Cell genomicsPub Date : 2025-03-04DOI: 10.1016/j.xgen.2025.100807
Jeffrey K Ng, Yilin Chen, Titilope M Akinwe, Hillary B Heins, Elvisa Mehinovic, Yoonhoo Chang, David H Gutmann, Christina A Gurnett, Zachary L Payne, Juana G Manuel, Rachel Karchin, Tychele N Turner
{"title":"Proteome-wide assessment of differential missense variant clustering in neurodevelopmental disorders and cancer.","authors":"Jeffrey K Ng, Yilin Chen, Titilope M Akinwe, Hillary B Heins, Elvisa Mehinovic, Yoonhoo Chang, David H Gutmann, Christina A Gurnett, Zachary L Payne, Juana G Manuel, Rachel Karchin, Tychele N Turner","doi":"10.1016/j.xgen.2025.100807","DOIUrl":"10.1016/j.xgen.2025.100807","url":null,"abstract":"<p><p>Prior studies examining genomic variants suggest that some proteins contribute to both neurodevelopmental disorders (NDDs) and cancer. While there are several potential etiologies, here, we hypothesize that missense variation in proteins occurs in different clustering patterns, resulting in distinct phenotypic outcomes. This concept was first explored in 1D protein space and expanded using 3D protein structure models. Missense de novo variants were examined from 39,883 families with NDDs and missense somatic variants from 10,543 sequenced tumors covering five The Cancer Genome Atlas (TCGA) cancer types and two Catalog of Somatic Mutations in Cancer (COSMIC) pan-cancer aggregates of tissue types. We find 18 proteins with differential missense variation clustering in NDDs compared to cancers and 19 in cancers relative to NDDs. These proteins may be important for detailed assessments in thinking of future prognostic and therapeutic applications. We establish a framework for interpreting missense patterns in NDDs and cancer, using advances in 3D protein structure prediction.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100807"},"PeriodicalIF":11.1,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-20DOI: 10.1016/j.xgen.2025.100779
Abner Herbert Lim, Cedric Chuan Young Ng, Jing Han Hong, Ewe Choon Lee, Kenneth Kwek, Patrick Tan, Hazri Kifle, Ivy Ng, Bin Tean Teh
{"title":"Genomic garden: From societal and scientific impacts to biodiversity conservation.","authors":"Abner Herbert Lim, Cedric Chuan Young Ng, Jing Han Hong, Ewe Choon Lee, Kenneth Kwek, Patrick Tan, Hazri Kifle, Ivy Ng, Bin Tean Teh","doi":"10.1016/j.xgen.2025.100779","DOIUrl":"https://doi.org/10.1016/j.xgen.2025.100779","url":null,"abstract":"<p><p>Because of urbanization, deforestation, pollution, climate change, and natural disasters, the loss of biodiversity is a pressing concern globally. As part of our efforts toward biodiversity conservation, we propose the establishment of a genomic garden, where the genome of each plant in the garden is elucidated. Combining science, horticulture, and a digital content hub accessible with any handheld device, the genomic garden serves multiple purposes, from enhancing urban landscapes, facilitating biomedical research, and improving population health to providing entertainment and education for visitors.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100779"},"PeriodicalIF":11.1,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143532138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-12DOI: 10.1016/j.xgen.2025.100773
Wen Zhang, Xiaohong Wu, Jing Gong
{"title":"Overcoming collaboration barriers in quantitative trait loci analysis.","authors":"Wen Zhang, Xiaohong Wu, Jing Gong","doi":"10.1016/j.xgen.2025.100773","DOIUrl":"10.1016/j.xgen.2025.100773","url":null,"abstract":"<p><p>In this issue of Cell Genomics, Choi et al.<sup>1</sup> report a novel approach, privateQTL, which leverages secure multiparty computation (MPC) to enable federated expression quantitative trait loci (eQTL) mapping across institutions without compromising data privacy. Zhang et al. preview their approach and discuss its application in future genetic analyses.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"5 2","pages":"100773"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-12Epub Date: 2025-01-29DOI: 10.1016/j.xgen.2025.100762
Nauman Javed, Thomas Weingarten, Arijit Sehanobish, Adam Roberts, Avinava Dubey, Krzysztof Choromanski, Bradley E Bernstein
{"title":"A multi-modal transformer for cell type-agnostic regulatory predictions.","authors":"Nauman Javed, Thomas Weingarten, Arijit Sehanobish, Adam Roberts, Avinava Dubey, Krzysztof Choromanski, Bradley E Bernstein","doi":"10.1016/j.xgen.2025.100762","DOIUrl":"10.1016/j.xgen.2025.100762","url":null,"abstract":"<p><p>Sequence-based deep learning models have emerged as powerful tools for deciphering the cis-regulatory grammar of the human genome but cannot generalize to unobserved cellular contexts. Here, we present EpiBERT, a multi-modal transformer that learns generalizable representations of genomic sequence and cell type-specific chromatin accessibility through a masked accessibility-based pre-training objective. Following pre-training, EpiBERT can be fine-tuned for gene expression prediction, achieving accuracy comparable to the sequence-only Enformer model, while also being able to generalize to unobserved cell states. The learned representations are interpretable and useful for predicting chromatin accessibility quantitative trait loci (caQTLs), regulatory motifs, and enhancer-gene links. Our work represents a step toward improving the generalization of sequence-based deep neural networks in regulatory genomics.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100762"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143070069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-12DOI: 10.1016/j.xgen.2025.100771
Peisen Sun, Stephen J Bush, Songbo Wang, Peng Jia, Mingxuan Li, Tun Xu, Pengyu Zhang, Xiaofei Yang, Chengyao Wang, Linfeng Xu, Tingjie Wang, Kai Ye
{"title":"STMiner: Gene-centric spatial transcriptomics for deciphering tumor tissues.","authors":"Peisen Sun, Stephen J Bush, Songbo Wang, Peng Jia, Mingxuan Li, Tun Xu, Pengyu Zhang, Xiaofei Yang, Chengyao Wang, Linfeng Xu, Tingjie Wang, Kai Ye","doi":"10.1016/j.xgen.2025.100771","DOIUrl":"10.1016/j.xgen.2025.100771","url":null,"abstract":"<p><p>Analyzing spatial transcriptomics data from tumor tissues poses several challenges beyond those of healthy samples, including unclear boundaries between different regions, uneven cell densities, and relatively higher cellular heterogeneity. Collectively, these bias the background against which spatially variable genes are identified, which can result in misidentification of spatial structures and hinder potential insight into complex pathologies. To overcome this problem, STMiner leverages 2D Gaussian mixture models and optimal transport theory to directly characterize the spatial distribution of genes rather than the capture locations of the cells expressing them (spots). By effectively mitigating the impacts of both background bias and data sparsity, STMiner reveals key gene sets and spatial structures overlooked by spot-based analytic tools, facilitating novel biological discoveries. The core concept of directly analyzing overall gene expression patterns also allows for a broader application beyond spatial transcriptomics, positioning STMiner for continuous expansion as spatial omics technologies evolve.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"5 2","pages":"100771"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-12DOI: 10.1016/j.xgen.2025.100770
Dahlia Rohm, Joshua B Black, Sean R McCutcheon, Alejandro Barrera, Shanté S Berry, Daniel J Morone, Xander Nuttle, Celine E de Esch, Derek J C Tai, Michael E Talkowski, Nahid Iglesias, Charles A Gersbach
{"title":"Activation of the imprinted Prader-Willi syndrome locus by CRISPR-based epigenome editing.","authors":"Dahlia Rohm, Joshua B Black, Sean R McCutcheon, Alejandro Barrera, Shanté S Berry, Daniel J Morone, Xander Nuttle, Celine E de Esch, Derek J C Tai, Michael E Talkowski, Nahid Iglesias, Charles A Gersbach","doi":"10.1016/j.xgen.2025.100770","DOIUrl":"10.1016/j.xgen.2025.100770","url":null,"abstract":"<p><p>Epigenome editing with DNA-targeting technologies such as CRISPR-dCas9 can be used to dissect gene regulatory mechanisms and potentially treat associated disorders. For example, Prader-Willi syndrome (PWS) results from loss of paternally expressed imprinted genes on chromosome 15q11.2-q13.3, although the maternal allele is intact but epigenetically silenced. Using CRISPR repression and activation screens in human induced pluripotent stem cells (iPSCs), we identified genomic elements that control the expression of the PWS gene SNRPN from the paternal and maternal chromosomes. We showed that either targeted transcriptional activation or DNA demethylation can activate the silenced maternal SNRPN and downstream PWS transcripts. However, these two approaches function at unique regions, preferentially activating different transcript variants and involving distinct epigenetic reprogramming mechanisms. Remarkably, transient expression of the targeted demethylase leads to stable, long-term maternal SNRPN expression in PWS iPSCs. This work uncovers targeted epigenetic manipulations to reprogram a disease-associated imprinted locus and suggests possible therapeutic interventions.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"5 2","pages":"100770"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872474/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-12Epub Date: 2025-01-21DOI: 10.1016/j.xgen.2024.100744
Gladys Poon, Aditi Vedi, Mathijs Sanders, Elisa Laurenti, Peter Valk, Jamie R Blundell
{"title":"Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution.","authors":"Gladys Poon, Aditi Vedi, Mathijs Sanders, Elisa Laurenti, Peter Valk, Jamie R Blundell","doi":"10.1016/j.xgen.2024.100744","DOIUrl":"10.1016/j.xgen.2024.100744","url":null,"abstract":"<p><p>The representation of driver mutations in preleukemic hematopoietic stem cells (pHSCs) provides a window into the somatic evolution that precedes acute myeloid leukemia (AML). Here, we isolate pHSCs from the bone marrow of 16 patients diagnosed with AML and perform single-cell DNA sequencing on thousands of cells to reconstruct phylogenetic trees of the major driver clones in each patient. We develop a computational framework that can infer levels of positive selection operating during preleukemic evolution from the statistical properties of these phylogenetic trees. Combining these data with 67 previously published phylogenetic trees, we find that the highly variable structures of preleukemic trees emerge naturally from a simple model of somatic evolution with pervasive positive selection typically in the range of 9%-24% per year. At these levels of positive selection, we show that the identification of early multiple-mutant clones could be used to identify individuals at risk of future AML.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100744"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872528/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cell genomicsPub Date : 2025-02-12Epub Date: 2025-02-05DOI: 10.1016/j.xgen.2025.100768
Peifeng Ji, Ning Wang, You Yu, Junjie Zhu, Zhenqiang Zuo, Bing Zhang, Fangqing Zhao
{"title":"Single-cell delineation of the microbiota-gut-brain axis: Probiotic intervention in Chd8 haploinsufficient mice.","authors":"Peifeng Ji, Ning Wang, You Yu, Junjie Zhu, Zhenqiang Zuo, Bing Zhang, Fangqing Zhao","doi":"10.1016/j.xgen.2025.100768","DOIUrl":"10.1016/j.xgen.2025.100768","url":null,"abstract":"<p><p>Emerging research underscores the gut microbiome's impact on the nervous system via the microbiota-gut-brain axis, yet comprehensive insights remain limited. Using a CHD8-haploinsufficient model for autism spectrum disorder (ASD), we explored host-gut microbiota interactions by constructing a single-cell transcriptome atlas of brain and intestinal tissues in wild-type and mutant mice across three developmental stages. CHD8 haploinsufficiency caused delayed development of radial glial precursors and excitatory neural progenitors in the E14.5 brain, inflammation in the adult brain, immunodeficiency, and abnormal intestinal development. Selective CHD8 knockdown in intestinal epithelial cells generated Chd8<sup>ΔIEC</sup> mice, which exhibited normal sociability but impaired social novelty recognition. Probiotic intervention with Lactobacillus murinus selectively rescued social deficits in Chd8<sup>ΔIEC</sup> mice, with single-cell transcriptome analysis revealing underlying mechanisms. This study provides a detailed single-cell transcriptomic dataset of ASD-related neural and intestinal changes, advancing our understanding of the gut-brain axis and offering potential therapeutic strategies for ASD.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100768"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143366925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Genetic mapping of serum metabolome to chronic diseases among Han Chinese.","authors":"Chunxiao Cheng, Fengzhe Xu, Xiong-Fei Pan, Cheng Wang, Jiayao Fan, Yunhaonan Yang, Yuanjiao Liu, Lingyun Sun, Xiaojuan Liu, Yue Xu, Yuan Zhou, Congmei Xiao, Wanglong Gou, Zelei Miao, Jiaying Yuan, Luqi Shen, Yuanqing Fu, Xiaohui Sun, Yimin Zhu, Yuming Chen, An Pan, Dan Zhou, Ju-Sheng Zheng","doi":"10.1016/j.xgen.2024.100743","DOIUrl":"10.1016/j.xgen.2024.100743","url":null,"abstract":"<p><p>Serum metabolites are potential regulators for chronic diseases. To explore the genetic regulation of metabolites and their roles in chronic diseases, we quantified 2,759 serum metabolites and performed genome-wide association studies (GWASs) among Han Chinese individuals. We identified 184 study-wide significant (p < 1.81 × 10<sup>-11</sup>) metabolite quantitative trait loci (metaboQTLs), 88.59% (163) of which were novel. Notably, we identified Asian-ancestry-specific metaboQTLs, including the SNP rs2296651 for taurocholic acid and taurochenodesoxycholic acid. Leveraging the GWAS for 37 clinical traits from East Asians, Mendelian randomization analyses identified 906 potential causal relationships between metabolites and clinical traits, including 27 for type 2 diabetes and 38 for coronary artery disease. Integrating genetic regulation of the transcriptome and proteome revealed putative regulators of several metabolites. In summary, we depict a landscape of the genetic architecture of the serum metabolome among Han Chinese and provide insights into the role of serum metabolites in chronic diseases.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100743"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143017205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Secure and federated quantitative trait loci mapping with privateQTL.","authors":"Yoolim Annie Choi, Yebin Kim, Peihan Miao, Tuuli Lappalainen, Gamze Gürsoy","doi":"10.1016/j.xgen.2025.100769","DOIUrl":"10.1016/j.xgen.2025.100769","url":null,"abstract":"<p><p>Understanding the relationship between genotypes and phenotypes is crucial for advancing personalized medicine. Expression quantitative trait loci (eQTL) mapping plays a significant role by correlating genetic variants to gene expression levels. Despite the progress made by large-scale projects, eQTL mapping still faces challenges in statistical power and privacy concerns. Multi-site studies can increase sample sizes but are hindered by privacy issues. We present privateQTL, a novel framework leveraging secure multi-party computation for secure and federated eQTL mapping. When tested in a real-world scenario with data from different studies, privateQTL outperformed meta-analysis by accurately correcting for covariates and batch effect and retaining higher accuracy and precision for both eGene-eVariant mapping and effect size estimation. In addition, privateQTL is modular and scalable, making it adaptable for other molecular phenotypes and large-scale studies. Our results indicate that privateQTL is a practical solution for privacy-preserving collaborative eQTL mapping.</p>","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"5 2","pages":"100769"},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11872535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143416454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}