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Cancer epigenetics and diagnostics

Section information

Section Editors : Carmen Jeronimo and Maria Berdasco

Associate Editors : Nita Ahuja, James Chim (haematological-based cancers only); Jim Davie, James Flanagan, Mario Fraga, Michéle Hoffmann, Bozena Kaminska (gliomas), Gwen Lomberk, Graham K Packham, Arpad Patai (colorectal/GI cancers), Qian Tao, Raul Urrutia, Keishi Yamashita

The development of genome-wide techniques has rapidly improved the comprehensive knowledge of epigenetic alterations in cancer. Currently, a vast number of genes and their associated molecular pathways that show epigenetic differences between normal and tumoral cells have been identified, emphasizing the crucial role of epigenetic factors in cancer etiology and progression.  This section publishes original epigenetic research focused on the identification of epigenetic biomarkers associated with cancer diagnosis or tumor progression. Manuscripts on epigenetic biomarkers leading to a better definition of therapy response are also accepted (pharmacoepigenetics). Submissions on reports from human clinical trials providing insights on the clinical application of epigenetic biomarkers are welcomed.

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  1. Lung cancer is the leading cause of cancer-related mortality. The alteration of DNA methylation plays a major role in the development of lung cancer. Methylation biomarkers become a possible method for lung ca...

    Authors: Lei Li, Zhujia Ye, Sai Yang, Hao Yang, Jing Jin, Yingying Zhu, Jinsheng Tao, Siyu Chen, Jiehan Xu, Yanying Liu, Weihe Liang, Bo Wang, Mengzhu Yang, Qiaoyun Huang, Zhiwei Chen, Weimin Li…

    Citation: Clinical Epigenetics 2021 13:185

    Content type: Research

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  2. Current clinical guidelines suggest that breast cancers with low hormone receptor expression (LowHR) in 1–10% of tumor cells should be regarded as hormone receptor positive. However, clinical data show that th...

    Authors: Philipp Jurmeister, Karsten Weber, Sonia Villegas, Thomas Karn, Michael Untch, Anne Thieme, Volkmar Müller, Eliane Taube, Peter Fasching, Wolfgang D. Schmitt, Frederik Marmé, Elmar Stickeler, Bruno V. Sinn, Paul Jank, Christian Schem, Frederick Klauschen…

    Citation: Clinical Epigenetics 2021 13:184

    Content type: Research

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  3. Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression ...

    Authors: Jingwei Li, Kun Fang, Lavanya Choppavarapu, Ke Yang, Yini Yang, Junbai Wang, Ruifeng Cao, Ismail Jatoi and Victor X. Jin

    Citation: Clinical Epigenetics 2021 13:175

    Content type: Research

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  4. Multiple myeloma (MM) is a malignancy of plasma cells that largely remains incurable. The search for new therapeutic targets is therefore essential. In addition to a wide panel of genetic mutations, epigenetic...

    Authors: Laurie Herviou, Sara Ovejero, Fanny Izard, Ouissem Karmous-Gadacha, Claire Gourzones, Celine Bellanger, Eva De Smedt, Anqi Ma, Laure Vincent, Guillaume Cartron, Jian Jin, Elke De Bruyne, Charlotte Grimaud, Eric Julien and Jérôme Moreaux

    Citation: Clinical Epigenetics 2021 13:174

    Content type: Research

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  5. Thymic epithelial tumors (TETs) are rare neoplasms, originating from epithelial thymic cells. The oncogenic potential of these rare neoplasms is still largely undefined, and a deeper molecular characterization...

    Authors: Alessia Iaiza, Claudia Tito, Zaira Ianniello, Federica Ganci, Valentina Laquintana, Enzo Gallo, Andrea Sacconi, Silvia Masciarelli, Luciana De Angelis, Sara Aversa, Daniele Diso, Marco Anile, Vincenzo Petrozza, Francesco Facciolo, Enrico Melis, Edoardo Pescarmona…

    Citation: Clinical Epigenetics 2021 13:173

    Content type: Research

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  6. Pancreatic cancer is one of the lethal cancers among solid malignancies. Pathological diagnosis of surgical margins is sometimes unreliable due to tissue shrinkage, invisible field cancerization and skipped le...

    Authors: Yuki Sunagawa, Masamichi Hayashi, Suguru Yamada, Hiroshi Tanabe, Keisuke Kurimoto, Nobutake Tanaka, Fuminori Sonohara, Yoshikuni Inokawa, Hideki Takami, Mitsuro Kanda, Chie Tanaka, Goro Nakayama, Masahiko Koike and Yasuhiro Kodera

    Citation: Clinical Epigenetics 2021 13:172

    Content type: Research

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  7. BCOR (BCL6 corepressor) is an epigenetic regulator gene involved in the specification of cell differentiation and body structure development. Recurrent somatic BCOR mutations have been identified in myelodyspl...

    Authors: Xiao Li, Feng Xu, Zheng Zhang, Juan Guo, Qi He, Lu-Xi Song, Dong Wu, Li-Yu Zhou, Ji-Ying Su, Chao Xiao, Chun-Kang Chang and Ling-Yun Wu

    Citation: Clinical Epigenetics 2021 13:169

    Content type: Research

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  8. Disease progression and therapeutic resistance are hallmarks of advanced stage prostate cancer (PCa), which remains a major cause of cancer-related mortality around the world. Longitudinal studies, coupled wit...

    Authors: Romina Silva, Bruce Moran, Anne-Marie Baird, Colm J. O’Rourke, Stephen P. Finn, Ray McDermott, William Watson, William M. Gallagher, Donal J. Brennan and Antoinette S. Perry

    Citation: Clinical Epigenetics 2021 13:168

    Content type: Research

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  9. In an effort to contribute to overcoming the platinum resistance exhibited by most solid tumors, we performed an array of epigenetic approaches, integrating next-generation methodologies and public clinical da...

    Authors: Javier Andrés Soto, Carlos Rodríguez-Antolín, Olga Vera, Olga Pernía, Isabel Esteban-Rodríguez, Maria Dolores Diestro, Javier Benitez, Fátima Sánchez-Cabo, Rafael Alvarez, Javier De Castro and Inmaculada Ibanez de Cáceres

    Citation: Clinical Epigenetics 2021 13:167

    Content type: Research

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  10. DNA methylation, an epigenetic modification, regulates gene transcription and maintains genome stability. DNA methyltransferase (DNMT) inhibitors can activate silenced genes at low doses and cause cytotoxicity...

    Authors: Chunhong Hu, Xiaohan Liu, Yue Zeng, Junqi Liu and Fang Wu

    Citation: Clinical Epigenetics 2021 13:166

    Content type: Review

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  11. DNA methylation is involved in the regulation of gene expression and phenotypic variation, but the inter-relationship between genetic variation, DNA methylation and gene expression remains poorly understood. H...

    Authors: Anna Díez-Villanueva, Mireia Jordà, Robert Carreras-Torres, Henar Alonso, David Cordero, Elisabet Guinó, Xavier Sanjuan, Cristina Santos, Ramón Salazar, Rebeca Sanz-Pamplona and Victor Moreno

    Citation: Clinical Epigenetics 2021 13:162

    Content type: Research

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  12. Aberrant DNA hypomethylation of the long interspersed nuclear elements (LINE-1 or L1) has been recognized as an early event of colorectal transformation. Simultaneous genetic and epigenetic analysis of colorec...

    Authors: Carla Debernardi, Laura Libera, Enrico Berrino, Nora Sahnane, Anna Maria Chiaravalli, Cristiana Laudi, Mattia Berselli, Anna Sapino, Fausto Sessa, Tiziana Venesio and Daniela Furlan

    Citation: Clinical Epigenetics 2021 13:154

    Content type: Research

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    The Correction to this article has been published in Clinical Epigenetics 2021 13:178

  13. Glioblastoma (GBM) is the most aggressive primary brain tumor, having a poor prognosis and a median overall survival of less than two years. Over the last decade, numerous findings regarding the distinct molec...

    Authors: Borja Sesé, Miquel Ensenyat-Mendez, Sandra Iñiguez, Pere Llinàs-Arias and Diego M. Marzese

    Citation: Clinical Epigenetics 2021 13:150

    Content type: Review

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    The Correction to this article has been published in Clinical Epigenetics 2021 13:194

  14. In contrast to stable genetic events, epigenetic changes are highly plastic and play crucial roles in tumor evolution and development. Epithelial ovarian cancer (EOC) is a highly heterogeneous disease that is ...

    Authors: David W. Chan, Wai-Yip Lam, Fushun Chen, Mingo M. H. Yung, Yau-Sang Chan, Wai-Sun Chan, Fangfang He, Stephanie S. Liu, Karen K. L. Chan, Benjamin Li and Hextan Y. S. Ngan

    Citation: Clinical Epigenetics 2021 13:142

    Content type: Research

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    The Correction to this article has been published in Clinical Epigenetics 2021 13:151

  15. Primary or acquired chemoresistance is a key link in the high mortality rate of ovarian cancer. There is no reliable method to predict chemoresistance in ovarian cancer. We hypothesized that specific methylati...

    Authors: Li-yuan Feng, Bing-bing Yan, Yong-zhi Huang and Li Li

    Citation: Clinical Epigenetics 2021 13:141

    Content type: Research

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  16. Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4 (H3K4me3) located after first exons and around transcription start sites. This epigenetic mark is typically restricted ...

    Authors: Tasnim H. Beacon, Geneviève P. Delcuve, Camila López, Gino Nardocci, Igor Kovalchuk, Andre J. van Wijnen and James R. Davie

    Citation: Clinical Epigenetics 2021 13:138

    Content type: Review

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  17. Patients with metastatic prostate cancer (PC) are treated with androgen deprivation therapy (ADT) that initially reduces metastasis growth, but after some time lethal castration-resistant PC (CRPC) develops. A...

    Authors: Erik Bovinder Ylitalo, Elin Thysell, Mattias Landfors, Maria Brattsand, Emma Jernberg, Sead Crnalic, Anders Widmark, Magnus Hultdin, Anders Bergh, Sofie Degerman and Pernilla Wikström

    Citation: Clinical Epigenetics 2021 13:133

    Content type: Research

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  18. Liver metastases can occur even in CRC patients who underwent curative surgery. While evidence suggested that adjuvant chemotherapy can help to reduce the occurrence of liver metastases for certain patients, i...

    Authors: Weihua Li, Lei Guo, Wanxiangfu Tang, Yutong Ma, Xiaonan Wang, Yang Shao, Hong Zhao and Jianming Ying

    Citation: Clinical Epigenetics 2021 13:126

    Content type: Research

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  19. Resistance to DNA damaging chemotherapies leads to cancer treatment failure and poor patient prognosis. We investigated how genomic distribution of accessible chromatin sites is altered during acquisition of c...

    Authors: John Gallon, Erick Loomis, Edward Curry, Nicholas Martin, Leigh Brody, Ian Garner, Robert Brown and James M. Flanagan

    Citation: Clinical Epigenetics 2021 13:122

    Content type: Research

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  20. At present, after extensive studies in the field of cancer, cancer stem cells (CSCs) have been proposed as a major factor in tumor initiation, progression, metastasis, and recurrence. CSCs are a subpopulation ...

    Authors: Saeedeh Keyvani-Ghamsari, Khatereh Khorsandi, Azhar Rasul and Muhammad Khatir Zaman

    Citation: Clinical Epigenetics 2021 13:120

    Content type: Review

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  21. Mutations in the POLE gene result in an ultra-hypermutated phenotype in colorectal cancer (CRC); however, the molecular characterisation of epigenetic alterations remains unclear. We examined the genetic and epig...

    Authors: Takashi Kawai, Akihiro Nyuya, Yoshiko Mori, Takehiro Tanaka, Hiroaki Tanioka, Kazuya Yasui, Toshiaki Toshima, Fumitaka Taniguchi, Kunitoshi Shigeyasu, Yuzo Umeda, Toshiyoshi Fujiwara, Makoto Okawaki, Yoshiyuki Yamaguchi, Ajay Goel and Takeshi Nagasaka

    Citation: Clinical Epigenetics 2021 13:117

    Content type: Research

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  22. Long-term stored serum is considered challenging for epigenomic analyses: as there are no cells, circulating DNA is scarce, and amplification removes epigenetic signals. Additionally, pre-analytical treatments...

    Authors: Marcin W. Wojewodzic, Magnus Leithaug, Marianne Lauritzen, Robert Lyle, Sofia Haglund, Carl-Johan Rubin, Philip A. Ewels, Tom Grotmol and Trine B. Rounge

    Citation: Clinical Epigenetics 2021 13:107

    Content type: Research

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  23. DNA methylation profiling has facilitated and improved the classification of a wide variety of tumors of the central nervous system. In this study, we investigated the potential utility of DNA methylation prof...

    Authors: Sandra Ferreyra Vega, Thomas Olsson Bontell, Alba Corell, Anja Smits, Asgeir Store Jakola and Helena Carén

    Citation: Clinical Epigenetics 2021 13:102

    Content type: Research

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  24. Although esophageal squamous cell carcinoma (ESCC)-oriented mechanism has been widely explored, the integrated action of histone deacetylase 2 (HDAC2), microRNA (miR)-503-5p and C-X-C motif chemokine 10 (CXCL1...

    Authors: Jindong Li, Chengyan Jin, Lihua Sun, Bin Wang, Peiyan Hua and Yan Zhang

    Citation: Clinical Epigenetics 2021 13:96

    Content type: Research

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  25. Current non-invasive tests have limited sensitivities and lack capabilities of pre-operative risk stratification for bladder cancer (BC) diagnosis. We aimed to develop and validate a urine-based DNA methylatio...

    Authors: Weimei Ruan, Xu Chen, Ming Huang, Hong Wang, Jiaxin Chen, Zhixin Liang, Jingtong Zhang, Yanqi Yu, Shang Chen, Shizhong Xu, Tianliang Hu, Xia Li, Yuanjie Guo, Zeyu Jiang, Zhiwei Chen, Jian Huang…

    Citation: Clinical Epigenetics 2021 13:91

    Content type: Research

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  26. Colorectal cancer (CRC) is a leading cause of cancer-related deaths worldwide. Early detection of CRC can significantly reduce its mortality rate. Current method of CRC diagnosis relies on the invasive endosco...

    Authors: Yunfeng Zhang, Qian Wu, Linhao Xu, Hong Wang, Xin Liu, Sihui Li, Tianliang Hu, Yanying Liu, Quanzhou Peng, Zhiwei Chen, Xianrui Wu and Jian-Bing Fan

    Citation: Clinical Epigenetics 2021 13:90

    Content type: Research

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  27. Aberrant DNA methylation has been firmly established as a factor contributing to the pathogenesis of colorectal cancer (CRC) via its capacity to silence tumour suppressor genes. However, the methylation status...

    Authors: Keke Shao, Weilin Pu, Jianfeng Zhang, Shicheng Guo, Fei Qian, Ingrid Glurich, Qing Jin, Yanyun Ma, Shaoqing Ju, Zhao Zhang and Weifeng Ding

    Citation: Clinical Epigenetics 2021 13:89

    Content type: Research

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  28. Cancer initiation and progression are driven by genetic and epigenetic changes. Although genome/exome sequencing has significantly contributed to the characterization of the genetic driver alterations, further...

    Authors: Sarah Bazzocco, Higinio Dopeso, Águeda Martínez-Barriocanal, Estefanía Anguita, Rocío Nieto, Jing Li, Elia García-Vidal, Valentina Maggio, Paulo Rodrigues, Priscila Guimarães de Marcondes, Simo Schwartz Jr, Lauri A. Aaltonen, Alex Sánchez, John M. Mariadason and Diego Arango

    Citation: Clinical Epigenetics 2021 13:88

    Content type: Research

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  29. Bladder cancer (BC) is the 5th most common cancer in the USA. Non-muscle invasive bladder cancer represents about 70% of all cases and has generally a favorable outcome. However, recurrence rates as high as 60...

    Authors: Paolo Piatti, Yap Ching Chew, Michiko Suwoto, Taikun Yamada, Benjamin Jara, Xi-Yu Jia, Wei Guo, Saum Ghodoussipour, Siamak Daneshmand, Hamed Ahmadi, Jeffrey Rice, Jeffrey Bhasin, Faith Holloway, Yvonne Tsai, Yoshitomo Chihara and Gangning Liang

    Citation: Clinical Epigenetics 2021 13:84

    Content type: Research

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  30. Epigenetic (“above genetics”) modifications can alter the gene expression without altering the DNA sequence. Aberrant epigenetic regulations in cancer include DNA methylation, histone methylation, histone acet...

    Authors: Ning Jin, Tiffany L. George, Gregory A. Otterson, Claire Verschraegen, Haitao Wen, David Carbone, James Herman, Erin M. Bertino and Kai He

    Citation: Clinical Epigenetics 2021 13:83

    Content type: Review

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  31. Mutations in the EZH2 gene are recurrently found in patients with myeloid neoplasms and are associated with a poor prognosis. We aimed to characterize genetic and epigenetic alterations of EZH2 in 58 patients (51...

    Authors: Julia Stomper, Ruth Meier, Tobias Ma, Dietmar Pfeifer, Gabriele Ihorst, Nadja Blagitko-Dorfs, Gabriele Greve, Dennis Zimmer, Uwe Platzbecker, Anne Hagemeijer, Ingrid Schmitt-Graeff and Michael Lübbert

    Citation: Clinical Epigenetics 2021 13:77

    Content type: Research

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    The Correction to this article has been published in Clinical Epigenetics 2021 13:94

  32. The development of new biomarkers with diagnostic, prognostic and therapeutic prominence will greatly enhance the management of breast cancer (BC). Several reports suggest the involvement of the histone acetyl...

    Authors: Wafaa S. Ramadan, Iman M. Talaat, Mahmood Y. Hachim, Annette Lischka, Timo Gemoll and Raafat El-Awady

    Citation: Clinical Epigenetics 2021 13:72

    Content type: Research

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  33. Epigenetic alterations are known contributors to cancer development and aggressiveness. Additional to alterations in cancer cells, aberrant epigenetic marks are present in cells of the tumor microenvironment, ...

    Authors: Iris Lodewijk, Sandra P. Nunes, Rui Henrique, Carmen Jerónimo, Marta Dueñas and Jesús M. Paramio

    Citation: Clinical Epigenetics 2021 13:63

    Content type: Review

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  34. The promoter hypermethylation of the methylguanine-DNA methyltransferase gene is a frequently used biomarker in daily clinical practice as it is associated with a favorable prognosis in glioblastoma patients t...

    Authors: Rocio Rosas-Alonso, Julian Colmenarejo-Fernandez, Olga Pernia, Carlos Rodriguez-Antolín, Isabel Esteban, Ismael Ghanem, Dario Sanchez-Cabrero, Itsaso Losantos-Garcia, Sara Palacios-Zambrano, Gema Moreno-Bueno, Javier de Castro, Virginia Martinez-Marin and Inmaculada Ibanez-de-Caceres

    Citation: Clinical Epigenetics 2021 13:52

    Content type: Research

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  35. Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation ...

    Authors: Suleyman Vural, Alida Palmisano, William C. Reinhold, Yves Pommier, Beverly A. Teicher and Julia Krushkal

    Citation: Clinical Epigenetics 2021 13:49

    Content type: Research

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  36. Chromatin modifiers and their implications in oncogenesis have been an exciting area of cancer research. These are enzymes that modify chromatin via post-translational modifications such as methylation, acetyl...

    Authors: Benjamin J. Bernard, Nupur Nigam, Kyunghee Burkitt and Vassiliki Saloura

    Citation: Clinical Epigenetics 2021 13:45

    Content type: Review

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  37. Trimethylation of lysine 27 and dimethylation of lysine 9 of histone-H3 catalyzed by the histone methyltransferases EZH2 and G9a impede gene transcription in cancer. Our human bronchial epithelial (HBEC) pre-m...

    Authors: Carmen S. Tellez, Maria A. Picchi, Daniel Juri, Kieu Do, Dhimant H. Desai, Shantu G. Amin, Julie A. Hutt, Piotr T. Filipczak and Steven A. Belinsky

    Citation: Clinical Epigenetics 2021 13:44

    Content type: Research

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  38. Epigenetic alterations may contribute to early detection of cancer. We evaluated the association of blood DNA methylation with lymphatic–hematopoietic cancers and, for comparison, with solid cancers. We also e...

    Authors: Arce Domingo-Relloso, Tianxiao Huan, Karin Haack, Angela L. Riffo-Campos, Daniel Levy, M. Daniele Fallin, Mary Beth Terry, Ying Zhang, Dorothy A. Rhoades, Miguel Herreros-Martinez, Esther Garcia-Esquinas, Shelley A. Cole, Maria Tellez-Plaza and Ana Navas-Acien

    Citation: Clinical Epigenetics 2021 13:43

    Content type: Research

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  39. Lung cancer is the leading cause of cancer-related death in most western countries in both, males and females, accounting for roughly 20–25% of all cancer deaths. For choosing the most appropriate therapy regi...

    Authors: Torsten Goldmann, Bernhard Schmitt, Julia Müller, Maren Kröger, Swetlana Scheufele, Sebastian Marwitz, Dörte Nitschkowski, Marc A. Schneider, Michael Meister, Thomas Muley, Michael Thomas, Christian Kugler, Klaus F. Rabe, Reiner Siebert, Martin Reck and Ole Ammerpohl

    Citation: Clinical Epigenetics 2021 13:38

    Content type: Research

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  40. BRG1 (encoded by SMARCA4) is a catalytic component of the SWI/SNF chromatin remodelling complex, with key roles in modulating DNA accessibility. Dysregulation of BRG1 is observed, but functionally uncharacterised...

    Authors: Katherine A. Giles, Cathryn M. Gould, Joanna Achinger-Kawecka, Scott G. Page, Georgia R. Kafer, Samuel Rogers, Phuc-Loi Luu, Anthony J. Cesare, Susan J. Clark and Phillippa C. Taberlay

    Citation: Clinical Epigenetics 2021 13:37

    Content type: Research

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  41. Glycosylation, one of the most fundamental post-translational modifications, is altered in cancer and is subject in part, to epigenetic regulation. As there are many epigenetic-targeted therapies currently in ...

    Authors: Gordon Greville, Esther Llop, Jane Howard, Stephen F. Madden, Antoinette S. Perry, Rosa Peracaula, Pauline M. Rudd, Amanda McCann and Radka Saldova

    Citation: Clinical Epigenetics 2021 13:34

    Content type: Research

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  42. Although R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) remains the standard chemotherapy regimen for diffuse large B cell lymphoma (DLBCL) patients, not all patients are respon...

    Authors: Hang-Yu Chen, Wei-Long Zhang, Lei Zhang, Ping Yang, Fang Li, Ze-Ruo Yang, Jing Wang, Meng Pang, Yun Hong, Changjian Yan, Wei Li, Jia Liu, Nuo Xu, Long Chen, Xiu-Bing Xiao, Yan Qin…

    Citation: Clinical Epigenetics 2021 13:33

    Content type: Research

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  43. Patients suffering from the BCR-ABL1-negative myeloproliferative disease prefibrotic primary myelofibrosis (pre-PMF) have a certain risk for progression to myelofibrosis. Accurate risk estimation for this fibroti...

    Authors: Ulrich Lehmann, Helge Stark, Stephan Bartels, Jerome Schlue, Guntram Büsche and Hans Kreipe

    Citation: Clinical Epigenetics 2021 13:28

    Content type: Research

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  44. Early detection of colorectal carcinoma (CRC) would help to identify tumors when curative treatments are available and beneficial. However, current screening methods for CRC, e.g., colonoscopy, may affect pati...

    Authors: Jinke Sui, Xianrui Wu, Chenyang Wang, Guoqiang Wang, Chengcheng Li, Jing Zhao, Yuzi Zhang, Jianxing Xiang, Yu Xu, Weiqi Nian, Fuao Cao, Guanyu Yu, Zheng Lou, Liqiang Hao, Lianjie Liu, Bingsi Li…

    Citation: Clinical Epigenetics 2021 13:26

    Content type: Research

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  45. The recent discovery of cancer/tissue specificity of miRNA has indicated its great potential as a therapeutic target. In Epstein–Barr virus-associated gastric cancer (EBVaGC), host genes are affected by extens...

    Authors: Mansheng Zhu, Qixiang Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Liu, Yanfeng Hu, Jiang Yu and Guoxin Li

    Citation: Clinical Epigenetics 2021 13:22

    Content type: Research

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