Cell Reports Methods最新文献

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276074","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

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144235395","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

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144276073","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

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

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

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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267477","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

Precise estimation of in-depth relatedness in biobank-scale datasets using deepKin. 使用deepKin精确估计生物库规模数据集的深度相关性。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-05-27 DOI: 10.1016/j.crmeth.2025.101053

Qi-Xin Zhang, Dovini Jayasinghe, Zhe Zhang, Sang Hong Lee, Hai-Ming Xu, Guo-Bo Chen

引用次数: 0

Encapsulation of protein/DNA complexes into unilamellar liposomes via annexin-mediated membrane recruitment and sonication. 通过膜联蛋白介导的膜募集和超声将蛋白质/DNA复合物封装到单层脂质体中。

IF 4.3

Cell Reports Methods Pub Date : 2025-06-16 Epub Date: 2025-06-09 DOI: 10.1016/j.crmeth.2025.101073

Michael Burger, Finn Brigger, Valeria Mantella, Jean-Christophe Leroux

引用次数: 0