Cell Reports Methods最新文献_第7页

Automated denoising of CITE-seq data with ThresholdR. 基于ThresholdR的CITE-seq数据自动去噪。

IF 4.5

Cell Reports Methods Pub Date : 2025-07-21 Epub Date: 2025-07-08 DOI: 10.1016/j.crmeth.2025.101088

Mohammad Oliaeimotlagh, Sunil Kumar, Aleksandr Taraskin, Sujit Silas Armstrong Suthahar, Vasantika Suryawanshi, Austin W T Chiang, Klaus Ley

{"title":"Automated denoising of CITE-seq data with ThresholdR.","authors":"Mohammad Oliaeimotlagh, Sunil Kumar, Aleksandr Taraskin, Sujit Silas Armstrong Suthahar, Vasantika Suryawanshi, Austin W T Chiang, Klaus Ley","doi":"10.1016/j.crmeth.2025.101088","DOIUrl":"10.1016/j.crmeth.2025.101088","url":null,"abstract":"Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) is a potent addition to single-cell RNA sequencing (scRNA-seq). This method enriches transcriptomic insights by incorporating information about the cell surface phenotype through the application of oligonucleotide-tagged monoclonal antibodies. Similar to observations in flow cytometry, the CITE-seq signal (antibody-derived tag [ADT]) contains technical noise originating from ambient antibodies within the reaction compartment, non-specific binding, and/or imperfect titration. To denoise ADT data provided through CITE-seq experiments, we present ThresholdR, an R-based automated tool, to reliably and systematically find the threshold that separates the signal from the noise for each antibody. We assess the performance of ThresholdR across different datasets and platforms and benchmark it against two alternative methods, DSB (denoised and scaled by background) and CellBender. We show that ThresholdR remedies the high false negative rates of DSB and CellBender. We propose that denoising with ThresholdR can improve cell-type annotation and improve downstream analyses.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101088"},"PeriodicalIF":4.5,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12296422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144601756","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

Joint processing of long- and short-read sequencing data with deep learning improves variant calling. 利用深度学习对长、短读序列数据进行联合处理，提高了变异调用的效率。

IF 4.5

Cell Reports Methods Pub Date : 2025-07-21 Epub Date: 2025-07-15 DOI: 10.1016/j.crmeth.2025.101107

Gennaro Gambardella

引用次数: 0

Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing. 利用PerCell染色质测序对差异蛋白-基因组结合进行高度定量测量。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-05-19 DOI: 10.1016/j.crmeth.2025.101052

Alexi Tallan, Jack Kucinski, Benjamin Sunkel, Cenny Taslim, Stephanie LaHaye, Qi Liu, Jun Qi, Meng Wang, Genevieve C Kendall, Benjamin Z Stanton

引用次数: 0

Engineering high-efficiency matriptase substrates using E. coli display for applications in prodrug activation. 利用大肠杆菌显示器设计高效基质酶底物用于前药活化。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-06-10 DOI: 10.1016/j.crmeth.2025.101077

Anna Mestre Borras, Hanna Mehari, Stefan Ståhl, John Löfblom

{"title":"Engineering high-efficiency matriptase substrates using E. coli display for applications in prodrug activation.","authors":"Anna Mestre Borras, Hanna Mehari, Stefan Ståhl, John Löfblom","doi":"10.1016/j.crmeth.2025.101077","DOIUrl":"10.1016/j.crmeth.2025.101077","url":null,"abstract":"Proteases play a crucial role in biological functions such as tumor progression and tissue homeostasis. Recently, protease-activated prodrugs have gained attention for their potential to enhance selectivity in tumor-targeted therapies. In this study, we report the engineering of substrate sequences for matriptase, a protease overexpressed in tumors and previously explored for prodrug activation in vivo. A peptide library containing millions of potential substrates was displayed on Escherichia coli, and flow cytometric sorting was used to isolate improved substrates based on cleavage efficiency. Hits were ranked by flow cytometry, and the top substrates exhibited kcat/KM values over 40-fold higher than previously reported sequences. These substrates were further evaluated in an antibody-prodrug format, demonstrating exceptional activation. The matriptase substrates hold broad potential for applications such as cleavable linkers in next-generation antibody prodrugs. Furthermore, the developed bacterial display platform shows promise for discovering substrates of other proteases.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101077"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12272249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276074","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

Expansion microscopy reveals nano-scale insights into the human neuromuscular junction. 扩展显微镜揭示了纳米尺度对人类神经肌肉连接处的洞察。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 DOI: 10.1016/j.crmeth.2025.101082

Abdullah Ramadan, Thomas M D Sheard, Abrar Alhindi, Philippa A Rust, Ross A Jones, Izzy Jayasinghe, Thomas H Gillingwater

引用次数: 0

Microendoscopy for periodic intravital end-to-end tumor imaging of cancer cells. 显微内镜用于肿瘤细胞的周期性活体端到端肿瘤成像。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-06-04 DOI: 10.1016/j.crmeth.2025.101056

Toshiyuki Goto, Masayuki Nakano, Sally Danno, Chie Ueda, Asako Sakaue-Sawano, Atsushi Miyawaki, Anna Wrabel, Ichiro Nakahara, Takahito Nishikata, Akira Mizoguchi, Yasuhisa Tamura, Kei Mizuno, Yosky Kataoka, Kazuo Funabiki

{"title":"Microendoscopy for periodic intravital end-to-end tumor imaging of cancer cells.","authors":"Toshiyuki Goto, Masayuki Nakano, Sally Danno, Chie Ueda, Asako Sakaue-Sawano, Atsushi Miyawaki, Anna Wrabel, Ichiro Nakahara, Takahito Nishikata, Akira Mizoguchi, Yasuhisa Tamura, Kei Mizuno, Yosky Kataoka, Kazuo Funabiki","doi":"10.1016/j.crmeth.2025.101056","DOIUrl":"10.1016/j.crmeth.2025.101056","url":null,"abstract":"The spatiotemporal heterogeneity in intratumor proliferative behavior of cancer cells deeply affects tumor environment characteristics and the efficacy of anticancer treatments. Thus, intravital imaging with unlimited imaging depth and cellular-level resolution is greatly desired. We developed an optical-fiber-bundle-based microendoscope with a genetically encoded fluorescent ubiquitination-based cell-cycle indicator (Fucci) system to achieve the intravital, periodic, and multicolor end-to-end imaging of the proliferative activity of cancer cells at a cellular-level resolution. This technique enabled the periodic visualization of spatiotemporal cellular responses, including cell-cycle arrest and resumption, and nuclear enlargement following the administration of anticancer drugs in living mice. It was suggested that proliferating cell ratio and nuclear enlargement in cancer cells at the surface region of tumor characterized by abundant vascular invasion contribute to aggressive tumor regrowth after chemotherapy. The application of this technique can accelerate innovation in cancer biology and therapeutics.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101056"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12272250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235395","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

CRISPR GENome and epigenome engineering improves loss-of-function genetic-screening approaches. CRISPR基因组和表观基因组工程改进了功能丧失基因筛选方法。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-06-10 DOI: 10.1016/j.crmeth.2025.101078

Jannis Stadager, Chiara Bernardini, Laura Hartmann, Henrik May, Jessica Wiepcke, Monika Kuban, Zeynab Najafova, Steven A Johnsen, Stefan Legewie, Franziska R Traube, Julian Jude, Philipp Rathert

{"title":"CRISPR GENome and epigenome engineering improves loss-of-function genetic-screening approaches.","authors":"Jannis Stadager, Chiara Bernardini, Laura Hartmann, Henrik May, Jessica Wiepcke, Monika Kuban, Zeynab Najafova, Steven A Johnsen, Stefan Legewie, Franziska R Traube, Julian Jude, Philipp Rathert","doi":"10.1016/j.crmeth.2025.101078","DOIUrl":"10.1016/j.crmeth.2025.101078","url":null,"abstract":"CRISPR-Cas9 technology has revolutionized genotype-to-phenotype assignments through large-scale loss-of-function (LOF) screens. However, limitations like editing inefficiencies and unperturbed genes cause significant noise in data collection. To address this, we introduce CRISPR gene and epigenome engineering (CRISPRgenee), which uses two specific single guide RNAs (sgRNAs) to simultaneously repress and cleave the target gene within the same cell, increasing LOF efficiencies and reproducibility. CRISPRgenee outperforms conventional CRISPR knockout (CRISPRko), CRISPR interference (CRISPRi), and CRISPRoff systems in suppressing challenging targets and regulators of cell proliferation. Additionally, it efficiently suppresses modulators of epithelial-to-mesenchymal transition (EMT) and impairs neuronal differentiation in a human induced pluripotent stem cell (iPSC) model. CRISPRgenee exhibits improved depletion efficiency, reduced sgRNA performance variance, and accelerated gene depletion compared to individual CRISPRi or CRISPRko screens, ensuring consistency in phenotypic effects and identifying more significant gene hits. By combining CRISPRko and CRISPRi, CRISPRgenee increases LOF rates without increasing genotoxic stress, facilitating library size reduction for advanced LOF screens.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101078"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12272254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276073","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

Enhancement of CRISPR-Cas12a system through universal circular RNA design. 通过通用环状RNA设计增强CRISPR-Cas12a系统。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 DOI: 10.1016/j.crmeth.2025.101076

Jiaqi Wang, Wei Zhang, Wentao Li, Qinyuan Xie, Ziyu Zang, Chaoxing Liu

{"title":"Enhancement of CRISPR-Cas12a system through universal circular RNA design.","authors":"Jiaqi Wang, Wei Zhang, Wentao Li, Qinyuan Xie, Ziyu Zang, Chaoxing Liu","doi":"10.1016/j.crmeth.2025.101076","DOIUrl":"10.1016/j.crmeth.2025.101076","url":null,"abstract":"Precise control of Cas12a activity is crucial to address incompatibility in isothermal amplification-CRISPR-Cas12a one-pot nucleic acid detection. We developed a light-triggerable circular RNA system for dynamic LbCas12a regulation. By employing circular CRISPR guide RNA (crRNA) or a split circular universal direct repeat region with a replaceable spacer, we resolved the incompatibility between isothermal amplification and CRISPR detection. This system demonstrated robust performance in detecting trace nucleic acids in clinical samples. Furthermore, DNA modifications on circular crRNA enabled CRISPR-Cas12a regulation via base excision repair (BER) enzymes, offering potential for BER enzyme detection and modulation of LbCas12a cleavage activity by BER enzymes. This programmable strategy holds promise for selective gene editing in cells with elevated BER enzyme expression, such as uracil DNA glycosylase (UDG) in colon cancer cells. The circular RNA-assisted approach represents a resource-efficient method with significant potential for medical diagnostics and future clinical gene therapy applications.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 6","pages":"101076"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12272218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318150","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

Visualizing chromatin communication in living cells through Oligo-LiveFISH. 通过Oligo-LiveFISH可视化活细胞中的染色质通讯。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-06-09 DOI: 10.1016/j.crmeth.2025.101079

Mattia Conte, Mario Nicodemi

引用次数: 0

Preserving spatial and quantitative information in unpaired biomedical image-to-image translation. 在非配对生物医学图像到图像的翻译中保留空间和定量信息。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-06-09 DOI: 10.1016/j.crmeth.2025.101074

Joshua Yedam You, Minho Eom, Tae-Ik Choi, Eun-Seo Cho, Jieun Choi, Minyoung Lee, Changyeop Shin, Jieun Moon, Eunji Kim, Pilhan Kim, Cheol-Hee Kim, Young-Gyu Yoon

{"title":"Preserving spatial and quantitative information in unpaired biomedical image-to-image translation.","authors":"Joshua Yedam You, Minho Eom, Tae-Ik Choi, Eun-Seo Cho, Jieun Choi, Minyoung Lee, Changyeop Shin, Jieun Moon, Eunji Kim, Pilhan Kim, Cheol-Hee Kim, Young-Gyu Yoon","doi":"10.1016/j.crmeth.2025.101074","DOIUrl":"10.1016/j.crmeth.2025.101074","url":null,"abstract":"Analysis of biological samples often requires integrating diverse imaging modalities to gain a comprehensive understanding. While supervised biomedical image translation methods have shown success in synthesizing images across different modalities, they require paired data, which are often impractical to obtain due to challenges in data alignment and sample preparation. Unpaired methods, while not requiring paired data, struggle to preserve the precise spatial and quantitative information essential for accurate analysis. To address these challenges, we introduce STABLE (spatial and quantitative information preserving biomedical image translation), an unpaired image-to-image translation method that emphasizes the preservation of spatial and quantitative information by enforcing information consistency and employing dynamic, learnable upsampling operators to achieve pixel-level accuracy. We validate STABLE across various biomedical imaging tasks, including translating calcium imaging data from zebrafish brains and virtual histological staining, demonstrating its superior ability to preserve spatial details, signal intensities, and accurate alignment compared to existing methods.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101074"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12272260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267477","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