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Genomic basis for RNA alterations in cancer

Claudia Calabrese, PCAWG Transcriptome Core Group, Natalie R. Davidson, Deniz Demircioğlu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban (+41 others)
2020 Nature  
This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.  ...  Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes  ...  collation, realignment and harmonized variant calling of the cancer genomes used in this study.  ... 
doi:10.1038/s41586-020-1970-0 pmid:32025019 pmcid:PMC7054216 fatcat:mlq5hbjn4rd6xp5ej6t42i4mqe

Genomic basis for RNA alterations in cancer

Claudia Calabrese, Natalie R. Davidson, Deniz Demircioğlu, Nuno A. Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M. Soulette, Lara Urban, Liliana Greger (+63 others)
2021
This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.  ...  Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes  ...  Identified eQTLs are in https://dcc.icgc.org/releases/PCAWG/transcriptome/eQTL and a binarized table indicating all RNA and DNA alterations for each gene can be found in the subfolder https://dcc.icgc.org  ... 
doi:10.17863/cam.64275 fatcat:lspoy33h7fdyxnla5w43dksxmy

Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers

Xiaohui Yan, Zhongyi Hu, Yi Feng, Xiaowen Hu, Jiao Yuan, Sihai D. Zhao, Youyou Zhang, Lu Yang, Weiwei Shan, Qun He, Lingling Fan, Lana E. Kandalaft (+18 others)
2015 Cancer Cell  
RNA (lncRNA) has dramatically altered our understanding of cancer.  ...  Graphical Abstract Highlights d lncRNA dysregulation was characterized in 5,037 tumor samples across 13 cancer types d lncRNAs are altered in cancers at transcriptional, genomic, and epigenetic levels  ...  This work was supported, in whole or in part, by the Basser Center for BRCA (L.Z.), the Harry Fields Professorship (L.Z.); the NIH (grants R01CA142776 to L.Z., R01CA190415 to L.Z.,  ... 
doi:10.1016/j.ccell.2015.09.006 pmid:26461095 pmcid:PMC4777353 fatcat:reoj3omeqvdgrdo7ruc6hefsm4

Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study

Emilie Lalonde, Adrian S Ishkanian, Jenna Sykes, Michael Fraser, Helen Ross-Adams, Nicholas Erho, Mark J Dunning, Silvia Halim, Alastair D Lamb, Nathalie C Moon, Gaetano Zafarana, Anne Y Warren (+30 others)
2014 The Lancet Oncology  
We identifi ed four genomic subtypes for prostate cancer, which had diff erent 5-year biochemical relapse-free survival.  ...  We aimed to test combined genomic and microenvironmental indices in prostate cancer to improve risk stratifi cation and complement clinical prognostic factors.  ...  Acknowledgments We thank study volunteers for their participation, and staff at the Wellcome  ... 
doi:10.1016/s1470-2045(14)71021-6 pmid:25456371 fatcat:qw6sp5xitfgk7jzr3mcwcezldm

Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers

Babak Alaei-Mahabadi, Joydeep Bhadury, Joakim W. Karlsson, Jonas A. Nilsson, Erik Larsson
2016 Proceedings of the National Academy of Sciences of the United States of America  
of cancer genomes.  ...  For somatic SVs to be functional in cancer, they need to have an influence on transcription in some way, by altering mRNA structures or levels.  ...  A detailed description of the methods used in the study is provided in SI Methods.  ... 
doi:10.1073/pnas.1606220113 pmid:27856756 pmcid:PMC5137778 fatcat:htzutidxcjhkdliwjmebmyhi5y

New Views into the Prostate Cancer Genome

Lloyd Trotman, Scott Powers
2010 Cancer Cell  
Thus, both RNA expression profiling and DNA expression profiling work for breast cancer. So the real question is why doesn't RNA expression profiling work for prostate cancer?  ...  This integrated approach paid off in this case, as the authors were able to test two classes of alterations for their ability to predict recurrence, RNA expression profiling, and DNA copy-number profiling  ... 
doi:10.1016/j.ccr.2010.06.011 pmid:20609345 fatcat:mbcwngm24zettfnwoizpqmewwi

Noncoding RNAs serve as the deadliest regulators for cancer [article]

Anyou Wang, Hai Rong
2019 arXiv   pre-print
Strikingly, noncoding RNAs serves as the universal strongest regulators for all cancer types although personal clinic variables such as alcohol and smoking significantly alter cancer genome.  ...  Therefore, noncoding RNAs overall serve as the deadliest cancer regulators, which refreshes the basic concept of cancer mechanism and builds a novel basis for cancer research and therapy.  ...  We further ranked these 428 regulators in basis of their absolute coefficients (coef), higher coefficient, more important in regulating cancer death.  ... 
arXiv:1910.03934v1 fatcat:rf4v7fdsbbga7jws7zxwjqtj6q

Non-coding RNAs for Medical Practice in Oncology

Tetsuro Setoyama, Hui Ling, Shoji Natsugoe, George A. Calin
2011 The Keio Journal of Medicine  
Alterations in microRNA (miRNA) and other short or long non-coding RNA (ncRNA) are involved in the initiation, progression, and metastasis of human cancer.  ...  These discoveries could be exploited for the development of useful markers for diagnosis and prognosis in cancer, as well as for the development of new RNA-based cancer therapies.  ...  May Result in Cancer Predisposition Despite extensive research, the molecular basis for most familial cancers is unknown.  ... 
doi:10.2302/kjm.60.106 pmid:22200634 fatcat:kswhts3vznhp7ofmrv2bl7xbbm

Exploring cancer genomic data from the cancer genome atlas project

Ju-Seog Lee
2016 BMB Reports  
The Cancer Genome Atlas (TCGA) has compiled genomic, epigenomic, and proteomic data from more than 10,000 samples derived from 33 types of cancer, aiming to improve our understanding of the molecular basis  ...  Availability of these genome-wide information provides an unprecedented opportunity for uncovering new key regulators of signaling pathways or new roles of pre-existing members in pathways.  ...  The GCCs aim to identify all genomic alterations in the tumors in each cancer type.  ... 
doi:10.5483/bmbrep.2016.49.11.145 pmid:27530686 pmcid:PMC5346320 fatcat:2g3o7hrzsnft3hsrnfa5gjx6mi

Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of the gene regulatory program in cancers [article]

Jaime Abraham Castro-Mondragon, Miriam Ragle Aure, Ole Christian Lingærde, Anita Langerød, John W.M. Martens, Anne-Lise Børresen-Dale, Vessela Kristensen, Anthony Mathelier
2020 bioRxiv   pre-print
Most cancer alterations occur in the noncoding portion of the human genome, which contains important regulatory regions acting as genetic switches to ensure gene expression occurs at correct times and  ...  By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluated the combined effects of transcriptional and post-transcriptional alteration on the dysregulation  ...  We thank Jiarui Ding for his help on using xseq for this study; Marcel Smid for providing raw RNA-seq data for the BASIS cohort; Georgios Magklaras and Georgios Marselis for their IT support; Ingrid Kjelsvik  ... 
doi:10.1101/2020.06.25.170738 fatcat:j6cxqjqdonafvbkntw22jqehku

The Non-Coding Oncogene: A Case of Missing DNA Evidence?

Puja Shahrouki, Erik Larsson
2012 Frontiers in Genetics  
However, in comparison with coding cancer genes, the genomic (DNA-level) evidence is sparse for ncRNAs.  ...  Multiple lines of proof show how random somatic genomic alteration of such genes (e.g., mutation, deletion, or amplification), followed by selection and clonal expansion, forms the main molecular basis  ...  Anders Jacobsen and Nicholas Gauthier for critical review of the manuscript.  ... 
doi:10.3389/fgene.2012.00170 pmid:22988449 pmcid:PMC3439828 fatcat:2mkyfpj7tjaxngbtta5z4crtay

Sequencing Technologies and their Importance in the Field of Oncology

Sonakshi Madan, Bhavya lamba, Sonia Purswani, Chakresh K Jain
2017 Indo global journal of pharmaceutical sciences  
approaches in cancer genomics.  ...  It has been at the forefront of medical research with huge leaps in the field of cancer genomics.  ...  approaches in cancer genomics.  ... 
doi:10.35652/igjps.2017.86 fatcat:66hufdg7rjhkbi7wx6rvgjwn7q

Integrated analysis of expression and genome alteration reveals putative amplified target genes in esophageal cancer

Takashi Sugimoto, Makoto Arai, Hideaki Shimada, Akira Hata, Naohiko Seki
2007 Oncology Reports  
Thus, the integration of DNA and RNA profiles provides a highly productive entry point for the discovery of genes involved in the development and progression of esophageal cancer.  ...  Microarray and comparative genomic hybridization (CGH) studies have provided a wide range of information about esophageal cancer, but the correlations between gene expression and copy number alteration  ...  Many of these genome alterations were observed in all cell lines (Fig. 1 ).  ... 
doi:10.3892/or.18.2.465 fatcat:ewcghthng5bfpoknplggfegkwy

An expanding universe of the non-coding genome in cancer biology

Bin Xue, Lin He
2014 Carcinogenesis  
A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs  ...  Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor  ...  which L1 mobilize to alter cancer genome.  ... 
doi:10.1093/carcin/bgu099 pmid:24747961 pmcid:PMC4110481 fatcat:2pxpsytdpvgpre6xs6iramtaxi

Prediction of breast cancer proteins involved in immunotherapy, metastasis, and RNA-binding using molecular descriptors and artificial neural networks

Andrés López-Cortés, Alejandro Cabrera-Andrade, José M. Vázquez-Naya, Alejandro Pazos, Humberto Gonzáles-Díaz, César Paz-y-Miño, Santiago Guerrero, Yunierkis Pérez-Castillo, Eduardo Tejera, Cristian R. Munteanu
2020 Scientific Reports  
Breast cancer (BC) is a heterogeneous disease where genomic alterations, protein expression deregulation, signaling pathway alterations, hormone disruption, ethnicity and environmental determinants are  ...  Scripts can be downloaded at https://github.com/muntisa/neural-networks-for-breast-cancer-proteins.  ...  Additionally, Fig. 9B shows the most altered RNA-binding proteins per genomic alteration type.  ... 
doi:10.1038/s41598-020-65584-y pmid:32444848 fatcat:ee6xzbzlqrgafeug5fu4rsxbd4
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