Article
Respiratory System
Mina Gaga, Joanna Chorostowska-Wynimko, Ildiko Horvath, Martin C. Tammemagi, David Shitrit, Vered H. Eisenberg, Hao Liang, David Stav, Dan Levy Faber, Maarten Jansen, Yael Raviv, Vasileios Panagoulias, Piotr Rudzinski, Gabriel Izbicki, Ohad Ronen, Adiv Goldhaber, Rawia Moalem, Nadir Arber, Ilana Haas, Qinghua Zhou
Summary: The study validated the performance of the methylation-based blood test Lung EpiCheck in the detection of lung cancer in European and Chinese samples, showing high detection rates for early-stage non-small cell lung cancer and small cell lung cancer.
EUROPEAN RESPIRATORY JOURNAL
(2021)
Article
Oncology
Kala Visvanathan, Leslie Cope, Mary Jo Fackler, Michael Considine, Lori Sokoll, Lisa A. Carey, Andres Forero-Torres, James N. Ingle, Nancy U. Lin, Rita Nanda, Anna Maria Storniolo, Suzana Tulac, Neesha Venkatesan, Natalie C. Wu, Sudhakar Marla, Scott Campbell, Michael Bates, Christopher B. Umbricht, Antonio C. Wolff, Saraswati Sukumar
Summary: This study evaluated the clinical utility of a novel liquid biopsy-breast cancer methylation (LBx-BCM) prototype assay for early assessment of disease progression in women with metastatic breast cancer (MBC). The results showed that high levels of cumulative methylation (CM) were associated with shorter median progression-free survival (PFS) and overall survival (OS) at week 4. The CM levels at week 4 could be used to predict disease progression as early as 3 months after initiating a new treatment.
CLINICAL CANCER RESEARCH
(2023)
Review
Oncology
Harman Saman, Afsheen Raza, Kalyani Patil, Shahab Uddin, Tatjana Crnogorac-Jurcevic
Summary: This article reviews and assesses the effectiveness of different techniques, currently in use and upcoming, in early detection of lung cancer. It also discusses the principles of developing such techniques and the challenges faced by researchers in the field. Improvement in early detection would lower the rate of death and the societal burden of lung cancer.
Review
Oncology
Veronica Davalos, Manel Esteller
Summary: Cancer development is caused by changes in the structure and function of the genome. Epigenetic alterations regulate gene expression programs that promote tumorigenesis and can be used as useful tools in clinical decision making. Unlike genetic changes, epigenetic modifications can be reversed, making them an attractive target for drug development.
CA-A CANCER JOURNAL FOR CLINICIANS
(2023)
Article
Biochemistry & Molecular Biology
Hernan Guillermo Hernandez, Gloria Cristina Aranzazu-Moya, Efrain Hernando Pinzon-Reyes
Summary: The objective of this study was to identify DNA methylation patterns of heavy smokers in oral rinse samples. Genome-wide DNA methylation data from Gene Expression Omnibus GSE70977 was analyzed, including 71 epigenomes of cancer-free subjects and 139 oral-cancer patients' epigenomes. Differential DNA methylation was determined using bioinformatics packages, and candidate biomarker genes were identified. The results suggest that AHRR, ADAMTS2, and FAM184B genes may serve as biomarkers in oral rinse samples of heavy smokers.
Article
Biochemistry & Molecular Biology
Yu Kyeong Han, Ha Young Park, Sae-Gwang Park, Jae Joon Hwang, Hae Ryoun Park, Joo Mi Yi
Summary: Growing evidence suggests that genetic and epigenetic factors, including environmental factors, contribute to the development of oral squamous cell carcinoma (OSCC). This study investigated the transcriptional silencing and promoter methylation of CD24, CD44, CD133, and CD147 genes in OSCC cell lines, and found that CD133 and CD147 methylation status is associated with poor survival in OSCC patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Ruth Pidsley, Dilys Lam, Wenjia Qu, Timothy J. Peters, Phuc-Loi Luu, Darren Korbie, Clare Stirzaker, Roger J. Daly, Phillip Stricker, James G. Kench, Lisa G. Horvath, Susan J. Clark
Summary: This study used methylome sequencing to investigate the DNA methylation patterns in prostate cancer patients, and identified methylation patterns associated with prostate cancer-specific mortality, as well as prognostic biomarkers. The combination of DNA methylation biomarkers and clinicopathological measures improved the prognostic models for prostate cancer mortality.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Pathology
Lei Wang, Xiao Feng, Zonglin Jiao, Junqing Gan, Qingwei Meng
Summary: ALKBH family genes have prognostic and diagnostic values in NSCLC, with ALKBH2 identified as a potential novel diagnostic biomarker for LUAD.
PATHOLOGY RESEARCH AND PRACTICE
(2022)
Article
Oncology
John Adeoye, Chi Ching Joan Wan, Li-Wu Zheng, Peter Thomson, Siu-Wai Choi, Yu-Xiong Su
Summary: This study successfully utilized machine learning techniques to select optimal methylome biomarkers for oral cancer diagnoses. By applying genome-wide methylation analysis to saliva samples, ML-assisted platforms can be useful in stratifying oral squamous cell carcinoma (OSCC) during disease screening and monitoring.
Article
Oncology
Florian Janke, Arlou Kristina Angeles, Anja Lisa Riediger, Simone Bauer, Martin Reck, Albrecht Stenzinger, Marc A. Schneider, Thomas Muley, Michael Thomas, Petros Christopoulos, Holger Sueltmann
Summary: This study demonstrates the potential of DNA methylation biomarkers in prognosis and therapy monitoring of ALK-positive NSCLC patients. The research highlights the suitability of cfDNA methylation as a non-invasive biomarker for tumor detection and its correlation with other genomic alterations.
CLINICAL EPIGENETICS
(2022)
Article
Environmental Sciences
Yuan Chun Ding, Susan Hurley, June-Soo Park, Linda Steele, Michele Rakoff, Yun Zhu, Jinying Zhao, Mark LaBarge, Leslie Bernstein, Shiuan Chen, Peggy Reynolds, Susan L. Neuhausen
Summary: The study revealed associations between PBDE levels and DNA methylation, with these methylation changes being significantly associated with breast cancer risk.
ENVIRONMENT INTERNATIONAL
(2021)
Article
Multidisciplinary Sciences
Zirui Jia, Jiacheng Gao, Yuhang Wang, Tingting Zhou, Xiangwen Zhang, Guo Zu
Summary: Through meta-analysis and bioinformatics analysis, the study investigated the relationship between LOX expression and methylation level with clinicopathological parameters and prognosis in GC patients. Results showed that LOX expression was related to lymph node metastasis, tumor distant metastasis, and poor prognosis, while low methylation levels were associated with advanced tumor stage and poor prognosis.
SCIENTIFIC REPORTS
(2022)
Review
Biochemistry & Molecular Biology
Galateia Liouta, Maria Adamaki, Antonis Tsintarakis, Panagiotis Zoumpourlis, Anastasia Liouta, Sofia Agelaki, Vassilis Zoumpourlis
Summary: Head and neck squamous cell carcinoma (HNSCC) is a term used to describe cancers in the head and neck region. Most cases are diagnosed at a late stage and have poor prognosis. DNA methylation has been identified as a potential biomarker for HNSCC, and this study summarizes the current knowledge on how abnormally methylated DNA profiles may contribute to the development and progression of HNSCC, with the aim of improving management and survival outcomes for patients.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Oncology
Cora Palanca-Ballester, Aitor Rodriguez-Casanova, Susana Torres, Silvia Calabuig-Farinas, Francisco Exposito, Diego Serrano, Esther Redin, Karmele Valencia, Eloisa Jantus-Lewintre, Angel Diaz-Lagares, Luis Montuenga, Juan Sandoval, Alfonso Calvo
Summary: In addition to genetic changes, cancer is also characterized by epigenetic alterations that can be used for diagnosis, prognosis, and predicting drug response. These changes can be detected in early stages of cancer and through liquid biopsies, offering valuable information for personalized treatment. Validation and standardization of epigenetic biomarkers are needed for their successful transfer from research to clinical practice.
Article
Biochemistry & Molecular Biology
Yeongun Lee, So Hee Dho, Jiyeon Lee, Ji-Hyun Hwang, Minjung Kim, Won-Young Choi, Jin-Young Lee, Jongwon Lee, Woochul Chang, Min Young Lee, Jungmin Choi, Tae-You Kim, Lark Kyun Kim
Summary: A study has identified gene-specific alterations associated with worse outcomes in colorectal cancer patients through detecting patterns of DNA modification. The results could provide clinicians with an additional diagnostic tool and suggest the potential utility of performing such methylation profiling in other cancer types.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2022)
Article
Oncology
Amelia Acha-Sagredo, Bubaraye Uko, Paschalia Pantazi, Naiara G. Bediaga, Chryssanthi Moschandrea, Lucille Rainbow, Michael W. Marcus, Michael P. A. Davies, John K. Field, Triantafillos Liloglou
BRITISH JOURNAL OF CANCER
(2020)
Article
Oncology
Ahmed S. K. Al-Khafaji, Paschalia Pantazi, Amelia Acha-Sagredo, Andrew Schache, Janet M. Risk, Richard J. Shaw, Triantafillos Liloglou
Article
Oncology
Lawrence N. Barrera, Anthony Evans, Brian Lane, Sarah Brumskill, Frances E. Oldfield, Fiona Campbell, Timothy Andrews, Zipeng Lu, Pedro A. Perez-Mancera, Triantafillos Liloglou, Milton Ashworth, Mehdi Jalali, Rebecca Dawson, Quentin Nunes, Phoebe A. Phillips, John F. Timms, Christopher Halloran, William Greenhalf, John P. Neoptolemos, Eithne Costello
Article
Biochemistry & Molecular Biology
Ioannis Kanakis, Moussira Alameddine, Mattia Scalabrin, Rob J. van't Hof, Triantafillos Liloglou, Susan E. Ozanne, Katarzyna Goljanek-Whysall, Aphrodite Vasilaki
Review
Biochemistry & Molecular Biology
Minnatallah Al-Yozbaki, Amelia Acha-Sagredo, Alex George, Triantafillos Liloglou, Cornelia M. Wilson
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2020)
Article
Hematology
Emma Kennedy, Eve Coulter, Emma Halliwell, Nuria Profitos-Peleja, Elisabeth Walsby, Barnaby Clark, Elizabeth H. Phillips, Thomas A. Burley, Simon Mitchell, Stephen Devereux, Christopher D. Fegan, Christopher Jones, Rosalynd Johnston, Tim Chevassut, Ralph Schulz, Martina Seiffert, Angelo Agathanggelou, Ceri Oldreive, Nicholas Davies, Tatjana Stankovic, Triantafillos Liloglou, Chris Pepper, Andrea G. S. Pepper
Summary: Despite the advancements in B-cell receptor-targeted inhibitors, CLL remains incurable. TLR9 activation by unmethylated DNA is associated with disease progression in CLL. High TLR9 expression promotes CLL cell migration and disease progression, while dual targeting of TLR9 and BTK shows strong synergism as a potential treatment strategy for this incurable disease.
Article
Oncology
Yanhong Liu, Jun Xia, James McKay, Spiridon Tsavachidis, Xiangjun Xiao, Margaret R. Spitz, Chao Cheng, Jinyoung Byun, Wei Hong, Yafang Li, Dakai Zhu, Zhuoyi Song, Susan M. Rosenberg, Michael E. Scheurer, Farrah Kheradmand, Claudio W. Pikielny, Christine M. Lusk, Ann G. Schwartz, Ignacio I. Wistuba, Michael H. Cho, Edwin K. Silverman, Joan Bailey-Wilson, Susan M. Pinney, Marshall Anderson, Elena Kupert, Colette Gaba, Diptasri Mandal, Ming You, Mariza de Andrade, Ping Yang, Triantafillos Liloglou, Michael P. A. Davies, Jolanta Lissowska, Beata Swiatkowska, David Zaridze, Anush Mukeria, Vladimir Janout, Ivana Holcatova, Dana Mates, Jelena Stojsic, Ghislaine Scelo, Paul Brennan, Geoffrey Liu, John K. Field, Rayjean J. Hung, David C. Christiani, Christopher I. Amos
Summary: Recent studies indicate that rare variants could have a significant impact on the etiology of lung cancers. Through comprehensive sequencing, rare deleterious variants associated with lung cancer susceptibility were identified, including both known and novel susceptibility genes. Further mechanistic studies are needed to evaluate the pathogenic effects of these specific alleles.
NPJ PRECISION ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Rhian Jones, Susanne Wijesinghe, Claire Wilson, John Halsall, Triantafillos Liloglou, Aditi Kanhere
Summary: The nuclear lincRNA CCDC26 plays a crucial role in regulating DNMT1 activity and controlling DNA methylation levels. Its absence leads to mis-localization of DNMT1 to the cytoplasm, causing significant hypomethylation of genomic DNA, double-stranded DNA breaks, and increased cell death. This study reveals a previously unrecognized mechanism of lincRNA-mediated subcellular localization of DNMT1 and regulation of DNA methylation.
Article
Medicine, Research & Experimental
Caroline McCarthy, Joseph Sacco, Stefano Fedele, Michael Ho, Stephen Porter, Triantafillos Liloglou, Bill Greenhalf, Max Robinson, Bridget Young, Silvia Cicconi, Seema Chauhan, Binyam Tesfaye, Richard Jackson, Frances Sherratt, Richard Shaw
Summary: The SAVER trial aims to investigate the potential chemopreventive effects of VPA in patients with high-risk OED, while assessing the feasibility and acceptability of the trial.
Article
Biochemical Research Methods
Albert Rosenberger, Viola Tozzi, Heike Bickeboeller
Summary: This paper introduces an independent pair of accuracy measures, Iam hiQ, which can be applied to evaluate the output of all imputation software; by applying both measures to a large sample of the International Lung Cancer Consortium (ILCCO), meaningful thresholds for classifying markers of poor accuracy were found.
BMC BIOINFORMATICS
(2022)
Article
Oncology
Rachel C. Brooker, Philipp Antczak, Triantafillos Liloglou, Janet M. Risk, Joseph J. Sacco, Andrew G. Schache, Richard J. Shaw
Summary: This study identified a panel of genetic variants that can predict mandibular osteoradionecrosis (ORN) in head and neck cancer patients, offering new insight into personalized radiotherapy strategies for ORN management. The model developed achieved 92% accuracy and four SNPs were significantly associated with the absence of ORN, potentially guiding patient selection for personalized radiotherapy.
RADIOTHERAPY AND ONCOLOGY
(2021)
Article
Cell Biology
Michael Claxton, Michela Pulix, Michelle K. Y. Seah, Ralph Bernardo, Peng Zhou, Sultan Aljuraysi, Triantafillos Liloglou, Philippe Arnaud, Gavin Kelsey, Daniel M. Messerschmidt, Antonius Plagge
Summary: Genomic imprinting is an epigenetic process that leads to parent-of-origin specific gene expression. In this study, the researchers investigated the allelic expression biases in the brain and found variable states of allelic expression, especially for Trappc9 and Ago2 genes. They also discovered that Trappc9 and Ago2 are not imprinted in hippocampus-derived neural stem cells. The findings suggest the presence of variability and mosaicism in allelic expression between individual cells of the brain tissue.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Medicine, General & Internal
Michael P. A. Davies, Takahiro Sato, Haitham Ashoor, Liping Hou, Triantafillos Liloglou, Robert Yang, John K. Field
Summary: The study investigated the potential of plasma proteomes for lung cancer prediction and identified differentially expressed proteins and pathways associated with the presence and prediction of lung cancer.
Article
Medicine, Research & Experimental
Albert Rosenberger, Nils Muttray, Rayjean J. Hung, David C. Christiani, Neil E. Caporaso, Geoffrey Liu, Stig E. Bojesen, Loic Le Marchand, Demetrios Albanes, Melinda C. Aldrich, Adonina Tardon, Guillermo Fernandez-Tardon, Gad Rennert, John K. Field, Michael P. A. Davies, Triantafillos Liloglou, Lambertus A. Kiemeney, Philip Lazarus, Bernadette Wendel, Aage Haugen, Shanbeh Zienolddiny, Stephen Lam, Matthew B. Schabath, Angeline S. Andrew, Eric J. Duell, Susanne M. Arnold, Gary E. Goodman, Chu Chen, Jennifer A. Doherty, Fiona Taylor, Angela Cox, Penella J. Woll, Angela Risch, Thomas R. Muley, Mikael Johansson, Paul Brennan, Maria Teresa Landi, Sanjay S. Shete, Christopher Amos, Heike Bickeboeller
Summary: This study assessed the association and predictive ability of AhR/Wnt genes with lung cancer in individuals of European descent. The results showed no genome-wide significant association with overall lung cancer, but significant associations were observed in subgroups of ever smokers and never smokers. Although the predictability is poor, AhR/Wnt variants are overrepresented in optimized prediction scores for lung cancer.
EUROPEAN JOURNAL OF MEDICAL RESEARCH
(2022)
Article
Oncology
Athina Giannoudis, Mohammed Imad Malki, Bharath Rudraraju, Hisham Mohhamed, Suraj Menon, Triantafillos Liloglou, Simak Ali, Jason S. Carroll, Carlo Palmieri
BREAST CANCER RESEARCH
(2020)
