BIOMARKER DLEC1 FOR CANCER

• US 20200131584A1
• Filed: 08/02/2019
• Published: 04/30/2020
• Est. Priority Date: 08/03/2018
• Status: Active Grant

• Current Assignee: Chinese University of Hong Kong, Donaldson Company Incorporated
• Original Assignee: Chinese University of Hong Kong
• Inventors: Tao, Qian, Li, Lili
• Granted Patent: US 11,746,383 B2
• Time in Patent Office: Days
• CPC Class Codes: C12N 15/11 DNA or RNA fragments; Modified forms thereof DNA or RNA not used in recombinant technology, C07H21/00; Non-coding nucleic acids having a biological activity
• CPC Class Codes: C12N 5/0632 Cells of the oral mucosa
• CPC Class Codes: C12N 5/0693 Tumour cells; Cancer cells
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

The present invention provides a method for diagnosing and determining prognosis of certain cancers (e.g., esophageal squamous cell carcinoma or ESCC) in a subject by detecting suppressed expression of the DLEC1 gene, which in some cases is due to elevated methylation level in the genomic sequence of this gene. A kit and device useful for such a method are also provided. In addition, the present invention provides a method for treating cancer by increasing DLEC1 gene expression or activity.

Claims

1. A method for assessing risk for esophageal squamous cell carcinoma (ESCC) in a subject, comprising the steps of:

(a) measuring expression level of DLEC1 in a sample taken from the subject,

(b) comparing the expression level obtained in step (a) with a standard control, and

(c) determining the subject, who has a reduced DLEC1 expression level compared with the standard control, as having an increased risk for ESCC.

2. The method of claim 1, wherein the sample is a esophageal epithelial tissue sample.

3. The method of claim 1, wherein the expression level of DLEC1 is DLEC1 protein level.

4. The method of claim 1, wherein the expression level of DLEC1 is DLEC1 mRNA level.

5-12. -12. (canceled)

13. A method for assessing risk for ESCC in a subject, comprising the steps of:

(a) treating DNA from an esophageal epithelial tissue sample taken from the subject with an agent that differentially modifies methylated and unmethylated DNA;

(b) determining number of methylated CpGs in a genomic sequence, which is SEQ ID NO;

5 or 6 or a fragment thereof comprising at least 10 CpGs, and

(c) comparing the number of methylated CpGs from step (b) with the number of methylated CpGs in the genomic sequence from a non-ESCC sample and processed through steps (a) and (b); and

(d) determining the subject, whose sample contains more methylated CpGs in the genomic sequence determined in step (b) compared to the number of methylated CpGs with the number of methylated CpGs in the genomic sequence from a non-ESCC sample and processed through steps (1) to (3), as having an increased risk for ESCC compared with a healthy subject not diagnosed with ESCC.

14. The method of claim 13, wherein the genomic sequence is SEQ ID NO:

5.

15. The method of claim 13, wherein the genomic sequence is SEQ ID NO:

6.

16. The method of claim 13, wherein the agent that differentially modifies methylated DNA and unmethylated DNA is an enzyme that preferentially cleaves methylated DNA, an enzyme that preferentially cleaves unmethylated DNA, or a bisulfite.

17. (canceled)

18. A method for assessing likelihood of mortality from ESCC in an ESCC patient, comprising the steps of:

(a) treating DNA from an ESCC sample taken from a first ESCC patient with an agent that differentially modifies methylated and unmethylated DNA;

(b) determining number of methylated CpGs in a genomic sequence, which is SEQ ID NO;

5 or 6 or a fragment thereof comprising at least 10 CpGs, and

(c) comparing the number of methylated CpGs from step (b) with the number of methylated CpGs in the genomic sequence from another ESCC sample of the same type obtained from a second ESCC patient and processed through steps (a) and (b); and

(d) determining the first patient, whose ESCC sample contains more methylated CpGs in the genomic sequence determined in step (b) compared to the number of methylated CpGs with the number of methylated CpGs in the genomic sequence from the ESCC sample obtained from the second patient and processed through steps (1) to (3), as having an increased likelihood of mortality from ESCC compared with the second ESCC patient.

19. The method of claim 18, wherein the genomic sequence is SEQ ID NO:

5.

20. The method of claim 18, wherein the genomic sequence is SEQ ID NO:

6.

21. The method of claim 18, wherein the agent that differentially modifies methylated DNA and unmethylated DNA is an enzyme that preferentially cleaves methylated DNA, an enzyme that preferentially cleaves unmethylated DNA, or a bisulfite.

22. (canceled)

23. A kit for detecting ESCC in a subject, comprising (1) a standard control that provides an average amount of DLEC1 protein or DLEC1 mRNA;

and (2) an agent that specifically and quantitatively identifies DLEC1 protein or DLEC1 mRNA.

24. The kit of claim 23, wherein the agent is an antibody that specifically binds the DLEC1 protein.

25. The kit of claim 23, wherein the agent is a polynucleotide probe that hybridizes with the DLEC1 mRNA.

26. The kit of claim 23, wherein the agent comprises a detectable moiety.

27-28. -28. (canceled)

29. A method for inhibiting growth of an ESCC cell, comprising contacting the ESCC cell with an effective amount of a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:

4 or a nucleic acid comprising a polynucleotide sequence encoding SEQ ID NO;

4.

30. The method of claim 29, wherein the nucleic acid is an expression cassette comprising a promoter operably linked to the polynucleotide sequence encoding SEQ ID NO:

4.

31. The method of claim 30, wherein the promoter is an epithelium-specific promoter.

32. The method of claim 29, wherein the nucleic acid comprises the nucleotide sequence set forth in SEQ ID NO:

1 or 3.

33. (canceled)