Cell Reports Methods最新文献_第4页

Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS. 体内UFMylome的位点特异性量化揭示了肌球蛋白在ALS中的修饰。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-09 DOI: 10.1016/j.crmeth.2025.101048

Ronnie Blazev, Barry M Zee, Hayley Peckham, Yaan-Kit Ng, Christopher T A Lewis, Chengxin Zhang, James W McNamara, Craig A Goodman, Paul Gregorevic, Julien Ochala, Frederik J Steyn, Shyuan T Ngo, Matthew P Stokes, Benjamin L Parker

{"title":"Site-specific quantification of the in vivo UFMylome reveals myosin modification in ALS.","authors":"Ronnie Blazev, Barry M Zee, Hayley Peckham, Yaan-Kit Ng, Christopher T A Lewis, Chengxin Zhang, James W McNamara, Craig A Goodman, Paul Gregorevic, Julien Ochala, Frederik J Steyn, Shyuan T Ngo, Matthew P Stokes, Benjamin L Parker","doi":"10.1016/j.crmeth.2025.101048","DOIUrl":"10.1016/j.crmeth.2025.101048","url":null,"abstract":"UFMylation is a ubiquitin-like protein modification of Ubiquitin Fold Modifier 1 (UFM1) applied to substrate proteins and regulates several cellular processes such as protein quality control. Here, we describe the development of an antibody-based enrichment approach to immunoprecipitate remnant UFMylated peptides and identification by mass spectrometry. We used this approach to identify >200 UFMylation sites from various mouse tissues, revealing extensive modification in skeletal muscle. In vivo knockdown of the E2 ligase, UFC1, followed by enrichment and analysis of remnant UFMylated peptides quantified concomitant down-regulation and validation of a subset of modification sites, particularly myosin UFMylation. Furthermore, we show that UFMylation is increased in skeletal muscle biopsies from people living with amyotrophic lateral sclerosis (plwALS). Quantification of UFMylation sites in these biopsies with multiplexed isotopic labeling reveal prominent increases in myosin UFMylation. Our data suggest that in vivo UFMylation is more complex than previously thought.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101048"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013810","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

Accurate prediction of absolute prokaryotic abundance from DNA concentration. 从DNA浓度准确预测绝对原核生物丰度。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-04-28 DOI: 10.1016/j.crmeth.2025.101030

Jakob Wirbel, Tessa M Andermann, Erin F Brooks, Lanya Evans, Adam Groth, Mai Dvorak, Meenakshi Chakraborty, Bianca Palushaj, Gabriella Z M Reynolds, Imani E Porter, Monzr Al Malki, Andrew Rezvani, Mahasweta Gooptu, Hany Elmariah, Lyndsey Runaas, Teng Fei, Michael J Martens, Javier Bolaños-Meade, Mehdi Hamadani, Shernan Holtan, Rob Jenq, Jonathan U Peled, Mary M Horowitz, Kathleen L Poston, Wael Saber, Leslie S Kean, Miguel-Angel Perales, Ami S Bhatt

{"title":"Accurate prediction of absolute prokaryotic abundance from DNA concentration.","authors":"Jakob Wirbel, Tessa M Andermann, Erin F Brooks, Lanya Evans, Adam Groth, Mai Dvorak, Meenakshi Chakraborty, Bianca Palushaj, Gabriella Z M Reynolds, Imani E Porter, Monzr Al Malki, Andrew Rezvani, Mahasweta Gooptu, Hany Elmariah, Lyndsey Runaas, Teng Fei, Michael J Martens, Javier Bolaños-Meade, Mehdi Hamadani, Shernan Holtan, Rob Jenq, Jonathan U Peled, Mary M Horowitz, Kathleen L Poston, Wael Saber, Leslie S Kean, Miguel-Angel Perales, Ami S Bhatt","doi":"10.1016/j.crmeth.2025.101030","DOIUrl":"10.1016/j.crmeth.2025.101030","url":null,"abstract":"Quantification of the absolute microbial abundance in a human stool sample is crucial for a comprehensive understanding of the microbial ecosystem, but this information is lost upon metagenomic sequencing. While several methods exist to measure absolute microbial abundance, they are technically challenging and costly, presenting an opportunity for machine learning. Here, we observe a strong correlation between DNA concentration and the absolute number of 16S ribosomal RNA copies as measured by digital droplet PCR in clinical stool samples from individuals undergoing hematopoietic cell transplantation (BMT CTN 1801). Based on this correlation and additional measurements, we trained an accurate yet simple machine learning model for the prediction of absolute prokaryotic load, which showed exceptional prediction accuracy on an external cohort that includes people living with Parkinson's disease and healthy controls. We propose that, with further validation, this model has the potential to enable accurate absolute abundance estimation based on readily available sample measurements.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101030"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052505","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

Profiling human iPSC-derived sensory neurons for analgesic drug screening using a multi-electrode array. 利用多电极阵列分析人类ipsc来源的感觉神经元用于镇痛药物筛选。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-13 DOI: 10.1016/j.crmeth.2025.101051

Christian Kuete Fofie, Rafael Granja-Vazquez, Vincent Truong, Patrick Walsh, Theodore Price, Swati Biswas, Gregory Dussor, Joseph Pancrazio, Benedict Kolber

{"title":"Profiling human iPSC-derived sensory neurons for analgesic drug screening using a multi-electrode array.","authors":"Christian Kuete Fofie, Rafael Granja-Vazquez, Vincent Truong, Patrick Walsh, Theodore Price, Swati Biswas, Gregory Dussor, Joseph Pancrazio, Benedict Kolber","doi":"10.1016/j.crmeth.2025.101051","DOIUrl":"10.1016/j.crmeth.2025.101051","url":null,"abstract":"Chronic pain is a global health issue, yet effective treatments remain limited due to poor preclinical-to-human translation. To address this, we developed a high-content screening (HCS) platform using hiPSC-derived nociceptors to identify analgesics targeting the peripheral nervous system. These cells, cultured on multi-well microelectrode arrays, achieved nearly 100% active electrodes by week 2, maintaining stable activity for at least 2 weeks. After 28 days, we assessed drug effects on neuronal activity, achieving strong assay performance (robust Z' > 0.5). Pharmacological tests confirmed responses to key analgesic targets, including ion channels (Nav, Cav, Kv, and TRPV1), neurotransmitter receptors (AMPAR and GABA-R), and kinase inhibitors (tyrosine and JAK1/2). Transcriptomic analysis validated target expression, though levels differed from primary human DRG cells. The platform was used to screen over 700 natural compounds, demonstrating its potential for analgesic discovery. This HCS platform facilitates the rapid discovery of uncharacterized analgesics, reducing preclinical-to-human translation failure.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101051"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080953","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

Comparative analysis of gene regulation in single cells using Compass. Compass在单细胞中基因调控的比较分析。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-08 DOI: 10.1016/j.crmeth.2025.101035

Changxin Wan, Yilong Qu, Zhiyou Ye, Tianbei Zhang, Huifang Ma, Ming Chen, Wenpin Hou, Zhicheng Ji

引用次数: 0

A circadian behavioral analysis suite for real-time classification of daily rhythms in complex behaviors. 一个昼夜行为分析套件，用于复杂行为的日常节奏的实时分类。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 DOI: 10.1016/j.crmeth.2025.101050

Logan J Perry, Gavin E Ratcliff, Arthur Mayo, Blanca E Perez, Larissa Rays Wahba, K L Nikhil, William C Lenzen, Yangyuan Li, Jordan Mar, Isabella Farhy-Tselnicker, Wanhe Li, Jeff R Jones

{"title":"A circadian behavioral analysis suite for real-time classification of daily rhythms in complex behaviors.","authors":"Logan J Perry, Gavin E Ratcliff, Arthur Mayo, Blanca E Perez, Larissa Rays Wahba, K L Nikhil, William C Lenzen, Yangyuan Li, Jordan Mar, Isabella Farhy-Tselnicker, Wanhe Li, Jeff R Jones","doi":"10.1016/j.crmeth.2025.101050","DOIUrl":"10.1016/j.crmeth.2025.101050","url":null,"abstract":"Long-term analysis of animal behavior has been limited by reliance on real-time sensors or manual scoring. Existing machine learning tools can automate analysis but often fail under variable conditions or ignore temporal dynamics. We developed a scalable pipeline for continuous, real-time acquisition and classification of behavior across multiple animals and conditions. At its core is a self-supervised vision model paired with a lightweight classifier that enables robust performance with minimal manual labeling. Our system achieves expert-level performance and can operate indefinitely across diverse recording environments. As a proof-of-concept, we recorded 97 mice over 2 weeks to test whether sex hormones influence circadian behaviors. We discovered sex- and estrogen-dependent rhythms in behaviors such as digging and nesting. We introduce the Circadian Behavioral Analysis Suite (CBAS), a modular toolkit that supports high-throughput, long-timescale behavioral phenotyping, allowing for the temporal analysis of behaviors that were previously difficult or impossible to observe.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 5","pages":"101050"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112033","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

IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads. 使用PacBio高保真读数，IGLoo能够全面分析和组装淋巴母细胞样细胞系中的免疫球蛋白重链位点。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-01 DOI: 10.1016/j.crmeth.2025.101033

Mao-Jan Lin, Ben Langmead, Yana Safonova

{"title":"IGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads.","authors":"Mao-Jan Lin, Ben Langmead, Yana Safonova","doi":"10.1016/j.crmeth.2025.101033","DOIUrl":"10.1016/j.crmeth.2025.101033","url":null,"abstract":"High-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, LCLs pose technical challenges for profiling immunoglobulin (IG) genes, as their IG loci contain a mixture of germline and somatically recombined haplotypes, making genotyping and assembly difficult with widely used frameworks. To address this, we introduce IGLoo, a software tool that analyzes sequence data and assemblies derived from LCLs, characterizing somatic V(D)J recombination events and identifying breakpoints and missing IG genes in the assemblies. Furthermore, IGLoo implements a reassembly framework to improve germline assembly quality by integrating information on somatic events and population structural variations in IG loci. Applying IGLoo to the assemblies from the Human Pangenome Reference Consortium, we gained valuable insights into the mechanisms, gene usage, and patterns of V(D)J recombination and the causes of assembly artifacts in the IG heavy-chain (IGH) locus, and we improved the representation of IGH assemblies.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101033"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050631","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

CalliCog is an open-source cognitive neuroscience toolkit for freely behaving nonhuman primates. CalliCog是一个开源的认知神经科学工具包，用于自由行为的非人类灵长类动物。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-07 DOI: 10.1016/j.crmeth.2025.101034

Jack T Scott, Bruno L Mendivez Vasquez, Brian J Stewart, Dylan D Panacheril, Darren K J Rajit, Angela Y Fan, James A Bourne

{"title":"CalliCog is an open-source cognitive neuroscience toolkit for freely behaving nonhuman primates.","authors":"Jack T Scott, Bruno L Mendivez Vasquez, Brian J Stewart, Dylan D Panacheril, Darren K J Rajit, Angela Y Fan, James A Bourne","doi":"10.1016/j.crmeth.2025.101034","DOIUrl":"10.1016/j.crmeth.2025.101034","url":null,"abstract":"Nonhuman primates (NHPs) are pivotal for unlocking the complexities of human cognition, yet traditional cognitive studies remain constrained to specialized laboratories. To address this gap, we present CalliCog: an open-source, scalable in-cage platform tailored for experiments in small freely behaving primate species such as the common marmoset (Callithrix jacchus). CalliCog includes modular operant chambers that operate autonomously and integrate seamlessly with home cages, eliminating human intervention. Our results showcase the power of CalliCog to train experimentally naive marmosets in touchscreen-based cognitive tasks. Across two independent facilities, marmosets achieved touchscreen proficiency within 2 weeks and successfully completed tasks probing behavioral flexibility and working memory. Moreover, CalliCog enabled precise synchronization of behavioral data with electrocorticography (ECoG) recordings from freely moving animals, opening new frontiers for neurobehavioral research. By making CalliCog openly accessible, we aim to democratize cognitive experimentation with small NHPs, narrowing the translational gap between preclinical models and human cognition.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101034"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146646/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052843","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

An improved FLARE system for recording and manipulating neuronal activity. 用于记录和操纵神经元活动的改进的FLARE系统。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 Epub Date: 2025-03-21 DOI: 10.1016/j.crmeth.2025.101012

Guanwei Zhou, Ruonan Li, Ola Bartolik, Yuqian Ma, Wei Wei Wan, Jennifer Meng, Yujia Hu, Bing Ye, Wenjing Wang

引用次数: 0

Minimally invasive, wide-field two-photon imaging of the brainstem at cellular resolution. 脑干细胞分辨率的微创、宽视场双光子成像。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 Epub Date: 2025-04-04 DOI: 10.1016/j.crmeth.2025.101010

Masakazu Agetsuma, Azumi Hatakeyama, Daisuke Yamada, Hiroshi Kuniishi, Chihiro Ito, Eri Takeuchi, Shinji Tsuji, Motosuke Tsutsumi, Takako Ichiki, Kohei Otomo, Toshinori Yoshioka, Tomoko Kobayashi, Atsushi Noritake, Yoshitsugu Aoki, Tomomi Nemoto, Hiroshi Yukawa, Akiyoshi Saitoh, Junichi Nabekura, Masayuki Sekiguchi

{"title":"Minimally invasive, wide-field two-photon imaging of the brainstem at cellular resolution.","authors":"Masakazu Agetsuma, Azumi Hatakeyama, Daisuke Yamada, Hiroshi Kuniishi, Chihiro Ito, Eri Takeuchi, Shinji Tsuji, Motosuke Tsutsumi, Takako Ichiki, Kohei Otomo, Toshinori Yoshioka, Tomoko Kobayashi, Atsushi Noritake, Yoshitsugu Aoki, Tomomi Nemoto, Hiroshi Yukawa, Akiyoshi Saitoh, Junichi Nabekura, Masayuki Sekiguchi","doi":"10.1016/j.crmeth.2025.101010","DOIUrl":"10.1016/j.crmeth.2025.101010","url":null,"abstract":"Brain-viscera communication is crucial for regulating mental health, with the vagus nerve being a key structure mediating this interaction. Clinically, artificial vagus nerve stimulation (VNS) is used to treat various neuropsychiatric disorders, highlighting the importance of vagal afferent fibers in emotion regulation. The nucleus tractus solitarii (NTS) is a brainstem structure proposed to receive signals from vagal afferents and relay them to brain networks for emotion regulation. However, due to the anatomical complexity and difficulty in accessing the deep-brain NTS region in vivo, its underlying mechanisms remain unclear. Here, we developed a wide-field and deep-brain two-photon imaging method using a double-prism optical interface. This approach enables cellular-resolution imaging to specifically detect NTS neural activity while largely preserving the overlying cerebellum, a region also implicated in emotion regulation. We evaluated NTS neuronal responses to VNS and a gastrointestinal hormone, demonstrating the method's utility for investigating the vagus-NTS pathway in vivo.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101010"},"PeriodicalIF":4.3,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789245","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

Differential performance of strategies for single-cell whole-genome amplification. 单细胞全基因组扩增策略的差异表现。

IF 4.3

Cell Reports Methods Pub Date : 2025-04-21 DOI: 10.1016/j.crmeth.2025.101025

Nuria Estévez-Gómez, Tamara Prieto, Laura Tomás, Pilar Alvariño, Amy Guillaumet-Adkins, Holger Heyn, Sonia Prado-López, David Posada

{"title":"Differential performance of strategies for single-cell whole-genome amplification.","authors":"Nuria Estévez-Gómez, Tamara Prieto, Laura Tomás, Pilar Alvariño, Amy Guillaumet-Adkins, Holger Heyn, Sonia Prado-López, David Posada","doi":"10.1016/j.crmeth.2025.101025","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101025","url":null,"abstract":"Single-cell genomics enables studying tissues and organisms at the highest resolution. However, since a cell contains a small amount of DNA, single-cell DNA sequencing (scDNA-seq) typically requires single-cell whole-genome amplification (scWGA). Unfortunately, scWGA methods introduce technical biases that complicate the interpretation of scDNA-seq data. We compared six scWGA methods, three MDA (multiple displacement amplification; GenomiPhi, REPLI-g, and TruePrime) and three non-MDA (Ampli1, MALBAC, and PicoPLEX), on 206 tumoral and 24 healthy human cells. scWGA methods performed differently depending on the parameter of interest. REPLI-g minimized regional amplification bias, while non-MDA methods showed a more uniform and reproducible amplification. Ampli1 exhibited the lowest allelic imbalance and dropout, the most accurate insertion or deletion (indel) and copy-number detection, and a low polymerase error rate. However, REPLI-g yielded higher DNA quantities, longer amplicons, and greater genome coverage. We offer a comprehensive guide for selecting a scWGA approach, outlining trade-offs that influence the interpretation of scDNA-seq data.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 4","pages":"101025"},"PeriodicalIF":4.3,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144031525","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