Article
Biochemistry & Molecular Biology
Javier Ib, Lalla Hasna Zinelabidine, Rafael Torres-Perez, Jerome Grimplet, Elisa Baroja, Sergio Ibanez, Pablo Carbonell-Bejerano, Jose Miguel Martinez-Zapater, Javier Ibanez, Javier Tello
Summary: The study revealed that grape yield components are determined by complex polygenic factors, with certain SNPs showing additive effects on the phenotype. This suggests that superior grape cultivars with optimized fruit production can potentially be generated by pyramiding advantageous alleles from different genetic loci.
Article
Genetics & Heredity
Karlijn A. C. Meeks, Amy R. Bentley, Mateus H. Gouveia, Guanjie Chen, Jie Zhou, Lin Lei, Adebowale A. Adeyemo, Ayo P. Doumatey, Charles N. Rotimi
Summary: This study investigated the genetic architecture of obesity-related cytokines and hormones among Africans, identifying multiple significant loci and population differences in variants associated with adipocytokines. Sex, BMI, and T2D were found to have strong effects on the detected loci. Replication analyses successfully confirmed several novel loci, contributing to the understanding of the biology linking adipocytokines to cardiometabolic traits.
Article
Genetics & Heredity
Md Rafiqul Islam, Dale R. Int Headache Genetics Consortium IHGC, Dale Nyholt
Summary: The co-occurrence of migraine and glycemic traits has been observed in epidemiological studies, and this study aimed to investigate the genetic link between them. Cross-trait analysis of GWAS data revealed genetic correlations and shared genomic regions between migraine, headache, and various glycemic traits. Novel genetic markers associated with migraine and headache were identified, and gene-based association analyses showed overlaps across migraine, headache, and glycemic traits. Mendelian randomization analyses provided intriguing but inconsistent evidence for causal relationships. These findings shed light on the common genetic factors and molecular mechanisms underlying the comorbidity of migraine, headache, and glycemic traits.
Article
Clinical Neurology
Wenhui Chen, Jia Feng, Shuwen Jiang, Jie Guo, XiaoLin Zhang, Xiaoguan Zhang, Cunchuan Wang, Yi Ma, Zhiyong Dong
Summary: Using two-sample Mendelian randomization, we found that obesity was causally associated with attention deficit hyperactivity disorder, anorexia nervosa, post-traumatic stress disorder, major depressive disorder, and Alzheimer's disease, but was negatively associated with obsessive-compulsive disorder and schizophrenia. Additionally, there were bidirectional causal relationships between attention deficit hyperactivity disorder, major depressive disorder, schizophrenia, and Alzheimer's disease, and obesity.
JOURNAL OF AFFECTIVE DISORDERS
(2023)
Article
Multidisciplinary Sciences
Pascal Schlosser, Adrienne Tin, Pamela R. Matias-Garcia, Chris H. L. Thio, Roby Joehanes, Hongbo Liu, Antoine Weihs, Zhi Yu, Anselm Hoppmann, Franziska Grundner-Culemann, Josine L. Min, Adebowale A. Adeyemo, Charles Agyemang, Johan Arnlov, Nasir A. Aziz, Andrea Baccarelli, Murielle Bochud, Hermann Brenner, Monique M. B. Breteler, Cristian Carmeli, Layal Chaker, John C. Chambers, Shelley A. Cole, Josef Coresh, Tanguy Corre, Adolfo Correa, Simon R. Cox, Niek de Klein, Graciela E. Delgado, Arce Domingo-Relloso, Kai-Uwe Eckardt, Arif B. Ekici, Karlhans Endlich, Kathryn L. Evans, James S. Floyd, Myriam Fornage, Lude Franke, Eliza Fraszczyk, Xu Gao, Xin Gao, Mohsen Ghanbari, Sahar Ghasemi, Christian Gieger, Philip Greenland, Megan L. Grove, Sarah E. Harris, Gibran Hemani, Peter Henneman, Christian Herder, Steve Horvath, Lifang Hou, Mikko A. Hurme, Shih-Jen Hwang, Marjo-Riitta Jarvelin, Sharon L. R. Kardia, Silva Kasela, Marcus E. Kleber, Wolfgang Koenig, Jaspal S. Kooner, Holly Kramer, Florian Kronenberg, Brigitte Kuhnel, Terho Lehtimaki, Lars Lind, Dan Liu, Yongmei Liu, Donald M. Lloyd-Jones, Kurt Lohman, Stefan Lorkowski, Ake T. Lu, Riccardo E. Marioni, Winfried Marz, Daniel L. McCartney, Karlijn A. C. Meeks, Lili Milani, Pashupati P. Mishra, Matthias Nauck, Ana Navas-Acien, Christoph Nowak, Annette Peters, Holger Prokisch, Bruce M. Psaty, Olli T. Raitakari, Scott M. Ratliff, Alex P. Reiner, Sylvia E. Rosas, Ben Schottker, Joel Schwartz, Sanaz Sedaghat, Jennifer A. Smith, Nona Sotoodehnia, Hannah R. Stocker, Silvia Stringhini, Johan Sundstrom, Brenton R. Swenson, Maria Tellez-Plaza, Joyce B. J. van Meurs, Jana V. van Vliet-Ostaptchouk, Andrea Venema, Niek Verweij, Rosie M. Walker, Matthias Wielscher, Juliane Winkelmann, Bruce H. R. Wolffenbuttel, Wei Zhao, Yinan Zheng, Marie Loh, Harold Snieder, Daniel Levy, Melanie Waldenberger, Katalin Susztak, Anna Kottgen, Alexander Teumer
Summary: This study identified DNA methylation sites associated with kidney function measures, revealing potential regulatory mechanisms and pathways involved in kidney function and disease. Many of these findings were validated in kidney tissue and suggested causal effects on kidney function. Enrichment analyses indicated pathways related to hemostasis, blood cell migration, immune cell activation, and response in relation to estimated glomerular filtration rate and urinary albumin-to-creatinine ratio.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Hamzeh M. Tanha, Dale R. Nyholt
Summary: Using genome-wide association study, this study reveals pleiotropy between blood proteins and migraine, and identifies several proteins that have a significant causal effect on migraine. These findings suggest potential therapeutic targets for migraine treatment.
NATURE COMMUNICATIONS
(2022)
Article
Oncology
Apexa Modi, Gonzalo Lopez, Karina L. Conkrite, Chun Su, Tsz Ching Leung, Sathvik Ramanan, Elisabetta Manduchi, Matthew E. Johnson, Daphne Cheung, Samantha Gadd, Jinghui Zhang, Malcolm A. Smith, Jaime M. Guidry Auvil, Soheil Meshinchi, Elizabeth J. Perlman, Stephen P. Hunger, John M. Maris, Andrew D. Wells, Struan F. A. Grant, Sharon J. Diskin
Summary: This study curated and analyzed RNA sequencing data for 1,044 pediatric leukemia and solid tumors, revealing stable expression of lncRNAs in six pediatric cancers and their association with key processes such as proliferation, metabolism, and DNA damage. By integrating various analyses, several lncRNAs were prioritized for experimental validation.
Article
Biochemistry & Molecular Biology
Kathrin Landgraf, Andreas Kuhnapfel, Maria Schlanstein, Ronald Biemann, Berend Isermann, Elena Kempf, Holger Kirsten, Markus Scholz, Antje Korner
Summary: This study found that childhood obesity is associated with dysfunction and early signs of metabolic disease in adipose tissue. By analyzing gene expression profiles in adipose tissue samples from obese children, the researchers identified genes that are associated with obesity and related parameters. They also discovered that EGFL6 gene may play a role in the pathogenesis of metabolic disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Nikos Perdikopanis, Georgios K. Georgakilas, Dimitris Grigoriadis, Vasilis Pierros, Ioannis Kavakiotis, Panagiotis Alexiou, Artemis Hatzigeorgiou
Summary: Deregulation of miRNA expression is crucial in the shift from physiological to pathological states. The DIANA-miRGen v4 database offers cell-specific miRNA transcription start sites for over 1500 miRNAs, derived from analysis of >1000 CAGE samples across 133 tissues and cell lines. This resource greatly enhances our understanding of miRNA biogenesis regulation at the transcriptional level by integrating high-quality annotations for cell-specific miRNA promoters with experimentally derived TFBSs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Camila U. Braz, Troy N. Rowan, Robert D. Schnabel, Jared E. Decker
Summary: Understanding genotype-by-environment interactions is crucial for environmental adaptation and sustainability in mammals. This study explored the impact of GxE on growth traits in beef cattle, identifying functional loci with non-additive genetic effects and revealing biological mechanisms of environmental response through functional annotation and pathway analysis of GxE genes. The complexity of genetic basis underlying GxE provides new insights into how specific genes interact with different environmental conditions to influence adaptation and productivity.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Lucas Vicuna, Esteban Barrientos, Tomas Norambuena, Danilo Alvares, Juan Cristobal Gana, Valeria Leiva-Yamaguchi, Cristian Meza, Jose L. Santos, Veronica Mericq, Ana Pereira, Susana Eyheramendy
Summary: In this study, a cross-ethnic study was conducted on 904 admixed children, and regulatory variants of the immune gene HLA-DQB3 were found to be strongly associated with BMI in children aged 1.5-2.5 years old. A variant in the sex-determining gene DMRT1 was associated with the age at adiposity rebound in girls. BMI was significantly higher in Mapuche children than in Europeans between the ages of 5.5 and 16.5. Finally, compared with European children, Mapuche children had a significantly lower age at adiposity rebound by 1.94 years and a significantly higher BMI at adiposity rebound by 1.2 kg/m(2).
Article
Multidisciplinary Sciences
Karina Patasova, Annechien E. G. Haarman, Anthony M. Musolf, Omar A. Mahroo, Jugnoo S. Rahi, Mario Falchi, Virginie J. M. Verhoeven, Joan E. Bailey-Wilson, Caroline C. W. Klaver, Priya Duggal, Alison Klein, Jeremy A. Guggenheim, Chris J. Hammond, Pirro G. Hysi
Summary: This study demonstrates the importance of rare variants in the genetic risk of refractive errors, with strong associations found between the genes SIX6 and CRX and SPHE. These genes are related to eye, retina, optic disc development, photoreceptor specification, and expression in the retina.
Article
Genetics & Heredity
Hongbo Liu, Tomohito Doke, Dong Guo, Xin Sheng, Ziyuan Ma, Joseph Park, Ha My T. Vy, Girish N. Nadkarni, Amin Abedini, Zhen Miao, Matthew Palmer, Benjamin F. Voight, Hongzhe Li, Christopher D. Brown, Marylyn D. Ritchie, Yan Shu, Katalin Susztak
Summary: In this study, the genetic association with kidney function was analyzed in over 1.5 million individuals, leading to the identification of 878 loci and target genes. The role of methylation variation in heritability of kidney function was highlighted. The findings emphasize the importance of bulk and single-cell epigenomic information in understanding the mechanisms of complex traits.
Article
Plant Sciences
Ibrahim Al-Ashkar, Nasser Al-Suhaibani, Kamel Abdella, Mohammed Sallam, Majed Alotaibi, Mahmoud E. Seleiman
Summary: Water shortages have direct adverse effects on wheat productivity worldwide. Using high-throughput tools and genetic parameters, researchers identified key interpretative traits such as canopy temperature, relative water content, green leaf area, and leaf area index, which can improve genetic gain for yield in water-stressed environments. It was found that these four interpretive traits play a crucial role in enhancing wheat productivity under water shortage conditions.
Article
Plant Sciences
Hui Zhang, Lisa Dean, Ming Li Wang, Phat Dang, Marshall Lamb, Charles Chen
Summary: This research conducted a principal component analysis to identify the main traits related to peanut flavor. Genome-wide association studies revealed significant quantitative trait loci associated with total sugars and sucrose, and candidate genes for these traits were identified. The findings contribute valuable knowledge about the genetic control of peanut flavor.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Shan-Shan Dong, Wei-Xin Hu, Tie-Lin Yang, Xiao-Feng Chen, Han Yan, Xiang-Ding Chen, Li-Jun Tan, Qing Tian, Hong-Wen Deng, Yan Guo
SCIENTIFIC REPORTS
(2017)
Article
Genetics & Heredity
Xiao-Feng Chen, Dong-Li Zhu, Man Yang, Wei-Xin Hu, Yuan-Yuan Duan, Bing-Jie Lu, Yu Rong, Shan-Shan Dong, Ruo-Han Hao, Jia-Bin Chen, Yi-Xiao Chen, Shi Yao, Hlaing Nwe Thynn, Yan Guo, Tie-Lin Yang
AMERICAN JOURNAL OF HUMAN GENETICS
(2018)
Article
Endocrinology & Metabolism
Dong-Li Zhu, Xiao-Feng Chen, Wei-Xin Hu, Shan-Shan Dong, Bing-Jie Lu, Yu Rong, Yi-Xiao Chen, Hao Chen, Hlaing Nwe Thynn, Nai-Ning Wang, Yan Guo, Tie-Lin Yang
JOURNAL OF BONE AND MINERAL RESEARCH
(2018)
Article
Psychiatry
Hui-Min Niu, Ping Yang, Huan-Huan Chen, Ruo-Han Hao, Shan-Shan Dong, Shi Yao, Xiao-Feng Chen, Han Yan, Yu-Jie Zhang, Yi-Xiao Chen, Feng Jiang, Tie-Lin Yang, Yan Guo
TRANSLATIONAL PSYCHIATRY
(2019)
Article
Dermatology
Hlaing Nwe Thynn, Xiao-Feng Chen, Wei-Xin Hu, Yuan-Yuan Duan, Dong-Li Zhu, Hao Chen, Nai-Ning Wang, Huan-Huan Chen, Yu Rong, Bing-Jie Lu, Man Yang, Feng Jiang, Shan-Shan Dong, Yan Guo, Tie-Lin Yang
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2020)
Article
Endocrinology & Metabolism
Yan Zhang, Xiao-Feng Chen, Jing Li, Fang He, Xu Li, Yan Guo
JOURNAL OF BONE AND MINERAL RESEARCH
(2020)
Article
Biochemical Research Methods
Jia-Bin Chen, Shan-Shan Dong, Shi Yao, Yuan-Yuan Duan, Wei-Xin Hu, Hao Chen, Nai-Ning Wang, Xiao-Feng Chen, Ruo-Han Hao, Hlaing Nwe Thynn, Ming-Rui Guo, Yu-Jie Zhang, Yu Rong, Yi-Xiao Chen, Fu-Ling Zhou, Yan Guo, Tie-Lin Yang
Article
Medicine, Research & Experimental
Xiao-Feng Chen, Ming-Rui Guo, Yuan-Yuan Duan, Feng Jiang, Hao Wu, Shan-Shan Dong, Xiao-Rong Zhou, Hlaing Nwe Thynn, Cong-Cong Liu, Lin Zhang, Yan Guo, Tie-Lin Yang
Article
Genetics & Heredity
Shan-Shan Dong, Kun Zhang, Yan Guo, Jing-Miao Ding, Yu Rong, Jun-Cheng Feng, Shi Yao, Ruo-Han Hao, Feng Jiang, Jia-Bin Chen, Hao Wu, Xiao-Feng Chen, Tie-Lin Yang
Summary: The study identified potential causal effects of childhood obesity on 60 adult traits, but found that the detrimental effects on disease-related traits were no longer present after accounting for adult BMI. The associations between childhood BMI and increased risks of diseases in adulthood are likely attributed to individuals remaining obese in later life.
Article
Endocrinology & Metabolism
Dong-Li Zhu, Xiao-Feng Chen, Xiao-Rong Zhou, Shou-Ye Hu, Xiao-Mei Tuo, Ruo-Han Hao, Shan-Shan Dong, Feng Jiang, Yu Rong, Tie-Lin Yang, Zhi Yang, Yan Guo
Summary: Through bioinformatics and functional experiments, a potentially functional single-nucleotide polymorphism (SNP) located in an enhancer element was identified. This SNP, by altering the binding affinity of a transcription factor, increased the expression of the target gene SOX6, thus affecting the susceptibility to osteoporosis. This study revealed the mechanisms by which noncoding genetic variants impact osteoporosis through long-range gene regulatory mechanisms.
JOURNAL OF BONE AND MINERAL RESEARCH
(2022)
Article
Chemistry, Medicinal
Shuang Liang, Danyang Liu, Zhengwu Xiao, Jonathan Greenbaum, Hui Shen, Hongmei Xiao, Hongwen Deng
Summary: Sarcopenia, a condition characterized by age-related muscle loss, is a growing public health concern. This study used different approaches to identify potential drugs for repurposing, including analysis of gene expression in skeletal muscle, assessment of drug similarity, and validation in vitro. Vorinostat was found to be a promising drug for promoting muscle fiber formation. Although further validation is needed, this suggests a potential strategy for treating and preventing sarcopenia.
Review
Biology
Martin Nwadiugwu, Hui Shen, Hong-Wen Deng
Summary: This study systematically reviewed genetic research on Alzheimer's disease (AD) using single-cell transcriptomics (scRNA-seq) or spatial genomics to identify potential molecular mechanisms and explore differences from previous findings. It presented an overview of molecular imbalances in AD and their mechanisms across different factors. The study highlighted the importance of continuing research to identify common causes and solutions for AD. scRNA-seq and spatial transcriptomics provide more in-depth results, which are crucial for AD-modifying investigations.
Review
Biology
Lei Huang, Meng Song, Hui Shen, Huixiao Hong, Ping Gong, Hong-Wen Deng, Chaoyang Zhang
Summary: This review provides an overview of deep learning-based methods for imputing missing omics data, focusing on model architectures and multi-omics data imputation. These methods can model complex patterns and relationships in large and high-dimensional omics datasets, making them an increasingly popular choice for imputation. The review also discusses the challenges and opportunities associated with deep learning methods in this field.
Article
Biochemical Research Methods
Shan-Shan Dong, Yan Guo, Shi Yao, Yi-Xiao Chen, Mo-Nan He, Yu-Jie Zhang, Xiao-Feng Chen, Jia-Bin Chen, Tie-Lin Yang
BRIEFINGS IN BIOINFORMATICS
(2019)
Article
Oncology
Yi-Xiao Chen, Yan Guo, Shan-Shan Dong, Xiao-Feng Chen, Jia-Bin Chen, Yu-Jie Zhang, Shi Yao, Hlaing Nwe Thynn, Liqiang Zhi, Tie-Lin Yang