Article
Oncology
Xukun Li, Fang Ding, Luhua Wang, Hongyan Chen, Zhihua Liu
Summary: Studies have shown that enhancer-regulated S100A14 acts as a tumor suppressor in esophageal squamous cell carcinoma (ESCC). Deficiency in S100A14 promotes tumorigenesis and decreases the survival of mice. S100A14 expression is regulated by enhancers, and disruption of enhancers leads to decreased S100A14 expression. Mechanistic investigation reveals that S100A14 deficiency triggers abnormal differentiation. Downregulation of S100A14 in ESCC tissues is associated with poorer overall survival.
Review
Biochemistry & Molecular Biology
Yeon-Su Lee, Yong Sun Lee
Summary: nc886 is a medium-sized non-coding RNA transcribed by RNA polymerase III (Pol III) and has diverse roles in tumorigenesis, innate immunity, and other cellular processes. The expression of nc886 is controlled by multiple mechanisms, including promoter CpG DNA methylation and transcription factor activity. Additionally, its RNA instability contributes to its highly variable expression levels. This comprehensive review discusses nc886's variable expression in physiological and pathological conditions and examines the regulatory factors that determine its expression levels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Arnaud Carrier, Cecile Desjobert, Valerie Lobjois, Lise Rigal, Florence Busato, Jorg Tost, Miquel Ensenyat-Mendez, Diego M. Marzese, Anne Pradines, Gilles Favre, Laurence Lamant, Luisa Lanfrancone, Chantal Etievant, Paola B. Arimondo, Joelle Riond
Summary: Protocadherin proteins play an important role in cell adhesion and signaling pathways. The study found that the PCDHB15 gene's specific exon is hypermethylated in melanoma, leading to its silencing. This silencing contributes to the aggressiveness of melanoma.
CLINICAL EPIGENETICS
(2022)
Review
Biochemistry & Molecular Biology
Ting Xu, Hongmei Ding, Jie Chen, Jiahui Lei, Meng Zhao, Bingyu Ji, Youguo Chen, Songbing Qin, Qinqin Gao
Summary: This article provides an update on the roles of aberrant DNA methylation in endometrial carcinogenesis and discusses the opportunities and challenges of utilizing DNA methylation in the management and prevention of endometrial cancer.
Article
Neurosciences
Feifei Luo, Yifu Liao, Endong Cao, Yong Yang, Kai Tang, Dexiang Zhou, Dong Zhou, Haiping Cai
Summary: This study found that HIC2 gene is hypermethylated and expressed at low levels in glioma. Hypermethylation and low expression of HIC2 predict poor prognosis. Further experiments showed that HIC2 inhibits glioma proliferation in vitro and in vivo by interacting with RNF44 and PTPRN2.
CNS NEUROSCIENCE & THERAPEUTICS
(2023)
Review
Biotechnology & Applied Microbiology
Nasrullah, Abrar Hussain, Sagheer Ahmed, Mahmood Rasool, Abdul Jabbar Shah
Summary: DNA methylation is a process of adding methyl groups to the DNA molecule, which can alter the function of DNA. The importance and role of DNA methylation vary across different organisms, with mammals showing a strong relationship between DNA methylation and diseases such as cancer and placental development.
Article
Oncology
Gaurav Dube, Assia Tiamiou, Martin Bizet, Yasmine Boumahd, Imene Gasmi, Rebekah Crake, Justine Bellier, Marie-Julie Nokin, Emilie Calonne, Rachel Deplus, Tom Wissocq, Olivier Peulen, Vincent Castronovo, Francois Fuks, Akeila Bellahcene
Summary: A study reveals that methylglyoxal (MG), a by-product of glycolysis, can regulate gene expression by altering DNA methylation levels in breast cancer cells. The depletion of MG scavengers leads to the re-expression of metastasis-related tumor suppressor genes, suggesting the potential therapeutic role of MG scavengers in inhibiting tumor metastasis.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2023)
Article
Biochemical Research Methods
Jianxiong Tang, Jianxiao Zou, Mei Fan, Qi Tian, Jiyang Zhang, Shicai Fan
Summary: CaMelia, a CatBoost gradient boosting method, predicts missing methylation states based on locally paired intercellular methylation similarity. It significantly improves imputation performance on real single-cell methylation datasets, helping to discover intercellular differentially methylated loci masked by sparsity in raw data. The results demonstrate that CaMelia preserves cell-cell relationships, enhances cell type identification, and improves subpopulation detection.
Article
Biochemistry & Molecular Biology
Suman Abhishek, Naveen Kumar Nakarakanti, Waghela Deeksha, Eerappa Rajakumara
Summary: UHRF1 SRA can recognize non-mCpG DNA, with contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition. While the binding affinity for fully-mCpG is weaker, UHRF1 SRA exhibits higher affinity for fully-mCpHpG.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Environmental Sciences
Xingjie Zhang, Lin Ma, Yue Tang, Jiangyuan Han, Yongmei Qi, Dejun Huang
Summary: The study revealed that Cd-induced promoter hypermethylation of RASSF1A and DAPK1, decreasing their expression and leading to higher level of cell proliferation. Furthermore, Cd at low concentrations could influence DNA methylation, which may serve as the proliferative mechanism of Cd.
ENVIRONMENTAL TOXICOLOGY
(2021)
Article
Multidisciplinary Sciences
Sheersh Massey, Mohammad Aasif Khan, Safia Obaidur Rab, Saad Mustafa, Asifa Khan, Zoya Malik, Rahimunnisa Shaik, Mohit Kumar Verma, S. V. S. Deo, Syed Akhtar Husain
Summary: This study investigates the role of the MEN1 gene in breast cancer and finds that aberrant expression of MEN1 is associated with the development and progression of the disease.
Article
Medicine, Research & Experimental
Cheng-Huang Shen, Jin-Yi Wu, Shou-Chieh Wang, Chi-Hung Wang, Chen-Tai Hong, Pei-Yu Liu, Sin-Rong Wu, Yi-Wen Liu
Summary: Glutathione S-transferases (GSTs) play an important role in metabolism and detoxification of various substances. A study found that GSTM2 gene expression is lower in advanced stages of bladder urothelial carcinoma, and overexpression of GSTM2 inhibits invasion, migration, and tumor formation of bladder cancer cells. The study also identified an SP1 site and several phytochemicals that can affect GSTM2 expression, with berberrubine and resveratrol being the most effective. Furthermore, it was found that a DNA methylation inhibitor and berberrubine can influence the methylation level of the GSTM2 gene.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Review
Genetics & Heredity
Melva Gutierrez-Angulo, Maria de la Luz Ayala-Madrigal, Jose Miguel Moreno-Ortiz, Jorge Peregrina-Sandoval, Fernando Daniel Garcia-Ayala
Summary: Colorectal cancer is a complex disease influenced by genetics, epigenetics, and environmental factors. DNA methylation, particularly in tumor suppressor genes, plays a role in the development of cancer. The composition of gut microbiota, including enrichment of certain bacteria like Fusobacterium nucleatum and Hungatella hathewayi, is associated with changes in DNA methylation patterns in colorectal cancer. These changes can affect gene expression and impact the prognosis of colorectal cancer patients.
FRONTIERS IN GENETICS
(2023)
Article
Oncology
Tianyuan Liu, Xuan Zhao, Yuan Lin, Qi Luo, Shaosen Zhang, Yiyi Xi, Yamei Chen, Lin Lin, Wenyi Fan, Jie Yang, Yuling Ma, Alok K. Maity, Yanyi Huang, Jianbin Wang, Jiang Chang, Dongxin Lin, Andrew E. Teschendorff, Chen Wu
Summary: This study develops a computational strategy to identify stem-like preneoplastic cells that may drive cancer progression by dissecting the heterogeneity of differentiation states within a preneoplastic cell population.
Article
Oncology
Yijiao Ning, Chaoqun Deng, Chunhong Li, Weiyan Peng, Chun Yan, Jing Ran, Weihong Chen, Yujia Liu, Jiuyi Xia, Lin Ye, Zhengqiang Wei, Tingxiu Xiang
Summary: PCDH20 expression is attenuated in esophageal cancer, possibly due to promoter methylation. PCDH20 exerts anti-tumor effects through MAP3K9 downregulation and inhibition of AKT/β-catenin signaling in ESCC cells.
FRONTIERS IN ONCOLOGY
(2022)
Article
Gastroenterology & Hepatology
Jaffer A. Ajani, Yan Xu, Longfei Huo, Ruiping Wang, Yuan Li, Ying Wang, Melissa Pool Pizzi, Ailing Scott, Kazuto Harada, Lang Ma, Xiaodan Yao, Jiankang Jin, Wei Zhao, Xiaochuan Dong, Brian D. Badgwell, Namita Shanbhag, Ghia Tatlonghari, Jeannelyn Santiano Estrella, Sinchita Roy-Chowdhuri, Makoto Kobayashi, Jody V. Vykoukal, Samir M. Hanash, George Adrian Calin, Guang Peng, Ju-Seog Lee, Randy L. Johnson, Zhenning Wang, Linghua Wang, Shumei Song
Summary: YAP1 is highly upregulated in peritoneal carcinomatosis tumor cells, contributing to cancer stem cell properties and metastasis. Inhibition of YAP1 can significantly slow tumor growth and eliminate peritoneal carcinomatosis in preclinical models. Pharmacological inhibition of YAP1 can reduce cancer stem cell-like properties and suppress tumor growth, especially in combination with cytotoxic drugs in vivo models.
Article
Gastroenterology & Hepatology
Changyu Zhu, Yu-Jui Ho, Marcela A. Salomao, Dianne H. Dapito, Alberto Bartolome, Robert F. Schwabe, Ju-Seog Lee, Scott W. Lowe, Utpal B. Pajvani
Summary: The study revealed that Notch activity characterizes a distinct molecular subtype of HCC in humans, associated with unique histology and prognosis. Sustained Notch signaling in chronic liver diseases can drive tumor formation without acquiring specific genomic driver mutations.
JOURNAL OF HEPATOLOGY
(2021)
Article
Oncology
Changhee Park, Kyeonghun Jeong, Joon-Hyeong Park, Sohee Jung, Jeong Mo Bae, Kwangsoo Kim, Chan-Young Ock, Miso Kim, Bhumsuk Keam, Tae Min Kim, Yoon Kyung Jeon, Se-Hoon Lee, Ju-Seog Lee, Dong-Wan Kim, Gyeong Hoon Kang, Doo Hyun Chung, Dae Seog Heo
Summary: The study demonstrated a negative correlation between overall methylation aberrancy and tumor immunogenicity, indicating the importance of methylation aberrancy for tumors to evade immune surveillance. This highlights the need for further development of methylation biomarkers in cancer research.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Yeon-Su Lee, Xiaoyong Bao, Hwi-Ho Lee, Jiyoung Joan Jang, Enkhjin Saruuldalai, Gaeul Park, Wonkyun Ronny Im, Jong-Lyul Park, Seon-Young Kim, Sooyong Shin, Sung Ho Jeon, Sangmin Kang, Hyun-Sung Lee, Ju-Seog Lee, Ke Zhang, Eun Jung Park, In-Hoo Kim, Yong Sun Lee
Summary: The noncoding RNA nc886 acts as a novel suppressor for the IFN-beta signaling and inflammation by inhibiting the activation of IRF3, NF-kappa B, and AP-1 through inhibiting PKR. This leads to decreased expression of IFN-beta and IFN-stimulated genes. Its role is to restrict the IFN-beta signaling from hyperactivation, which may explain the variability of innate immune responses to pathogens based on biological settings.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Gastroenterology & Hepatology
Ji H. Nahm, Hye S. Lee, Haeryoung Kim, Sun Y. Yim, Ji-hyun Shin, Jeong E. Yoo, Sang H. Ahn, Jin S. Choi, Ju-Seog Lee, Young N. Park
Summary: This study developed a nomogram for predicting late recurrence of hepatocellular carcinoma (HCC) based on clinicopathological and molecular factors. The combination of pSTAT3, pERK1/2 and SYK immunoexpression with high lobular inflammatory activity and cirrhosis was found to predict late HCC recurrence.
LIVER INTERNATIONAL
(2021)
Review
Oncology
Sun Young Yim, Ju-Seog Lee
Summary: Tumor classifications based on alterations in the genome, epigenome, or proteome have shown promise in improving patient outcomes, especially with regards to personalized treatment. Understanding the molecular and genomic subtypes of hepatocellular carcinoma (HCC) is crucial for discovering new targets and biomarkers, and the development of new technical platforms for analyzing patient samples holds great potential for future advancements in treatment.
JOURNAL OF HEPATOCELLULAR CARCINOMA
(2021)
Article
Oncology
Soo-Mi Kweon, Gayeoun Kim, Yunseong Jeong, Wendong Huang, Ju-Seog Lee, Keane K. Y. Lai
Summary: Liver cancer, one of the deadliest cancers, may be influenced by the little-known gene midnolin, which has been found to correlate with poor prognosis in patients and may have a significant impact on liver cancer development.
Article
Oncology
Hee-Jin Jang, Hyun-Sung Lee, Wendong Yu, Maheshwari Ramineni, Cynthia Y. Truong, Daniela Ramos, Taylor Splawn, Jong Min Choi, Sung Yun Jung, Ju-Seog Lee, Daniel Y. Wang, Joel M. Sederstrom, Massimo Pietropaolo, Farrah Kheradmand, Christopher Amos, Thomas M. Wheeler, R. Taylor Ripley, Bryan M. Burt
Summary: Comprehensive single-cell proteomics analyses reveal the role of tumor-associated macrophages in resistance to PD-1 blockade therapy in lung adenocarcinoma progression. The spatiotemporal evolution of tumor-associated macrophages in the tumor-immune micro-environment governs tumor response to immunotherapy. PD-1 expression in a tumor-promoting subtype of tumor-associated macrophages controls tumor progression and protects tumor cells.
Article
Oncology
Thinh T. Nguyen, Hyun-Sung Lee, Bryan M. Burt, Christopher Amos, Chao Cheng
Summary: This study found that gene signature scores were more prognostic than genomic mutations, mRNA, and protein expression in malignant pleural mesothelioma (MPM). High immune infiltration levels were associated with prolonged survival. The integrated model combining intrinsic and extrinsic features provided independent prognostic values in MPM.
BRITISH JOURNAL OF CANCER
(2022)
Article
Oncology
Amanda M. Nash, Samira Aghlara-Fotovat, Bertha Castillio, Andrea Hernandez, Aarthi Pugazenthi, Hyun-Sung Lee, Hee-Jin Jang, Annie Nguyen, Alexander Lu, Bryan M. Burt, Ravi K. Ghanta, Omid Veiseh
Summary: The IL2 cytokine factories showed significant therapeutic efficacy in treating malignant mesothelioma in a mouse model, enhancing the effectiveness of therapy through activation of immune cells, and the safety and translatability of the treatment system were also validated.
CLINICAL CANCER RESEARCH
(2022)
Article
Oncology
Hyun-Sung Lee, Hee-Jin Jang, Maheshwari Ramineni, Daniel Y. Wang, Daniela Ramos, Jong Min Choi, Taylor Splawn, Monica Espinoza, Michelle Almarez, Leandria Hosey, Eunji Jo, Susan Hilsenbeck, Christopher I. Amos, R. Taylor Ripley, Bryan M. Burt
Summary: This study compared the effects of monotherapy and combination therapy on pathological response and survival in resectable patients. The results showed that combination therapy can alter the immune microenvironment of malignant pleural mesothelioma tumors and improve overall survival.
CLINICAL CANCER RESEARCH
(2023)
Article
Oncology
Joann Jung, Sowon Park, Yeonwoo Jang, Sung-Hwan Lee, Yun Seong Jeong, Sun Young Yim, Ju-Seog Lee
Summary: Hepatocellular carcinoma (HCC) is a common cancer that causes a large number of deaths worldwide. Metabolic reprogramming is a key feature of HCC, allowing cancer cells to meet the high energy demands for fast growth. By comparing genomic data from mice and humans, we identified three distinct metabolic subtypes of HCC and found clinical and molecular characteristics associated with each subtype. Notably, we discovered that the high metabolic subtype is resistant to immunotherapy and uncovered a potential mechanism for this resistance.
Letter
Gastroenterology & Hepatology
Sun Young Yim, Ju-Seog Lee
Article
Multidisciplinary Sciences
Younghun Y. Han, Jinyoung J. Byun, Catherine Zhu, Ryan R. Sun, Julia Y. Roh, Heather Cordell, Hyun-Sung A. Lee, Vikram R. Shaw, Sung Wook Kang, Javad Razjouyan, Matthew A. Cooley, Manal M. Hassan, Katherine A. Siminovitch, Trine Folseraas, David Ellinghaus, Annika Bergquist, Simon M. Rushbrook, Andre Franke, Tom H. Karlsen, Konstantinos N. Lazaridis, Katherine A. McGlynn, Lewis R. Roberts, Christopher Amos, Christoph Schramm, David Shapiro, Elizabeth Goode
Summary: This study used multitrait joint analyses to explore the genetic contribution and correlations between various clinical and epidemiological traits associated with PSC. Several new risk loci and potential susceptibility genes such as MANBA and IRF5 were identified, and in silico drug screening provided candidate agents for further investigation of pharmacological effects in PSC.
NATURE COMMUNICATIONS
(2023)