Cell Reports Methods最新文献

Harmonizing TUNEL with multiplexed iterative immunofluorescence enriches spatial contextualization of cell death. TUNEL与多路迭代免疫荧光的协调丰富了细胞死亡的空间语境化。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-12 DOI: 10.1016/j.crmeth.2025.101047

Marc S Sherman, Thomas McMahon-Skates, Lindsey S Gaston, Sonya W Katzen, Joseph A Majzoub, Wolfram Goessling

{"title":"Harmonizing TUNEL with multiplexed iterative immunofluorescence enriches spatial contextualization of cell death.","authors":"Marc S Sherman, Thomas McMahon-Skates, Lindsey S Gaston, Sonya W Katzen, Joseph A Majzoub, Wolfram Goessling","doi":"10.1016/j.crmeth.2025.101047","DOIUrl":"10.1016/j.crmeth.2025.101047","url":null,"abstract":"Terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) is an essential tool for detecting cell death in tissues, but its compatibility with spatial proteomic methods is unknown. We evaluated variations of the TUNEL protocol for compatibility with multiple iterative labeling by antibody neodeposition (MILAN) in acetaminophen-induced hepatocyte necrosis and dexamethasone-induced adrenocortical apoptosis. Using a commercial Click-iT-based assay as a standard, TUNEL signal could be reliably produced independent of the antigen retrieval method, with tissue-specific minor differences in signal to noise. In contrast, proteinase K treatment consistently reduced or even abrogated protein antigenicity, while pressure cooker treatment enhanced protein antigenicity for the targets tested. Antibody-based TUNEL with pressure cooker retrieval could be flexibly integrated into a MILAN staining series, and first-round TUNEL was also compatible with a second spatial proteomic method, cyclic immunofluorescence (CycIF). We anticipate that this harmonization of TUNEL with spatial proteomics will enhance the spatial contextualization of cell death in complex tissues.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101047"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144022130","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

Understanding how genetically encoded tags and crowding agents affect phase separation by heterochromatin protein HP1α. 了解基因编码标签和拥挤因子如何影响异染色质蛋白HP1α的相分离。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-04-21 DOI: 10.1016/j.crmeth.2025.101029

Ziling Kate Zhou, Kibeom Hong, Bo Huang, Geeta J Narlikar

引用次数: 0

Fluorescence microscopy through scattering media with robust matrix factorization. 荧光显微镜通过散射介质与鲁棒矩阵分解。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-04-28 DOI: 10.1016/j.crmeth.2025.101031

Zijun Gao, Zhi Ling, Wenhao Liu, Keyi Han, Hongmanlin Zhang, Xuanwen Hua, Edward A Botchwey, Shu Jia

{"title":"Fluorescence microscopy through scattering media with robust matrix factorization.","authors":"Zijun Gao, Zhi Ling, Wenhao Liu, Keyi Han, Hongmanlin Zhang, Xuanwen Hua, Edward A Botchwey, Shu Jia","doi":"10.1016/j.crmeth.2025.101031","DOIUrl":"10.1016/j.crmeth.2025.101031","url":null,"abstract":"Biological tissues, as natural scattering media, inherently disrupt structural information, presenting significant challenges for optical imaging. Complex light propagation through tissue severely degrades image quality, limiting conventional fluorescence imaging techniques to superficial depths. Extracting meaningful information from random speckle patterns is, therefore, critical for deeper tissue imaging. In this study, we present RNP (robust non-negative principal matrix factorization), an approach that enables fluorescence microscopy under diverse scattering conditions. By integrating robust feature extraction with non-negativity constraints, RNP effectively addresses challenges posed by non-sparse signals and background interference in scattering tissue environments. The framework operates on a standard epi-fluorescence platform, eliminating the need for complex instrumentation or precise alignment. The results from imaging scattered cells and tissues demonstrate substantial improvements in robustness, field of view, depth of field, and image clarity. We anticipate that RNP will become a valuable tool for overcoming scattering challenges in fluorescence microscopy and driving advancements in biomedical research.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101031"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144038578","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

CHAS infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders. CHAS在神经和精神疾病的大量脑组蛋白乙酰化研究中推断细胞类型特异性特征。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-04-28 DOI: 10.1016/j.crmeth.2025.101032

Kitty B Murphy, Yuqian Ye, Maria Tsalenchuk, Alexi Nott, Sarah J Marzi

{"title":"CHAS infers cell type-specific signatures in bulk brain histone acetylation studies of neurological and psychiatric disorders.","authors":"Kitty B Murphy, Yuqian Ye, Maria Tsalenchuk, Alexi Nott, Sarah J Marzi","doi":"10.1016/j.crmeth.2025.101032","DOIUrl":"10.1016/j.crmeth.2025.101032","url":null,"abstract":"Epigenomic profiling of the brain has largely been done on bulk tissues, limiting our understanding of cell type-specific epigenetic changes in disease states. Here, we introduce cell type-specific histone acetylation score (CHAS), a computational tool for inferring cell type-specific signatures in bulk brain H3K27ac profiles. We applied CHAS to >300 H3K27ac chromatin immunoprecipitation sequencing samples from studies of Alzheimer's disease, Parkinson's disease, autism spectrum disorder, schizophrenia, and bipolar disorder in bulk postmortem brain tissue. In addition to recapitulating known disease-associated shifts in cellular proportions, we identified cell type-specific biological insights into brain-disorder-associated regulatory variation. In most cases, genetic risk and epigenetic dysregulation targeted different cell types, suggesting independent mechanisms. For instance, genetic risk of Alzheimer's disease was exclusively enriched within microglia, while epigenetic dysregulation predominantly fell within oligodendrocyte-specific H3K27ac regions. In addition, reanalysis of the original datasets using CHAS enabled identification of biological pathways associated with each neurological and psychiatric disorder at cellular resolution.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101032"},"PeriodicalIF":4.3,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050630","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

Generation of T cell responses against broad KRAS hotspot neoantigens for cell therapy or TCR discovery. 产生针对广泛的KRAS热点新抗原的T细胞应答，用于细胞治疗或TCR的发现。

IF 4.3

Cell Reports Methods Pub Date : 2025-05-19 Epub Date: 2025-05-12 DOI: 10.1016/j.crmeth.2025.101049

Brandon P Conn, Jared L Dietze, Christian J Yee, Margaret M Hallisey, Irais Ortiz-Caraveo, Marit M van Buuren, Richard B Gaynor, Kendra C Foley, Jaewon Choi, Vikram R Juneja

引用次数: 0

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013810","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

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144052505","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

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080953","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

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

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144050631","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