Cell Reports Methods最新文献_第6页

Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. CITE-seq数据的多模式分层分类描绘了跨谱系和组织的免疫细胞状态。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2025-01-14 DOI: 10.1016/j.crmeth.2024.100938

Daniel P Caron, William L Specht, David Chen, Steven B Wells, Peter A Szabo, Isaac J Jensen, Donna L Farber, Peter A Sims

{"title":"Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues.","authors":"Daniel P Caron, William L Specht, David Chen, Steven B Wells, Peter A Szabo, Isaac J Jensen, Donna L Farber, Peter A Sims","doi":"10.1016/j.crmeth.2024.100938","DOIUrl":"10.1016/j.crmeth.2024.100938","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins. Cellular indexing of transcriptomes and epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes; however, accurate cell-type annotation requires a classifier that integrates multimodal data. Here, we describe multimodal classifier hierarchy (MMoCHi), a marker-based approach for accurate cell-type classification across multiple single-cell modalities that does not rely on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal subset markers. MMoCHi is designed for adaptability and can integrate annotation of cell types and developmental states across diverse lineages, samples, or modalities.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100938"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013083","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

Unifying community whole-brain imaging datasets enables robust neuron identification and reveals determinants of neuron position in C. elegans. 统一的社区全脑成像数据集可以实现稳健的神经元识别，并揭示秀丽隐杆线虫神经元位置的决定因素。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2025-01-17 DOI: 10.1016/j.crmeth.2024.100964

Daniel Y Sprague, Kevin Rusch, Raymond L Dunn, Jackson M Borchardt, Steven Ban, Greg Bubnis, Grace C Chiu, Chentao Wen, Ryoga Suzuki, Shivesh Chaudhary, Hyun Jee Lee, Zikai Yu, Benjamin Dichter, Ryan Ly, Shuichi Onami, Hang Lu, Koutarou D Kimura, Eviatar Yemini, Saul Kato

{"title":"Unifying community whole-brain imaging datasets enables robust neuron identification and reveals determinants of neuron position in C. elegans.","authors":"Daniel Y Sprague, Kevin Rusch, Raymond L Dunn, Jackson M Borchardt, Steven Ban, Greg Bubnis, Grace C Chiu, Chentao Wen, Ryoga Suzuki, Shivesh Chaudhary, Hyun Jee Lee, Zikai Yu, Benjamin Dichter, Ryan Ly, Shuichi Onami, Hang Lu, Koutarou D Kimura, Eviatar Yemini, Saul Kato","doi":"10.1016/j.crmeth.2024.100964","DOIUrl":"10.1016/j.crmeth.2024.100964","url":null,"abstract":"We develop a data harmonization approach for C. elegans volumetric microscopy data, consisting of a standardized format, pre-processing techniques, and human-in-the-loop machine-learning-based analysis tools. Using this approach, we unify a diverse collection of 118 whole-brain neural activity imaging datasets from five labs, storing these and accompanying tools in an online repository WormID (wormid.org). With this repository, we train three existing automated cell-identification algorithms, CPD, StatAtlas, and CRF_ID, to enable accuracy that generalizes across labs, recovering all human-labeled neurons in some cases. We mine this repository to identify factors that influence the developmental positioning of neurons. This growing resource of data, code, apps, and tutorials enables users to (1) study neuroanatomical organization and neural activity across diverse experimental paradigms, (2) develop and benchmark algorithms for automated neuron detection, segmentation, cell identification, tracking, and activity extraction, and (3) share data with the community and comply with data-sharing policies.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100964"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013087","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

A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex. 针对普通包柔氏包虫病的核心基因组多基因组测序技术（MLST）方案有助于深入了解该物种复合体的进化历史。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2024-12-18 DOI: 10.1016/j.crmeth.2024.100935

Sabrina Hepner, Keith A Jolley, Santiago Castillo-Ramirez, Evangelos Mourkas, Alexandra Dangel, Andreas Wieser, Johannes Hübner, Andreas Sing, Volker Fingerle, Gabriele Margos

{"title":"A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex.","authors":"Sabrina Hepner, Keith A Jolley, Santiago Castillo-Ramirez, Evangelos Mourkas, Alexandra Dangel, Andreas Wieser, Johannes Hübner, Andreas Sing, Volker Fingerle, Gabriele Margos","doi":"10.1016/j.crmeth.2024.100935","DOIUrl":"10.1016/j.crmeth.2024.100935","url":null,"abstract":"Multi-locus sequence typing (MLST) based on eight genes has become the method of choice for Borrelia typing and is extensively used for population studies. Whole-genome sequencing enables studies to scale up to genomic levels but necessitates extended schemes. We have developed a 639-loci core genome MLST (cgMLST) scheme for Borrelia burgdorferi sensu lato (s.l.) that enables unambiguous genotyping and improves the robustness of phylogenies and lineage resolution within species. Notably, all inner nodes of the cgMLST phylogenies had consistently high statistical support. Analyses of the genetically homogeneous European B. bavariensis population support the notion that cgMLST provides high discriminatory power even for closely related isolates. While isolates differed maximally in one MLST locus, there were up to 179 cgMLST loci differences. Thus, the developed cgMLST scheme for B. burgdorferi s.l. resolves lineages at a finer resolution than MLST and improves insights into the evolutionary history of the species complex.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100935"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865597","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

The FIRE biosensor illuminates iron regulatory protein activity and cellular iron homeostasis. FIRE生物传感器照亮铁调节蛋白活性和细胞铁稳态。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2025-01-16 DOI: 10.1016/j.crmeth.2024.100960

Carolyn Sangokoya

引用次数: 0

Accelerated protein retention expansion microscopy using microwave radiation. 利用微波辐射加速蛋白质保留扩展显微镜。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-11-22 DOI: 10.1016/j.crmeth.2024.100907

Meghan R Bullard, Juan Carlos Martinez-Cervantes, Norisha B Quaicoe, Amanda Jin, Danya A Adams, Jessica M Lin, Elena Iliadis, Tess M Seidler, Isaac Cervantes-Sandoval, Hai-Yan He

{"title":"Accelerated protein retention expansion microscopy using microwave radiation.","authors":"Meghan R Bullard, Juan Carlos Martinez-Cervantes, Norisha B Quaicoe, Amanda Jin, Danya A Adams, Jessica M Lin, Elena Iliadis, Tess M Seidler, Isaac Cervantes-Sandoval, Hai-Yan He","doi":"10.1016/j.crmeth.2024.100907","DOIUrl":"10.1016/j.crmeth.2024.100907","url":null,"abstract":"Protein retention expansion microscopy (ExM) retains fluorescent signals in fixed tissue and isotropically expands the tissue to allow nanoscale (<70 nm) resolution on diffraction-limited confocal microscopes. Despite the numerous advantages of ExM, the protocol is time-consuming. Here, we adapted an ExM protocol to vibratome-sectioned brain tissue of Xenopus laevis tadpoles and implemented a microwave (M/W)-assisted protocol (M/WExM) to reduce the workflow from days to hours. Our M/WExM protocol maintains the superior resolution of the original ExM protocol and yields a higher magnitude of expansion, suggesting that M/W radiation may also facilitate the expansion process. We then adapted the M/W protocol to the whole-mount brain of Drosophila melanogaster fruit flies, and successfully reduced the processing time of a widely used Drosophila IHC-ExM protocol from 6 to 2 days. This demonstrates that with appropriate adjustment of M/W parameters, this protocol can be readily adapted to different organisms and tissue types to greatly increase the efficiency of ExM experiments.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100907"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704622/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142695867","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

Ensemble and consensus approaches to prediction of recessive inheritance for missense variants in human disease. 人类疾病中错义变异隐性遗传预测的集合和共识方法。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-09 DOI: 10.1016/j.crmeth.2024.100914

Ben O Petrazzini, Daniel J Balick, Iain S Forrest, Judy Cho, Ghislain Rocheleau, Daniel M Jordan, Ron Do

{"title":"Ensemble and consensus approaches to prediction of recessive inheritance for missense variants in human disease.","authors":"Ben O Petrazzini, Daniel J Balick, Iain S Forrest, Judy Cho, Ghislain Rocheleau, Daniel M Jordan, Ron Do","doi":"10.1016/j.crmeth.2024.100914","DOIUrl":"10.1016/j.crmeth.2024.100914","url":null,"abstract":"Mode of inheritance (MOI) is necessary for clinical interpretation of pathogenic variants; however, the majority of variants lack this information. Furthermore, variant effect predictors are fundamentally insensitive to recessive-acting diseases. Here, we present MOI-Pred, a variant pathogenicity prediction tool that accounts for MOI, and ConMOI, a consensus method that integrates variant MOI predictions from three independent tools. MOI-Pred integrates evolutionary and functional annotations to produce variant-level predictions that are sensitive to both dominant-acting and recessive-acting pathogenic variants. Both MOI-Pred and ConMOI show state-of-the-art performance on standard benchmarks. Importantly, dominant and recessive predictions from both tools are enriched in individuals with pathogenic variants for dominant- and recessive-acting diseases, respectively, in a real-world electronic health record (EHR)-based validation approach of 29,981 individuals. ConMOI outperforms its component methods in benchmarking and validation, demonstrating the value of consensus among multiple prediction methods. Predictions for all possible missense variants are provided in the \"Data and code availability\" section.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100914"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808086","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

RFW captures species-level metagenomic functions by integrating genome annotation information. RFW通过整合基因组注释信息捕获物种水平的宏基因组功能。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-10 DOI: 10.1016/j.crmeth.2024.100932

Kai Mi, Rui Xu, Xingyin Liu

引用次数: 0

Synthetic mismatches enable specific CRISPR-Cas12a-based detection of genome-wide SNVs tracked by ARTEMIS. 合成错配使基于crispr - cas12的全基因组snv特异性检测成为可能。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-06 DOI: 10.1016/j.crmeth.2024.100912

Kavish A V Kohabir, Jasper Linthorst, Lars O Nooi, Rick Brouwer, Rob M F Wolthuis, Erik A Sistermans

{"title":"Synthetic mismatches enable specific CRISPR-Cas12a-based detection of genome-wide SNVs tracked by ARTEMIS.","authors":"Kavish A V Kohabir, Jasper Linthorst, Lars O Nooi, Rick Brouwer, Rob M F Wolthuis, Erik A Sistermans","doi":"10.1016/j.crmeth.2024.100912","DOIUrl":"10.1016/j.crmeth.2024.100912","url":null,"abstract":"Detection of pathogenic DNA variants is vital in cancer diagnostics and treatment monitoring. While CRISPR-based diagnostics (CRISPRdx) offer promising avenues for cost-effective, rapid, and point-of-care testing, achieving single-nucleotide detection fidelity remains challenging. We present an in silico pipeline that scans the human genome for targeting pathogenic mutations in the seed region (ARTEMIS), the most stringent crRNA domain. ARTEMIS identified 12% of pathogenic SNVs as Cas12a recognizable, including 928 cancer-associated variants such as BRAFV600E, BRCA2E1953∗, TP53V272M, and ALDH2E504K. Cas12a exhibited remarkable tolerance to single mismatches within the seed region. Introducing deliberate synthetic mismatches within the seed region yielded on-target activity with single-nucleotide fidelity. Both positioning and nucleobase types of mismatches influenced detection accuracy. With improved specificity, Cas12a could accurately detect and semi-quantify BRAFV600E in cfDNA from cell lines and patient liquid biopsies. These results provide insights toward rationalized crRNA design for high-fidelity CRISPRdx, supporting personalized and cost-efficient healthcare solutions in oncologic diagnostics.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100912"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142792444","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

Single-cell RNA sequencing algorithms underestimate changes in transcriptional noise compared to single-molecule RNA imaging. 与单分子RNA成像相比，单细胞RNA测序算法低估了转录噪声的变化。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-10 DOI: 10.1016/j.crmeth.2024.100933

Neha Khetan, Binyamin Zuckerman, Giuliana P Calia, Xinyue Chen, Ximena Garcia Arceo, Leor S Weinberger

{"title":"Single-cell RNA sequencing algorithms underestimate changes in transcriptional noise compared to single-molecule RNA imaging.","authors":"Neha Khetan, Binyamin Zuckerman, Giuliana P Calia, Xinyue Chen, Ximena Garcia Arceo, Leor S Weinberger","doi":"10.1016/j.crmeth.2024.100933","DOIUrl":"10.1016/j.crmeth.2024.100933","url":null,"abstract":"Stochastic fluctuations (noise) in transcription generate substantial cell-to-cell variability. However, how best to quantify genome-wide noise remains unclear. Here, we utilize a small-molecule perturbation (5'-iodo-2'-deoxyuridine [IdU]) to amplify noise and assess noise quantification from numerous single-cell RNA sequencing (scRNA-seq) algorithms on human and mouse datasets and then compare it to noise quantification from single-molecule RNA fluorescence in situ hybridization (smFISH) for a panel of representative genes. We find that various scRNA-seq analyses report amplified noise-without altered mean expression levels-for ∼90% of genes and that smFISH analysis verifies noise amplification for the vast majority of tested genes. Collectively, the analyses suggest that most scRNA-seq algorithms (including a simple normalization approach) are appropriate for quantifying noise, although all algorithms appear to systematically underestimate noise changes compared to smFISH. For practical purposes, this analysis further argues that IdU noise enhancement is globally penetrant-i.e., homeostatically increasing noise without altering mean expression levels-and could enable investigations of the physiological impacts of transcriptional noise.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100933"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814498","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

High-throughput specificity profiling of antibody libraries using ribosome display and microfluidics. 利用核糖体展示和微流体技术对抗体文库进行高通量特异性分析。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 DOI: 10.1016/j.crmeth.2024.100934

Ellen K Wagner, Kyle P Carter, Yoong Wearn Lim, Geeyun Jenny Chau, Alexis Enstrom, Nicholas P Wayham, Jessica-Mae Hanners, Chiann-Ling C Yeh, Marc Fouet, Jackson Leong, Adam S Adler, Jan Fredrik Simons

{"title":"High-throughput specificity profiling of antibody libraries using ribosome display and microfluidics.","authors":"Ellen K Wagner, Kyle P Carter, Yoong Wearn Lim, Geeyun Jenny Chau, Alexis Enstrom, Nicholas P Wayham, Jessica-Mae Hanners, Chiann-Ling C Yeh, Marc Fouet, Jackson Leong, Adam S Adler, Jan Fredrik Simons","doi":"10.1016/j.crmeth.2024.100934","DOIUrl":"10.1016/j.crmeth.2024.100934","url":null,"abstract":"In this work, we developed PolyMap (polyclonal mapping), a high-throughput method for mapping protein-protein interactions. We demonstrated the mapping of thousands of antigen-antibody interactions between diverse antibody libraries isolated from convalescent and vaccinated COVID-19 donors and a set of clinically relevant SARS-CoV-2 spike variants. We identified over 150 antibodies with a variety of distinctive binding patterns toward the antigen variants and found a broader binding profile, including targeting of the Omicron variant, in the antibody repertoires of more recent donors. We then used these data to select mixtures of a small number of clones with complementary reactivity that together provide strong potency and broad neutralization. PolyMap is a generalizable platform that can be used for one-pot epitope mapping, immune repertoire profiling, and therapeutic design and, in the future, could be expanded to other families of interacting proteins.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"4 12","pages":"100934"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11704616/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142847770","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