A vexing observation in genome-wide association studies (GWASs) is that parallel analyses in different species may not identify orthologous genes. Here, we demonstrate that cross-species translation of GWASs can be greatly improved by an analysis of co-localization within molecular networks. Using body mass index (BMI) as an example, we show that the genes associated with BMI in humans lack significant agreement with those identified in rats. However, the networks interconnecting these genes show substantial overlap, highlighting common mechanisms including synaptic signaling, epigenetic modification, and hormonal regulation. Genetic perturbations within these networks cause abnormal BMI phenotypes in mice, too, supporting their broad conservation across mammals. Other mechanisms appear species specific, including carbohydrate biosynthesis (humans) and glycerolipid metabolism (rodents). Finally, network co-localization also identifies cross-species convergence for height/body length. This study advances a general paradigm for determining whether and how phenotypes measured in model species recapitulate human biology.
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http://dx.doi.org/10.1016/j.celrep.2023.112873 | DOI Listing |
Bioinform Adv
December 2024
Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, United States.
Motivation: The expansion of genetic association data from genome-wide association studies has increased the importance of methodologies like Polygenic Risk Scores (PRS) and Mendelian Randomization (MR) in genetic epidemiology. However, their application is often impeded by complex, multi-step workflows requiring specialized expertise and the use of disparate tools with varying data formatting requirements. Existing solutions are frequently standalone packages or command-line based-largely due to dependencies on tools like PLINK-limiting accessibility for researchers without computational experience.
View Article and Find Full Text PDFArch Dermatol Res
January 2025
Jiangxi Medical College, Nanchang University, Nanchang, China.
Multiple studies have suggested that psoriasis may increase the risk of atrial fibrillation (AF). However, the molecular and immune mechanisms underlying this association remain unclear. This study initially downloaded gene expression profiles for psoriasis and AF from the Gene Expression Omnibus database.
View Article and Find Full Text PDFMol Biol Evol
January 2025
Institut de Biologie, École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research University, Paris, F-75005, France.
Modifiers of recombination rates have been described but the selective pressures acting on them and their effect on adaptation to novel environments remain unclear. We performed experimental evolution in the nematode Caenorhabditis elegans using alternative rec-1 alleles modifying the position of meiotic crossovers along chromosomes without detectable direct fitness effects. We show that adaptation to a novel environment is impaired by the allele that decreases recombination rates in the genomic regions containing fitness variation.
View Article and Find Full Text PDFInt Urol Nephrol
January 2025
Department of Nuclear Medicine, Linyi People's Hospital, Shandong Second Medical University, 27 Jiefang Road, Linyi, 276003, Shandong, China.
Purpose: The aim of our report was to recognize bladder cancer (BC)-specific serum exosome-derived long non-coding RNAs (lncRNAs) profile for early diagnosis of BC.
Methods: Potential BC-specific exosomal lncRNA indicators were discerned by genome-wide microarray profiling analysis of serum exosomes from 10 healthy participants and 10 early stage BC patients (Ta and T1), followed by multi-stage validation through quantitative real-time PCR (qRT-PCR) in BC cells, culture solution as well as 200 serum specimens and 50 tissue specimens from non-muscle-invasive bladder cancer (NMIBC) patients. The diagnostic panel was established using logistic regression and evaluated by receiver-operating characteristic (ROC) curve.
JAMA Psychiatry
January 2025
Max Planck Institute of Psychiatry, Munich, Germany.
Importance: As an accessible part of the central nervous system, the retina provides a unique window to study pathophysiological mechanisms of brain disorders in humans. Imaging and electrophysiological studies have revealed retinal alterations across several neuropsychiatric and neurological disorders, but it remains largely unclear which specific cell types and biological mechanisms are involved.
Objective: To determine whether specific retinal cell types are affected by genomic risk for neuropsychiatric and neurological disorders and to explore the mechanisms through which genomic risk converges in these cell types.
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