Journal ArticleDOI
Clinical epigenetics: seizing opportunities for translation.
María Berdasco,Manel Esteller +1 more
TLDR
Beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.Abstract:
Biomarker discovery and validation are necessary for improving the prediction of clinical outcomes and patient monitoring. Despite considerable interest in biomarker discovery and development, improvements in the range and quality of biomarkers are still needed. The main challenge is how to integrate preclinical data to obtain a reliable biomarker that can be measured with acceptable costs in routine clinical practice. Epigenetic alterations are already being incorporated as valuable candidates in the biomarker field. Furthermore, their reversible nature offers a promising opportunity to ameliorate disease symptoms by using epigenetic-based therapy. Thus, beyond helping to understand disease biology, clinical epigenetics is being incorporated into patient management in oncology, as well as being explored for clinical applicability for other human pathologies such as neurological and infectious diseases and immune system disorders.read more
Citations
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Clinical characteristics and risk factors for mortality in cancer patients with COVID-19.
Junnan Liang,Guannan Jin,Tongtong Liu,Jingyuan Wen,Ganxun Li,Lin Chen,Wei Wang,Yuwei Wang,Wei Liao,Jia Song,Zeyang Ding,Xiaoping Chen,Bixiang Zhang +12 more
TL;DR: In this article, the authors found that cancer patients with high risk of COVID-19 infection had a poorer prognosis than patients without cancer, especially those with hematological malignancies.
Journal ArticleDOI
Epigenetic loss of the transfer RNA-modifying enzyme TYW2 induces ribosome frameshifts in colon cancer
Margalida Rosselló-Tortella,Pere Llinàs-Arias,Yuriko Sakaguchi,Kenjyo Miyauchi,Veronica Davalos,Fernando Setien,Maria E. Calleja-Cervantes,David Piñeyro,Jesús Martínez-Gómez,Sonia Guil,Ricky S. Joshi,Alberto Villanueva,Tsutomu Suzuki,Manel Esteller +13 more
TL;DR: It is reported that the tRNA-yW Synthesizing Protein 2 (TYW2) undergoes promoter hypermethylation-associated transcriptional silencing in human cancer, particularly in colorectal tumors, and this finding provides an illustrative example of how epigenetic changes can modify the epitranscriptome and further support a role for tRNA modifications in cancer biology.
Journal ArticleDOI
A chemical probe of CARM1 alters epigenetic plasticity against breast cancer cell invasion.
Xiao-Chuan Cai,Tuo Zhang,Eui-jun Kim,Ming Jiang,Ming Jiang,Ke Wang,Junyi Wang,Shi Chen,Nawei Zhang,Nawei Zhang,Hong Wu,Fengling Li,Carlo C. dela Seña,Hong Zeng,Victor Vivcharuk,Xiang Niu,Weihong Zheng,Jonghan P Lee,Yuling Chen,Dalia Barsyte,Magda Szewczyk,Taraneh Hajian,Glorymar Ibáñez,Aiping Dong,Ludmila Dombrovsky,Zhenyu Zhang,Haiteng Deng,Haiteng Deng,Jinrong Min,Jinrong Min,Cheryl H. Arrowsmith,Cheryl H. Arrowsmith,Linas Mazutis,Lei Shi,Masoud Vedadi,Masoud Vedadi,Peter Brown,Jenny Xiang,Li-Xuan Qin,Wei Xu,Minkui Luo,Minkui Luo +41 more
TL;DR: A CARM1-addiction mechanism of cancer metastasis is discovered and a chemical probe is developed to target this process, suggesting distinct modes of action for small-molecule and genetic perturbations.
Journal ArticleDOI
Use of DNA methylation profiling in translational oncology.
TL;DR: In this article, the role of DNA methylation in normal cellular function is discussed, as well as how epigenetic aberrations override normal cellular cues that lead to tumor initiation and propagation.
Journal ArticleDOI
Cell-Free DNA-Methylation-Based Methods and Applications in Oncology.
Francesca Galardi,Francesca De Luca,Dario Romagnoli,Chiara Biagioni,Erica Moretti,Laura Biganzoli,Angelo Di Leo,Ilenia Migliaccio,Luca Malorni,Matteo Benelli +9 more
TL;DR: Recent advances on experimental strategies for the analysis of DNAm in cfDNA samples are reported, including protocols, biomolecular techniques, and computational strategies enabling DNAm evaluation in the context of cfDNA analysis, along with practical considerations on input sample requirements and costs.
References
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TL;DR: This paper examined potential sources of missing heritability and proposed research strategies, including and extending beyond current genome-wide association approaches, to illuminate the genetics of complex diseases and enhance its potential to enable effective disease prevention or treatment.
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Journal ArticleDOI
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Wouter Meuleman,Jason Ernst,Misha Bilenky,Angela Yen,Angela Yen,Alireza Heravi-Moussavi,Pouya Kheradpour,Pouya Kheradpour,Zhizhuo Zhang,Zhizhuo Zhang,Jianrong Wang,Jianrong Wang,Michael J. Ziller,Viren Amin,John W. Whitaker,Matthew D. Schultz,Lucas D. Ward,Lucas D. Ward,Abhishek Sarkar,Abhishek Sarkar,Gerald Quon,Gerald Quon,Richard Sandstrom,Matthew L. Eaton,Matthew L. Eaton,Yi-Chieh Wu,Yi-Chieh Wu,Andreas R. Pfenning,Andreas R. Pfenning,Xinchen Wang,Xinchen Wang,Melina Claussnitzer,Melina Claussnitzer,Yaping Liu,Yaping Liu,Cristian Coarfa,R. Alan Harris,Noam Shoresh,Charles B. Epstein,Elizabeta Gjoneska,Elizabeta Gjoneska,Danny Leung,Wei Xie,R. David Hawkins,Ryan Lister,Chibo Hong,Philippe Gascard,Andrew J. Mungall,Richard A. Moore,Eric Chuah,Angela Tam,Theresa K. Canfield,R. Scott Hansen,Rajinder Kaul,Peter J. Sabo,Mukul S. Bansal,Mukul S. Bansal,Mukul S. Bansal,Annaick Carles,Jesse R. Dixon,Kai How Farh,Soheil Feizi,Soheil Feizi,Rosa Karlic,Ah Ram Kim,Ah Ram Kim,Ashwinikumar Kulkarni,Daofeng Li,Rebecca F. Lowdon,Ginell Elliott,Tim R. Mercer,Shane Neph,Vitor Onuchic,Paz Polak,Paz Polak,Nisha Rajagopal,Pradipta R. Ray,Richard C Sallari,Richard C Sallari,Kyle Siebenthall,Nicholas A Sinnott-Armstrong,Nicholas A Sinnott-Armstrong,Michael Stevens,Robert E. Thurman,Jie Wu,Bo Zhang,Xin Zhou,Arthur E. Beaudet,Laurie A. Boyer,Philip L. De Jager,Philip L. De Jager,Peggy J. Farnham,Susan J. Fisher,David Haussler,Steven J.M. Jones,Steven J.M. Jones,Wei Li,Marco A. Marra,Michael T. McManus,Shamil R. Sunyaev,Shamil R. Sunyaev,James A. Thomson,Thea D. Tlsty,Li-Huei Tsai,Li-Huei Tsai,Wei Wang,Robert A. Waterland,Michael Q. Zhang,Lisa Helbling Chadwick,Bradley E. Bernstein,Bradley E. Bernstein,Bradley E. Bernstein,Joseph F. Costello,Joseph R. Ecker,Martin Hirst,Alexander Meissner,Aleksandar Milosavljevic,Bing Ren,John A. Stamatoyannopoulos,Ting Wang,Manolis Kellis,Manolis Kellis +123 more
TL;DR: It is shown that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease.
Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal ArticleDOI
Non-coding RNAs in human disease
TL;DR: Dysregulation of these ncRNAs is being found to have relevance not only to tumorigenesis, but also to neurological, cardiovascular, developmental and other diseases, and there is great interest in therapeutic strategies to counteract these perturbations.