Cell genomics最新文献

How exposomic tools complement and enrich genomic research. 暴露体工具如何补充和丰富基因组研究。

IF 11.1

Cell genomics Pub Date : 2025-07-22 DOI: 10.1016/j.xgen.2025.100952

Konstantinos C Makris, Andrea Baccarelli, Edwin K Silverman, Robert O Wright

引用次数: 0

Genomic insights into the demographic history and local adaptation of wild boars across Eurasia. 对欧亚大陆野猪的人口历史和当地适应的基因组见解。

IF 11.1

Cell genomics Pub Date : 2025-07-17 DOI: 10.1016/j.xgen.2025.100954

Zishuai Wang, Zixin Li, Tao Huang, Jianhai Chen, Pan Xu, Ruimin Qiao, Hongwei Yin, Chengyi Song, Dongjie Zhang, Di Liu, Shuhong Zhao, Martien A M Groenen, Ole Madsen, Yanlin Zhang, Lijing Bai, Kui Li

{"title":"Genomic insights into the demographic history and local adaptation of wild boars across Eurasia.","authors":"Zishuai Wang, Zixin Li, Tao Huang, Jianhai Chen, Pan Xu, Ruimin Qiao, Hongwei Yin, Chengyi Song, Dongjie Zhang, Di Liu, Shuhong Zhao, Martien A M Groenen, Ole Madsen, Yanlin Zhang, Lijing Bai, Kui Li","doi":"10.1016/j.xgen.2025.100954","DOIUrl":"https://doi.org/10.1016/j.xgen.2025.100954","url":null,"abstract":"Wild boars exhibit genetic and phenotypic diversity shaped by migrations and local adaptations. Their expansion across Eurasia, especially in Central Asia, remains underexplored. Here, we present newly sequenced whole-genome data of 47 wild boars from Eastern Asia, Central Asia, and Europe, combined with 49 existing genomes, creating a comprehensive dataset of 96 individuals. Our analyses show that Asian wild boars and Southeast Asian Suids split ∼3.6 million years ago (mya), with Central Asian and Southern Chinese ancestors diverging ∼1.8 mya. The split between Central Asian and European-Near East ancestors occurred ∼0.9 mya, followed by a European-Near East divergence ∼0.6 mya. We identify signatures of local adaptation in Central Asian populations, including two positively selected variants in LPIN1, associated with lipid metabolism, and a missense mutation in ALPK2, linked to meat traits. These findings provide insights into wild boar dispersal and adaptation and shed light on domestic pig breeding.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100954"},"PeriodicalIF":11.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719235","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}

引用次数: 0

Impact of polymorphisms on gene expression and splicing in response to exercise and diet-induced weight loss in human skeletal muscle tissues. 运动和饮食诱导的人体骨骼肌组织体重减轻对基因表达和剪接多态性的影响

IF 11.1

Cell genomics Pub Date : 2025-07-16 DOI: 10.1016/j.xgen.2025.100951

Wenjing Wang, Wei Lin Liew, Shiqi Huang, Edmund Chan, Amelia Li Min Tan, Chi Tian, Yihan Tong, Yuntian Zhang, Fei Liu, Yixian Qin, Sean Jun Leong Ou, Suresh Anand Sadananthan, Sambasivam Sendhil Velan, Kavita Venkataraman, Sarah R Langley, Petretto Enrico, Shawn Hoon, Kwang Wei Tham, Yap Seng Chong, Yung Seng Lee, Melvin Khee-Shing Leow, Xueling Sim, Chin Meng Khoo, E Shyong Tai, Eric Yin Hao Khoo, Mei Hui Liu, Boxiang Liu

{"title":"Impact of polymorphisms on gene expression and splicing in response to exercise and diet-induced weight loss in human skeletal muscle tissues.","authors":"Wenjing Wang, Wei Lin Liew, Shiqi Huang, Edmund Chan, Amelia Li Min Tan, Chi Tian, Yihan Tong, Yuntian Zhang, Fei Liu, Yixian Qin, Sean Jun Leong Ou, Suresh Anand Sadananthan, Sambasivam Sendhil Velan, Kavita Venkataraman, Sarah R Langley, Petretto Enrico, Shawn Hoon, Kwang Wei Tham, Yap Seng Chong, Yung Seng Lee, Melvin Khee-Shing Leow, Xueling Sim, Chin Meng Khoo, E Shyong Tai, Eric Yin Hao Khoo, Mei Hui Liu, Boxiang Liu","doi":"10.1016/j.xgen.2025.100951","DOIUrl":"10.1016/j.xgen.2025.100951","url":null,"abstract":"Weight loss through exercise and diet reduces the risk of type 2 diabetes, but the genetic regulation of gene expression and splicing in response to weight loss remains unclear in humans. We collected clinical data and skeletal muscle biopsies from 54 overweight/obese Asian individuals before and after a 16-week lifestyle intervention, which resulted in an average of ∼10% weight loss, accompanied by an ∼30% increase in insulin-stimulated glucose uptake. Improvements were observed in 118 of 252 clinical traits and six blood lipids. Transcriptomic analysis of paired skeletal muscle biopsies identified 505 differentially expressed genes enriched in mitochondrial function and insulin sensitivity. Thousands of muscle-specific expression/splicing quantitative trait loci (e/sQTLs) were detected pre- and post-intervention, including hundreds of lifestyle-responsive e/sQTLs. Notably, approximately 4.2% of eQTLs and 7.3% of sQTLs showed Asian specificity. Joint analysis with genome-wide association study (GWAS) identified 16 putative metabolic risk genes. Our study reveals gene-by-lifestyle interactions and how lifestyle modulates gene regulation in skeletal muscle.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100951"},"PeriodicalIF":11.1,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669103","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}

引用次数: 0

Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy. 年轻人类新生基因的致瘤作用及其在癌症免疫治疗中作为新抗原的潜力。

IF 11.1

Cell genomics Pub Date : 2025-07-14 DOI: 10.1016/j.xgen.2025.100928

Chunfu Xiao, Xiaoge Liu, Peiyu Liu, Xinwei Xu, Chao Yao, Chunqiong Li, Qi Xiao, Tiannan Guo, Li Zhang, Yongjun Qian, Chao Wang, Yiting Dong, Yingxuan Wang, Zhi Peng, Chuanhui Han, Qiang Cheng, Ni A An, Chuan-Yun Li

{"title":"Oncogenic roles of young human de novo genes and their potential as neoantigens in cancer immunotherapy.","authors":"Chunfu Xiao, Xiaoge Liu, Peiyu Liu, Xinwei Xu, Chao Yao, Chunqiong Li, Qi Xiao, Tiannan Guo, Li Zhang, Yongjun Qian, Chao Wang, Yiting Dong, Yingxuan Wang, Zhi Peng, Chuanhui Han, Qiang Cheng, Ni A An, Chuan-Yun Li","doi":"10.1016/j.xgen.2025.100928","DOIUrl":"10.1016/j.xgen.2025.100928","url":null,"abstract":"Young human de novo genes, recently emerging from non-coding regions, are expected to contribute to human-specific traits and diseases. However, systematic explorations of this connection have been lacking. Here, we report 37 recently originated de novo genes in humans, with their evolution and characteristics defined within an updated genomic context. The expression of these genes is significantly upregulated and temporospatially expanded in tumors, partially associated with extrachromosomal DNA amplification. Depletion of 57.1% of these genes suppresses tumor cell proliferation, underscoring their roles in tumorigenesis. As a proof of concept, we developed mRNA vaccines expressing ELFN1-AS1 and TYMSOS-young genes specifically expressed during early development but reactivated exclusively in tumors. In humanized mice, these vaccines triggered specific T cell activation and inhibited tumor growth. The antigens derived from these genes are immunogenic and capable of eliciting antigen-specific T cell activation in colorectal cancer patients. These findings underscore young human de novo genes as neoantigens in cancer immunotherapy.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100928"},"PeriodicalIF":11.1,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144669104","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}

引用次数: 0

Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics. 通过菌株水平宏基因组学探索工程厌氧生态系统的遗传适应和微生物动力学。

IF 11.1

Cell genomics Pub Date : 2025-07-10 DOI: 10.1016/j.xgen.2025.100949

Gabriele Ghiotto, Aikaterini Xirostylidou, Maria Gaspari, Panagiotis G Kougias, Stefano Campanaro, Laura Treu

{"title":"Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.","authors":"Gabriele Ghiotto, Aikaterini Xirostylidou, Maria Gaspari, Panagiotis G Kougias, Stefano Campanaro, Laura Treu","doi":"10.1016/j.xgen.2025.100949","DOIUrl":"https://doi.org/10.1016/j.xgen.2025.100949","url":null,"abstract":"Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100949"},"PeriodicalIF":11.1,"publicationDate":"2025-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651381","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}

引用次数: 0

Early establishment and life course stability of sex biases in the human brain transcriptome. 人类大脑转录组性别偏见的早期建立和生命过程稳定性。

IF 11.1

Cell genomics Pub Date : 2025-07-09 Epub Date: 2025-05-26 DOI: 10.1016/j.xgen.2025.100890

Clara Benoit-Pilven, Juho V Asteljoki, Jaakko T Leinonen, Juha Karjalainen, Mark J Daly, Taru Tukiainen

引用次数: 0

Integrative characterization of MYC RNA-binding function. MYC rna结合功能的综合表征。

IF 11.1

Cell genomics Pub Date : 2025-07-09 Epub Date: 2025-05-15 DOI: 10.1016/j.xgen.2025.100878

Sihan Li, Zehua Wang, Xiaofei Wang, Yifei Wang, Dhamotharan Pattarayan, Yu Zhang, Phuong Nguyen, Avishek Bhuniya, Yuang Chen, Haozhe Huang, Yixian Huang, Luxuan Wang, Junmei Wang, Song Li, Min Zhang, Yang Liu, Nara Lee, Da Yang

{"title":"Integrative characterization of MYC RNA-binding function.","authors":"Sihan Li, Zehua Wang, Xiaofei Wang, Yifei Wang, Dhamotharan Pattarayan, Yu Zhang, Phuong Nguyen, Avishek Bhuniya, Yuang Chen, Haozhe Huang, Yixian Huang, Luxuan Wang, Junmei Wang, Song Li, Min Zhang, Yang Liu, Nara Lee, Da Yang","doi":"10.1016/j.xgen.2025.100878","DOIUrl":"10.1016/j.xgen.2025.100878","url":null,"abstract":"Emerging evidence suggests that MYC interacts with RNAs. Here, we performed an integrative characterization of MYC as an RNA-binding protein in six cell lines. We found that MYC binds to a myriad of RNAs with high affinity for guanosine-rich RNAs. Global and specific depletion of RNAs reduces MYC chromatin occupancy. Mechanistically, two highly conserved sequences, amino acids 355-357 KRR and 364-367 RQRR, within the basic region of MYC are necessary for its RNA binding. Notably, alanine substitution of KRR abolishes MYC's RNA-binding ability both in vitro and in vivo, without affecting its ability to bind E-box DNA as part of the MYC:MAX dimer in vitro. The loss of RNA-binding function decreases MYC chromatin binding in vivo and attenuates its ability to promote gene expression, cell-cycle progression, and proliferation. Our study lays a foundation for future investigation into the role of RNAs in MYC-mediated transcriptional activation and oncogenic functions.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100878"},"PeriodicalIF":11.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12278643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087059","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}

引用次数: 0

CellWalker2: Multi-omic discovery using hierarchical cell type relationships. CellWalker2：使用分层细胞类型关系的多组学发现。

IF 11.1

Cell genomics Pub Date : 2025-07-09 Epub Date: 2025-05-22 DOI: 10.1016/j.xgen.2025.100886

Zhirui Hu, Pawel F Przytycki, Katherine S Pollard

引用次数: 0

Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay. 无义变异的系统分析揭示了肽释放率作为无义介导的mRNA衰变的新修饰因子。

IF 11.1

Cell genomics Pub Date : 2025-07-09 Epub Date: 2025-05-19 DOI: 10.1016/j.xgen.2025.100882

Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortázar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, Elena Alkalaeva, Zeynep H Coban-Akdemir, Sujatha Jagannathan

{"title":"Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay.","authors":"Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortázar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, Elena Alkalaeva, Zeynep H Coban-Akdemir, Sujatha Jagannathan","doi":"10.1016/j.xgen.2025.100882","DOIUrl":"10.1016/j.xgen.2025.100882","url":null,"abstract":"The phenotypic impact of nonsense variants is determined by nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). Despite the clinical importance of nonsense variants, transcript-specific and context-dependent variations in NMD activity remain poorly understood. Here, we show that the amino acid preceding the PTC strongly influences NMD activity. Glycine codons promote robust NMD efficiency and show striking enrichment before PTCs but are depleted before normal termination codons. Glycine-PTC enrichment is particularly pronounced in genes tolerant to loss-of-function variants, suggesting efficient elimination of truncated proteins from nonessential genes. We further demonstrate that the peptide release rate during translation termination is an important determinant of NMD activity. We propose a \"window of opportunity\" model where translation termination kinetics modulate NMD activity. By revealing how sequence context shapes NMD activity through translation termination dynamics, our findings provide a mechanistic framework for improved clinical interpretation of nonsense variants.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100882"},"PeriodicalIF":11.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12278647/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112930","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}

引用次数: 0

Pisces: A multi-modal data augmentation approach for drug combination synergy prediction. 双鱼座：药物联合协同作用预测的多模态数据增强方法。

IF 11.1

Cell genomics Pub Date : 2025-07-09 Epub Date: 2025-06-03 DOI: 10.1016/j.xgen.2025.100892

Hanwen Xu, Jiacheng Lin, Addie Woicik, Zixuan Liu, Jianzhu Ma, Sheng Zhang, Hoifung Poon, Liewei Wang, Sheng Wang

{"title":"Pisces: A multi-modal data augmentation approach for drug combination synergy prediction.","authors":"Hanwen Xu, Jiacheng Lin, Addie Woicik, Zixuan Liu, Jianzhu Ma, Sheng Zhang, Hoifung Poon, Liewei Wang, Sheng Wang","doi":"10.1016/j.xgen.2025.100892","DOIUrl":"10.1016/j.xgen.2025.100892","url":null,"abstract":"Drug combination therapy is promising for cancer treatment by reducing resistance and improving efficacy. Machine learning approaches to predicting drug combinations require massive training data. Here, we propose Pisces, a novel machine learning approach for drug combination synergy prediction. The key idea is to augment the sparse dataset by creating multiple views for each drug combination based on different modalities. We combined eight modalities of a drug to create 64 augmented views. By treating each augmented view as a separate instance, Pisces can process any number of drug modalities, circumventing the issue of missing modality. Pisces obtained state-of-the-art results on cell-line-based and xenograft-based drug synergy predictions and drug-drug interaction prediction. By interpreting Pisces's predictions using a genetic interaction network, we identified a breast cancer drug-sensitive pathway from BRCA cell lines. Collectively, the results show that Pisces effectively predicts drug synergy and drug-drug interactions through data augmentation and can be applied to various biological applications.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100892"},"PeriodicalIF":11.1,"publicationDate":"2025-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12278649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144227827","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}

引用次数: 0