion gene present within one or more cells of a subject to produce an anti-cancer effect.

First claim

1 - 51 . (canceled)

52 . A method of treating a subject, comprising determining that at least one fusion gene is present in a sample obtained from a subject and then performing a genome editing technique targeting the fusion gene within one or more cells of the subject to achieve an anti-neoplastic effect or an anti-cancer effect, wherein the subject does not have prostate cancer.

53 . The method of claim 52 , wherein the at least one fusion gene is selected from the group consisting of TRMT11-GRIK2, SLC45A2-AMACR, MTOR-TP53BP1, LRRC59-FLJ60017, TMEM135-CCDC67, KDM4B-AC011523.2, MAN2A1-FER, PTEN-NOLC1, CCNH-C5orf30, ZMPSTE24-ZMYM4, CLTC-ETV1, ACPP-SEC13, DOCK7-OLR1, PCMTD1-SNTG1 and a combination thereof.

54 . The method of claim 52 , wherein the subject has a pre-malignant or a neoplastic condition.

55 . The method of claim 52 , wherein the subject has cancer.

56 . The method of claim 55 , wherein the cancer is breast cancer, liver cancer, lung cancer, cervical cancer, endometrial cancer, pancreatic cancer, ovarian cancer, gastric cancer, thyroid cancer, glioblastoma multiforme, colorectal cancer, diffuse large B cell-lymphoma, sarcoma, acute and chronic lymphocytic leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma, or esophageal adenocarcinoma.

57 . The method of claim 52 , wherein the at least one fusion gene is detected by FISH analysis or by reverse transcription polymerase chain reaction.

58 . The method of claim 52 , wherein the genome editing technique uses a CRISPR/Cas system.

59 . The method of claim 58 , wherein the CRISPR/Cas system cleaves a sequence within the fusion gene genomic sequence to insert a nucleic acid within the at least one fusion gene to induce cell death.

60 . The method of claim 58 , wherein the CRISPR/Cas system uses a Cas endonuclease selected from the group consisting of Casl, CaslB, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7, Cas8, Cas9 (also known as Csnl or Csxl2), CaslO, Csyl, Csy2, Csy3, Cse 1, Cse2, Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3, Csxl, CsxlS, Csfl, Csf2, CsO, Csf4, Cpfl, c2cl, c2c3, Cas9HiFi and a combination thereof.

61 . The method of claim 52 , wherein the genome editing technique comprises: transducing the one or more cells with (i) a vector comprising a nucleic acid encoding a Cas protein and two guide RNAs (gRNA) and (ii) a vector comprising a donor nucleic acid and one or more targeting sequences.

62 . The method of claim 61 , wherein one of the gRNAs is complementary to a region within a first gene of the at least one fusion gene and the other gRNA is complementary to a region within a second gene of the at least one fusion gene.

63 . The method of claim 61 , wherein the donor nucleic acid encodes HSV-1 thymidine kinase.

64 . The method of claim 61 , wherein the method further comprises administering to the subject a therapeutically effective amount of ganciclovir or valganciclovir.

65 . The method of claim 61 , wherein one of the gRNAs is complementary to a region within a MAN2A1 gene of a MAN2A1-FER fusion gene and the other gRNA can be complementary to a region within a FER gene.

66 . The method of claim 61 , wherein one of the gRNAs is complementary to a region within a TMEM135 gene of a TMEM135-CCDC67 fusion gene and the other gRNA can be complementary to a region within a CCDC67 gene.

67 . The method of claim 66 , wherein the one or more cells of the subject are cancer cells.

68 . The method of claim 67 , wherein the cancer cells are breast cancer, liver cancer, lung cancer, cervical cancer, endometrial cancer, pancreatic cancer, ovarian cancer, gastric cancer, thyroid cancer, glioblastoma multiforme, colorectal cancer, diffuse large B cell lymphoma, sarcoma, acute and chronic lymphocytic leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma or esophageal adenocarcinoma cells.

69 . The method of claim 55 , wherein the cancer is not lung adenocarcinoma, glioblastoma multiforme or hepatocellular carcinoma.

70 . A kit for performing a genome editing technique targeting one or more fusion genes present within a cell, where the cell is not a prostate cancer cell, wherein the kit comprises: (i) a vector comprising a nucleic acid encoding a Cas protein and one or more guide RNAs (gRNA) and (ii) a vector comprising a donor nucleic acid and one or more targeting sequences.

71 . The kit of claim 70 , wherein a first gRNA is complementary to a region within a first gene of the fusion gene and a second gRNA is complementary to a region within a second gene of the fusion gene.

72 . The kit of claim 70 , wherein the donor nucleic acid encodes HSV-1 thymidine kinase.

73 . The kit of claim 70 , wherein the kit further comprises ganciclovir and/or valganciclovir.

74 . The kit of claim 70 , wherein the one or more fusion genes is selected from the group consisting of TRMT11-GRIK2, SLC45A2-AMACR, MTOR-TP53BP1, LRRC59-FLJ60017, TMEM135-CCDC67, KDM4B-AC011523.2, MAN2A1-FER, PTEN-NOLC1, CCNH-C5orf30, ZMPSTE24-ZMYM4, CLTC-ETV1, ACPP-SEC13, DOCK7-OLR1, PCMTD1-SNTG1 and a combination thereof.

75 . The kit of claim 70 , further comprising nucleic acid primers for PCR analysis or nucleic acid probes for FISH analysis of the one or more fusion genes selected from the group consisting of TRMT11-GRIK2, SLC45A2-AMACR, MTOR-TP53BP1, LRRC59-FLJ60017, TMEM135-CCDC67, PTEN-NOLC1, CCNH-C5orf30, TRMT11-GRIK2, SLC45A2-AMACR, KDM4B-AC011523.2, MAN2A1-FER, MTOR-TP53BP, ZMPSTE24-ZMYM4, CLTC-ETV1, ACPP-SEC13, DOCK7-OLR1 or PCMTD1-SNTG11.

76 . The kit of claim 70 , wherein the cell is a cell from a breast cancer, liver cancer, lung cancer, cervical cancer, endometrial cancer, pancreatic cancer, ovarian cancer, gastric cancer, thyroid cancer, glioblastoma multiforme, colorectal cancer, diffuse large B cell lymphoma, sarcoma, acute and chronic lymphocytic leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma or esophageal adenocarcinoma cell.

77 . The kit of claim 70 , wherein the cell is a neoplastic and/or pre-malignant cell.

78 . The kit of claim 70 , wherein the Cas protein is Cas9 or Cas9 D10A .

79 . The kit of claim 70 , wherein the cell is not a cell from a lung adenocarcinoma, a glioblastoma multiforme or a hepatocellular carcinoma.

80 . An agent capable of targeted genome editing for use in a method to treat a subject, the method comprising (i) determining whether a sample of the subject contains one or more fusion genes; and (ii) where the sample contains the one or more fusion genes, then performing a genome editing procedure using the agent to target the one or more fusion genes in one or more cells within the subject, where the subject does not have prostate cancer.

81 . The agent of claim 80 , wherein the agent is a Cas9 protein.

82 . The agent of claim 81 , wherein the Cas9 protein is Cas9 D10A .

83 . The agent of claim 80 , wherein the subject has cancer, and wherein the cancer is breast cancer, liver cancer, lung cancer, cervical cancer, endometrial cancer, pancreatic cancer, ovarian cancer, gastric cancer, thyroid cancer, glioblastoma multiforme, colorectal cancer, diffuse large B cell lymphoma, sarcoma, acute and chronic lymphocytic leukemia, Hodgkin's lymphoma, non-Hodgkin's lymphoma or esophageal ad

Assignees

• Univ Pittsburgh Commonwealth Sys Higher Education

Inventors

• Luo Jianhua
• Chen Zhanghui
• Yu Yanping
• Michalopoulos George
• Nelson Joel B
• Tseng Chien-Cheng

Classifications

• A61K48/005 Primary

  characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered · CPC title

• A61K38/465

  acting on ester bonds (3.1), e.g. lipases, ribonucleases · CPC title

• C12Q2600/106

  Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism · CPC title

• A61K31/7088

  Compounds having three or more nucleosides or nucleotides · CPC title

• A61P35/00

  Antineoplastic agents · CPC title