US 12,442,042 B2
Epigenomic profiling reveals the somatic promoter landscape of primary gastric adenocarcinoma
Patrick Tan, Singapore (SG); Aditi Qamra, Singapore (SG); Manjie Xing, Singapore (SG); and Wen Fong Ooi, Singapore (SG)
Assigned to AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH, Singapore (SG)
Appl. No. 15/999,597
Filed by AGENCY FOR SCIENCE, TECHNOLOGY AND RESEARCH, Singapore (SG)
PCT Filed Feb. 16, 2017, PCT No. PCT/SG2017/050072
§ 371(c)(1), (2) Date Aug. 16, 2018,
PCT Pub. No. WO2017/142484, PCT Pub. Date Aug. 24, 2017.
Claims priority of application No. 10201601142V (SG), filed on Feb. 16, 2016.
Prior Publication US 2021/0301348 A1, Sep. 30, 2021
Int. Cl. C12Q 1/68 (2018.01); C12P 19/34 (2006.01); C12Q 1/6886 (2018.01)
CPC C12Q 1/6886 (2013.01) [C12Q 2600/118 (2013.01); C12Q 2600/154 (2013.01)] 16 Claims
 
1. A method for detecting the presence of at least one promoter in a cancerous biological sample that is associated with tumor immunity, comprising:
i) contacting the cancerous biological sample with at least one antibody specific for histone modification H3K4me3 and at least one antibody specific for histone modification H3K4me1;
ii) isolating nucleic acid from the cancerous biological sample having a signal ratio of H3K4me3 relative to H3K4me1 greater than 1, wherein the isolated nucleic acid comprises at least one region specific to said histone modifications;
iii) detecting an increase in signal intensity of H3K4me3 in the isolated nucleic acid relative to the signal intensity of H3K4me3 in a non-cancerous biological sample of greater than 1.5 fold thereby identifying at least one cancer-associated alternative promoter that is associated with a canonical promoter; and
iv) detecting the presence of a transcript variant in the cancerous biological sample driven by the at least one cancer-associated alternative promoter of step iii), wherein the at least one cancer-associated promoter is a promoter of a gene encoding a polypeptide associated with tumor immunity,
wherein the transcript variant encodes an N-terminal truncated peptide and wherein said truncated peptide is a non-immunogenic peptide compared to an untruncated variant of the peptide encoded by a transcript expressed from the associated canonical promoter.