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Research: Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
- Suhaida A. Selamat,
- Brian S. Chung,
- Luc Girard,
- Wei Zhang,
- Ying Zhang,
- Mihaela Campan,
- Kimberly D. Siegmund,
- Michael N. Koss,
- Jeffrey A. Hagen,
- Wan L. Lam,
- Stephen Lam,
- Adi F. Gazdar,
- and Ite A. Laird-Offringa
Genome Res. July 2012 22: 1197-1211; Published in Advance May 21, 2012, doi:10.1101/gr.132662.111
...on 59 matched lung adenocarcinoma/non-tumor lung pairs, with genome-scale verification on an independent set of tissues. We identified 766 genes showing altered DNA methylation between tumors and non-tumor lung. By integrating DNA methylation and mRNA expression data, we identified 164 hypermethylated...
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Method: ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens
- Diane D. Shao,
- Aviad Tsherniak,
- Shuba Gopal,
- Barbara A. Weir,
- Pablo Tamayo,
- Nicolas Stransky,
- Steven E. Schumacher,
- Travis I. Zack,
- Rameen Beroukhim,
- Levi A. Garraway,
- Adam A. Margolin,
- David E. Root,
- William C. Hahn,
- and Jill P. Mesirov
Genome Res. April 2013 23: 665-678; Published in Advance December 26, 2012, doi:10.1101/gr.143586.112
...to this work. ↵ Present addresses: 7 Blueprint Medicines, Cambridge, MA 02142, USA; ↵ 8 Sage Bionetworks, Seattle, WA 98109, USA. Abstract Genome-scale RNAi libraries enable the systematic interrogation of gene function. However, the interpretation of RNAi screens...
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Research: Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors
- Andrew Feber,
- Gareth A. Wilson,
- Lu Zhang,
- Nadege Presneau,
- Bernadine Idowu,
- Thomas A. Down,
- Vardhman K. Rakyan,
- Luke A. Noon,
- Alison C. Lloyd,
- Elia Stupka,
- Vassia Schiza,
- Andrew E. Teschendorff,
- Gary P. Schroth,
- Adrienne Flanagan,
- and Stephan Beck
Genome Res. April 2011 21: 515-524; Published in Advance February 1, 2011, doi:10.1101/gr.109678.110
..., University College London, London WC1E 6BT, United Kingdom Abstract Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However...
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Research: Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer
- Milad Razavi-Mohseni,
- Weitai Huang,
- Yu A. Guo,
- Dustin Shigaki,
- Shamaine Wei Ting Ho,
- Patrick Tan,
- Anders J. Skanderup,
- and Michael A. Beer
Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123
...activity in Mes-like GC versus Epi-like GC, as well as TCGA-STAD compared with normal stomach. Survival analysis shows that activation of Mes-like TFs and their target genes is predictive of disease severity and suggests both prognostic and therapeutic utility.Taken together, we identified altered...
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Resource: Recounting the FANTOM CAGE-Associated Transcriptome
- Eddie Luidy Imada,
- Diego Fernando Sanchez,
- Leonardo Collado-Torres,
- Christopher Wilks,
- Tejasvi Matam,
- Wikum Dinalankara,
- Aleksey Stupnikov,
- Francisco Lobo-Pereira,
- Chi-Wai Yip,
- Kayoko Yasuzawa,
- Naoto Kondo,
- Masayoshi Itoh,
- Harukazu Suzuki,
- Takeya Kasukawa,
- Chung-Chau Hon,
- Michiel J.L. de Hoon,
- Jay W. Shin,
- Piero Carninci,
- Andrew E. Jaffe,
- Jeffrey T. Leek,
- Alexander Favorov,
- Gloria R. Franco,
- Ben Langmead,
- and Luigi Marchionni
Genome Res. July 2020 30: 1073-1081; Published in Advance February 20, 2020, doi:10.1101/gr.254656.119
...did not identify any cancer association for common e-lncRNAs, one among those we identified, LINC02884, has been previously reported to be up-regulated in late-onset Alzheimer's disease (Humphries et al. 2015). Furthermore, the enhancer lncRNA class also yielded the lowest number of genes in common...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
...silencing of some tumor suppressor genes, such as BRCA1 (Dobrovic and Simpfendorfer 1997), RB1 (Greger et al. 1994), and MLH1 (Herman et al. 1998). However, the primary role of this defect in the widespread cancer-associated genes silencing, and more broadly in cancer biology, is still being questioned...
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Research: Characterization of colibactin-associated mutational signature in an Asian oral squamous cell carcinoma and in other mucosal tumor types
- Arnoud Boot,
- Alvin W.T. Ng,
- Fui Teen Chong,
- Szu-Chi Ho,
- Willie Yu,
- Daniel S.W. Tan,
- N. Gopalakrishna Iyer,
- and Steven G. Rozen
Genome Res. June 2020 30: 803-813; Published in Advance July 6, 2020, doi:10.1101/gr.255620.119
...mutation, with bases indicated by color as in panel B. (D) Transcriptional strand bias as a function of gene expression level.In 62074759, the mutational spectra of SBSs in trinucleotide context were essentially identical at a wide range of variant allele frequencies (VAFs) (Supplemental Fig. S5...
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Research: Transcriptional consequences of genomic structural aberrations in breast cancer
- Koichiro Inaki,
- Axel M. Hillmer,
- Leena Ukil,
- Fei Yao,
- Xing Yi Woo,
- Leah A. Vardy,
- Kelson Folkvard Braaten Zawack,
- Charlie Wah Heng Lee,
- Pramila Nuwantha Ariyaratne,
- Yang Sun Chan,
- Kartiki Vasant Desai,
- Jonas Bergh,
- Per Hall,
- Thomas Choudary Putti,
- Wai Loon Ong,
- Atif Shahab,
- Valere Cacheux-Rataboul,
- Radha Krishna Murthy Karuturi,
- Wing-Kin Sung,
- Xiaoan Ruan,
- Guillaume Bourque,
- Yijun Ruan,
- and Edison T. Liu
Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
...by the duplication event. Certain other structural mutations, however, tend to attenuate gene expression. From these candidate gene fusions, we have found a fusion transcript ( RPS6KB1–VMP1 ) recurrently expressed in ∼30% of breast cancers associated with potential clinical consequences. This gene fusion is caused...
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Method: Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
- Aaron L. Statham,
- Mark D. Robinson,
- Jenny Z. Song,
- Marcel W. Coolen,
- Clare Stirzaker,
- and Susan J. Clark
Genome Res. June 2012 22: 1120-1127; Published in Advance March 30, 2012, doi:10.1101/gr.132076.111
...methylation on Lys27 of histone H3 pre-marks genes for de novo methylation in cancer. Nat Genet 39: 232–236. Song JZ, Stirzaker C, Harrison J, Melki JR, Clark SJ. 2002. Hypermethylation trigger of the glutathione-S-transferase gene (GSTP1) in prostate cancer cells. Oncogene 21: 1048–1061. Statham AL, Strbenac...
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Research: Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
- Phillippa C. Taberlay,
- Aaron L. Statham,
- Theresa K. Kelly,
- Susan J. Clark,
- and Peter A. Jones
Genome Res. September 2014 24: 1421-1432; Published in Advance June 10, 2014, doi:10.1101/gr.163485.113
...-translational histone modifications, and nucleosome occupancy (Coolen et al. 2010; Taberlay and Jones 2011; Bert et al. 2013), can lead to global changes of the cancer epi coupled with associated deregulation of cancer gene expression signatures. DNA methylation currently remains the most characterized epigenetic...
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