Cell genomics最新文献_第5页

Coordinated regulation by lncRNAs results in tight lncRNA-target couplings. lncrna的协同调控导致lncrna -靶标紧密耦合。

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-07-07 DOI: 10.1016/j.xgen.2025.100927

Hua-Sheng Chiu, Sonal Somvanshi, Chung-Te Chang, Eric James de Bony de Lavergne, Zhaowen Wei, Chih-Hung Hsieh, Wim Trypsteen, Kathleen A Scorsone, Ektaben Patel, Tien T Tang, David B Flint, Mohammad Javad Najaf Panah, Hyunjae Ryan Kim, Purva Rathi, Yan-Hwa Wu Lee, Sarah E Woodfield, Sanjeev A Vasudevan, Andras Attila Heczey, M Waleed Gaber, Gabriel O Sawakuchi, Ting-Wen Chen, Pieter Mestdagh, Xuerui Yang, Pavel Sumazin

{"title":"Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.","authors":"Hua-Sheng Chiu, Sonal Somvanshi, Chung-Te Chang, Eric James de Bony de Lavergne, Zhaowen Wei, Chih-Hung Hsieh, Wim Trypsteen, Kathleen A Scorsone, Ektaben Patel, Tien T Tang, David B Flint, Mohammad Javad Najaf Panah, Hyunjae Ryan Kim, Purva Rathi, Yan-Hwa Wu Lee, Sarah E Woodfield, Sanjeev A Vasudevan, Andras Attila Heczey, M Waleed Gaber, Gabriel O Sawakuchi, Ting-Wen Chen, Pieter Mestdagh, Xuerui Yang, Pavel Sumazin","doi":"10.1016/j.xgen.2025.100927","DOIUrl":"10.1016/j.xgen.2025.100927","url":null,"abstract":"The determination of long non-coding RNA (lncRNA) function is a major challenge in RNA biology with applications to basic, translational, and medical research. We developed BigHorn to computationally infer lncRNA-DNA interactions that mediate transcription and chromatin-remodeling factor activity. Its accurate inference enabled the identification of lncRNAs that coordinately regulate both the transcriptional and post-transcriptional processing of their targets. These lncRNAs may act as molecular chaperones, regulating the stability and translation of mRNAs they helped transcribe, leading to tightly coupled expression profiles. Our analysis suggests that lncRNAs regulate cancer genes across tumor contexts, thus propagating the effects of non-coding alterations to effectively dysregulate cancer programs. As a proof of principle, we studied the regulation of DICER1, a cancer gene that plays a key role in microRNA biogenesis, by the lncRNA ZFAS1. We showed that ZFAS1 helps activate DICER1 transcription and block its mRNA degradation to phenomimic DICER1 and regulate its target microRNAs.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100927"},"PeriodicalIF":11.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12367320/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593054","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

Temporal multi-omics analysis of COVID-19 in end-stage kidney disease. COVID-19在终末期肾脏疾病中的时间多组学分析

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-06-17 DOI: 10.1016/j.xgen.2025.100918

Emily Stephenson, Erin Macdonald-Dunlop, Lisa M Dratva, Rik G H Lindeboom, Zewen Kelvin Tuong, Win Min Tun, Lorenz Kretschmer, Norzawani B Buang, Stephane Ballereau, Mia Cabantaus, Ana Peñalver, Elena Prigmore, John R Ferdinand, Benjamin J Stewart, Jack Gisby, Talat H Malik, Candice L Clarke, Nicholas Medjeral-Thomas, Maria Prendecki, Stephen McAdoo, Anais Portet, Michelle Willicombe, Eleanor Sandhu, Matthew C Pickering, Marina Botto, Sarah A Teichmann, Muzlifah Haniffa, Menna R Clatworthy, David C Thomas, James E Peters

{"title":"Temporal multi-omics analysis of COVID-19 in end-stage kidney disease.","authors":"Emily Stephenson, Erin Macdonald-Dunlop, Lisa M Dratva, Rik G H Lindeboom, Zewen Kelvin Tuong, Win Min Tun, Lorenz Kretschmer, Norzawani B Buang, Stephane Ballereau, Mia Cabantaus, Ana Peñalver, Elena Prigmore, John R Ferdinand, Benjamin J Stewart, Jack Gisby, Talat H Malik, Candice L Clarke, Nicholas Medjeral-Thomas, Maria Prendecki, Stephen McAdoo, Anais Portet, Michelle Willicombe, Eleanor Sandhu, Matthew C Pickering, Marina Botto, Sarah A Teichmann, Muzlifah Haniffa, Menna R Clatworthy, David C Thomas, James E Peters","doi":"10.1016/j.xgen.2025.100918","DOIUrl":"10.1016/j.xgen.2025.100918","url":null,"abstract":"Patients with end-stage kidney disease (ESKD) are at high risk of severe COVID-19. We performed longitudinal single-cell immune profiling of ESKD patients with COVID-19. Transcriptome, surface proteome, and immunoreceptor sequencing data were generated on 580,040 high-quality cells, derived from 187 samples from 61 patients. For a subset of individuals, we obtained samples before and during infection, allowing intra-individual comparison. Longitudinal profiling demonstrated distinct temporal gene expression trajectories in severe/critical versus mild/moderate COVID-19. We identified a population of transcriptionally distinct monocytes that emerged in peripheral blood following glucocorticoid treatment. Evaluation of clonal T cell dynamics showed that the fastest expanding clones were enriched in known SARS-CoV-2-specific sequences and shared across multiple patients. Comparison with external datasets revealed upregulation of immune cell TGF-β pathway expression in ESKD, irrespective of COVID-19 status. Our data delineate the temporal dynamics of the immune response in COVID-19 in a high-risk population.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100918"},"PeriodicalIF":11.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144327898","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

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 : 2025-08-13 Epub Date: 2025-07-24 DOI: 10.1016/j.xgen.2025.100952

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

引用次数: 0

Take the bull by the horns: A computational framework to predict lncRNA function. 迎难而上：预测lncRNA功能的计算框架。

IF 11.1

Cell genomics Pub Date : 2025-08-13 DOI: 10.1016/j.xgen.2025.100972

Amit Felach, Assaf C Bester

引用次数: 0

A rare, evolutionarily conserved venom protein benefits endoparasitism across parasitoids. 一种罕见的，进化上保守的毒液蛋白有利于寄生蜂的内寄生。

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-06-19 DOI: 10.1016/j.xgen.2025.100920

Zhi Dong, Yueqi Lu, Gangqi Fang, Qichao Zhang, Yifeng Sheng, Lan Pang, Jiani Chen, Wenqi Shi, Ting Feng, Junwei Zhang, Yixiang Zhang, Guiyun Li, Xuexin Chen, Jianhua Huang, Shuai Zhan

{"title":"A rare, evolutionarily conserved venom protein benefits endoparasitism across parasitoids.","authors":"Zhi Dong, Yueqi Lu, Gangqi Fang, Qichao Zhang, Yifeng Sheng, Lan Pang, Jiani Chen, Wenqi Shi, Ting Feng, Junwei Zhang, Yixiang Zhang, Guiyun Li, Xuexin Chen, Jianhua Huang, Shuai Zhan","doi":"10.1016/j.xgen.2025.100920","DOIUrl":"10.1016/j.xgen.2025.100920","url":null,"abstract":"Although many venom proteins and other parasitic effectors have been identified in various specific systems of parasitoids, key elements that contribute to parasitic success across a broad range of taxa remain largely unexplored. Here, we focus on Leptopilina and conduct a large-scale, multi-omics study to explore common venom proteins for these drosophilid parasitoids. We find that this genus has undergone extensive chromosome rearrangements and a rapid turnover of venom gene repertoires between species. Interestingly, we identified a lineage-specific venom lipase, Leptopilina-specific venom lipase (LVL), as a rare venom protein that is subject to evolutionary constraint and recruited by all Leptopilina species. Functional genetics studies on LVL reveal its critical role in hydrolyzing host lipids under acidic conditions, which in turn ensures the nutrition supply for the embryonic development of parasitoids. Our study provides a paradigm to characterize adaptive effectors across diverse insects and highlights the importance of host lipid utilization in the parasitization of parasitoids.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100920"},"PeriodicalIF":11.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366661/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144337297","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

Benchmarking of T cell receptor-epitope predictors with ePytope-TCR. 用表位- tcr对T细胞受体表位预测因子进行基准测试。

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-07-07 DOI: 10.1016/j.xgen.2025.100946

Felix Drost, Anna Chernysheva, Mahmoud Albahah, Katharina Kocher, Kilian Schober, Benjamin Schubert

{"title":"Benchmarking of T cell receptor-epitope predictors with ePytope-TCR.","authors":"Felix Drost, Anna Chernysheva, Mahmoud Albahah, Katharina Kocher, Kilian Schober, Benjamin Schubert","doi":"10.1016/j.xgen.2025.100946","DOIUrl":"10.1016/j.xgen.2025.100946","url":null,"abstract":"Understanding the recognition of disease-derived epitopes through T cell receptors (TCRs) has the potential to serve as a stepping stone for the development of efficient immunotherapies and vaccines. While a plethora of sequence-based prediction methods for TCR-epitope binding exists, their pre-trained models have not been comparatively evaluated. To alleviate this shortcoming, we integrated 21 TCR-epitope prediction models into the immune-prediction framework ePytope, offering interoperable interfaces with standard TCR repertoire data formats. We showcase the applicability of ePytope-TCR by evaluating the performance of these publicly available prediction models on two challenging datasets. While novel predictors successfully predicted binding to frequently observed epitopes, all methods failed for less frequently observed epitopes. Further, we detected a strong bias in the prediction scores between different epitope classes. We envision this benchmark to guide researchers in their choice of a predictor and to accelerate the method development by defining standardized evaluation settings.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100946"},"PeriodicalIF":11.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144593053","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

CXCR4-LASP1-G9a-SNAIL axis drives NEPC transdifferentiation via induction of EMT and downregulation of REST. CXCR4-LASP1-G9a-SNAIL轴通过诱导EMT和下调REST驱动NEPC转分化。

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-06-10 DOI: 10.1016/j.xgen.2025.100916

Liangliang Liu, Itzel Astiazarán Rascón, Dong Lin, Yuchao Ni, Xin Dong, Hui Xue, Yen-Yi Lin, Anne Haegert, Funda Sar, James W Peacock, Tabitha Tombe, Christopher Dusek, Amina Zoubeidi, Martin E Gleave, Colin Collins, Francois Bénard, Yuzhuo Wang, Christopher J Ong

{"title":"CXCR4-LASP1-G9a-SNAIL axis drives NEPC transdifferentiation via induction of EMT and downregulation of REST.","authors":"Liangliang Liu, Itzel Astiazarán Rascón, Dong Lin, Yuchao Ni, Xin Dong, Hui Xue, Yen-Yi Lin, Anne Haegert, Funda Sar, James W Peacock, Tabitha Tombe, Christopher Dusek, Amina Zoubeidi, Martin E Gleave, Colin Collins, Francois Bénard, Yuzhuo Wang, Christopher J Ong","doi":"10.1016/j.xgen.2025.100916","DOIUrl":"10.1016/j.xgen.2025.100916","url":null,"abstract":"Phenotypic switching is an emerging driver of cancer treatment resistance, yet early signals regulating this process remain unclear. Here, using longitudinal single-cell RNA sequencing, we mapped differentiation trajectories in the LTL331 prostate adenocarcinoma patient-derived xenograft (PDX) model undergoing neuroendocrine prostate cancer (NEPC) transformation post castration. Our analyses identified a key differentiation node marked by epithelial-mesenchymal transition (EMT) and repressor element-1 silencing transcription factor (REST) downregulation driven by the CXCR4-LASP1-G9a-SNAIL axis. Mechanistically, CXCR4 activation promotes nuclear translocation of LASP1 that links G9a and SNAIL via SH3/proline-rich motif and LIM/SNAG domain interactions, enabling SNAIL-mediated REST repression via promoter E-box motifs. Inhibition of CXCR4 or G9a reversed LTL331R NEPC cells toward a luminal androgen receptor-active phenotype. CXCR4-targeted radioligands enabled both imaging and inhibition of NEPC tumors in vivo. These findings highlight the CXCR4-LASP1-G9a-SNAIL axis as a key regulator of epigenetic and transcriptional reprogramming in NEPC transdifferentiation and support its therapeutic targeting in aggressive NEPC.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100916"},"PeriodicalIF":11.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366657/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276917","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

Disentangling cell-intrinsic and cell-extrinsic factors underlying evolution. 解开进化背后的细胞内在和细胞外在因素。

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-05-29 DOI: 10.1016/j.xgen.2025.100891

Alexander L Starr, Toshiya Nishimura, Kyomi J Igarashi, Chihiro Funamoto, Hiromitsu Nakauchi, Hunter B Fraser

{"title":"Disentangling cell-intrinsic and cell-extrinsic factors underlying evolution.","authors":"Alexander L Starr, Toshiya Nishimura, Kyomi J Igarashi, Chihiro Funamoto, Hiromitsu Nakauchi, Hunter B Fraser","doi":"10.1016/j.xgen.2025.100891","DOIUrl":"10.1016/j.xgen.2025.100891","url":null,"abstract":"A long-standing question in biology is the extent to which cells function autonomously as opposed to requiring interactions with other cells or environmental factors. Here, we develop a framework to use interspecies chimeras to precisely decompose evolutionary divergence in any cellular trait into cell-intrinsic and cell-extrinsic components. Applying this framework to thousands of gene expression levels in reciprocal rat-mouse chimeras, we found that most divergence is cell intrinsic, though extrinsic factors also play an integral role. For example, cell-extrinsic regulation of a transcription factor can propagate to its target genes, leading to cell-type-specific extrinsic regulation of both their mRNA and their protein levels. We also show that imprinted genes are dramatically misexpressed in chimeras, suggesting a mismatch between rapidly evolving intrinsic and extrinsic imprinting mechanisms. Overall, our conceptual framework opens up new avenues to investigate the mechanistic basis of the evolution, development, and regulation of myriad cellular traits in any multicellular organism.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100891"},"PeriodicalIF":11.1,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144188616","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

Depletion of aneuploid cells is shaped by cell-to-cell interactions. 非整倍体细胞的损耗是由细胞间相互作用形成的。

IF 11.1

Cell genomics Pub Date : 2025-08-13 Epub Date: 2025-06-03 DOI: 10.1016/j.xgen.2025.100894

Elena Fusari, Mariana Muzzopappa, Juliette Gracia, Marco Milán

引用次数: 0

Predicting TCR-epitope recognition: How good are we? 预测tcr表位识别：我们做得有多好？

IF 11.1

Cell genomics Pub Date : 2025-08-13 DOI: 10.1016/j.xgen.2025.100975

David Gfeller

引用次数: 0