Article
Cell Biology
Mariana Andrawus, Lital Sharvit, Noga Touitou, Batia Lerrer, Haim Y. Cohen, Gil Atzmon
Summary: Copy number variations (CNV) play a significant role in genome variability and have been associated with aging and pregnancy physiology. By studying CNVs in pregnant mice, researchers have found that most of the selected CNVs showed an opposite trend during pregnancy and post-partum. Additionally, significant differential expression was observed in the nearby genes of the candidate CNVs. This study highlights the importance of using pregnancy as a model for aging and reveals the mechanisms and similarities between pregnancy and aging.
Article
Multidisciplinary Sciences
Wouter Steyaert, Lonneke Haer-Wigman, Rolph Pfundt, Debby Hellebrekers, Marloes Steehouwer, Juliet Hampstead, Elke de Boer, Alexander Stegmann, Helger Yntema, Erik-Jan Kamsteeg, Han Brunner, Alexander Hoischen, Christian Gilissen
Summary: This paper presents a method called "Chameleolyser" that accurately identifies variants in duplicated genomic regions. Application of this method to a large cohort of exome samples led to the identification of a significant number of rare variants, including those that resulted in direct molecular diagnoses for previously undiagnosed patients.
NATURE COMMUNICATIONS
(2023)
Article
Oncology
Vincent Vuaroqueaux, Alexandra Musch, Dennis Kobelt, Thomas Risch, Pia Herrmann, Susen Burock, Anne-Lise Peille, Marie-Laure Yaspo, Heinz-Herbert Fiebig, Ulrike Stein
Summary: This study investigates the contribution of chromosomal instability and somatic copy number alterations (SCNA) to the dysregulation of MACC1 in colorectal cancer (CRC). The findings suggest that elevated MACC1 expression is largely driven by chromosomal instability (CIN), SCNA gains, and molecular subtypes, and it has prognostic and predictive impacts on metastasis and survival. These insights could potentially serve as a basis for personalized treatment decisions.
Article
Cell Biology
Aditi Hazra, Andrea O'Hara, Kornelia Polyak, Faina Nakhlis, Beth T. Harrison, Antonio Giordano, Beth Overmoyer, Filipa Lynce
Summary: The goal of this study was to identify biomarkers associated with de novo inflammatory breast cancer (IBC). Through examination of breast biopsies, significant copy number variations (CNVs) on chromosome 7p11.2 and 21 were identified. These findings provide insights into the biology of IBC and may lead to the optimization of treatment strategies.
Article
Biochemistry & Molecular Biology
Alejandro Martin-Trujillo, Paras Garg, Nihir Patel, Bharati Jadhav, Andrew J. Sharp
Summary: Short tandem repeats (STRs) contribute significantly to genetic diversity in humans, including disease-causing variation. In this study, the researchers investigated the impact of STR variation on DNA methylation levels and the risk of common human traits. They analyzed two independent data sets and identified a large number of STRs associated with DNA methylation levels. By fine-mapping, they identified the likely causal variants and linked them to previously reported genetic association study signals. Furthermore, they observed that some of these variants also modulate gene expression levels. Overall, this study highlights the importance of incorporating STRs in genetic association analysis and understanding genome regulation.
Article
Cell Biology
Wei Chen, Jian Zhang, Huafeng Fu, Xun Hou, Qiao Su, Yulong He, Dongjie Yang
Summary: Gastric cancer is the third leading cause of cancer death globally. This study revealed that KLF5 amplification and over-expression in gastric cancer may support cell proliferation, suggesting an oncogene-like role for KLF5 in gastric cancer. The findings also showed a correlation between higher KLF5 expression and more locally invasive gastric cancer with higher T stage.
Article
Agronomy
Jinlong Li, Xin Xin, Fangyao Sun, Zhenzhen Zhu, Xiangru Xu, Jiatian Yang, Xiaoming Xie, Jiazheng Yu, Xiaobo Wang, Sen Li, Shilin Tian, Baoyun Li, Chaojie Xie, Jun Ma
Summary: This study identified a dominant locus on chromosome 5AL associated with awn length in wheat. The B1 gene, which inhibits awn growth, was found to have increased copy number in awnless wheat, leading to enhanced gene expression and inhibition of awn length.
Article
Biochemical Research Methods
Xia Wang, Dechun Xing, Zheng Liu, Yujing Zhang, Bo Cheng, Suozhu Sun, Qingtao Wang, Lianhua Dong
Summary: Accurate measurement of HER2 copy number variation is crucial for guiding tumor target therapy in breast cancer. Digital PCR (dPCR) is a sensitive and quantitative method that can detect HER2 CNV. The study established and validated three HER2 exon-specific dPCR assays along with three new reference gene assays, which showed high concordance rates with the diagnostic results of clinical FFPE samples by fluorescence in situ hybridization (FISH). The proposed dPCR method accurately provides the absolute copy number of HER2 and reference genes, improving molecular typing and diagnosis of breast cancer.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Ming-Hung Shen, Chi-Jung Huang, Thien-Fiew Ho, Chih-Yi Liu, Ying-Yih Shih, Ching-Shui Huang, Chi-Cheng Huang
Summary: This study aims to enhance the prognostication of colorectal cancer by integrating SNP and GE microarrays and identifying genes with concurrent gains and losses to develop a prognostic signature. The results show that the colorectal cancer concurrent gene signature has the potential to predict recurrence, metastasis, or mortality among 1746 patients.
Article
Medicine, General & Internal
Weinan Zheng, Fuyuan Jin, Fang Wang, Luyue Wang, Shaowei Fu, Zemin Pan, Haichen Long
Summary: This study aimed to explore and analyze the expression of eukaryotic translation elongation factor 1 alpha 2 (eEF1A2) gene in cervical cancer tissues and its relationship with patient survival, gene mutations, and changes in copy number. Gene expression profile interactive analysis and cBioPortal were used to analyze eEF1A2 expression and gene changes in cervical cancer tissues. The eEF1A2 copy number was determined using real-time fluorescence quantitative polymerase chain reaction. The Human Protein Atlas was utilized to analyze the relationship between eEF1A2 protein expression and clinical stage, pathological grade, and patient survival.
Article
Multidisciplinary Sciences
Matthew H. Larson, Wenying Pan, Hyunsung John Kim, Ruth E. Mauntz, Sarah M. Stuart, Monica Pimentel, Yiqi Zhou, Per Knudsgaard, Vasiliki Demas, Alexander M. Aravanis, Arash Jamshidi
Summary: Cell-free RNA is a promising analyte for cancer detection, with the potential to identify tissue- and subtype-specific biomarkers in breast and lung cancer patients. The presence of dark channel biomarker (DCB) genes in cfRNA from individuals with cancer suggests they could enhance cancer detection in patients with low levels of circulating tumor DNA.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Luca Denti, Parsoa Khorsand, Paola Bonizzoni, Fereydoun Hormozdiari, Rayan Chikhi
Summary: Structural variants (SVs) contribute to sequence variability in genomes and are significant in human genomics and precision medicine. However, due to the complexities of the human genome, SV discovery in individuals has been challenging. The introduction of low-error long-read sequencing technologies, such as PacBio HiFi, may provide a solution to these challenges.
Article
Plant Sciences
Robin Nicole Bosman, Jessica Anne-Marie Vervalle, Danielle Lisa November, Phyllis Burger, Justin Graham Lashbrooke
Summary: Volatile organic compounds, such as terpenes, play a vital role in influencing the quality parameters of grapevine through their contribution to the flavor and aroma profile of grapes. The biosynthesis of these compounds is complex and controlled by multiple genes, many of which are unidentified. By analyzing volatile metabolic data from a grapevine mapping population, researchers identified several significant genomic regions associated with terpene modulation in grape berries. These findings provide insights into the molecular mechanisms of terpene accumulation and offer potential applications in developing grape cultivars with desired terpene profiles.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Oncology
Fumi Murakami, Yumi Tsuboi, Yuka Takahashi, Yoshiya Horimoto, Kaoru Mogushi, Takeshi Ito, Mitsuru Emi, Daisuke Matsubara, Tatsuhiro Shibata, Mitsue Saito, Yoshinori Murakami
Summary: Copy number variation (CNV) is a common polymorphism in the human genome, with somatic alterations at CNV sites detected in 39.9% of the CNV probes examined in invasive breast cancers. The most frequently altered regions included gains of 1q21-22, 8q21-24, 1q44, 3q11, and losses of 16q22-24. Gene ontology analysis revealed correlations between CNAs and transcription/RNA metabolism in relation to HER2 positivity and menopausal status in breast cancer patients.
Article
Agriculture, Dairy & Animal Science
Yong-Zhen Huang, Qiao Ting Shi, Shu-Yue Shi, Peng Yang, Zi-Jing Zhang, Shi-Jie Lyu, Fu-Ying Chen, Jia-Wei Xu, Xian Liu, Zhiming Li, Baorui Ru, Cuicui Cai, Jianliang Xie, ChuZhao Lei, Hong Chen, Zhaoxue Xu, Eryao Wang
Summary: This study examined the copy number variation (CNV) of the SERPINA3-1 gene in Chinese cattle and its association with growth traits. The Duplication type of the SERPINA3-1 gene performed better on growth traits and showed significant correlation with multiple growth traits. Additionally, the gene exhibited different expression conditions in different tissues, with low expression in muscle. These findings suggest that the SERPINA3-1 gene could serve as a molecular marker for beef cattle growth and development.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Oncology
Zhengyu Fang, Shanshan Zhang, Yufan Wang, Shiyue Shen, Feng Wang, Yinghua Hao, Yuxia Li, Bingyue Zhang, You Zhou, Hongyu Yang
Article
Oncology
Xiao-su Zhao, Yi-nuo Wang, Meng-Lv, Yuan-Kong, Hong-xue Luo, Xiao-yang Ye, Qi Wu, Tong-feng Zhao, Yue-huan Hu, Hong-yu Zhang, Ming-rui-Huo, Jun-Wan, Xiao-jun Huang
Article
Geriatrics & Gerontology
Chunying Fan, Qi Wu, Xiaoyang Ye, Hongxue Luo, Dongdong Yan, Yi Xiong, Haili Zhu, Yarui Diao, Wei Zhang, Jun Wan
FRONTIERS IN AGING NEUROSCIENCE
(2016)
Article
Oncology
Ran Cheng, Ya-Jing Liu, Jun-Wei Cui, Man Yang, Xiao-Ling Liu, Peng Li, Zhan Wang, Li-Zhang Zhu, Si-Yi Lu, Li Zou, Xiao-Qin Wu, Yu-Xia Li, You Zhou, Zheng-Yu Fang, Wei Wei
Article
Genetics & Heredity
Zhengyu Fang, Dongyi He, Bo Yu, Feng Liu, Jianping Zuo, Yuxia Li, Qi Lin, Xiaodong Zhou, Qingwen Wang
Article
Oncology
Yuxia Li, Jie Zhang, Yajing Liu, Bingyue Zhang, Fubo Zhong, Shubin Wang, Zhengyu Fang
Article
Gastroenterology & Hepatology
Zhen Liu, Chuanhai Guo, Yujie He, Yun Chen, Ping Ji, Zhengyu Fang, Fenglei Li, Yuefei Tang, Xiujian Chen, Ping Xiao, Chengwen Wang, Weihua Yin, Hai Guo, Mengfei Liu, Yaqi Pan, Fangfang Liu, Ying Liu, Zhonghu He, Yang Ke
GASTROINTESTINAL ENDOSCOPY
(2020)
Article
Immunology
Zhengyu Fang, Jiyang Lv, Jing Wang, Qingxia Qin, Juan He, Meiying Wang, Gengmin Zhou, Guoyu Liu, Fubo Zhong, Yadan Zheng, Hui-Yao Lan, Qingwen Wang
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Xin-le Han, Jun Du, Ya-dan Zheng, Jia-jing Dai, Su-wen Lin, Bing-yue Zhang, Fu-bo Zhong, Zhe-guang Lin, Shu-qi Jiang, Wei Wei, Zheng-yu Fang
Summary: Triple-negative breast cancer (TNBC) is a deadly subtype with limited treatment options and often develops resistance to chemotherapy. The study identified that belinostat treatment induced the expression of CXCL1 in TNBC cell lines, possibly as a result of cellular stress clone evolution. These findings shed light on clone evolution during HDACi treatment and suggest the implementation of mutation-targeted treatments throughout the treatment cycle.
BIOMED RESEARCH INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Zhengyu Fang, Yiping Hu, Jiajing Dai, Lianhua He, Juan He, Bihua Xu, Xinle Han, Fubo Zhong, Huiyao Lan, Qingwen Wang
Summary: The combination treatment with CS12192 and MTX is shown to have a better therapeutic effect on collagen-induced arthritis (CIA) in rats, with a stronger suppressive effect on T cells and macrophage-mediated joint inflammation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Xinle Han, Jun Du, Dandan Shi, Lingjie Li, Dandan Li, Kun Zhang, Suwen Lin, Jingzhong Zhu, Zoufang Huang, You Zhou, Zhengyu Fang
Summary: This study used a reporter gene system to confirm the differences in biological activity between wild-type and mutant P53, and tentatively applied it to related mechanism research and compound activity evaluation. The results provide a reliable reference and calculation model for relevant basic research and drug development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Endocrinology & Metabolism
Suwen Lin, Shengjian Huang, Zhou Deng, Yu Zhang, Lin Huang, Yanyi Wu, Shuyan Lv, Zhiyi Wang, Ning Huang, Lan Wang, Ziqi Chen, Guangyin Yu, Weihua Yin, You Zhou, Zhengyu Fang
Summary: In this study, a novel THR-beta agonist called CS271011 was discovered and its safety and efficiency compared to MGL-3196 were assessed. Results showed that CS271011 exhibited higher THR-beta activation in vitro compared to MGL-3196 and demonstrated favorable pharmacokinetic properties and liver enrichment in a diet-induced obesity mice model. Furthermore, CS271011 improved dyslipidemia and liver steatosis. Overall, CS271011 is a potent and liver-targeted THR-beta agonist for treating lipid metabolism disorders.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Yajing Liu, Yinghua Hao, Yuxia Li, Yadan Zheng, Jiajing Dai, Fubo Zhong, Wei Wei, Zhengyu Fang
SCIENTIFIC REPORTS
(2020)
Article
Oncology
You Zhou, Yinghua Hao, Yuxia Li, Ruizhen Li, Ruifang Wu, Shubin Wang, Zhengyu Fang
Article
Medicine, General & Internal
Hongrui Tian, Wei Yang, Yanjun Hu, Zhen Liu, Lei Chen, Liang Lei, Fan Zhang, Fen Cai, Huawen Xu, Mengfei Liu, Chuanhai Guo, Yun Chen, Ping Xiao, Junhui Chen, Ping Ji, Zhengyu Fang, Fangfang Liu, Ying Liu, Yaqi Pan, Isabel dos-Santos-Silva, Zhonghu He, Yang Ke
