Article
Gastroenterology & Hepatology
Swathi Eluri, Anna Paterson, Brianna N. Lauren, Maria O'Donovan, Pradeep Bhandari, Massimiliano di Pietro, Minyi Lee, Rehan Haidry, Laurence Lovat, Krish Ragunath, Chin Hur, Rebecca C. Fitzgerald, Nicholas J. Shaheen
Summary: This study assessed the application value of Cytosponge in BE patients after RFA. The results showed that Cytosponge testing is a cost-effective surveillance method and is strongly associated with residual BE after ablation.
CLINICAL GASTROENTEROLOGY AND HEPATOLOGY
(2022)
Article
Oncology
Chaonan Liang, Nan Liu, Qin Zhang, Mingming Deng, Jiangwei Ma, Jingwen Lu, Yan Yin, Jian Wang, Yuan Miao, Bin She, Qingchang Li, Gang Hou
Summary: This study established a novel combination of cancer-specific methylated genes for the differential diagnosis of malignant pleural effusion (MPE). The results showed that this combination had high sensitivity and specificity in detecting MPE, making it a potential biomarker for MPE.
FRONTIERS IN ONCOLOGY
(2022)
Article
Genetics & Heredity
Madonna R. Peter, Misha Bilenky, Yuliang Shi, Jiajie Pu, Shivani Kamdar, Aaron R. Hansen, Neil E. Fleshner, Srikala S. Sridhar, Anthony M. Joshua, Martin Hirst, Wei Xu, Bharati Bapat
Summary: This study identifies a methylated cfDNA marker panel associated with androgen treatment resistance in metastatic prostate cancer, which could aid in its clinical management.
Article
Multidisciplinary Sciences
Georg A. Busslinger, Buys de Barbanson, Rurika Oka, Bas L. A. Weusten, Michiel de Maat, Richard van Hillegersberg, Lodewijk A. A. Brosens, Ruben van Boxtel, Alexander van Oudenaarden, Hans Clevers
Summary: Barrett's esophagus is categorized into different stages based on morphological appearance, which correlate with the risk of developing esophageal adenocarcinoma. Single-cell sequencing experiments revealed chromosomal instabilities in dysplastic BE cells, with stable cells predominantly found in nondysplastic BE biopsies. The datasets provide insight into the mutational landscape and gene expression patterns at different stages of BE development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Immunology
Ikenna C. Okereke, Aaron L. Miller, Daniel C. Jupiter, Catherine F. Hamilton, Gabriel L. Reep, Timothy Krill, Clark R. Andersen, Richard B. Pyles
Summary: The microbial community structures differ between patients with and without Barrett's esophagus, with certain organisms less likely to be detected as the severity of Barrett's esophagus worsens.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Review
Cell Biology
Deqiang Han, Chao Zhang
Summary: Barrett's esophagus is a major complication of gastro-esophageal reflux disease and an important precursor lesion for the development of Barrett's metaplasia and esophageal adenocarcinoma. This review discusses the mechanisms of Barrett's metaplasia and adenocarcinoma underlying oxidative DNA damage in gastro-esophageal reflux disease patients based on recent clinical and basic findings.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Oncology
Lisa M. Marinelli, John B. Kisiel, Seth W. Slettedahl, Douglas W. Mahoney, Maureen A. Lemens, Vijayalakshmi Shridhar, William R. Taylor, Julie K. Staub, Xiaoming Cao, Patrick H. Foote, Kelli N. Burger, Calise K. Berger, Maria C. O'Connell, Karen A. Doering, Maria Giakoumopoulos, Hannah Berg, Carla Volkmann, Adam Solsrud, Hatim T. Allawi, Michael Kaiser, Abram M. Vaccaro, Catherine Albright Crawford, Cynthia Moehlenkamp, Gracie Shea, Melissa S. Deist, J. Kenneth Schoolmeester, Sarah E. Kerr, Mark E. Sherman, Jamie N. Bakkum-Gamez
Summary: This study identified candidate methylation markers (MDMs) that are highly methylated in ovarian cancer and demonstrated high sensitivity and specificity in plasma. Further studies are needed to validate these findings in larger plasma-based cohorts.
GYNECOLOGIC ONCOLOGY
(2022)
Article
Oncology
Yi Bai, Juan Xu, Deqiang Li, Xiaoyu Zhang, Dapeng Chen, Fucun Xie, Longmei Huang, Xiaotian Yu, Haitao Zhao, Yamin Zhang
Summary: We developed a multimarker HCC detection panel (HepaClear) containing 3 hypermethylated CpG sites and 2 protein markers, which showed high sensitivity for early-stage HCC.
CLINICAL EPIGENETICS
(2023)
Article
Oncology
Rita Pinto, Tobias Hauge, Marine Jeanmougin, Heidi D. Pharo, Stine H. Kresse, Hilde Honne, Sara B. Winge, May-Britt Five, Theresa Kumar, Tom Mala, Truls Hauge, Egil Johnson, Guro E. Lind
Summary: This study investigates the distribution of genetic and epigenetic modifications in esophageal adenocarcinoma (EAC) and its precursor lesion Barrett's esophagus (BE). The study confirms the frequent occurrence of TP53 mutations in EAC, while no mutations were found in BE. MSI and MLH1 promoter hypermethylation were rare events in both EAC and BE. APC, CDKN2A, MGMT, and TIMP3 promoter hypermethylation were frequently observed in both lesions.
CLINICAL EPIGENETICS
(2022)
Article
Gastroenterology & Hepatology
Abhiram Duvvuri, Madhav Desai, Sreekar Vennelaganti, April Higbee, Venkat Subhash Gorrepati, Chandra Dasari, Viveksandeep Thoguluva Chandrasekar, Prashanth Vennalaganti, Divyanshoo Kohli, Anjana Sathyamurthy, Tarun Rai, Prateek Sharma
Summary: In this pilot study, it was found that the novel esophageal capsule is not suitable for population screening of Barrett's esophagus. Further studies integrating artificial intelligence into improved quality novel esophageal capsule should be conducted for BE screening.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Oncology
Graeme P. Young, Erin L. Symonds, Hans Jorgen 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, Susanne K. Pedersen
Summary: The study developed a multiplexed real-time PCR assay for methylation detection in BCAT1, IKZF1, and IRF4 for colorectal cancer (CRC) screening. By combining the PCR signals for DMRs in the three genes, the assay achieved high sensitivity and specificity for CRC, advanced adenomas, and high-grade dysplastic (HGD) adenomas. Detection of methylation in all three genes was more likely in CRC cases than in those without it, and the multi-panel test maintained high sensitivity for CRC and HGD adenomas while significantly improving specificity.
CLINICAL EPIGENETICS
(2021)
Article
Genetics & Heredity
Takuya Shijimaya, Tomomitsu Tahara, Jumpei Yamazaki, Sanshiro Kobayashi, Anna Horitani, Yasushi Matsumoto, Naohiro Nakamura, Takashi Okazaki, Yu Takahashi, Takashi Tomiyama, Yusuke Honzawa, Norimasa Fukata, Toshiro Fukui, Makoto Naganuma
Summary: This study examined the microarchitectures of non-neoplastic Barrett's esophagus (BE) associated with DNA methylation status using magnifying narrow-band imaging (NBI) endoscopy. The results showed that the magnifying NBI endoscopic features of non-neoplastic BE were correlated with DNA methylation as an independent factor. Conclusion: Microarchitectures of BE visualized by magnifying NBI endoscopy correlated with DNA methylation.
Article
Biology
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst, Steven J. M. Jones
Summary: This study used nanopore sequencing data to map the imprinted intervals in the human genome. It successfully phased the human methylome and detected both known and novel imprinted DMRs. The study also found several conserved imprinted DMRs in mouse, rhesus monkey, and chimpanzee. These findings expand our understanding of imprinting and demonstrate the potential of nanopore sequencing in identifying imprinting regions.
Article
Multidisciplinary Sciences
Weilin Peng, Guangxu Tu, Zhenyu Zhao, Boxue He, Qidong Cai, Pengfei Zhang, Xiong Peng, Shuai Shi, Xiang Wang
Summary: This study identified a diagnostic model involving methylation of four genes for early diagnosis of EAC by analyzing DNA methylome and gene expression data from EAC tissues. The model was validated in other datasets and may have potential applications in prospective EAC cases.
Article
Medicine, General & Internal
Min-Kyung So, Jong-Ho Park, Jong-Won Kim, Ja-Hyun Jang
Summary: This study aimed to evaluate the analytical validity of the Oncomine Pan-Cancer Cell-Free Assay, showing high sensitivity and precision in detecting EGFR mutations in lung cancer patients. The assay demonstrated comparable performance to the Cobas EGFR Mutation Test v2 and 100% concordance on clinical samples. Further studies are needed to assess the analytical validity for other gene types and aberrations in clinical samples.