BARD1 isoforms in lung and colorectal cancer and use thereof

Patent metadata

Field	Value
Publication number	US-9599624-B2
Application number	US-201113817013-A
Country	US
Kind code	B2
Filing date	Aug 17, 2011
Priority date	Aug 17, 2010
Publication date	Mar 21, 2017
Grant date	Mar 21, 2017

Abstract

The present invention relates to new BARD1 isoforms specific to lung cancer and colorectal cancer, a method for detecting thereof and a method for treating and/or preventing lung cancer and colorectal cancer.

First claim

The invention claimed is:

1. A method for detecting the presence of a BARD1 isoform specific to lung cancer and colorectal cancer, the method comprising the steps of:
obtaining a biological sample from a subject;
providing at least one polynucleotide primer or probe, wherein said polynucleotide primer or probe is specific for an mRNA that encodes the BARD1 isoform π consisting of SEQ ID NO:1 or a sequence having at least 99% homology to SEQ ID NO:1 and for an mRNA that encodes BARD1 isoform π′ consisting of SEQ ID NO: 105 or a sequence having at least 99% homology to SEQ ID NO:105, wherein said BARD1 isoform π consisting of SEQ ID NO:1, said sequence having at least 99% homology to SEQ ID NO:1, said BARD1 isoform π′ consisting of SEQ ID NO:105, and said sequence having at least 99% homology to SEQ ID NO:105 comprise a deletion within exon 4 of said BARD1 isoform, and wherein said primer or probe specifically binds to said mRNA at the deletion junction of said deletion within exon 4; and
detecting in said sample the mRNA encoding said sequence by detecting specific binding of said polynucleotide primer or probe to said mRNA, thereby detecting the presence of said BARD1 isoform specific to lung cancer and colorectal cancer,
wherein the presence of said BARD1 isoform π or isoform π′ specific to lung cancer and colorectal cancer in a sample from said subject is an indication that said subject is afflicted with lung cancer and/or colorectal cancer, has an increased risk of lung cancer and/or colorectal cancer, a risk of recurrence after a treatment for lung cancer and/or colorectal cancer, and/or is an indication of reduced survival of a patient afflicted with lung cancer.

2. The method of claim 1 , wherein said method comprises the step of detecting in said biological sample BARD1 isoform π consisting of SEQ ID NO:1 and BARD1 isoform κ consisting of SEQ ID NO:2.

3. The method of claim 1 , wherein said method further comprises detecting in said biological sample at least one of the BARD1 isoforms selected from the group comprising
isoform π′ comprising SEQ ID NO:105, a biologically active fragment thereof, or a sequence having at least 95% homology to SEQ ID NO:105,
isoform β comprising SEQ ID NO:5, a biologically active fragment thereof, or a sequence having at least 95% homology to SEQ ID NO:5,
isoform δ comprising SEQ ID NO:6, a biologically active fragment thereof, or a sequence having at least 95% homology to SEQ ID NO:6, and
isoform γ comprising SEQ ID NO:7, a biologically active fragment thereof, or a sequence having at least 95% homology to SEQ ID NO:7,
isoform β′ comprising SEQ ID NO:106, a biologically active fragment thereof, or a sequence having at least 95% homology to SEQ ID NO:106.

4. The method of claim 3 , wherein said method comprises detecting in said biological sample BARD1 isoform π consisting of SEQ ID NO:1, BARD1 isoform κ consisting of SEQ
ID NO:2 and BARD1 isoform β consisting of SEQ ID NO:5.

5. The method according to claim 1 , wherein said biological sample is selected from the group comprising a biopsy sample, a histology sample, lung liquids, frozen tissue sample, tumor tissue sample, feces sample, cerebrospinal fluid (CSF), circulating tumour cells (CTC) and blood sample.

6. The method according to claim 1 , wherein said subject is a human.

7. The method of claim 1 , wherein the presence of said BARD1 isoforms is detected by using antibodies specific to said BARD1 isoforms.

8. The method of claim 7 , wherein said antibodies are a combination of antibodies or fragments thereof that specifically bind to different epitopes of at least one of the BARD1 isoforms comprising amino acid sequences selected from the group comprising SEQ ID NOs:1-7, 105-106 biologically active fragments thereof, or sequences having at least 95% homology to SEQ ID NOs:1-7, 105-106.

9. The method of claim 1 , wherein the presence of said BARD1 isoforms is detected by detecting the level of mRNA that encodes at least one of the BARD1 isoforms comprising amino acid sequences selected from the group comprising SEQ ID NOs:1-7, 105-106, biologically active fragments thereof, or sequences having at least 95% homology to SEQ ID NOs:1-7, 105-106.

10. A method for discriminating lung cancer and colorectal cancer from gynecological cancers, said method comprising the steps of:
obtaining a biological sample from a subject;
providing at least one polynucleotide primer or probe, wherein said polynucleotide primer or probe is specific for an mRNA that encodes the BARD1 isoform π consisting of SEQ ID NO:1 or a sequence having at least 99% homology to SEQ ID NO:1 and for an mRNA that encodes BARD1 isoform π′ consisting of SEQ ID NO:105 or a sequence having at least 99% homology to SEQ ID NO:105, wherein said BARD1 isoform π consisting of SEQ ID NO:1, said sequence having at least 99% homology to SEQ ID NO:1, said BARD1 isoform π′ consisting of SEQ ID NO:105, and said sequence having at least 99% homology to SEQ ID NO:105 comprise a deletion within exon 4 of said BARD1 isoform, and wherein said primer or probe specifically binds to a deletion junction of said deletion within exon 4; and
detecting in said sample the mRNA encoding said sequence by detecting specific binding of said polynucleotide primer or probe to said mRNA, thereby detecting the presence of said BARD1 isoform π or π′ specific to lung cancer and colorectal cancer,
wherein the presence of said BARD1 isoform π or π′ specific to lung cancer and colorectal cancer is an indication for lung cancer and/or colorectal cancer.

11. The method of claim 1 , wherein said mRNA that encodes said sequence is detected in circulating tumor cells present in said sample.

12. A method for detecting the presence of a BARD1 isoform specific to lung cancer and colorectal cancer, the method comprising the steps of:
obtaining a biological sample from a subject;
detecting in said biological sample autoantibodies specific for a BARD1 isoform π consisting of sequence SEQ ID NO:1 or a sequence having at least 99% homology to SEQ ID NO:1 by performing an immunoassay, wherein said step of performing an immunoassay comprises the steps:
a) providing at least four different antigen peptides selected from the group consisting of SEQ ID NOs:16, 17, 18, 23, 68, 69, 74 and 75, wherein said antigen peptides are immobilized on a solid support,
b) bringing said biological sample into contact with said immobilized solid support, and
c) detecting complexes formed between autoimmune antibodies and antigen peptides, thereby detecting the presence of a BARD1 isoform specific to lung cancer and colorectal cancer,
wherein the presence of said BARD1 isoform π specific to lung cancer and colorectal cancer in a sample from said subject is an indication that said subject is afflicted with lung cancer and/or colorectal cancer, has an increased risk of lung cancer and/or colorectal cancer, a risk of recurrence after a treatment for lung cancer and/or colorectal cancer, and/or is an indication of reduced survival of a patient afflicted with lung cancer.

13. The method of claim 1 , wherein said primer or probe is specific for a nucleotide sequence of SEQ ID NO:8 encoding BARD1 isoform n or an nucleotide sequence having 95% homology to SEQ ID NO:8, and for a nucleotide sequence of SEQ ID NO:141 encoding BARD1 isoform n′ or an nucleotide sequence having 95% homology to SEQ ID NO:141.

14. The method of claim 1 , wherein said primer or probe specifically binds to said mRNA at said deletion junction at an annealing temperature of 56° C. and at salt conditions conducive for binding of a primer or probe to said mRNA.

Assignees

• Irminger-Finger Irmgard
• Zhang yong-qiang
• Hopitaux Univ De Geneve
• Univ Geneve

Inventors

• Irminger-Finger Irmgard
• Zhang yong-qiang

Classifications

• A61P35/00

  Antineoplastic agents · CPC title

• C12N2310/14

  interfering nucleic acids [NA] · CPC title

• C12Q2600/158

  Expression markers · CPC title

• A61P1/00

  Drugs for disorders of the alimentary tract or the digestive system · CPC title

• C12Y603/02

  Acid—amino-acid ligases (peptide synthases)(6.3.2) · CPC title