Literature DB >> 26318634

The impact of the Cancer Genome Atlas on lung cancer.

Jeremy T-H Chang1, Yee Ming Lee2, R Stephanie Huang3.   

Abstract

The Cancer Genome Atlas (TCGA) has profiled more than 10,000 samples derived from 33 types of cancer to date, with the goal of improving our understanding of the molecular basis of cancer and advancing our ability to diagnose, treat, and prevent cancer. This review focuses on lung cancer as it is the leading cause of cancer-related mortality worldwide in both men and women. Particularly, non-small cell lung cancers (including lung adenocarcinoma and lung squamous cell carcinoma) were evaluated. Our goal was to demonstrate the impact of TCGA on lung cancer research under 4 themes: diagnostic markers, disease progression markers, novel therapeutic targets, and novel tools. Examples are given related to DNA mutation, copy number variation, messenger RNA, and microRNA expression along with methylation profiling.
Copyright © 2015 Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 26318634      PMCID: PMC4656061          DOI: 10.1016/j.trsl.2015.08.001

Source DB:  PubMed          Journal:  Transl Res        ISSN: 1878-1810            Impact factor:   7.012


  104 in total

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Authors:  Andrew D Sharrocks
Journal:  Genes Dev       Date:  2006-04-01       Impact factor: 11.361

2.  A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Authors:  Marc Sultan; Marcel H Schulz; Hugues Richard; Alon Magen; Andreas Klingenhoff; Matthias Scherf; Martin Seifert; Tatjana Borodina; Aleksey Soldatov; Dmitri Parkhomchuk; Dominic Schmidt; Sean O'Keeffe; Stefan Haas; Martin Vingron; Hans Lehrach; Marie-Laure Yaspo
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Review 3.  A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes.

Authors:  O A Kent; J T Mendell
Journal:  Oncogene       Date:  2006-10-09       Impact factor: 9.867

4.  NRF2 Pathway Activation and Adjuvant Chemotherapy Benefit in Lung Squamous Cell Carcinoma.

Authors:  David W Cescon; Desmond She; Shingo Sakashita; Chang-Qi Zhu; Melania Pintilie; Frances A Shepherd; Ming-Sound Tsao
Journal:  Clin Cancer Res       Date:  2015-03-04       Impact factor: 12.531

5.  SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples.

Authors:  Patrick K Kimes; Christopher R Cabanski; Matthew D Wilkerson; Ni Zhao; Amy R Johnson; Charles M Perou; Liza Makowski; Christopher A Maher; Yufeng Liu; J S Marron; D Neil Hayes
Journal:  Nucleic Acids Res       Date:  2014-07-16       Impact factor: 16.971

Review 6.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

7.  CLCA2 as a novel immunohistochemical marker for differential diagnosis of squamous cell carcinoma from adenocarcinoma of the lung.

Authors:  Kazuya Shinmura; Hisaki Igarashi; Hisami Kato; Yuichi Kawanishi; Yusuke Inoue; Satoki Nakamura; Hiroshi Ogawa; Takashi Yamashita; Akikazu Kawase; Kazuhito Funai; Haruhiko Sugimura
Journal:  Dis Markers       Date:  2014-12-07       Impact factor: 3.434

8.  Novel candidate key drivers in the integrative network of genes, microRNAs, methylations, and copy number variations in squamous cell lung carcinoma.

Authors:  Tao Huang; Jing Yang; Yu-Dong Cai
Journal:  Biomed Res Int       Date:  2015-02-23       Impact factor: 3.411

9.  PIAS3 expression in squamous cell lung cancer is low and predicts overall survival.

Authors:  Rime Abbas; Karen S McColl; Adam Kresak; Michael Yang; Yanwen Chen; Pingfu Fu; Gary Wildey; Afshin Dowlati
Journal:  Cancer Med       Date:  2015-01-09       Impact factor: 4.711

10.  An eight-miRNA signature as a potential biomarker for predicting survival in lung adenocarcinoma.

Authors:  Xuelian Li; Yunrui Shi; Zhihua Yin; Xiaoxia Xue; Baosen Zhou
Journal:  J Transl Med       Date:  2014-06-04       Impact factor: 5.531

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  39 in total

1.  Novel genetic variants in KIF16B and NEDD4L in the endosome-related genes are associated with nonsmall cell lung cancer survival.

Authors:  Sen Yang; Dongfang Tang; Yu C Zhao; Hongliang Liu; Sheng Luo; Thomas E Stinchcombe; Carolyn Glass; Li Su; Sipeng Shen; David C Christiani; Qiming Wang; Qingyi Wei
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2.  T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling.

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Journal:  Bioinformatics       Date:  2021-11-10       Impact factor: 6.937

3.  Identification and Validation of a Novel Signature Based on NK Cell Marker Genes to Predict Prognosis and Immunotherapy Response in Lung Adenocarcinoma by Integrated Analysis of Single-Cell and Bulk RNA-Sequencing.

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Journal:  Front Immunol       Date:  2022-06-10       Impact factor: 8.786

4.  Integrated analysis of single-cell and bulk RNA-sequencing identifies a signature based on B cell marker genes to predict prognosis and immunotherapy response in lung adenocarcinoma.

Authors:  Peng Song; Wenbin Li; Xiaoxuan Wu; Zhirong Qian; Jianming Ying; Shugeng Gao; Jie He
Journal:  Cancer Immunol Immunother       Date:  2022-02-13       Impact factor: 6.630

5.  Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers.

Authors:  Theresa Ryan Stueve; Wen-Qing Li; Jianxin Shi; Crystal N Marconett; Tongwu Zhang; Chenchen Yang; Daniel Mullen; Chunli Yan; William Wheeler; Xing Hua; Beiyun Zhou; Zea Borok; Neil E Caporaso; Angela C Pesatori; Jubao Duan; Ite A Laird-Offringa; Maria Teresa Landi
Journal:  Hum Mol Genet       Date:  2017-08-01       Impact factor: 6.150

6.  The International Epidemiology of Lung Cancer: Latest Trends, Disparities, and Tumor Characteristics.

Authors:  Ting-Yuan David Cheng; Susanna M Cramb; Peter D Baade; Danny R Youlden; Chukwumere Nwogu; Mary E Reid
Journal:  J Thorac Oncol       Date:  2016-06-27       Impact factor: 15.609

7.  hsa_circ_0008234 inhibits the progression of lung adenocarcinoma by sponging miR-574-5p.

Authors:  Wei Jiang; Yaozhou He; Zijian Ma; Yu Zhang; Chengpeng Zhang; Nianpeng Zheng; Xing Tang
Journal:  Cell Death Discov       Date:  2021-05-28

8.  Targeting the Golgi apparatus to overcome acquired resistance of non-small cell lung cancer cells to EGFR tyrosine kinase inhibitors.

Authors:  Yoshimi Ohashi; Mutsumi Okamura; Ryohei Katayama; Siyang Fang; Saki Tsutsui; Akinobu Akatsuka; Mingde Shan; Hyeong-Wook Choi; Naoya Fujita; Kentaro Yoshimatsu; Isamu Shiina; Takao Yamori; Shingo Dan
Journal:  Oncotarget       Date:  2017-12-06

9.  SLC15A4 Serves as a Novel Prognostic Biomarker and Target for Lung Adenocarcinoma.

Authors:  Hui Huang; Junwei Wang; Shibin Chen; HongJiang He; Yu Shang; Xiaorong Guo; Ge Lou; Jingjing Ji; Mian Guo; Hong Chen; Shan Yu
Journal:  Front Genet       Date:  2021-06-08       Impact factor: 4.599

10.  Downregulation of m6A Reader YTHDC2 Promotes the Proliferation and Migration of Malignant Lung Cells via CYLD/NF-κB Pathway.

Authors:  Jin Wang; Lirong Tan; Beibei Jia; Xiaofan Yu; Ruixin Yao; Nan OUYang; Xueting Yu; Xiyuan Cao; Jian Tong; Tao Chen; Rui Chen; Jianxiang Li
Journal:  Int J Biol Sci       Date:  2021-06-22       Impact factor: 6.580

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