Cancer epigenetics and diagnostics

Section information

Section edited by Maria Berdasco, James Chim, Roderick Dashwood, Carmen Jerónimo, Eckart Meese, Arpad Patai and Ed Seto

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 epigenetic profiling and its clinical value for future diagnosis, prognosis and prediction of response to therapies (pharmacoepigenetics). 

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  1. Review

    Histone code and long non-coding RNAs (lncRNAs) aberrations in lung cancer: implications in the therapy response

    Respiratory diseases hold several genome, epigenome, and transcriptional aberrations as a cause of the accumulated damage promoted by, among others, environmental risk factors. Such aberrations can also come a...

    Abril Marcela Herrera-Solorio, Leonel Armas-López, Oscar Arrieta, Joaquín Zúñiga, Patricia Piña-Sánchez and Federico Ávila-Moreno

    Clinical Epigenetics 2017 9:98

    Published on: 8 September 2017

  2. Research

    Prognostic relevance of an epigenetic biomarker panel in sentinel lymph nodes from colon cancer patients

    Patients with early colorectal cancer (stages I–II) generally have a good prognosis, but a subgroup of 15–20% experiences relapse and eventually die of disease. Occult metastases have been suggested as a marke...

    Guro E. Lind, Marianne Guriby, Terje Ahlquist, Israr Hussain, Marine Jeanmougin, Kjetil Søreide, Hartwig Kørner, Ragnhild A. Lothe and Oddmund Nordgård

    Clinical Epigenetics 2017 9:97

    Published on: 5 September 2017

  3. Research

    Pyrosequencing quantified methylation level of miR-124 predicts shorter survival for patients with myelodysplastic syndrome

    Aberrant CpG island methylation has been increasingly recognized as a common event in myelodysplastic syndrome (MDS). To date, most of the previous studies of miR-124 in MDS have focused on epigenetic changes ...

    Hong Wang, Tong-Tong Zhang, Song Jin, Hong Liu, Xiang Zhang, Chang-Geng Ruan, De-Pei Wu, Yue Han and Xiao-Qin Wang

    Clinical Epigenetics 2017 9:91

    Published on: 30 August 2017

  4. Research

    Epigenetic response of imprinted domains during carcinogenesis

    Imprinted domains have been identified as targets for aberrant DNA methylation during carcinogenesis, but it remains unclear when these epigenetic alterations occur and how they contribute to tumor progression...

    Corey L. Bretz, Ingeborg M. Langohr and Joomyeong Kim

    Clinical Epigenetics 2017 9:90

    Published on: 25 August 2017

  5. Research

    Seven-CpG-based prognostic signature coupled with gene expression predicts survival of oral squamous cell carcinoma

    DNA methylation has started a recent revolution in genomics biology by identifying key biomarkers for multiple cancers, including oral squamous cell carcinoma (OSCC), the most common head and neck squamous cel...

    Sipeng Shen, Guanrong Wang, Qianwen Shi, Ruyang Zhang, Yang Zhao, Yongyue Wei, Feng Chen and David C. Christiani

    Clinical Epigenetics 2017 9:88

    Published on: 24 August 2017

  6. Research

    CpG location and methylation level are crucial factors for the early detection of oral squamous cell carcinoma in brushing samples using bisulfite sequencing of a 13-gene panel

    Oral squamous cell carcinoma (OSCC) is usually diagnosed at an advanced stage and is commonly preceded by oral premalignant lesions. The mortality rates have remained unchanged (50% within 5 years after diagno...

    Luca Morandi, Davide Gissi, Achille Tarsitano, Sofia Asioli, Andrea Gabusi, Claudio Marchetti, Lucio Montebugnoli and Maria Pia Foschini

    Clinical Epigenetics 2017 9:85

    Published on: 15 August 2017

  7. Research

    Tri-methylation of H3K79 is decreased in TGF-β1-induced epithelial-to-mesenchymal transition in lung cancer

    The epithelial-to-mesenchymal transition (EMT) enables epithelial cancer cells to acquire mesenchymal features and contributes to metastasis and resistance to treatment. This process involves epigenetic reprog...

    Emilie Evanno, Julie Godet, Nathalie Piccirilli, Joëlle Guilhot, Serge Milin, Jean Marc Gombert, Benoit Fouchaq and Joëlle Roche

    Clinical Epigenetics 2017 9:80

    Published on: 8 August 2017

  8. Research

    A long-range interactive DNA methylation marker panel for the promoters of HOXA9 and HOXA10 predicts survival in breast cancer patients

    Most DNA cancer methylation markers are based on the transcriptional regulation of the promoter-gene relationship. Recently, the importance of long-range interactions between distal CpGs and target genes has b...

    Seong-Min Park, Eun-Young Choi, Mingyun Bae, Jung Kyoon Choi and Youn-Jae Kim

    Clinical Epigenetics 2017 9:73

    Published on: 24 July 2017

  9. Research

    MicroRNA profiling of ovarian granulosa cell tumours reveals novel diagnostic and prognostic markers

    The aim of this study was to explore the clinical utility of microRNAs (miRNAs) as improved markers of ovarian granulosa cell tumours (GCTs) for cancer diagnosis and prognosis prediction. Current histopatholog...

    Wei-Tzu Cheng, Roseanne Rosario, Anita Muthukaruppan, Michelle K Wilson, Kathryn Payne, Peter C. Fong, Andrew N. Shelling and Cherie Blenkiron

    Clinical Epigenetics 2017 9:72

    Published on: 21 July 2017

  10. Methodology

    Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers

    The DNA modification 5-hydroxymethylcytosine (5hmC) is now referred to as the sixth base of DNA with evidence of tissue-specific patterns and correlation with gene regulation and expression. This epigenetic ma...

    Noa Gilat, Tzlil Tabachnik, Amit Shwartz, Tamar Shahal, Dmitry Torchinsky, Yael Michaeli, Gil Nifker, Shahar Zirkin and Yuval Ebenstein

    Clinical Epigenetics 2017 9:70

    Published on: 14 July 2017

  11. Methodology

    PAT-H-MS coupled with laser microdissection to study histone post-translational modifications in selected cell populations from pathology samples

    Aberrations in histone post-translational modifications (hPTMs) have been linked with various pathologies, including cancer, and could not only represent useful biomarkers but also suggest possible targetable ...

    Roberta Noberini, Rémi Longuespée, Cristina Richichi, Giancarlo Pruneri, Mark Kriegsmann, Giuliana Pelicci and Tiziana Bonaldi

    Clinical Epigenetics 2017 9:69

    Published on: 11 July 2017

  12. Research

    Epigenetic silencing of SALL3 is an independent predictor of poor survival in head and neck cancer

    This study examined Sal-like protein (SALL)3 methylation profiles of head and neck cancer (HNSCC) patients at diagnosis and follow-up and evaluated their prognostic significance and value as a biomarker. SALL3 ex...

    Kiyoshi Misawa, Daiki Mochizuki, Atsushi Imai, Yuki Misawa, Shiori Endo, Masato Mima, Hideya Kawasaki, Thomas E. Carey and Takeharu Kanazawa

    Clinical Epigenetics 2017 9:64

    Published on: 12 June 2017

  13. Research

    ZAR1 is a novel epigenetically inactivated tumour suppressor in lung cancer

    Lung cancer is the leading cause of cancer-related deaths with 1.8 million new cases each year and poor 5-year prognosis. Promoter hypermethylation of tumour suppressors leads to their inactivation and thereby...

    Antje M. Richter, Steffen Kiehl, Nicole Köger, Janina Breuer, Thorsten Stiewe and Reinhard H. Dammann

    Clinical Epigenetics 2017 9:60

    Published on: 2 June 2017

  14. Research

    Genome-wide DNA methylation profiling integrated with gene expression profiling identifies PAX9 as a novel prognostic marker in chronic lymphocytic leukemia

    In chronic lymphocytic leukemia (CLL), epigenomic and genomic studies have expanded the existing knowledge about the disease biology and led to the identification of potential biomarkers relevant for implement...

    Lata Rani, Nitin Mathur, Ritu Gupta, Ajay Gogia, Gurvinder Kaur, Jaspreet Kaur Dhanjal, Durai Sundar, Lalit Kumar and Atul Sharma

    Clinical Epigenetics 2017 9:57

    Published on: 30 May 2017

  15. Research

    Prognostic significance of LINE-1 hypomethylation in oropharyngeal squamous cell carcinoma

    Inclusion of new biomarkers to improve a personalized treatment approach for oropharyngeal squamous cell carcinoma (OPSCC) is urgently needed. Hypomethylation of the Long interspersed nucleotide element-1 (LIN...

    Carlo Furlan, Jerry Polesel, Luigi Barzan, Giovanni Franchin, Sandro Sulfaro, Salvatore Romeo, Francesca Colizzi, Aurora Rizzo, Vittorio Baggio, Vittorio Giacomarra, Angelo Paolo Dei Tos, Paolo Boscolo-Rizzo, Emanuela Vaccher, Riccardo Dolcetti, Luca Sigalotti and Elisabetta Fratta

    Clinical Epigenetics 2017 9:58

    Published on: 30 May 2017

  16. Research

    Analysis of the DNA methylation level of cancer-related genes in colorectal cancer and the surrounding normal mucosa

    Two molecular pathways promote the development of colorectal cancer (CRC). One is termed “microsatellite stable” (MSS) whereas the other is characterized by “microsatellite instability” (MSI or MIN). In additi...

    Tamotsu Sugai, Masakazu Yoshida, Makoto Eizuka, Noriyuki Uesugii, Wataru Habano, Kouki Otsuka, Akira Sasaki, Eiichiro Yamamoto, Takayuki Matsumoto and Hiromu Suzuki

    Clinical Epigenetics 2017 9:55

    Published on: 18 May 2017

  17. Research

    Circulating nucleosomes as new blood-based biomarkers for detection of colorectal cancer

    Colonoscopy is currently widely accepted as the gold standard for detection of colorectal cancer (CRC) providing detection of up to 95% of pre-cancerous lesions during the procedure. However, certain limitatio...

    Jean-François Rahier, Anne Druez, Laurence Faugeras, Jean-Paul Martinet, Myriam Géhénot, Eléonore Josseaux, Marielle Herzog, Jake Micallef, Fabienne George, Monique Delos, Thierry De Ronde, Abdenor Badaoui and Lionel D’Hondt

    Clinical Epigenetics 2017 9:53

    Published on: 15 May 2017

  18. Letter to the Editor

    Epigenetic modifications of the immune-checkpoint genes CTLA4 and PDCD1 in non-small cell lung cancer results in increased expression

    Targeting checkpoint inhibitors using monoclonal antibodies results in significantly better outcome of cancer patients compared to conventional chemotherapy. However, the current companion diagnostics to predi...

    Sebastian Marwitz, Swetlana Scheufele, Sven Perner, Martin Reck, Ole Ammerpohl and Torsten Goldmann

    Clinical Epigenetics 2017 9:51

    Published on: 11 May 2017

  19. Research

    The CpG island methylator phenotype is concordant between primary colorectal carcinoma and matched distant metastases

    The CpG island methylator phenotype (CIMP) in stage III colon cancer (CRC) has been associated with improved survival after treatment with adjuvant irinotecan-based chemotherapy. In this analysis, we determine...

    Stacey A. Cohen, Ming Yu, Kelsey Baker, Mary Redman, Chen Wu, Tai J. Heinzerling, Ralph M. Wirtz, Elpida Charalambous, George Pentheroudakis, Vassiliki Kotoula, Konstantine T. Kalogeras, George Fountzilas and William M. Grady

    Clinical Epigenetics 2017 9:46

    Published on: 2 May 2017

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