Article
Multidisciplinary Sciences
Heyang Cui, Yong Zhou, Fang Wang, Caixia Cheng, Weimin Zhang, Ruifang Sun, Ling Zhang, Yanghui Bi, Min Guo, Yan Zhou, Xinhui Wang, Jiaxin Ren, Ruibing Bai, Ning Ding, Chen Cheng, Longlong Wang, Xuehan Zhuang, Mingwei Gao, Yongjia Weng, Yueguang Wu, Huijuan Liu, Shuaicheng Li, Shubin Wang, Xiaolong Cheng, Yongping Cui, Zhihua Liu, Qimin Zhan
Summary: This study analyzed 528 whole genomes to investigate the landscape and molecular mechanisms of structural variations in esophageal squamous cell carcinoma (ESCC). The findings revealed different types of structural variations associated with biological characteristics, identified a rearrangement type correlated with poor outcomes, and discovered specific rearrangement signatures linked to chromatin accessibility and early replication region. The study further confirmed the oncogenic effect of certain genes and their interaction with enhancers. Additionally, extrachromosomal circular DNAs were found in ESCC, showing strong selective advantages to driver genes.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Liang Chen, Na Zhao, Jiabao Cao, Xiaolin Liu, Jiayue Xu, Yue Ma, Ying Yu, Xuan Zhang, Wenhui Zhang, Xiangyu Guan, Xiaotong Yu, Zhipeng Liu, Yanqun Fan, Yang Wang, Fan Liang, Depeng Wang, Linhua Zhao, Moshi Song, Jun Wang
Summary: In this study, the researchers used a combination of short and long sequencing reads to analyze the genetic variations in human gut microbiomes. They found that these structural variations are highly distinct between individuals and stable within an individual, and they have significant impacts on the functional differences and correlations with metabolites.
NATURE COMMUNICATIONS
(2022)
Review
Biochemical Research Methods
Dohun Yi, Jin-Wu Nam, Hyobin Jeong
Summary: Structural variants (SVs) are diverse genomic rearrangements that accumulate in the genome during cell development and aging, potentially impacting cancer development. Detecting somatic SVs is challenging but crucial for understanding their functional implications. This review summarizes recent advances in whole-genome sequencing (WGS)-based approaches for somatic SV detection, including computational algorithms for bulk WGS data and cutting-edge single-cell techniques. The advantages and limitations of bulk and single-cell approaches are discussed, along with their potential for linking somatic SVs to functional readouts.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
Bin Jia, Jin Jin, Mingzhe Han, Bingzhi Li, Yingjin Yuan
Summary: In this study, researchers developed a yeast strain prone to SVs using the SCRaMbLE technology and demonstrated the potential of SVs in industries by using astaxanthin biosynthesis as a readout. The complex SVs induced the formation of new chromosomes and increased the astaxanthin yield. The study also identified genetic targets that further enhanced astaxanthin production, providing insights into the mechanism of complex SVs and their ability to alter phenotypes.
SCIENCE CHINA-LIFE SCIENCES
(2022)
Article
Plant Sciences
Shenjian Xu, Ke Teng, Hui Zhang, Juying Wu, Liusheng Duan, Hongyu Zhang, Haifeng Wen, Wenjun Teng, Yuesen Yue, Xifeng Fan
Summary: The mitochondrial genome of Carex breviculmis was sequenced and assembled, revealing its genomic features and possible structures. The major conformation of the mitochondrial genome is a circular molecule with 33 protein-coding genes, 15 tRNA genes, and three rRNA genes. The reduction in RNA editing sites could be attributed to point mutations and retroprocessing events.
Article
Plant Sciences
Ben N. Mansfeld, Adam Boyher, Jeffrey C. Berry, Mark Wilson, Shujun Ou, Seth Polydore, Todd P. Michael, Noah Fahlgren, Rebecca S. Bart
Summary: This study utilized a combination of high-throughput sequencing technologies to resolve the highly heterozygous genome of cassava, revealing a large number of haplotype-specific structural variations that impact important agronomic traits, as well as exploring gene hemizygosity and allele-specific gene expression.
Article
Biotechnology & Applied Microbiology
Maulik Upadhyay, Martijn F. L. Derks, Goran Andersson, Ivica Medugorac, Martien A. M. Groenen, Richard P. M. A. Crooijmans
Summary: This study identified 16,738 SVs in cattle using 72 whole genome sequences representing taurine and zebu cattle, with 1575 of them being novel. The distribution of SVs in cattle is influenced by factors such as demographic differences and gene flow, as demonstrated by the presence of unique SVs in different cattle breeds. This research provides valuable insights into the genetic diversity and evolutionary history of cattle populations.
Article
Multidisciplinary Sciences
Yu Chen, Amy Y. Wang, Courtney A. Barkley, Yixin Zhang, Xinyang Zhao, Min Gao, Mick D. Edmonds, Zechen Chong
Summary: The authors developed DeBreak, an algorithm for comprehensive and accurate structural variant (SV) detection in long-read sequencing data, which outperforms existing SV callers.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Rubi Campos Gudino, Ally C. Farrell, Nicole M. Neudorf, Kirk J. McManus
Summary: Genetic and epigenetic alterations in SCF complex member genes occur frequently in many types of cancer, which adversely affect the normal targeting and degradation of protein substrates, potentially contributing to the development and progression of a wide range of cancer types.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Henry Cm Leung, Huijing Yu, Yifan Zhang, Wing Sze Leung, Ivan Fm Lo, Ho Ming Luk, Wai-Chun Law, Ka Kui Ma, Chak Lim Wong, Yat Sing Wong, Ruibang Luo, Tak-Wah Lam
Summary: In this paper, the researchers demonstrate that low-depth whole-genome sequencing using a single Oxford Nanopore MinION flow cell is sufficient for sensitive detection of structural variations (SV), particularly pathogenic SV for clinical diagnosis. They developed a new SV calling software called SENSV, which showed high sensitivity and breakpoint precision within 100 bp. Evaluation using real and simulated data showed that SENSV outperformed existing software in detecting pathogenic SV, achieving detection rates of over 90%.
SCIENTIFIC REPORTS
(2022)
Review
Cell Biology
Laura L. Thompson, Kailee A. Rutherford, Chloe C. Lepage, Kirk J. McManus
Summary: SKP1 plays a central role in regulating essential cellular processes, and its aberrant expression and function may lead to genome instability and cancer pathogenesis.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Engineering, Biomedical
Nuphar Bianco-Stein, Iryna Polishchuk, Arad Lang, Galit Atiya, Julie Villanova, Paul Zaslansky, Alexander Katsman, Boaz Pokroy
Summary: The calcareous alga Jania sp. exhibits a highly intricate structure with helical inner pores, and each cell wall nanocrystal comprises Mg-rich calcite nanoparticles demonstrating various crystallographic orientations. This unique structure assists in preventing fracture and enhancing the alga's fracture toughness, and the presence of Mg-rich nanoparticles is also observed in another species of coralline red algae, pointing to the generality of this phenomenon.
ACTA BIOMATERIALIA
(2021)
Article
Agronomy
Georgiy A. Lihodeevskiy, Elena P. Shanina
Summary: Research conducted whole-genome sequencing on three backcrossed potato varieties, identifying over 24,000 structural variants, with deletions being the most common type. The majority of these variants were found in non-coding regions, but a quarter of the genes exhibited chromosomal mutations.
Article
Biotechnology & Applied Microbiology
Zhaowu Zhang, Rob van Treuren, Ting Yang, Yulan Hu, Wenhui Zhou, Huan Liu, Tong Wei
Summary: This study characterized a large number of SVs in the lettuce genome, uncovering potential causal SVs associated with agronomic traits like seed coat color and leaf anthocyanin content. The findings provide a valuable genomic resource for future lettuce breeding.
Article
Genetics & Heredity
Luming Xu, Xingyue Wang, Xiaohuan J. Lu, Fan Liang, Zhibo J. Liu, Hongyan Zhang, Xiaoqiong J. Li, ShaoBo Tian, Lin J. Wang, Zheng Wang
Summary: This study used long-read sequencing to accurately and reliably detect 494 somatic structural variants (SVs) in colorectal cancer (CRC) samples, significantly more than previous short-read sequencing studies. Large scale inversions (>10 kbp) that are often missed by short-read sequencing and affect key tumor suppressor genes (APC and CFTR) were identified. A novel gene fusion RNF38-RAD51B was also discovered, which functionally enhances migration, invasion, and metastasis capabilities of CRC cells. This work provides a comprehensive SV landscape of CRC and offers a genetic basis for personalized medicine.
Article
Genetics & Heredity
Chunyu Liu, Ying Shen, Shuyan Tang, Jiaxiong Wang, Yiling Zhou, Shixiong Tian, Huan Wu, Jiangshan Cong, Xiaojin He, Li Jin, Yunxia Cao, Yihong Yang, Feng Zhang
Summary: In this study, we investigated a group of Han Chinese men with asthenoteratozoospermia, a common type of male infertility. Through whole-exome sequencing, we identified AKAP3 as a novel gene associated with multiple morphological abnormalities of the sperm flagella (MMAF). Two different deleterious variants of AKAP3 were found in unrelated MMAF-affected men, and subsequent experiments confirmed the impact of these variants on AKAP3 expression in spermatozoa. Interestingly, the clinical outcomes after intracytoplasmic sperm injection (ICSI) were different between these two cases, suggesting that AKAP3 dosage may influence the prognosis of ICSI treatment.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Clinical Neurology
Yingzhe Wang, Yanfeng Jiang, Wanqing Wu, Kelin Xu, Qianhua Zhao, Ziyi Tan, Xiaoniu Liang, Min Fan, Zhenxu Xiao, Li Zheng, Saineng Ding, Qiang Dong, Zhen Hong, Li Jin, Xingdong Chen, Ding Ding, Mei Cui
Summary: The study found that older adults with higher educational attainment showed slower cognitive decline. Education is especially important for maintaining cognitive health in disadvantaged living environments.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemistry & Molecular Biology
Yimin Wang, Yunchao Ling, Jiao Gong, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, Shaohua Fan, Guoqing Zhang, Shuhua Xu
Summary: PGG.SV is a practical platform that provides large-scale structural variation data, including 1030 long-read sequencing genomes representing 177 global populations. The database offers high-quality SVs with precise genomic locations, estimates of SV prevalence in different geographical populations, informative annotations of related genes, and an analysis platform and visualization tools for association studies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Rheumatology
Fangyi Wu, Xuling Han, Jing Liu, Zhenghua Zhang, Kexiang Yan, Beilan Wang, Lin Yang, Hejian Zou, Chengde Yang, Wei Huang, Li Jin, Jiucun Wang, Feng Qian, Zhenmin Niu
Summary: This study explores the association between variants in non MHC proteasome gene and AS, and finds that the rs12717 SNP in PSMB1 gene is significantly associated with AS. The study also discovers that PSMB1 regulates the RANK/RANKL signaling pathway and affects bone formation by inhibiting osteoclast differentiation.
Letter
Genetics & Heredity
Chengqiu Tao, Tingting Zhu, Shuyan Tang, Jiaqi Lu, Xiaoqi Lin, Xiuqin Li, Xiaomei Liu, Yicun Pang, Huan Zhao, Jie Liang, Feng Zhang, Xin Lu, Ling Zhang
Article
Biochemistry & Molecular Biology
Mingrong Lv, Dongdong Tang, Hui Yu, Hao Geng, Yiling Zhou, Zhongmei Shao, Kuokuo Li, Yang Gao, Senchao Guo, Chuan Xu, Qing Tan, Chunyu Liu, Rui Guo, Huan Wu, Zongliu Duan, Jingjing Zhang, Guanxiong Wang, Rong Hua, Feifei Fu, Kai Wang, Yuping Xu, Ping Zhou, Zhaolian Wei, Feng Zhang, Yunxia Cao, Xiaojin He
Summary: Compound heterozygous variants of FSIP2 were identified in three unrelated individuals with asthenoteratozoospermia, causing severe defects in fibrous sheath and axoneme. Additionally, other morphological abnormalities and successful pregnancies through ICSI were observed.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Letter
Biochemistry & Molecular Biology
Shixiong Tian, Ziqi Wang, Liting Liu, Yiling Zhou, Yue Lv, Dongdong Tang, Jiaxiong Wang, Jing Jiang, Huan Wu, Shuyan Tang, Guanxiong Wang, Hao Geng, Fangbiao Tao, Hongbin Liu, Xiaojin He, Feng Zhang, Jinsong Li, Li Jin, Tao Huang, Chunyu Liu, Yunxia Cao
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Genetics & Heredity
Shixiong Tian, Chaofeng Tu, Xiaojin He, Lanlan Meng, Jiaxiong Wang, Shuyan Tang, Yang Gao, Chunyu Liu, Huan Wu, Yiling Zhou, Mingrong Lv, Ge Lin, Li Jin, Yunxia Cao, Dongdong Tang, Feng Zhang, Yue-Qiu Tan
Summary: This study identified biallelic deleterious mutations of CFAP54 in three unrelated men with severe MMAF or NOA. These mutations were associated with abnormal sperm morphology, reduced sperm concentration and motility. Immunofluorescence assays showed reduced staining of four flagellar assembly-associated proteins in the spermatozoa of CFAP54-deficient men.
JOURNAL OF MEDICAL GENETICS
(2023)
Article
Oncology
Huangbo Yuan, Tao Qing, Sibo Zhu, Xiaorong Yang, Weicheng Wu, Kelin Xu, Hui Chen, Yanfeng Jiang, Chengkai Zhu, Ziyu Yuan, Tiejun Zhang, Li Jin, Chen Suo, Ming Lu, Xingdong Chen, Weimin Ye
Summary: Defects in DNA damage repair pathways can lead to genomic instability and oncogenesis. DDR alterations in esophageal squamous cell carcinoma (ESCC) affect mutational processes and tumor immune microenvironment.
Article
Genetics & Heredity
Chunyu Liu, Wei Si, Chaofeng Tu, Shixiong Tian, Xiaojin He, Shengnan Wang, Xiaoyu Yang, Chencheng Yao, Cong Li, Zine-Eddine Kherraf, Maosen Ye, Zixue Zhou, Yuhua Ma, Yang Gao, Yu Li, Qiwei Liu, Shuyan Tang, Jiaxiong Wang, Hexige Saiyin, Liangyu Zhao, Liqun Yang, Lanlan Meng, Bingbing Chen, Dongdong Tang, Yiling Zhou, Huan Wu, Mingrong Lv, Chen Tan, Ge Lin, Qingpeng Kong, Hong Shi, Zhixi Su, Zheng Li, Yong-Gang Yao, Li Jin, Ping Zheng, Pierre F. Ray, Yue-Qiu Tan, Yunxia Cao, Feng Zhang
Summary: Primate-specific genes (PSGs) expressed in the brain and testis are consistent with brain evolution in primates. The identification of deleterious variants of the X-linked SSX1 gene in men with asthenoteratozoospermia highlights its crucial role in spermatogenesis. Knocking down Ssx1 expression in non-human primate and tree shrew models resulted in reduced sperm motility and abnormal sperm morphology, reflecting the phenotype observed in humans. This study has important implications for genetic counseling and clinical diagnosis, and provides insights into the functions of testis-enriched PSGs in spermatogenesis.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Reproductive Biology
Wei Luo, Hanni Ke, Shuyan Tang, Xue Jiao, Zhuqing Li, Shidou Zhao, Feng Zhang, Ting Guo, Yingying Qin
Summary: This study screened 500 Chinese Han patients with premature ovarian insufficiency using a next generation sequencing panel and identified 61 pathogenic or likely pathogenic variants. 58 of these variants were first identified in patients with POI. Further analysis revealed that specific variants in certain genes may result in isolated POI, while multiple gene defects could worsen the severity of POI.
JOURNAL OF OVARIAN RESEARCH
(2023)
Article
Urology & Nephrology
Sarah Kimmins, Richard A. Anderson, Christopher L. R. Barratt, Hermann M. Behre, Sarah R. Catford, Christopher J. De Jonge, Geraldine Delbes, Michael L. Eisenberg, Nicolas Garrido, Brendan J. Houston, Niels Jorgensen, Csilla Krausz, Ariane Lismer, Robert I. Mclachlan, Suks Minhas, Tim Moss, Allan Pacey, Laerke Priskorn, Stefan Schlatt, Jacquetta Trasler, Leonardo Trasande, Frank Tuettelmann, Monica Hebe Vazquez-Levin, Joris A. Veltman, Feng Zhang, Moira K. O'Bryan
Summary: Currently, there is a lack of understanding and awareness about the causes of male infertility and the importance of male reproductive health. This leads to standardized treatment strategies using medically assisted reproduction techniques, which overlook the potential co-morbidities and shift the burden to women. To improve male reproductive health, it is essential to establish centers for data and sample collection and study the effects of genetics, epigenetics, and environment on fertility and offspring health. Personalized treatment protocols should be developed and education about infertility should be increased.
NATURE REVIEWS UROLOGY
(2023)
Editorial Material
Biology
Chunyu Liu, Feng Zhang
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Genetics & Heredity
Jialin Li, Qingxia Huang, Yingzhe Wang, Mei Cui, Kelin Xu, Chen Suo, Zhenqiu Liu, Yanpeng An, Li Jin, Huiru Tang, Xingdong Chen, Yanfeng Jiang
Summary: Cardiovascular health is linked to a lower risk of cognitive decline, and this association may be mediated by metabolic perturbations. The study found that better cardiovascular health was associated with a lower risk of concentration and orientation decline. Certain blood components, such as apolipoprotein-A1 and high-density lipoprotein cholesterol, were also associated with a lower risk of memory and orientation decline. Mediation analysis suggested that cholesterol ester and total lipids in medium-size HDL may partially mediate the negative association between health status and the risk of orientation decline. These findings highlight the potential of using lipoproteins as targets for early stage dementia screening and intervention.
Article
Cell Biology
Eduardo A. Maury, Maxwell A. Sherman, Giulio Genovese, Thomas G. Gilgenast, Tushar Kamath, S. J. Burris, Prashanth Rajarajan, Erin Flaherty, Schahram Akbarian, Andrew Chess, Steven A. McCarroll, Po-Ru Loh, Jennifer E. Phillips-Cremins, Kristen J. Brennand, Evan Z. Macosko, James T. R. Walters, Michael O'Donovan, Patrick Sullivan, Jonathan Sebat, Eunjung A. Lee, Christopher A. Walsh
Summary: This study suggests that somatic copy-number variants (sCNVs) may play a potential role in the risk of schizophrenia (SCZ). Early-developmental sCNVs were more common in SCZ cases, including recurrent somatic deletions in the NRXN1 gene. Additionally, recurrent intragenic deletions of the ABCB11 gene were observed in treatment-resistant SCZ cases.