Cell Reports Methods最新文献

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 : 2025-04-02 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":"https://doi.org/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":"2025-04-02","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

Rapid and robust generation of cardiomyocyte-specific crispants in zebrafish using the cardiodeleter system. 使用cardiodeleter系统在斑马鱼中快速稳健地生成心肌细胞特异性criscriss。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 DOI: 10.1016/j.crmeth.2025.101003

Sean Keeley, Miriam Fernández-Lajarín, David Bergemann, Nicolette John, Lily Parrott, Brittany E Andrea, Juan Manuel González-Rosa

{"title":"Rapid and robust generation of cardiomyocyte-specific crispants in zebrafish using the cardiodeleter system.","authors":"Sean Keeley, Miriam Fernández-Lajarín, David Bergemann, Nicolette John, Lily Parrott, Brittany E Andrea, Juan Manuel González-Rosa","doi":"10.1016/j.crmeth.2025.101003","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101003","url":null,"abstract":"CRISPR-Cas9 has accelerated loss-of-function studies in zebrafish, but creating tissue-specific mutant lines is still labor intensive. While some tissue-specific Cas9 zebrafish lines exist, standardized methods for gene targeting, including guide RNA (gRNA) delivery, are lacking, limiting broader use in the community. To tackle these limitations, we develop a cardiomyocyte-specific Cas9 line, the cardiodeleter, that efficiently generates biallelic mutations in combination with gene-specific gRNAs. We create transposon-based guide shuttles that deliver gRNAs targeting a gene of interest while permanently labeling cells susceptible to becoming mutant. We validate this modular approach by deleting five genes (ect2, tnnt2a, cmlc2, amhc, and erbb2), resulting in the loss of the corresponding protein or phenocopy of established mutants. We provide detailed protocols for generating guide shuttles, facilitating the adoption of these techniques in the zebrafish community. Our approach enables rapid generation of tissue-specific crispants and analysis of mosaic phenotypes, making it a valuable tool for cell-autonomous studies and genetic screening.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 3","pages":"101003"},"PeriodicalIF":4.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711481","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

AVID enables sensitive and accurate viral integration detection across human cancers. AVID能够在人类癌症中进行敏感和准确的病毒整合检测。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 DOI: 10.1016/j.crmeth.2025.101007

Xueying Lyu, Russell Wing-Yeung Mok, Hoi-Ying Chan, Tina Suoangbaji, Qian Li, Fanhong Zeng, Renwen Long, Irene Oi-Lin Ng, Loey Lung-Yi Mak, Daniel Wai-Hung Ho

{"title":"AVID enables sensitive and accurate viral integration detection across human cancers.","authors":"Xueying Lyu, Russell Wing-Yeung Mok, Hoi-Ying Chan, Tina Suoangbaji, Qian Li, Fanhong Zeng, Renwen Long, Irene Oi-Lin Ng, Loey Lung-Yi Mak, Daniel Wai-Hung Ho","doi":"10.1016/j.crmeth.2025.101007","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101007","url":null,"abstract":"Oncovirus infection is a key etiological risk factor of human cancers, which triggers virus integration in the host genome. Viral integration can lead to structural variation, gene dysfunction, and genome instability, promoting tumorigenesis. To support the investigation of virus-associated cancer and improve the detection of virus infection, we developed an algorithm called AVID (accurate viral integration detector) for viral integration detection. AVID was built by overcoming the existing detection limitations, enhancing sensitivity and accuracy, and expanding additional functions of viral integration detection. The performance of AVID was estimated in simulated datasets and experimentally validated datasets compared with other tools. To demonstrate its wide applicability, we also tested AVID on viral integration detection in multiple oncovirus-associated human cancers, including hepatocellular carcinoma (HCC), cervical cancer, and nasopharyngeal carcinoma. Taken together, our study developed an improved and applicable tool for viral integration detection and visualization to facilitate further exploration of virus-infected diseases.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 3","pages":"101007"},"PeriodicalIF":4.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711473","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

A sequence context-based approach for classifying tumor structural variants without paired normal samples. 一个序列上下文为基础的方法分类肿瘤结构变异没有配对正常样本。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 Epub Date: 2025-03-12 DOI: 10.1016/j.crmeth.2025.100991

Wolu Chukwu, Siyun Lee, Alexander Crane, Shu Zhang, Sophie Webster, Oumayma Dakhama, Ipsa Mittra, Carlos Rauert, Marcin Imielinski, Rameen Beroukhim, Frank Dubois, Simona Dalin

引用次数: 0

Directing microbial co-culture composition using cybernetic control. 利用控制论控制指导微生物共培养组成。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 DOI: 10.1016/j.crmeth.2025.101009

Ting An Lee, Jan Morlock, John Allan, Harrison Steel

引用次数: 0

Thickness- and quality-controlled fabrication of fluorescence-targeted frozen-hydrated lamellae. 厚度和质量控制制备荧光靶向冷冻水合薄片。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 DOI: 10.1016/j.crmeth.2025.101004

Daan B Boltje, Radim Skoupý, Clémence Taisne, Wiel H Evers, Arjen J Jakobi, Jacob P Hoogenboom

{"title":"Thickness- and quality-controlled fabrication of fluorescence-targeted frozen-hydrated lamellae.","authors":"Daan B Boltje, Radim Skoupý, Clémence Taisne, Wiel H Evers, Arjen J Jakobi, Jacob P Hoogenboom","doi":"10.1016/j.crmeth.2025.101004","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101004","url":null,"abstract":"Cryogenic focused ion beam (FIB) milling is essential for fabricating thin lamella-shaped samples out of frozen-hydrated cells for high-resolution structure determination. Structural information can only be resolved at high resolution if the lamella thickness is between 100 and 200 nm. While the lamella fabrication workflow has improved significantly since its conception, quantitative, live feedback on lamella thickness, quality, and biological target inclusion remains lacking. Using coincident light microscopy integrated into the FIB scanning electron microscope (FIB-SEM), we present three strategies that enable accurate, live control during lamella fabrication. First, we combine four-dimensional (4D) STEM with fluorescence microscopy (FM) targeting to determine lamella thickness. Second, with reflected light microscopy (RLM), we screen target sites for ice contamination and monitor lamella thickness and protective Pt coating integrity during FIB milling. Third, we exploit thin-film interference for fine-grained feedback on thickness uniformity below 500 nm. Finally, we present a fluorescence-targeted, quality-controlled workflow for frozen-hydrated lamellae, benchmarked with excellent agreement with energy-filtered transmission electron microscopy (EFTEM) measurements and tomograms from electron cryotomography.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 3","pages":"101004"},"PeriodicalIF":4.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711493","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

The development of a canine single-chain phage antibody library to isolate recombinant antibodies for use in translational cancer research. 犬单链噬菌体抗体文库的建立，分离重组抗体用于转化性癌症研究。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 DOI: 10.1016/j.crmeth.2025.101008

Małgorzata Lisowska, Erin G Worrall, Filip Zavadil-Kokas, Keith Charlton, Euan Murray, M Aiman Mohtar, Radovan Krejcir, Vaclav Hrabal, Jack Brydon, Ainhoa Gonzalez Urionabarrenetxea, David G Saliba, Mariana Grima, Umesh Kalathiya, Petr Muller, Adam Krejci, Borivoj Vojtesek, Kathryn L Ball, Robin Fahraeus, David J Argyle, Maciej Parys, Ted R Hupp

{"title":"The development of a canine single-chain phage antibody library to isolate recombinant antibodies for use in translational cancer research.","authors":"Małgorzata Lisowska, Erin G Worrall, Filip Zavadil-Kokas, Keith Charlton, Euan Murray, M Aiman Mohtar, Radovan Krejcir, Vaclav Hrabal, Jack Brydon, Ainhoa Gonzalez Urionabarrenetxea, David G Saliba, Mariana Grima, Umesh Kalathiya, Petr Muller, Adam Krejci, Borivoj Vojtesek, Kathryn L Ball, Robin Fahraeus, David J Argyle, Maciej Parys, Ted R Hupp","doi":"10.1016/j.crmeth.2025.101008","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101008","url":null,"abstract":"The development of canine immunotolerant monoclonal antibodies can accelerate the invention of new medicines for both canine and human diseases. We develop a methodology to clone the naive, somatically mutated variable domain repertoire from canine B cell mRNA using 5'RACE PCR. A set of degenerate primers were then designed and used to clone variable domain genes into archival \"holding\" plasmid libraries. These archived variable domain genes were then combinatorially ligated to produce a scFv M13 phage library. Next-generation long-read and short-read DNA sequencing methodologies were developed to annotate features of the cloned library including CDR diversity and IGHV/IGKV/IGLV subfamily distribution. A synthetic immunoglobulin G was developed from this scFv library to the canine immune checkpoint receptor PD-1. This synthetic platform can be used to clone and annotate archived antibody variable domain genes for use in perpetuity in order to develop improved preclinical models for the treatment of complex human diseases.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 3","pages":"101008"},"PeriodicalIF":4.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711486","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

Comprehensive assessment of computational methods for cancer immunoediting. 癌症免疫编辑计算方法的综合评估。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 DOI: 10.1016/j.crmeth.2025.101006

Shengyuan He, Shangqin Sun, Kun Liu, Bo Pang, Yun Xiao

{"title":"Comprehensive assessment of computational methods for cancer immunoediting.","authors":"Shengyuan He, Shangqin Sun, Kun Liu, Bo Pang, Yun Xiao","doi":"10.1016/j.crmeth.2025.101006","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101006","url":null,"abstract":"Cancer immunoediting reflects the role of the immune system in eliminating tumor cells and shaping tumor immunogenicity, which leaves marks in the genome. In this study, we systematically evaluate four methods for quantifying immunoediting. In colorectal cancer samples from The Cancer Genome Atlas, we found that these methods identified 78.41%, 46.17%, 36.61%, and 4.92% of immunoedited samples, respectively, covering 92.90% of all colorectal cancer samples. Comparison of 10 patient-derived xenografts (PDXs) with their original tumors showed that different methods identified reduced immune selection in PDXs ranging from 44.44% to 60.0%. The proportion of such PDX-tumor pairs increases to 77.78% when considering the union of results from multiple methods, indicating the complementarity of these methods. We find that observed-to-expected ratios highly rely on neoantigen selection criteria and reference datasets. In contrast, HLA-binding mutation ratio, immune dN/dS, and enrichment score of cancer cell fraction were less affected by these factors. Our findings suggest integration of multiple methods may benefit future immunoediting analyses.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 3","pages":"101006"},"PeriodicalIF":4.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143711474","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

A comprehensive and standardized pipeline for automated profiling of higher cognition in mice. 用于自动分析小鼠高级认知能力的综合标准化管道。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 Epub Date: 2025-03-17 DOI: 10.1016/j.crmeth.2025.101011

Vinicius Daguano Gastaldi, Martin Hindermann, Justus B H Wilke, Anja Ronnenberg, Sahab Arinrad, Sabine Kraus, Anne-Fleur Wildenburg, Antonios Ntolkeras, Micah J Provost, Liu Ye, Yasmina Curto, Jonathan-Alexis Cortés-Silva, Umer Javed Butt, Klaus-Armin Nave, Kamilla Woznica Miskowiak, Hannelore Ehrenreich

{"title":"A comprehensive and standardized pipeline for automated profiling of higher cognition in mice.","authors":"Vinicius Daguano Gastaldi, Martin Hindermann, Justus B H Wilke, Anja Ronnenberg, Sahab Arinrad, Sabine Kraus, Anne-Fleur Wildenburg, Antonios Ntolkeras, Micah J Provost, Liu Ye, Yasmina Curto, Jonathan-Alexis Cortés-Silva, Umer Javed Butt, Klaus-Armin Nave, Kamilla Woznica Miskowiak, Hannelore Ehrenreich","doi":"10.1016/j.crmeth.2025.101011","DOIUrl":"10.1016/j.crmeth.2025.101011","url":null,"abstract":"In rodent behavior research, observer-independent methods, such as the IntelliCage, enhance data collection in a social, and thus stress-reduced, environment. The IntelliCage system allows experimenters to create cognitive challenges for mice motivated by rewards. Given the extensive and diverse data from IntelliCage, there is a high demand for automated analysis. Here, we introduce IntelliR, a free and standardized pipeline for analyzing IntelliCage data, including a cognition index for performance comparison across challenges. IntelliR supports the automatic analysis of three challenges that cover spatial, episodic-like, and working memory with their reversal tests and can also be adapted for other designs. Results from three cohorts of adult female C57B6 mice showed improved task proficiency over time. To validate cognitive impairment detection, we used adult female NexCreERT2xRosa26-eGFP-DTA mice after neuron ablation in cortex and hippocampus, in which we observed reduced learning capabilities. IntelliR integrates easily into research, improving time management and reproducibility.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101011"},"PeriodicalIF":4.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658871","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

Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes. 顺序共同组装减少了计算资源和元基因组组装基因组的错误。

IF 4.3

Cell Reports Methods Pub Date : 2025-03-24 Epub Date: 2025-03-17 DOI: 10.1016/j.crmeth.2025.101005

Hannah M Lynn, Jeffrey I Gordon

引用次数: 0