Cell Reports Methods最新文献_第10页

Precise detection of cell-type-specific domains in spatial transcriptomics. 在空间转录组学中精确检测细胞类型特异性结构域

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-09 DOI: 10.1016/j.crmeth.2024.100841

Zhihan Ruan, Weijun Zhou, Hong Liu, Jinmao Wei, Yichen Pan, Chaoyang Yan, Xiaoyi Wei, Wenting Xiang, Chengwei Yan, Shengquan Chen, Jian Liu

{"title":"Precise detection of cell-type-specific domains in spatial transcriptomics.","authors":"Zhihan Ruan, Weijun Zhou, Hong Liu, Jinmao Wei, Yichen Pan, Chaoyang Yan, Xiaoyi Wei, Wenting Xiang, Chengwei Yan, Shengquan Chen, Jian Liu","doi":"10.1016/j.crmeth.2024.100841","DOIUrl":"10.1016/j.crmeth.2024.100841","url":null,"abstract":"Cell-type-specific domains are the anatomical domains in spatially resolved transcriptome (SRT) tissues where particular cell types are enriched coincidentally. It is challenging to use existing computational methods to detect specific domains with low-proportion cell types, which are partly overlapped with or even inside other cell-type-specific domains. Here, we propose De-spot, which synthesizes segmentation and deconvolution as an ensemble to generate cell-type patterns, detect low-proportion cell-type-specific domains, and display these domains intuitively. Experimental evaluation showed that De-spot enabled us to discover the co-localizations between cancer-associated fibroblasts and immune-related cells that indicate potential tumor microenvironment (TME) domains in given slices, which were obscured by previous computational methods. We further elucidated the identified domains and found that Srgn may be a critical TME marker in SRT slices. By deciphering T cell-specific domains in breast cancer tissues, De-spot also revealed that the proportions of exhausted T cells were significantly increased in invasive vs. ductal carcinoma.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100841"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384096/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914181","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

Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics. Nova-ST：用于空间转录组学的纳米图案超密集平台。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-06 DOI: 10.1016/j.crmeth.2024.100831

Suresh Poovathingal, Kristofer Davie, Lars E Borm, Roel Vandepoel, Nicolas Poulvellarie, Annelien Verfaillie, Nikky Corthout, Stein Aerts

引用次数: 0

Discovery and generalization of tissue structures from spatial omics data. 从空间 omics 数据中发现和归纳组织结构。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-09 DOI: 10.1016/j.crmeth.2024.100838

Zhenqin Wu, Ayano Kondo, Monee McGrady, Ethan A G Baker, Benjamin Chidester, Eric Wu, Maha K Rahim, Nathan A Bracey, Vivek Charu, Raymond J Cho, Jeffrey B Cheng, Maryam Afkarian, James Zou, Aaron T Mayer, Alexandro E Trevino

{"title":"Discovery and generalization of tissue structures from spatial omics data.","authors":"Zhenqin Wu, Ayano Kondo, Monee McGrady, Ethan A G Baker, Benjamin Chidester, Eric Wu, Maha K Rahim, Nathan A Bracey, Vivek Charu, Raymond J Cho, Jeffrey B Cheng, Maryam Afkarian, James Zou, Aaron T Mayer, Alexandro E Trevino","doi":"10.1016/j.crmeth.2024.100838","DOIUrl":"10.1016/j.crmeth.2024.100838","url":null,"abstract":"Tissues are organized into anatomical and functional units at different scales. New technologies for high-dimensional molecular profiling in situ have enabled the characterization of structure-function relationships in increasing molecular detail. However, it remains a challenge to consistently identify key functional units across experiments, tissues, and disease contexts, a task that demands extensive manual annotation. Here, we present spatial cellular graph partitioning (SCGP), a flexible method for the unsupervised annotation of tissue structures. We further present a reference-query extension pipeline, SCGP-Extension, that generalizes reference tissue structure labels to previously unseen samples, performing data integration and tissue structure discovery. Our experiments demonstrate reliable, robust partitioning of spatial data in a wide variety of contexts and best-in-class accuracy in identifying expertly annotated structures. Downstream analysis on SCGP-identified tissue structures reveals disease-relevant insights regarding diabetic kidney disease, skin disorder, and neoplastic diseases, underscoring its potential to drive biological insight and discovery from spatial datasets.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100838"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914177","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

Genome editing using type I-E CRISPR-Cas3 in mice and rat zygotes. 利用 I-E 型 CRISPR-Cas3 在小鼠和大鼠子代中进行基因组编辑。

IF 4.3

Cell Reports Methods Pub Date : 2024-08-19 Epub Date: 2024-08-08 DOI: 10.1016/j.crmeth.2024.100833

Kazuto Yoshimi, Akihiro Kuno, Yuko Yamauchi, Kosuke Hattori, Hiromi Taniguchi, Kouya Mikamo, Ryuya Iida, Saeko Ishida, Motohito Goto, Kohei Takeshita, Ryoji Ito, Riichi Takahashi, Satoru Takahashi, Tomoji Mashimo

{"title":"Genome editing using type I-E CRISPR-Cas3 in mice and rat zygotes.","authors":"Kazuto Yoshimi, Akihiro Kuno, Yuko Yamauchi, Kosuke Hattori, Hiromi Taniguchi, Kouya Mikamo, Ryuya Iida, Saeko Ishida, Motohito Goto, Kohei Takeshita, Ryoji Ito, Riichi Takahashi, Satoru Takahashi, Tomoji Mashimo","doi":"10.1016/j.crmeth.2024.100833","DOIUrl":"10.1016/j.crmeth.2024.100833","url":null,"abstract":"The type I CRISPR system has recently emerged as a promising tool, especially for large-scale genomic modification, but its application to generate model animals by editing zygotes had not been established. In this study, we demonstrate genome editing in zygotes using the type I-E CRISPR-Cas3 system, which efficiently generates deletions of several thousand base pairs at targeted loci in mice with 40%-70% editing efficiency without off-target mutations. To overcome the difficulties associated with detecting the variable deletions, we used a newly long-read sequencing-based multiplex genotyping approach. Demonstrating remarkable versatility, our Cas3-based technique was successfully extended to rats as well as mice, even by zygote electroporation methods. Knockin for SNP exchange and genomic replacement with a donor plasmid were also achieved in mice. This pioneering work with the type I CRISPR zygote editing system offers increased flexibility and broader applications in genetic engineering across different species.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100833"},"PeriodicalIF":4.3,"publicationDate":"2024-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11384072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914178","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

Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue. 抗体辅助选择性分离小鼠小脑组织中的浦肯野细胞核。

IF 4.3

Cell Reports Methods Pub Date : 2024-07-15 Epub Date: 2024-07-08 DOI: 10.1016/j.crmeth.2024.100816

Luke C Bartelt, Mouad Fakhri, Grazyna Adamek, Magdalena Trybus, Anna Samelak-Czajka, Paulina Jackowiak, Agnieszka Fiszer, Craig B Lowe, Albert R La Spada, Pawel M Switonski

{"title":"Antibody-assisted selective isolation of Purkinje cell nuclei from mouse cerebellar tissue.","authors":"Luke C Bartelt, Mouad Fakhri, Grazyna Adamek, Magdalena Trybus, Anna Samelak-Czajka, Paulina Jackowiak, Agnieszka Fiszer, Craig B Lowe, Albert R La Spada, Pawel M Switonski","doi":"10.1016/j.crmeth.2024.100816","DOIUrl":"10.1016/j.crmeth.2024.100816","url":null,"abstract":"We developed a method that utilizes fluorescent labeling of nuclear envelopes alongside cytometry sorting for the selective isolation of Purkinje cell (PC) nuclei. Beginning with SUN1 reporter mice, we GFP-tagged envelopes to confirm that PC nuclei could be accurately separated from other cell types. We then developed an antibody-based protocol to make PC nuclear isolation more robust and adaptable to cerebellar tissues of any genotypic background. Immunofluorescent labeling of the nuclear membrane protein RanBP2 enabled the isolation of PC nuclei from C57BL/6 cerebellum. By analyzing the expression of PC markers, nuclear size, and nucleoli number, we confirmed that our method delivers a pure fraction of PC nuclei. To demonstrate its applicability, we isolated PC nuclei from spinocerebellar ataxia type 7 (SCA7) mice and identified transcriptional changes in known and new disease-associated genes. Access to pure PC nuclei offers insights into PC biology and pathology, including the nature of selective neuronal vulnerability.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100816"},"PeriodicalIF":4.3,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141564709","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

Detection of fluorescent protein mechanical switching in cellulo. 检测细胞中的荧光蛋白机械开关。

IF 4.3

Cell Reports Methods Pub Date : 2024-07-15 Epub Date: 2024-07-09 DOI: 10.1016/j.crmeth.2024.100815

T Curtis Shoyer, Kasie L Collins, Trevor R Ham, Aaron T Blanchard, Juilee N Malavade, Benjamin A Johns, Jennifer L West, Brenton D Hoffman

{"title":"Detection of fluorescent protein mechanical switching in cellulo.","authors":"T Curtis Shoyer, Kasie L Collins, Trevor R Ham, Aaron T Blanchard, Juilee N Malavade, Benjamin A Johns, Jennifer L West, Brenton D Hoffman","doi":"10.1016/j.crmeth.2024.100815","DOIUrl":"10.1016/j.crmeth.2024.100815","url":null,"abstract":"The ability of cells to sense and respond to mechanical forces is critical in many physiological and pathological processes. However, determining the mechanisms by which forces affect protein function inside cells remains challenging. Motivated by in vitro demonstrations of fluorescent proteins (FPs) undergoing reversible mechanical switching of fluorescence, we investigated whether force-sensitive changes in FP function could be visualized in cells. Guided by a computational model of FP mechanical switching, we develop a formalism for its detection in Förster resonance energy transfer (FRET)-based biosensors and demonstrate its occurrence in cellulo within a synthetic actin crosslinker and the mechanical linker protein vinculin. We find that in cellulo mechanical switching is reversible and altered by manipulation of cell force generation, external stiffness, and force-sensitive bond dynamics of the biosensor. This work describes a framework for assessing FP mechanical stability and provides a means of probing force-sensitive protein function inside cells.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100815"},"PeriodicalIF":4.3,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141580964","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

Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation. Fatecode 利用分类监督自动编码器扰动技术实现细胞命运调节器预测。

IF 4.3

Cell Reports Methods Pub Date : 2024-07-15 Epub Date: 2024-07-09 DOI: 10.1016/j.crmeth.2024.100819

Mehrshad Sadria, Anita Layton, Sidhartha Goyal, Gary D Bader

{"title":"Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation.","authors":"Mehrshad Sadria, Anita Layton, Sidhartha Goyal, Gary D Bader","doi":"10.1016/j.crmeth.2024.100819","DOIUrl":"10.1016/j.crmeth.2024.100819","url":null,"abstract":"Cell reprogramming, which guides the conversion between cell states, is a promising technology for tissue repair and regeneration, with the ultimate goal of accelerating recovery from diseases or injuries. To accomplish this, regulators must be identified and manipulated to control cell fate. We propose Fatecode, a computational method that predicts cell fate regulators based only on single-cell RNA sequencing (scRNA-seq) data. Fatecode learns a latent representation of the scRNA-seq data using a deep learning-based classification-supervised autoencoder and then performs in silico perturbation experiments on the latent representation to predict genes that, when perturbed, would alter the original cell type distribution to increase or decrease the population size of a cell type of interest. We assessed Fatecode's performance using simulations from a mechanistic gene-regulatory network model and scRNA-seq data mapping blood and brain development of different organisms. Our results suggest that Fatecode can detect known cell fate regulators from single-cell transcriptomics datasets.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100819"},"PeriodicalIF":4.3,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294839/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141580965","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

Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics. 在近距离标记蛋白质组学中利用自裂解肽进行定制控制。

IF 4.3

Cell Reports Methods Pub Date : 2024-07-15 Epub Date: 2024-07-09 DOI: 10.1016/j.crmeth.2024.100818

Louis Delhaye, George D Moschonas, Daria Fijalkowska, Annick Verhee, Delphine De Sutter, Tessa Van de Steene, Margaux De Meyer, Hanna Grzesik, Laura Van Moortel, Karolien De Bosscher, Thomas Jacobs, Sven Eyckerman

{"title":"Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics.","authors":"Louis Delhaye, George D Moschonas, Daria Fijalkowska, Annick Verhee, Delphine De Sutter, Tessa Van de Steene, Margaux De Meyer, Hanna Grzesik, Laura Van Moortel, Karolien De Bosscher, Thomas Jacobs, Sven Eyckerman","doi":"10.1016/j.crmeth.2024.100818","DOIUrl":"10.1016/j.crmeth.2024.100818","url":null,"abstract":"Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods and has quickly become the current state of the art in the field. Nevertheless, tight control of proximity-labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein of interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split/link design, we applied it to identify protein interactions of the glucocorticoid receptor and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid and non-structural protein 7 (NSP7) proteins by TurboID proximity labeling. Our results demonstrate that our T2A split/link provides an opportune control that builds upon previously established control requirements in the field.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100818"},"PeriodicalIF":4.3,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141580966","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 mammalian model reveals inorganic polyphosphate channeling into the nucleolus and induction of a hyper-condensate state. 哺乳动物模型揭示了无机多磷酸进入核仁的通道和诱导高凝状态。

IF 4.3

Cell Reports Methods Pub Date : 2024-07-15 Epub Date: 2024-07-08 DOI: 10.1016/j.crmeth.2024.100814

Filipy Borghi, Cristina Azevedo, Errin Johnson, Jemima J Burden, Adolfo Saiardi

{"title":"A mammalian model reveals inorganic polyphosphate channeling into the nucleolus and induction of a hyper-condensate state.","authors":"Filipy Borghi, Cristina Azevedo, Errin Johnson, Jemima J Burden, Adolfo Saiardi","doi":"10.1016/j.crmeth.2024.100814","DOIUrl":"10.1016/j.crmeth.2024.100814","url":null,"abstract":"Inorganic polyphosphate (polyP) is a ubiquitous polymer that controls fundamental processes. To overcome the absence of a genetically tractable mammalian model, we developed an inducible mammalian cell line expressing Escherichia coli polyphosphate kinase 1 (EcPPK1). Inducing EcPPK1 expression prompted polyP synthesis, enabling validation of polyP analytical methods. Virtually all newly synthesized polyP accumulates within the nucleus, mainly in the nucleolus. The channeled polyP within the nucleolus results in the redistribution of its markers, leading to altered rRNA processing. Ultrastructural analysis reveals electron-dense polyP structures associated with a hyper-condensed nucleolus resulting from an exacerbation of the liquid-liquid phase separation (LLPS) phenomena controlling this membraneless organelle. The selective accumulation of polyP in the nucleoli could be interpreted as an amplification of polyP channeling to where its physiological function takes place. Indeed, quantitative analysis of several mammalian cell lines confirms that endogenous polyP accumulates within the nucleolus.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100814"},"PeriodicalIF":4.3,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141564708","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

SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer. SingleCellGGM 可从单细胞转录组中识别基因表达程序，并促进通用细胞标签转移。

IF 4.3

Cell Reports Methods Pub Date : 2024-07-15 Epub Date: 2024-07-05 DOI: 10.1016/j.crmeth.2024.100813

Yupu Xu, Yuzhou Wang, Shisong Ma

{"title":"SingleCellGGM enables gene expression program identification from single-cell transcriptomes and facilitates universal cell label transfer.","authors":"Yupu Xu, Yuzhou Wang, Shisong Ma","doi":"10.1016/j.crmeth.2024.100813","DOIUrl":"10.1016/j.crmeth.2024.100813","url":null,"abstract":"Gene co-expression analysis of single-cell transcriptomes, aiming to define functional relationships between genes, is challenging due to excessive dropout values. Here, we developed a single-cell graphical Gaussian model (SingleCellGGM) algorithm to conduct single-cell gene co-expression network analysis. When applied to mouse single-cell datasets, SingleCellGGM constructed networks from which gene co-expression modules with highly significant functional enrichment were identified. We considered the modules as gene expression programs (GEPs). These GEPs enable direct cell-type annotation of individual cells without cell clustering, and they are enriched with genes required for the functions of the corresponding cells, sometimes at levels greater than 10-fold. The GEPs are conserved across datasets and enable universal cell-type label transfer across different studies. We also proposed a dimension-reduction method through averaging by GEPs for single-cell analysis, enhancing the interpretability of results. Thus, SingleCellGGM offers a unique GEP-based perspective to analyze single-cell transcriptomes and reveals biological insights shared by different single-cell datasets.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100813"},"PeriodicalIF":4.3,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11294836/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141545326","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