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Cancer Epigenetics - Solid Tumors

Section information

Section Editors : Maria Berdasco and Carmen Jeronimo 

Associate Editors : Nita Ahuja, Tiziana Bonaldi (histones), Rene Cortese, James Flanagan (cervical/ovarian), Mario Fraga, Michéle Hoffmann (prostate), Bozena Kaminska (gliomas), Gwen Lomberk, Arpad Patai (colorectal/GI cancers), Qian Tao, Raul Urrutia, Stefan Wiemann (breast), 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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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

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

  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Acute leukemia is an epigenetically heterogeneous disease. The intensity of treatment is currently guided by cytogenetic and molecular genetic risk classifications; however these incompletely predict outcomes,...

    Authors: A. D. van Dijk, F. W. Hoff, Y. H. Qiu, J. Chandra, E. Jabbour, E. S. J. M. de Bont, T. M. Horton and S. M. Kornblau
    Citation: Clinical Epigenetics 2021 13:21
  28. Hypoxia is a characteristic of the tumor microenvironments within pancreatic cancer (PC), which has been linked to its malignancy. Recently, hypoxia has been reported to regulate the activity of important carc...

    Authors: Hongzhen Li, Chunyan Peng, Chenhui Zhu, Shuang Nie, Xuetian Qian, Zhao Shi, Mengyue Shi, Yan Liang, Xiwei Ding, Shu Zhang, Bin Zhang, Xihan Li, Guifang Xu, Ying Lv, Lei Wang, Helmut Friess…
    Citation: Clinical Epigenetics 2021 13:18
  29. Obesity confers enhanced risk for multiple diseases including cancer. The DNA methylation alterations in obesity-related genes have been implicated in several human solid tumors. However, the underlying role a...

    Authors: Ting-juan Zhang, Zi-jun Xu, Yu Gu, Ji-chun Ma, Xiang-mei Wen, Wei Zhang, Zhao-qun Deng, Jun Qian, Jiang Lin and Jing-dong Zhou
    Citation: Clinical Epigenetics 2021 13:16
  30. To date, no predictive or prognostic molecular biomarkers except BRCA mutations are clinically established for epithelial ovarian cancer (EOC) despite being the deadliest gynecological malignancy. Aim of this bio...

    Authors: Karolin Heinze, Matthias Rengsberger, Mieczyslaw Gajda, Lars Jansen, Linea Osmers, Leticia Oliveira-Ferrer, Barbara Schmalfeldt, Matthias Dürst, Norman Häfner and Ingo B. Runnebaum
    Citation: Clinical Epigenetics 2021 13:15
  31. Differentially-methylated regions (DMRs) are characteristic of colorectal cancer (CRC) and some occur more frequently than common mutations. This study aimed to evaluate the clinical utility of assaying circul...

    Authors: Graeme P. Young, Erin L. Symonds, Hans Jørgen Nielsen, Linnea Ferm, Ib J. Christensen, Evelien Dekker, Manon van der Vlugt, Rosalie C. Mallant-Hent, Nicky Boulter, Betty Yu, Michelle Chan, Gregor Tevz, Lawrence C. LaPointe and Susanne K. Pedersen
    Citation: Clinical Epigenetics 2021 13:14
  32. Despite using prognostic algorithms and standard surveillance guidelines, 17% of patients initially diagnosed with low risk clear cell renal cell carcinoma (ccRCC) ultimately relapse and die of recurrent disea...

    Authors: Louis Y. El Khoury, Shuang Fu, Ryan A. Hlady, Ryan T. Wagner, Liguo Wang, Jeanette E. Eckel-Passow, Erik P. Castle, Melissa L. Stanton, R. Houston Thompson, Alexander S. Parker, Thai H. Ho and Keith D. Robertson
    Citation: Clinical Epigenetics 2021 13:12
  33. Tumour DNA methylation profiling has shown potential to refine disease subtyping and improve the diagnosis and prognosis prediction of breast cancer. However, limited data exist regarding invasive lobular brea...

    Authors: Medha Suman, Pierre-Antoine Dugué, Ee Ming Wong, JiHoon Eric Joo, John L. Hopper, Tu Nguyen-Dumont, Graham G. Giles, Roger L. Milne, Catriona McLean and Melissa C. Southey
    Citation: Clinical Epigenetics 2021 13:11
  34. Blood DNA methylation-based aging algorithms predict mortality in the general population. We investigated the prognostic value of five established DNA methylation aging algorithms for patients with colorectal ...

    Authors: Xīn Gào, Yan Zhang, Daniel Boakye, Xiangwei Li, Jenny Chang-Claude, Michael Hoffmeister and Hermann Brenner
    Citation: Clinical Epigenetics 2020 12:184
  35. Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer worldwide, with human papillomavirus (HPV)-related HNSCC rising to concerning levels. Extensive clinical, genetic and epigenetic...

    Authors: Siyu Liu, Marcell Costa de Medeiros, Evan M. Fernandez, Katie R. Zarins, Raymond G. Cavalcante, Tingting Qin, Gregory T. Wolf, Maria E. Figueroa, Nisha J. D’Silva, Laura S. Rozek and Maureen A. Sartor
    Citation: Clinical Epigenetics 2020 12:175
  36. The utility of O6-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation status as a prognostic marker in patients with glioblastoma (GBM) has been established. However, the number of CpG sites that...

    Authors: Mitsuto Hanihara, Kunio Miyake, Atsushi Watanabe, Yuriko Yamada, Naoki Oishi, Tomoyuki Kawataki, Takeshi Inukai, Tetsuo Kondo and Hiroyuki Kinouchi
    Citation: Clinical Epigenetics 2020 12:174
  37. Zinc-finger protein 471 (ZNF471) is a member of the Krüppel-associated box domain zinc finger protein (KRAB-ZFP) family. ZNF471 is methylated in squamous cell carcinomas of tongue, stomach and esophageal. However...

    Authors: Chunfang Tao, Juan Luo, Jun Tang, Danfeng Zhou, Shujun Feng, Zhu Qiu, Thomas C. Putti, Tingxiu Xiang, Qiao Tao, Lili Li and Guosheng Ren
    Citation: Clinical Epigenetics 2020 12:173

    The Correction to this article has been published in Clinical Epigenetics 2022 14:17

  38. Previous studies suggest the tumor suppressor role of long non-coding RNA (lncRNA) STXBP5-AS1 in cervical and gastric cancer, but its expression pattern and functional mechanism are still elusive in pancreatic ca...

    Authors: Shi Chen, Long Huang, Ge Li, Funan Qiu, Yaodong Wang, Can Yang, Jingjing Pan, Zhangwei Wu, Jiangzhi Chen and Yifeng Tian
    Citation: Clinical Epigenetics 2020 12:168
  39. Multiple myeloma (MM) is a heterogeneous plasma cell malignancy that remains challenging to cure. Global hypomethylation correlates with an aggressive phenotype of the disease, while hypermethylation is observ...

    Authors: Jean-Baptiste Alberge, Florence Magrangeas, Mirko Wagner, Soline Denié, Catherine Guérin-Charbonnel, Loïc Campion, Michel Attal, Hervé Avet-Loiseau, Thomas Carell, Philippe Moreau, Stéphane Minvielle and Aurélien A. Sérandour
    Citation: Clinical Epigenetics 2020 12:163
  40. Stool DNA testing is an emerging and attractive option for colorectal cancer (CRC) screening. We previously evaluated the feasibility of a stool DNA (sDNA) test of methylated SDC2 for CRC detection. The aim of th...

    Authors: Jianping Wang, Side Liu, Hui Wang, Lei Zheng, Changchun Zhou, Guoxin Li, Rongkang Huang, Huaiming Wang, Chujun Li, Xinjuan Fan, Xinhui Fu, Xinying Wang, Hongliang Guo, Jie Guan, Yanlai Sun, Xilin Song…
    Citation: Clinical Epigenetics 2020 12:162
  41. Gastric cancer (GC) is a digestive system cancer with a high mortality rate globally. Previous experiences and studies have provided clinicians with ample evidence to diagnose and treat patients with reasonabl...

    Authors: Tengda Li, Xin Chen, Mingli Gu, Anmei Deng and Cheng Qian
    Citation: Clinical Epigenetics 2020 12:161
  42. Variation in intercellular methylation patterns can complicate the use of methylation biomarkers for clinical diagnostic applications such as blood-based cancer testing. Here, we describe development and valid...

    Authors: Brendan F. Miller, Thomas R. Pisanic II, Gennady Margolin, Hanna M. Petrykowska, Pornpat Athamanolap, Alexander Goncearenco, Akosua Osei-Tutu, Christina M. Annunziata, Tza-Huei Wang and Laura Elnitski
    Citation: Clinical Epigenetics 2020 12:154
  43. miR-342-3p, localized to 14q32, is a tumor suppressor miRNA implicated in carcinogenesis. Given the presence of a promotor-associated CpG island for its host gene, EVL, we hypothesized that intronic miR-342-3p is...

    Authors: Min Yue Zhang, George A. Calin, Kit San Yuen, Dong Yan Jin and Chor Sang Chim
    Citation: Clinical Epigenetics 2020 12:150
  44. Protein lysine methyltransferases (PKMTs) constitute a large family of approximately 50 chromatin modifiers that mono-, di- and/or tri-methylate lysine residues on histone and non-histone substrates. With the ...

    Authors: Theodore Vougiouklakis, Benjamin J. Bernard, Nupur Nigam, Kyunghee Burkitt, Yusuke Nakamura and Vassiliki Saloura
    Citation: Clinical Epigenetics 2020 12:146
  45. Inflammation has been associated with higher rates of recurrence and mortality in head and neck cancer (HNC). While the biological mechanisms predisposing patients to heightened inflammatory states remain larg...

    Authors: Laura Moody, Sylvia L. Crowder, Andrew D. Fruge, Julie L. Locher, Wendy Demark-Wahnefried, Laura Q. Rogers, Ashley Delk-Licata, William R. Carroll, Sharon A. Spencer, Molly Black, John W. Erdman Jr, Hong Chen, Yuan-Xiang Pan and Anna E. Arthur
    Citation: Clinical Epigenetics 2020 12:138