Article
Biotechnology & Applied Microbiology
Shu Zhao, Peng Song, Gang Zhou, Dong Zhang, Yi Hu
Summary: This study aimed to investigate the roles of METTL3, a regulator of m6A, in NSCLC. They found that METTL3 was overexpressed in NSCLC and its downregulation restrained the proliferation, migration and invasion of NSCLC cells. They also discovered that METTL3 negatively regulated SFRP2 and its silencing enhanced the stability of SFRP2. Furthermore, downregulation of SFRP2 induced by METTL3 activated the Wnt/beta-catenin signaling pathway in NSCLC. Thus, METTL3 might be a promising predictor and therapeutic target for NSCLC.
CANCER GENE THERAPY
(2023)
Article
Oncology
Shaobo Li, Nicholas Mancuso, Catherine Metayer, Xiaomei Ma, Adam J. de Smith, Joseph L. Wiemels
Summary: This study investigated the associations between DNA methylation and birthweight in newborns of diverse genetic ancestries. The results showed that genetic variation affects DNA methylation levels and incorporating genetic effects improved the significance of associations. This study highlights the importance of considering genetic effects in epigenome-wide association studies, especially for multiethnic populations.
CLINICAL EPIGENETICS
(2022)
Article
Plant Sciences
Rahul Chandnani, Changsoo Kim, Jinesh D. Patel, Hui Guo, Tariq Shehzad, Jason G. Wallace, Daohua He, Zhengsheng Zhang, Jeevan Adhikari, Sameer Khanal, Peng W. Chee, Andrew H. Paterson
Summary: This study investigated the genetic mapping of plant architecture, flowering time, and maturity traits in cotton, and identified a total of 27 QTLs associated with these traits. The findings suggest that this population structure can help reduce background noise and small effect QTLs, and the germplasm developed in this study may serve as potential pre-breeding material for improving cotton cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Medicine, General & Internal
Ying Zhu, Xiating Peng, Xiaoyang Wang, Pingting Ying, Haoxue Wang, Bin Li, Yue Li, Ming Zhang, Yimin Cai, Zequn Lu, Siyuan Niu, Nan Yang, Rong Zhong, Jianbo Tian, Jiang Chang, Xiaoping Miao
Summary: This study identified RFWD3 and its regulatory variant as novel genetic factors for PAAD prognosis. A total of 128 genes associated with PAAD prognosis were identified in the meta-analysis, and 14 regulatory loci in 12 of these genes were discovered. The functional variant rs4887783 in the promoter of RFWD3 showed significant association with PAAD prognosis in both stages of the population study.
CHINESE MEDICAL JOURNAL
(2022)
Article
Cell Biology
Jerome Levallet, Tiphaine Biojout, Celine Bazille, Manon Douyere, Fatemeh Dubois, Dimitri Leite Ferreira, Jasmine Taylor, Sylvain Teulier, Jerome Toutain, Nicolas Elie, Myriam Bernaudin, Samuel Valable, Emmanuel Bergot, Guenaelle Levallet
Summary: The over-activation of NDR2 kinase under hypoxia conditions promotes brain metastasis formation in NSCLC. NDR2 expression serves as a reliable indicator for predicting the risk of metastasis in NSCLC patients.
CELL DEATH & DISEASE
(2023)
Article
Biotechnology & Applied Microbiology
Jian-Rong Li, Mabel Tang, Yafang Li, Christopher Amos, Chao Cheng
Summary: In this study, a computational framework was proposed to infer mRNA stability of genes using RNA-seq data and identify stQTLs. The results revealed that stQTLs were enriched in the CDS and 3'UTR regions, while eQTLs were enriched in multiple regions. Additionally, stQTLs were more likely to overlap with RNA binding protein and microRNA binding sites. This study demonstrates that simultaneous identification of stQTLs and eQTLs provides more mechanistic insight into the association between genetic variants and gene expression levels.
Article
Computer Science, Interdisciplinary Applications
Tania Islam, Md Rezanur Rahman, Asaduzzaman Khan, Mohammad Ali Moni
Summary: This study aimed to identify putative functional causal gene biomarkers of stroke risk using a summary-based Mendelian randomisation (SMR) approach. Through integrative analysis, 45 candidate biomarker genes were identified that were pleiotropically or potentially causally associated with stroke risk. Among them, 10 genes exhibited differential expression in blood transcriptomics data from stroke and healthy individuals. This study provides insights into the influence of DNA methylation on the expression of genes linked to stroke risk.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Cell Biology
Fraser R. Millar, Adam Pennycuick, Morwenna Muir, Andrea Quintanilla, Priya Hari, Elisabeth Freyer, Philippe Gautier, Alison Meynert, Graeme Grimes, Carla Salomo Coll, Sofia Zdral, Stella Victorelli, Vitor H. Teixeira, John Connelly, Joao F. Passos, Marian A. Ros, William A. H. Wallace, Margaret C. Frame, Andrew H. Sims, Luke Boulter, Sam M. Janes, Simon Wilkinson, Juan Carlos Acosta
Summary: Targeting Toll-like receptor 2 (TLR2), a key regulator of oncogene-induced senescence, can impede early lung cancer progression by activating cell intrinsic cell cycle arrest pathways and the proinflammatory SASP. This discovery suggests TLR2 as a potential therapeutic target for lung cancer.
Article
Plant Sciences
Changyu Li, Yaoyao Li, Guangshu Song, Di Yang, Zhanchao Xia, Changhe Sun, Yuelei Zhao, Mei Hou, Mingyue Zhang, Zhi Qi, Baobao Wang, Haiyang Wang
Summary: In this study, we conducted phenotypic and gene expression analyses for 137 elite inbred lines of maize from different breeding eras in China. We identified four yield-related traits that significantly improved during modern maize breeding and identified several candidate genes associated with these traits. Our results demonstrate the effectiveness of our combined approaches for uncovering key candidate regulatory genes and functional variation underlying the improvement of important agronomic traits during modern maize breeding.
Article
Biochemical Research Methods
Jing Chen, Lindsey J. Leach, Zewei Luo
Summary: Mapping quantitative trait loci (QTL) in autotetraploid species is a timely and challenging task. Two papers by Wu and his colleagues proposed statistical methods for QTL mapping in these species, but have been criticized for fundamental conceptual errors from statistical and genetic perspectives.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Cell Biology
Sudipta Biswas, Kai Kang, Kwok Peng Ng, Tomas Radivoyevitch, Kurt Schalper, Hua Zhang, Daniel J. Lindner, Anish Thomas, David Macpherson, Brian Gastman, David S. Schrump, Kwok-Kin Wong, Vamsidhar Velcheti, Yogen Saunthararajah
Summary: Small cell lung cancers (SCLCs) rapidly develop resistance to chemotherapy and immune checkpoint inhibitor (ICI) treatments. This study found that DNMT1 plays a crucial role in the maturation arrest of SCLC cells. Inhibiting DNMT1/corepressors with clinical compounds extended the survival of mice with chemorefractory and ICI-refractory SCLC.
Article
Multidisciplinary Sciences
Kentaro Jingushi, Masaya Aoki, Kazuhiro Ueda, Takahiro Kogaki, Masaya Tanimoto, Yuya Monoe, Masayuki Ando, Takuya Matsumoto, Kentaro Minami, Yuko Ueda, Kaori Kitae, Hiroaki Hase, Toshiyuki Nagata, Aya Harada-Takeda, Masatatsu Yamamoto, Kohichi Kawahara, Kazuhiro Tabata, Tatsuhiko Furukawa, Masami Sato, Kazutake Tsujikawa
Summary: The study reveals that high expression of ALKBH4 is associated with the progression of non-small-cell lung cancer, and knockdown of ALKBH4 can inhibit cancer cell proliferation and affect cell cycle and E2F1 expression. Patients with high ALKBH4 expression have a poor prognosis, indicating that ALKBH4 plays a crucial tumour-promoting role in NSCLC.
SCIENTIFIC REPORTS
(2021)
Article
Neurosciences
Jianbo Zhang, Yajuan Fan, Jinting Zhou, Tengfei Ma, Keqiang Gao, Min Xu, Yifan Xiao, Yongsheng Zhu
Summary: The study revealed potential associations of genotypes and gene methylations of dopaminergic system genes with opioid use disorder. Several mQTLs were identified in both patients with heroin use disorder and healthy controls. Some mQTLs may be associated with traits of opioid use disorder.
PSYCHOPHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Balazs Gyorffy
Summary: This study established a comprehensive database of transcriptome-level data for lung cancer, which can be used to identify and rank the most promising biomarkers and therapeutic targets for different subtypes of lung cancer.
BRITISH JOURNAL OF PHARMACOLOGY
(2023)
Article
Genetics & Heredity
Yuzhuo Wang, Yue Ding, Su Liu, Cheng Wang, Erbao Zhang, Congcong Chen, Meng Zhu, Jing Zhang, Chen Zhu, Mengmeng Ji, Juncheng Dai, Guangfu Jin, Zhibin Hu, Hongbing Shen, Hongxia Ma
Summary: By performing a genome-wide study, we identified genetic variants that affect alternative splicing in lung tissues of individuals with Chinese ancestry. These variants, known as sQTLs, were found to be enriched in actively transcribed regions, genetic regulatory elements, and splicing-factor-binding sites. Moreover, they showed significant enrichment in potential risk loci of non-small-cell lung cancer (NSCLC). By integrating sQTLs into NSCLC GWAS datasets, we identified alternative splicing events in 19 genes that were significantly associated with NSCLC risk. Through functional annotation and experiments, we confirmed a specific sQTL variant that reduced the risk of lung adenocarcinoma by promoting exon skipping and downregulating the expression level of a long transcript. Overall, our study provides valuable resources and insights into the molecular mechanisms linking sQTL variants to NSCLC risk.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Shuanglin Gu, Li Lv, Xue Lin, Xingyu Li, Juncheng Dai, Jianqiong Zhang, Ren Kong, Wei Xie, Jian Li
Summary: This study identified important mutation sites in HBV and evaluated their impact using molecular dynamics simulation. The findings provide insights for immunotherapy.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Genetics & Heredity
Pei Ji, Jiang Chang, Xiaoyu Wei, Xueyao Song, Hua Yuan, Linnan Gong, Yuancheng Li, Dongsheng Ding, Erbao Zhang, Caiwang Yan, Meng Zhu, Xiaoping Miao, Chen Wu, Guangfu Jin, Zhibin Hu, Hongbing Shen, Hongxia Ma
Summary: This study identified three novel genetic variants associated with SCCHN risk. Functional analysis revealed that one variant could modulate TCF19 expression by regulating the binding affinity of SREBF1 to the promoter of TCF19. These findings suggest that TCF19 may serve as a susceptibility gene for SCCHN.
JOURNAL OF MEDICAL GENETICS
(2022)
Article
Clinical Neurology
Muhammed Lamin Sambou, Xiaoyu Zhao, Tongtong Hong, Muhammad Naveed, Alima Sambou, Fadoua El Hafa, TIl B. Basnet, Juncheng Dai
Summary: The study found that unhealthy sleep behaviors like insomnia, napping, daytime sleepiness, and difficulty getting up from bed are associated with an increased risk of shortened healthspan. Adherence to healthy sleep behavior is significant for extending healthspan.
SLEEP AND BREATHING
(2022)
Article
Oncology
Mengmeng Ji, Lingbin Du, Zhimin Ma, Junxing Xie, Yanqian Huang, Xiaoxia Wei, Xiangxiang Jiang, Jing Xu, Rong Yin, Yuzhuo Wang, Juncheng Dai, Guangfu Jin, Lin Xu, Chen Zhu, Zhibin Hu, Hongxia Ma, Meng Zhu, Hongbing Shen
Summary: Elevated CRP levels are associated with a 22% increased risk of lung cancer, with positive associations observed in small cell lung cancer, lung adenocarcinoma, and lung squamous cell carcinoma. However, no genetical association between circulating CRP levels and lung cancer risk was found. Adding CRP to the risk model of lung cancer can improve the model's performance in current smokers.
INTERNATIONAL JOURNAL OF CANCER
(2022)
Article
Biochemistry & Molecular Biology
Yafang Li, Xiangjun Xiao, Jianrong Li, Jinyoung Byun, Chao Cheng, Yohan Bosse, James McKay, Demetrios Albanes, Stephen Lam, Adonina Tardon, Chu Chen, Stig E. Bojesen, Maria T. Landi, Mattias Johansson, Angela Risch, Heike Bickeboeller, H-Erich Wichmann, David C. Christiani, Gad Rennert, Susanne Arnold, Gary Goodman, John K. Field, Michael P. A. Davies, Sanjay S. Shete, Loic Le Marchand, Olle Melander, Hans Brunnstrom, Geoffrey Liu, Rayjean J. Hung, Angeline S. Andrew, Lambertus A. Kiemeney, Hongbing Shen, Ryan Sun, Shan Zienolddiny, Kjell Grankvist, Mikael Johansson, Neil Caporaso, Dawn M. Teare, Yun-Chul Hong, Philip Lazarus, Matthew B. Schabath, Melinda C. Aldrich, Ann G. Schwartz, Ivan Gorlov, Kristen Purrington, Ping Yang, Yanhong Liu, Younghun Han, Joan E. Bailey-Wilson, Susan M. Pinney, Diptasri Mandal, James C. Willey, Colette Gaba, Paul Brennan, Christopher Amos
Summary: Sex differences in lung cancer risk have not been well studied despite the success in lung cancer association studies. By analyzing genotypes from a lung cancer cohort, we identified three low-frequency variants with differential risk effects in men and women. Further analysis suggested that one of the variants affects lung cancer risk through regulation of CXADR gene expression.
HUMAN MOLECULAR GENETICS
(2022)
Letter
Critical Care Medicine
Meng Zhu, Yanqian Huang, Hongxia Ma, Hongbing Shen
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE
(2022)
Article
Cardiac & Cardiovascular Systems
Xiangfeng Lu, Zhongying Liu, Qingmei Cui, Fangchao Liu, Jianxin Li, Xiaoge Niu, Chong Shen, Dongsheng Hu, Keyong Huang, Jichun Chen, Xiaolong Xing, Yingxin Zhao, Fanghong Lu, Xiaoqing Liu, Jie Cao, Shufeng Chen, Hongxia Ma, Ling Yu, Xianping Wu, Xigui Wu, Ying Li, Huan Zhang, Xingbo Mo, Liancheng Zhao, Jianfeng Huang, Laiyuan Wang, Wanqing Wen, Xiao-Ou Shu, Fumihiko Takeuchi, Woon-Puay Koh, E. Shyong Tai, Ching-Yu Cheng, Tien Yin Wong, Xuling Chang, Mark Yan-Yee Chan, Wei Gao, Hong Zheng, Kexin Chen, Jing Chen, Jiang He, Clara Sze-Man Tang, Karen Siu Ling Lam, Hung-Fat Tse, Chloe Yu Yan Cheung, Atsushi Takahashi, Michiaki Kubo, Norihiro Kato, Chikashi Terao, Yoichiro Kamatani, Pak Chung Sham, Chew-Kiat Heng, Zhibin Hu, Y. Eugene Chen, Tangchun Wu, Hongbing Shen, Cristen J. Willer, Dongfeng Gu
Summary: This study developed a polygenic risk score (PRS) for coronary artery disease (CAD) in Chinese populations and found that the PRS could refine risk stratification for CAD within clinical risk categories.
EUROPEAN HEART JOURNAL
(2022)
Article
Multidisciplinary Sciences
Yong-Qiao He, Tong-Min Wang, Mingfang Ji, Zhi-Ming Mai, Minzhong Tang, Ruozheng Wang, Yifeng Zhou, Yuming Zheng, Ruowen Xiao, Dawei Yang, Ziyi Wu, Changmi Deng, Jiangbo Zhang, Wenqiong Xue, Siqi Dong, Jiyun Zhan, Yonglin Cai, Fugui Li, Biaohua Wu, Ying Liao, Ting Zhou, Meiqi Zheng, Yijing Jia, Danhua Li, Lianjing Cao, Leilei Yuan, Wenli Zhang, Luting Luo, Xiating Tong, Yanxia Wu, Xizhao Li, Peifen Zhang, Xiaohui Zheng, Shaodan Zhang, Yezhu Hu, Weiling Qin, Bisen Deng, Xuejun Liang, Peiwen Fan, Yaning Feng, Jia Song, Shang-Hang Xie, Ellen T. Chang, Zhe Zhang, Guangwu Huang, Miao Xu, Lin Feng, Guangfu Jin, Jinxin Bei, Sumei Cao, Qing Liu, Zisis Kozlakidis, Haiqiang Mai, Ying Sun, Jun Ma, Zhibin Hu, Jianjun Liu, Maria Li Lung, Hans-Olov Adami, Hongbing Shen, Weimin Ye, Tai-Hing Lam, Yi-Xin Zeng, Wei-Hua Jia
Summary: The authors developed a polygenic risk score (PRS) for nasopharyngeal carcinoma using a large-scale genome-wide association study, which improved risk stratification and personalized screening.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Ting Tian, Jing Lu, Wei Zhao, Zhongming Wang, Hai Xu, Yuqing Ding, Wen Guo, Pei Qin, Wenfang Zhu, Ci Song, Hongxia Ma, Qun Zhang, Hongbing Shen
Summary: This study found that the systemic inflammation markers NLR, PLR, and SII were associated with poor lung cancer prognosis. Additionally, high levels of these markers were also found to be associated with an increased risk of positive nodules and lung cancer.
Article
Critical Care Medicine
Ni Li, Fengwei Tan, Wanqing Chen, Min Dai, Fei Wang, Sipeng Shen, Wei Tang, Jiang Li, Yiwen Yu, Wei Cao, Yongjie Xu, Chao Qin, Liang Zhao, Meng Zhu, Lanwei Guo, Zheng Wu, Zhuoyu Yang, Yadi Zheng, Hongda Chen, Yunyong Liu, Donghua Wei, Dong Dong, Ji Cao, Shaokai Zhang, Shipeng Yan, Ning Wang, Lingbin Du, Hongbing Shen, Ning Wu, Jie He
Summary: This study evaluated the effectiveness of one-off low-dose CT (LDCT) screening for the early detection of lung cancer in China. The results showed that one-off LDCT screening significantly reduced lung cancer mortality and all-cause mortality, indicating its potential in countries with limited medical resources.
LANCET RESPIRATORY MEDICINE
(2022)
Article
Oncology
Siwei Wang, Ming Li, Jingyuan Zhang, Peng Xing, Min Wu, Fancheng Meng, Feng Jiang, Jie Wang, Hua Bao, Jianfeng Huang, Binhui Ren, Mingfeng Yu, Ninglei Qiu, Houhuai Li, Fangliang Yuan, Zhi Zhang, Hui Jia, Xinxin Lu, Shuai Zhang, Xiaojun Wang, Youtao Xu, Wenjia Xia, Tongyan Liu, Weizhang Xu, Xinyu Xu, Mengting Sun, Xue Wu, Yang Shao, Qianghu Wang, Juncheng Dai, Mantang Qiu, Jinke Wang, Qin Zhang, Lin Xu, Hongbing Shen, Rong Yin
Summary: This study demonstrates that circulating tumor DNA can be used as a marker for monitoring minimal residual disease in early-to-mid-stage non-small cell lung cancer patients, and can predict the recurrence of high-risk patients.
JOURNAL OF HEMATOLOGY & ONCOLOGY
(2022)
Article
Oncology
Na Qin, Cheng Wang, Congcong Chen, Liu Yang, Su Liu, Jun Xiang, Yuan Xie, Shuang Liang, Jun Zhou, Xianfeng Xu, Xiaoyu Zhao, Meng Zhu, Guangfu Jin, Hongxia Ma, Juncheng Dai, Zhibin Hu, Hongbing Shen
Summary: Detection of mCAs can serve as a new indicator for lung cancer risk, and it may be combined with PRS for personalized risk stratification of lung cancer.
Article
Oncology
Xu Zhang, Na Qin, Jingyi Fan, Chang Zhang, Qi Sun, Yayun Gu, Meng Zhu, Erbao Zhang, Juncheng Dai, Guangfu Jin, Hongxia Ma, Zhibin Hu, Hongbing Shen
Summary: This study identified the causal variant rs3769823 in chromosome 2q33.1 and explored its biological functions in non-small cell lung cancer (NSCLC). The variant was found to inhibit the proliferation and metastasis of lung cancer cells and was involved in the apoptosis pathway.
CANCER BIOLOGY & MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Cheng Wang, Yayun Gu, Jun Zhou, Jie Zang, Xiufeng Ling, Hong Li, Lingmin Hu, Bei Xu, Bo Zhang, Na Qin, Hong Lv, Weiwei Duan, Yue Jiang, Yuanlin He, Tao Jiang, Congcong Chen, Xiumei Han, Kun Zhou, Bo Xu, Xiaoyu Liu, Shiyao Tao, Yangqian Jiang, Jiangbo Du, Juncheng Dai, Feiyang Diao, Chuncheng Lu, Xuejiang Guo, Ran Huo, Jiayin Liu, Yuan Lin, Yankai Xia, Guangfu Jin, Hongxia Ma, Hongbing Shen, Zhibin Hu
Summary: This study investigates the association between assisted reproductive technology (ART) and initial leukocyte telomere length (LTL) using whole-genome sequencing (WGS) data. The study finds that one-year-old children conceived by ART have shorter LTLs, especially in those conceived through blastocyst-stage embryo transfer. Mouse experiments also confirm that blastocyst-stage embryo transfer results in shorter telomere lengths.
Review
Public, Environmental & Occupational Health
Muhammed Lamin Sambou, Juncheng Dai, Xiaoyu Zhao, Tongtong Hong, Til Bahadur Basnet, Gifty Marley, Alima Sambou, El Hafa Fadoua, Muhammad Naveed
Summary: The study identified 8 significant determinants of VCT service uptake among adults in sub-Saharan Africa (SSA), including lower physical access, older age, higher education level, high knowledge of HIV and VCT awareness, unprotected sexual practices, discussion on HIV among partners and others, other STIs, and divorced/separated status. The findings suggest that HIV interventions and policy initiatives should be tailored to these determinants in order to increase VCT service uptake in SSA.
PUBLIC HEALTH REVIEWS
(2022)
