Novel chimeric gene atf7ip-pdgfrb of acute lymphoblastic leukemia

Patent metadata

Field	Value
Publication number	US-2016289663-A1
Application number	US-201415037907-A
Country	US
Kind code	A1
Filing date	Nov 17, 2014
Priority date	Nov 22, 2013
Publication date	Oct 6, 2016
Grant date	—

Abstract

To identify a mutation that can serve as an indicator for predicting the effectiveness of drug treatment in cancers such as leukemia; to provide a means for detecting said mutation; and to provide a means for identifying, based on said mutation, patients with cancer or subjects with a risk of cancer, in whom a drug targeting a gene having said mutation or a protein encoded by said gene shows a therapeutic effect.
A method for detecting a gene fusion serving as a responsible mutation (driver mutation) for cancer, the method comprising the step of detecting an ATF7IP-PDGFRB fusion polynucleotide or a polypeptide encoded thereby, in an isolated sample from a subject.

First claim

1 . A method for detecting a gene fusion, the method comprising the step of detecting an ATF7IP-PDGFRB fusion polypeptide comprising the SETDB1-binding domain of ATF7IP and the transmembrane region and kinase domain of PDGFRB, and having kinase activity, or a fusion polynucleotide encoding said polypeptide, in an isolated sample from a subject.

2 . The method according to claim 1 , wherein the fusion polypeptide is any one of (i) to (iii) mentioned below:
(i) a polypeptide consisting of the amino acid sequence of SEQ ID NO: 2 or 4, (ii) a polypeptide consisting of an amino acid sequence derived from the amino acid sequence of SEQ ID NO: 2 or 4 by deletion, substitution or addition of one or more amino acids, and the polypeptide having kinase activity, or (iii) a polypeptide consisting of an amino acid sequence having a sequence identity of at least 80% to the amino acid sequence of SEQ ID NO: 2 or 4, and the polypeptide having kinase activity.

3 . The method according to claim 1 , wherein the fusion polynucleotide is any one of (i) to (iv) mentioned below:
(i) a polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 1 or 3, (ii) a polynucleotide that hybridizes under stringent conditions with a polynucleotide consisting of a nucleotide sequence complementary to the polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 1 or 3, and which encodes a polypeptide having kinase activity, (iii) a polynucleotide that consists of a nucleotide sequence derived from the nucleotide sequence of SEQ ID NO: 1 or 3 by deletion, substitution or addition of one or more nucleotides, and which encodes a polypeptide having kinase activity, or (iv) a polynucleotide that has a sequence identity of at least 80% to the polynucleotide consisting of the nucleotide sequence of SEQ ID NO: 1 or 3, and which encodes a polypeptide having kinase activity.

4 . The method according to claim 1 , wherein the gene fusion is a responsible mutation (driver mutation) for cancer.

5 . The method according to claim 4 , wherein the cancer is acute lymphoblastic leukemia.

6 . A method for identifying a patient with cancer or a subject with a risk of cancer, in whom a substance suppressing the expression and/or activity of a polypeptide encoded by a fusion polynucleotide produced by a gene fusion serving as a responsible mutation (driver mutation) for cancer shows a therapeutic effect, the method comprising the steps of:
(1) detecting an ATF7IP-PDGFRB fusion polypeptide comprising the SETDB1-binding domain of ATF7IP and the transmembrane region and kinase domain of PDGFRB, and having kinase activity, or a fusion polynucleotide encoding said polypeptide, in an isolated sample from a subject, and (2) determining that the substance suppressing the expression and/or activity of the polypeptide shows a therapeutic effect in the subject, in the case where the fusion polypeptide or the fusion polynucleotide encoding said polypeptide is detected.

7 . A kit for detecting a gene fusion, the kit comprising any or a combination of (A) to (C) mentioned below:
(A) a polynucleotide that serves as a probe designed to specifically recognize an ATF7IP-PDGFRB fusion polynucleotide; (B) polynucleotides that serve as a pair of primers designed to enable specific amplification of an ATF7IP-PDGFRB fusion polynucleotide; or (C) an antibody that specifically recognizes an ATF7IP-PDGFRB fusion polypeptide.

8 . The kit according to claim 7 , wherein the gene fusion is a responsible mutation (driver mutation) for cancer.

9 . An isolated ATF7IP-PDGFRB fusion polypeptide or a fragment thereof, which comprises the SETDB1-binding domain of ATF7IP and the transmembrane region and kinase domain of PDGFRB, and has kinase activity.

10 . A polynucleotide encoding the fusion polypeptide or the fragment thereof according to claim 9 .

11 . A method for treating ATF7IP-PDGFRB gene fusion-positive cancer, comprising administering, to a patient in need thereof, an effective amount of a substance suppressing the expression and/or activity of an ATF7IP-PDGFRB fusion polypeptide comprising the SETDB1-binding domain of ATF7IP and the transmembrane region and kinase domain of PDGFRB, and having kinase activity.

12 . (canceled)

13 . The method according to claim 11 , wherein the cancer is acute lymphoblastic leukemia.

14 . The method according to claim 11 , wherein the substance suppressing the expression and/or activity of an ATF7IP-PDGFRB fusion polypeptide comprising the SETDB1-binding domain of ATF7IP and the transmembrane region and kinase domain of PDGFRB, and having kinase activity is a substance inhibiting the kinase activity of PDGFRB.

15 . The method according to claim 14 , wherein the substance inhibiting the kinase activity of PDGFRB is imatinib mesylate, dasatinib, nilotinib, ponatinib, rebastinib or bafetinib.

16 . The method according to claim 14 , wherein the substance inhibiting the kinase activity of PDGFRB is dasatinib.

17 . A method for screening a cancer therapeutic agent, the method comprising the steps of:
(1) bringing a test substance into contact with a cell that expresses an ATF7IP-PDGFRB fusion polypeptide comprising the SETDB1-binding domain of ATF7IP and the transmembrane region and kinase domain of PDGFRB, and having kinase activity; (2) determining whether the expression and/or activity of the fusion polypeptide is suppressed or not; and (3) selecting the substance determined to suppress the expression and/or activity of the fusion polypeptide, as a cancer therapeutic agent.

Assignees

• Nat Center For Child Health And Dev
• Nat Cancer Ct
• Lsip Llc

Inventors

• Kiyokawa Nobutaka
• Matsumoto Kenji
• Kobayashi Kenichiro
• Ichikawa Hitoshi

Classifications

• G01N2500/10

  involving cells · CPC title

• A61K45/06

  Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca · CPC title

• A61P35/02

  specific for leukemia · CPC title

• A61P35/00

  Antineoplastic agents · CPC title

• A61K31/404

  Indoles, e.g. pindolol · CPC title