Genome Medicine最新文献

{"title":"ERG is a regulator of dynamic and reversible endothelial plasticity.","authors":"Kristen Schulz, Steven R Botts, Kai Ellis, Corey A Scipione, Nadiya Khyzha, Christy Ho, Rathnakumar Kumaragurubaran, Kyoko E Yuki, Joshua D Wythe, Clint L Miller, Michael D Wilson, Kathryn L Howe, Jason E Fish","doi":"10.1186/s13073-026-01638-6","DOIUrl":"10.1186/s13073-026-01638-6","url":null,"abstract":"<p><strong>Background: </strong>Endothelial cells (ECs) orchestrate vascular homeostasis and resilience but can undergo reprogramming into a mesenchymal-like phenotype through an endothelial-to-mesenchymal transition (EndMT). Crucially, EndMT is a linchpin underlying several cardiometabolic diseases, but is almost universally studied as an endpoint. The transcription factor ERG (ETS-related gene) is critical to the maintenance of EC identity and function, yet the dynamic transcriptional and functional consequences of ERG loss on EndMT programs, and whether this can be reversed, has not been explored.</p><p><strong>Methods: </strong>We modeled both acute and chronic ERG loss in human aortic ECs using siRNA knockdown and CRISPR/Cas9-mediated ERG deletion. We profiled temporal changes in chromatin accessibility (ATAC-seq), transcriptomic responses (RNA-seq), and endothelial phenotypes, including migration and barrier integrity. The temporal kinetics of ERG loss and restoration was assessed by comparing stable ERG knockout to transient ERG knockdown and recovery over time. The implications to human disease were deciphered by examining ERG gene regulatory networks in human atherosclerosis and linkage with genetic variation associated with human cardiovascular disease.</p><p><strong>Results: </strong>Analysis of gene regulatory networks revealed profound and dynamic rewiring of endothelial and mesenchymal transcriptional programs upon loss of ERG. While endothelial identity was rapidly lost by 24 h of ERG knockdown, acquisition of mesenchymal identity, barrier dysfunction, and enhanced cell migration required 72 h to manifest. Loss of ERG was accompanied by a rapid reduction in accessibility of ETS motifs and an extensive gain in open chromatin containing AP1 motifs. Disease-relevant endothelial dysfunction programs were associated with dynamically reorganized transcriptional networks. Importantly, restoration of ERG expression reversed EndMT gene regulatory networks and phenotypes.</p><p><strong>Conclusions: </strong>Overall, this study highlights the ETS factor, ERG, as an essential transcriptional safeguard of endothelial identity and function, and demonstrates that ERG loss initiates a progressive, yet reversible, EndMT program with EC identity loss preceding a gain of mesenchymal gene regulatory networks and phenotypes. This study establishes loss of ERG as an early initiating event in EndMT and suggests that ERG-targeted therapies may hold promise for promoting endothelial resilience.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":"18 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13135260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147814041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative multi-omics profiling reveals distinct evolutionary and immunogenic features of brain oligometastasis in lung adenocarcinoma.","authors":"Rongxin Liao, Qian Yu, Yusheng Huang, Hengqiu He, Mengmeng Song, Xuan Gao, Lu Shen, Yihao Tao, Lin Li, Gang Xiao, Rui Kong, Cancan Wang, Shunping Huang, Xiaoyue Zhang, Zaicheng Xu, Rongrong Zhou, Zhenzhou Yang, Yuan Peng","doi":"10.1186/s13073-026-01664-4","DOIUrl":"10.1186/s13073-026-01664-4","url":null,"abstract":"<p><strong>Background: </strong>Emerging evidence has demonstrated that lung cancer patients with brain oligometastases (oligo-BMs) could benefit from local radical therapies. Despite rapid advancements in the treatment of oligometastatic disease, the molecular determinants governing the oligometastatic phenotype in the central nervous system remain elusive.</p><p><strong>Methods: </strong>We performed 1021-panel sequencing, transcriptome profiling, DNA methylation mapping, and multiplex immunohistochemistry on 20 paired primary lung adenocarcinoma and oligo-BMs specimens to delineate their evolutionary dynamics and microenvironmental characteristics.</p><p><strong>Results: </strong>A pronounced intertumor heterogeneity was observed between primary tumors (PTs) and oligo-BMs, while intratumoral heterogeneity was conserved across lesions. Subclonal analysis and phylogenetic reconstruction demonstrated that oligo-BMs exhibited predominant polyclonal seeding patterns and parallel progression trajectories. Moreover, oligo-BMs displayed a more immunosuppressed microenvironment compared to PTs, characterized by attenuated immunogenic cell death signatures, downregulation of immune-activated pathways, and diminished infiltration of activated immune cells (including B cells, NK cells, and Th1 cells). The methylation levels at functional genomic regions were highly concordant between PTs and oligo-BMs. Notably, we identified NLGN1 as a potential regulator of oligo-BM, where the hypermethylation at its genebody regions was mechanistically associated with transcriptional upregulation. Clinical validation revealed that NLGN1 was specifically overexpressed in BMs compared to PTs and extracranial metastases, correlating with advanced pathological stages and poor prognosis. In vivo studies further confirmed NLGN1 promotes BM in mice.</p><p><strong>Conclusions: </strong>Our findings provide novel insights into the evolutionary trajectory, immune landscape and methylation pattern of oligo-BMs, potentially paving the way for the development of innovative therapeutic strategies for lung cancer patients with oligo-BMs.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13248418/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147814017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional germline variants together with somatic mutations alter the integrity of cancer hallmark regulatory networks.","authors":"Jiawei Dai, Mate Posta, Michal Marczyk, Tao Qing, Balazs Gyorffy, Lajos Pusztai","doi":"10.1186/s13073-026-01644-8","DOIUrl":"10.1186/s13073-026-01644-8","url":null,"abstract":"","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13151107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.","authors":"Evgenia Dikareva, Niels van Best, Liene Bervoets, Christina E West, Connor Rossel, Christel Driessen, Monique Mommers, John Penders","doi":"10.1186/s13073-026-01660-8","DOIUrl":"10.1186/s13073-026-01660-8","url":null,"abstract":"<p><strong>Background: </strong>The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.</p><p><strong>Methods: </strong>Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.</p><p><strong>Results: </strong>Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value = 0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.</p><p><strong>Conclusions: </strong>This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13267274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single base focal hypermutation cooccurs with structural variation as an early event in advanced prostate tumourigenesis with ancestry specific independence: a multi-ancestral observational study.","authors":"Jue Jiang, Avraam Tapinos, Ruotian Huang, M S Riana Bornman, Phillip D Stricker, Shingai B A Mutambirwa, David C Wedge, Weerachai Jaratlerdsiri, Vanessa M Hayes","doi":"10.1186/s13073-026-01647-5","DOIUrl":"10.1186/s13073-026-01647-5","url":null,"abstract":"<p><p>BACKGROUND: Kataegis, the focal hypermutation of single base positions in tumour genomes, has received little attention with regards to prostate cancer (PCa) molecular features, tumour evolution and associated clinical presentation. Most notably, the impact of this phenomenon is yet to be explored across ancestral lineages representing the extremities of PCa presentation and outcomes, with men of African ancestry disproportionately disadvantaged. The purpose of this study is to address the knowledge gap through African inclusive multi-ancestral interrogation. METHODS: We assessed for ancestrally shared and unique molecular, evolutionary and clinical features of kataegis in 669 multi-ancestral whole PCa genomes. Access to raw whole-genome sequenced data allowed for direct single-pipeline comparative analysis between 109 southern African and 57 European derived treatment naïve high-risk-biased primary tumours (74% and 88%) with paired blood samples, further assessed against publicly available 207 Asian high-risk-leaning comparative (65%) and 296 European low-risk-biased alternative (79%) resources. Comparisons between ancestries and risk groups were through Wilcoxon’s rank sum test and Fisher’s exact tests, with P values adjusted by false discovery rate. RESULTS: Confirming relatively low burdens, we found kataegis to be significantly associated with genomic instability, cancer drivers, and clinical adversity across ancestries (false discovery rate = [Formula: see text]). Notably, kataegis-postive tumours were associated with elevated prostate-specific antigen levels at presentation in African (false discovery rate = [Formula: see text]) and higher risk for metastatic progression in European patients (Kaplan-Meier estimator, [Formula: see text]). Enrichment of APOBEC’s context preferences showed more attribution from APOBEC3B than APOBEC3A. Further through analyses of evolution and structural variant (SV) co-occurrence, commonly the ancestry agnostic SV-associated kataegis predominated in the clonal evolutionary state, while the less common the SV-independent kataegis ([Formula: see text]) and subclonal kataegis ([Formula: see text]) showed African specificity. CONCLUSIONS: We found kataegis-positivity to be associated with poor PCa presentation and prognosis, irrespective of patient ancestry. Kataegis-related genomic instability occurring early and late during African derived tumourigenesis, may partly explain the heightened tumour and clinical heterogeneity observed for patients of African ancestry.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13281657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond carrier frequency: a preliminary multicenter study of simultaneous couple-based comprehensive carrier screening for common and rare genetic disorders.","authors":"Bing Xiao, Hongqian Liu, Yu Sun, Xiaotian Su, Xiaoxiao Xie, Zhengfeng Xu, Feng Ren, Ying Peng, Ling Hui, Liangpu Xu, Chunhua Zhang, Jie Duan, Juan Zhang, Juan Li, Shuyuan Xue, Shixiu Liao, Ling Liu, Zhuoshu Zhao, Dejian Yuan, Juan Qiu, Fuqing Zhang, Yang Huang, Yingchun Ha, Lei Yu, Kai Tang, Xiaozhou Li, Wei Pan, Jing Shu, Jiansheng Zhu, Ling Meng, Chenming Xu, Aiping Mao, Nannan Yan, Yongguo Yu","doi":"10.1186/s13073-026-01628-8","DOIUrl":"10.1186/s13073-026-01628-8","url":null,"abstract":"<p><p>BACKGROUND: Currently, the American College of Medical Genetics and Genomics (ACMG) carrier screening (CS) guidelines do not recommend routinely screening for conditions with carrier frequencies ≤ 1:200. Advances in DNA sequencing and declining costs, alongside growing awareness, make it increasingly feasible to expand CS to cover a broader spectrum of conditions. We aimed to design a CS panel regardless of carrier frequency to evaluate its utility in less common disease. METHODS: We developed a large CS panel through gene curation, phenotypic severity evaluation, independent of carrier frequency. A cohort of 2010 couples across 24 Chinese cities underwent couple-based simultaneous screening. Gene carrier rate (GCR) was calculated, with subsequent assessment of at-risk couple rate (ACR) across varying GCR thresholds. RESULTS: The results obtained from testing 1736 genes were presented. Among 2010 couples undergoing CS, 106 were identified as having an increased risk of offspring with at least one genetic condition. The initial ACR is 5.3% (106/2010). After excluding couples not carrying high-risk CFTR variants based on the ACMG-recommended 100-variant panel for CFTR, the adjusted ACR was 5.2% (105/2010). Furthermore, after excluding GJB2: c.109 G > A and HFE, the adjusted ACR decreased to 2.2% (45/2,010). Fifty genes with a GCR ≥ 1/200 were identified through individual carrier analysis that were absent from the ACMG Tier 3 list. Setting a GCR ≥ 1/200 threshold would fail to detect 14 high-risk couples associated with 16 rare conditions: two couples carried pathogenic variants linked to two rare conditions each. Notably, 53.3% of identified high-risk couples would remain undetected under ACMG Tier 3-recommended conditions, with the majority of missed conditions representing rare yet severe disorders. The simultaneous couple-screening model maintained manageable ACR while resolving all reproductive concerns in a single phase, thereby reducing genetic counseling demands compared to sequential approaches. This methodology also minimized false-positive interpretations through integrated variant analysis. CONCLUSIONS: This study obtained preliminary Chinese population-specific GCR for both common and rare recessive conditions, providing a foundation for future CS panel optimization. Couples at risk of having a child with rare conditions are often undetectable using conventional CS paradigms that set GCR levels at ≥ 1/200 thresholds, emphasizing the need to expand beyond ACMG Tier 3 standards to address rare severe genetic disorders. For large CS panels, simultaneous couple-based screening is an effective strategy. </p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Empirical evaluation of analytic validity of polygenic scores.","authors":"Tian Lin, Jian Zeng, Scott D Gordon, Leanne Wallace, Laura Ziser, Sonia Shah, Oliver Pain, Ilja M Nolte, Harold Snieder, Paul A James, Nicholas G Martin, Peter M Visscher, Eric Lee, Loic Yengo, Anjali K Henders, Naomi R Wray","doi":"10.1186/s13073-026-01654-6","DOIUrl":"10.1186/s13073-026-01654-6","url":null,"abstract":"<p><p>BACKGROUND: Polygenic scores (PGSs) are weighted sum scores of trait-associated alleles from up to millions of SNPs. As PGS research pivots to translation into health care settings a key issue for laboratories providing PGS is demonstration of analytical validity of PGS. METHODS: We report data from 6 individuals who have been genotyped multiple times using the same and different technologies. These data were generated as part of standard experimental design for quality control purposes in two research settings over many studies and over many years. Using this opportunistic design of technical variability, we provide an empirical evaluation of technical reproducibility of PGS from 115 traits of different genetic architectures. RESULTS: Given a predefined set of SNP weights variability in PGS can reflect only SNP missingness or incorrect genotype call. We find very high reproducibility of SNP genotypes. In particular, the technical reproducibility of PGS generated from the same array technology and processed through the same quality control and imputation pipeline is very high. However, impact of missing SNPs varies between traits depending on the SNP’s weight for a trait. We provide a PGS quality score statistic (PGS:QS) that can be reported for each trait-specific score for an individual, to provide a quantitative assessment of the proportion of variation of the score that is captured by the SNPs genotyped/imputed for the individual. We provide an algorithm (PGS-impute) that updates the SNP weights of the scoring algorithm to the SNPs available for an individual, improving PGS accuracy. CONCLUSIONS: While validity of directly measured genotypes (whether from microarray or whole genome sequencing) is well-established, objective approaches to evaluate analytical reproducibility of PGS post-genotyping pipeline have been lacking. Here, we provide empirical data and an analysis framework which can be used by PGS providers to support understanding of analytical reproducibility and robustness.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13238075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vivo adenine base editing of mutant Galc gene ameliorates Krabbe disease progression.","authors":"Bae-Geun Nam, Jung Hwa Seo, Sung-Ah Hong, Ju-Hee Kim, Minju Kang, Geneva Rose Notario, Yoontaik Hong, Seunghee Cho, Sangsu Bae, Sung-Rae Cho","doi":"10.1186/s13073-026-01620-2","DOIUrl":"10.1186/s13073-026-01620-2","url":null,"abstract":"<p><p>BACKGROUND: Krabbe disease (KD) is caused by mutation of the galactosylceramidase (GALC) gene, leading to deficient sphingolipid metabolism, which is essential for functional myelination. The twitcher (Galctwi/twi) mouse, a KD model with a premature termination codon (PTC) caused by a single-nucleotide G-to-A substitution at the 355th codon of the Galc gene, is a model candidate for treatment with adenine base editors (ABEs). ABEs have emerged exclusively among genome editing systems as viable therapeutic candidates to correct mutant genes. METHODS: To confirm base editing efficiency of ABEs, mouse embryonic fibroblasts (MEFs) or mutant GALC HEK293T cells treated with three ABE variants (ABEmax, ABE8eWQ, ABE8e) were assessed using targeted deep sequencing. Each split-ABE8e vector was packaged into a dual-vector adeno-associated virus serotype 9 (AAV9) system and delivered to twitcher mice via intracerebroventricular injection on postnatal day 1. Thereafter, motor functions and survival rate were evaluated by rotarod test, clasping test and lifespan analysis. Various methods, including next-generation sequencing (NGS), qRT-PCR, enzyme activity assay, and flow cytometry, were used to measure the base correction rate of the target gene and verified restoration of GALC enzyme activity in the brain of ABE8e-treated mice. Additionally, myelin recovery was evaluated in the brain using histological analysis, magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), and transmission electron microscopy (TEM). RESULTS: The ABE8e-treated MEFs and mutant GALC HEK293T cells showed the most effective editing among the ABE variants tested. Three weeks after dual-AAV9 injection, the PTC was corrected in approximately 0.5% of genomic DNA and 5% of mRNA in twitcher mice. ABE8e treatment restored GALC enzymatic activity to approximately 5% of wild-type (WT) levels, while reducing the accumulation of psychosine—a major neurotoxic metabolite—by approximately 47% relative to WT. Moreover, histological analysis, TEM and, DTI and T2-weighted MRI showed preserved myelination and axonal integrity, along with amelioration of myelin deficits in the corpus callosum of ABE-treated twitcher mice. Five weeks after ABE8e administration, body weight recovered to approximately 64% of WT levels, accompanied by an extension of lifespan. In addition, clasping scores and rotarod performance improved to approximately 23% and 64% of WT levels, respectively. CONCLUSIONS: These data demonstrate a reliable application of base editing technology using ABEs as a potential treatment option for KD, progressing the development of therapeutics treating various genetic diseases.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":"18 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13104551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics identifies small interfering RNA with activity against all five human betacoronaviruses.","authors":"Julian Vogler, Shubhankar Ambike, Stoyan Velkov, Cho-Chin Cheng, Pauline Neubecker, Natalie Fischhaber, Pratik Mallick, Ivana Martan, Lucie Sauerhering, Albrecht von Brunn, Ulrike Protzer, Thomas Michler","doi":"10.1186/s13073-026-01659-1","DOIUrl":"10.1186/s13073-026-01659-1","url":null,"abstract":"<p><p>BACKGROUND: The Orthocoronavirinae virus subfamily (CoV) poses a continuous global health threat. Seven CoV species are known to infect humans and additional animal CoVs with potential for human spillover have been identified. Currently, antiviral drugs are available only against SARS-CoV-2, underscoring the need for broad-spectrum antivirals. Targeting the viral RNA genome with small interfering RNAs (siRNAs) induces its degradation by endogenous nucleases and represents an effective strategy to inhibit CoV replication. Previous studies have demonstrated the efficacy and feasibility of this approach against individual CoV species. However, its potential to serve as a broad-spectrum antiviral strategy effective across multiple members of the CoV subfamily has not been systematically explored. METHODS: The conservation of all potential siRNA target sites within the CoV genome (n ≈ 30,000) was analyzed using a custom database comprising 250,000 full-length genome sequences from 44 CoV species isolated from diverse mammalian and avian hosts. Antiviral activity of selected siRNA candidates was screened using a replication-competent recombinant SARS-CoV-2 expressing green fluorescent protein. The effect of target site mismatches was assessed using luciferase reporters, and cross-species antiviral activity was evaluated against six representative wild-type CoVs. Cellular toxicity was investigated by monitoring cell death, confluence, metabolic activity, and in silico prediction of siRNA off-target activity. RESULTS: Conservation of potential siRNA target sites correlated with the evolutionary distance between CoV species. Several genomic regions were conserved across different CoV subgenera and genera, but no site was universally preserved across all 44 analyzed species. The antiviral activity and tolerability of 347 siRNAs targeting the most promising sites were evaluated in multiple screening rounds. Following optimization of siRNA design and chemistry, we identified a lead candidate, si117m, which displayed high tolerability and potent silencing activity at picomolar concentrations against target sites of SARS-CoV-1, SARS-CoV-2, MERS-CoV, HCoV-OC43 and HCoV-HKU1. CONCLUSIONS: Our study demonstrates the potential of comparative genomics for developing broad-spectrum antiviral siRNAs. We identified a lead siRNA, si117m, which combines a favorable safety profile with cross-species activity against five human CoVs, supporting its potential for clinical translation and future pandemic preparedness.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":"18 1","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13101182/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147769498","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allele-specific suppression of pathogenic bestrophin-1 transcripts by CRISPR/Cas9-mediated genome editing.","authors":"Andrea Milenkovic, Bernhard H F Weber","doi":"10.1186/s13073-026-01649-3","DOIUrl":"10.1186/s13073-026-01649-3","url":null,"abstract":"<p><strong>Background: </strong>Treating autosomal dominant gene mutations remains challenging, particularly when mutations convey a gain-of-function or a dominant-negative effect, as standard gene supplementation strategies often fail to counteract the pathogenic allele.</p><p><strong>Methods: </strong>In this study, we employed human induced pluripotent stem cell-derived retinal pigment epithelium (hiPSC-RPE) to investigate allele-specific CRISPR/Cas9 genome editing as a potential treatment for Best disease (BD), an autosomal dominant macular dystrophy caused by over 250 distinct mutations in the bestrophin-1 (BEST1) gene. We designed and evaluated single guide RNAs (sgRNA) targeting three known BEST1 mutations (p.(R218C), p.(A243V), and p.(I295del)), assessing their impact on BD-associated hiPSC-RPE phenotypes and BEST1 channel function. Computationally predicted sgRNAs were rigorously tested for on-target efficiency, allele specificity and genome-wide off-target activities.</p><p><strong>Results: </strong>We found that shortening sgRNA length improved specificity in some cases, while introducing an additional mismatch generally compromised editing efficiency. Notably, only one of the three mutations yielded an sgRNA with both high cleavage efficiency and undetectable off-target effects in hiPSC-RPE cells. We then explored the consequences of allele-specific editing on BEST1 expression and function in clonal BD hiPSC-RPE lines. Eliminating the mutant BEST1 transcript led to enhanced BEST1 localization, improved protein stability and restoration of anion transport function.</p><p><strong>Conclusions: </strong>Taken together, our findings support allele-specific gene editing as a viable therapeutic strategy for selected BEST1 mutations, while underscoring the necessity for rigorous testing of computationally designed sgRNAs, given their mutation- and context-dependent variability.</p>","PeriodicalId":12645,"journal":{"name":"Genome Medicine","volume":" ","pages":""},"PeriodicalIF":10.8,"publicationDate":"2026-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13104400/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147729023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}