Systematic identification of genes with a cancer-testis expression pattern in 19 cancer types.
Cheng Wang,Yayun Gu,Kai Zhang,Kaipeng Xie,Meng Zhu,Ningbin Dai,Yue Jiang,Xuejiang Guo,Mingxi Liu,Juncheng Dai,Linxiang Wu,Guangfu Jin,Hongxia Ma,Tao Jiang,Rong Yin,Yankai Xia,Li Liu,Shouyu Wang,Bin Shen,Ran Huo,Qianghu Wang,Lin Xu,Liuqing Yang,Xingxu Huang,Hongbing Shen,Jiahao Sha,Zhibin Hu +26 more
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TLDR
This study integrates transcriptomics data from multiple databases and systematically identifies 876 new CT genes in 19 cancer types to propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms and provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.Abstract:
Cancer-testis (CT) genes represent the similarity between the processes of spermatogenesis and tumorigenesis. It is possible that their selective expression pattern can help identify driver genes in cancer. In this study, we integrate transcriptomics data from multiple databases and systematically identify 876 new CT genes in 19 cancer types. We explore their relationship with testis-specific regulatory elements. We propose that extremely highly expressed CT genes (EECTGs) are potential drivers activated through epigenetic mechanisms. We find mutually exclusive associations between EECTGs and somatic mutations in mutated genes, such as PIK3CA in breast cancer. We also provide evidence that promoter demethylation and close non-coding RNAs (namely, CT-ncRNAs) may be two mechanisms to reactivate EECTG gene expression. We show that the meiosis-related EECTG (MEIOB) and its nearby CT-ncRNA have a role in tumorigenesis in lung adenocarcinoma. Our findings provide methods for identifying epigenetic-driver genes of cancer, which could serve as targets of future cancer therapies.read more
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Genomic basis for RNA alterations in cancer
Claudia Calabrese,Natalie R. Davidson,Deniz Demircioğlu,Deniz Demircioğlu,Nuno A. Fonseca,Yao He,André Kahles,Kjong-Van Lehmann,Fenglin Liu,Yuichi Shiraishi,Cameron M. Soulette,Lara Urban,Liliana Greger,Siliang Li,Dongbing Liu,Marc D. Perry,Marc D. Perry,Qian Xiang,Fan Zhang,Junjun Zhang,Peter Bailey,Serap Erkek,Katherine A. Hoadley,Yong Hou,Matthew R. Huska,Helena Kilpinen,Jan O. Korbel,Maximillian G. Marin,Julia Markowski,Tannistha Nandi,Qiang Pan-Hammarström,Chandra Sekhar Pedamallu,Chandra Sekhar Pedamallu,Reiner Siebert,Stefan G. Stark,Hong Su,Patrick Tan,Patrick Tan,Sebastian M. Waszak,Christina K. Yung,Shida Zhu,Philip Awadalla,Philip Awadalla,Chad J. Creighton,Matthew Meyerson,Matthew Meyerson,B. F. Francis Ouellette,Kui Wu,Huanming Yang,Alvis Brazma,Angela N. Brooks,Angela N. Brooks,Angela N. Brooks,Jonathan Göke,Gunnar Rätsch,Roland F. Schwarz,Oliver Stegle,Oliver Stegle,Zemin Zhang +58 more
TL;DR: The most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Gome Atlas (TCGA) was presented in this article.
Journal ArticleDOI
A novel plasma circular RNA circFARSA is a potential biomarker for non-small cell lung cancer.
Dong Hang,Jing Zhou,Na Qin,Wen Zhou,Hongxia Ma,Guangfu Jin,Zhibin Hu,Juncheng Dai,Hongbing Shen +8 more
TL;DR: The circRNA profile of NSCLC is revealed for the first time and the evidence of plasma circFARSA as a potential noninvasive biomarker for this malignancy is provided.
Journal ArticleDOI
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy.
Ana Marcu,Leon Bichmann,Leon Kuchenbecker,Daniel J. Kowalewski,Lena Katharina Freudenmann,Linus Backert,Lena Mühlenbruch,András Szolek,Maren Lübke,Philipp Wagner,T Engler,Sabine Matovina,Jian Wang,Mathias Hauri-Hohl,Roland Martin,Konstantina Kapolou,Juliane S. Walz,Julia Velz,Holger Moch,Luca Regli,Manuela Silginer,Michael Weller,Markus W. Löffler,Florian Erhard,Andreas Schlosser,Oliver Kohlbacher,Stefan Stevanovic,Hans-Georg Rammensee,Marian Christoph Neidert,Marian Christoph Neidert +29 more
TL;DR: The HLA Ligand Atlas as discussed by the authors is a collection of paired HLAI and HLA-II immunopeptidomes from 227 benign human tissue samples, which facilitates a balanced comparison between tumor and benign tissues on HLA ligand level.
Journal ArticleDOI
Cancer-testis antigens: Unique cancer stem cell biomarkers and targets for cancer therapy.
TL;DR: Analysis of CTA expression patterns in embryonic germ and somatic cells, pluripotent and multipotent stem cells, cancer stem cells and their cell descendants indicates that rearrangements of characteristic CTA profiles (aberrant expression) could be associated with cancer transformation and failure of the developmental program of cell lineage specification and germ line restriction.
Journal ArticleDOI
Emerging Contributions of Cancer/Testis Antigens to Neoplastic Behaviors
TL;DR: Emerging evidence that demonstrates that CT antigens can confer a selective advantage to tumor cells by promoting oncogenic processes or permitting evasion of tumor-suppressive mechanisms is discussed.
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