Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-06-10DOI: 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":"<p><p>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.</p>","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-06-09DOI: 10.1016/j.crmeth.2025.101079
Mattia Conte, Mario Nicodemi
{"title":"Visualizing chromatin communication in living cells through Oligo-LiveFISH.","authors":"Mattia Conte, Mario Nicodemi","doi":"10.1016/j.crmeth.2025.101079","DOIUrl":"10.1016/j.crmeth.2025.101079","url":null,"abstract":"<p><p>Understanding genome regulation requires capturing chromatin dynamics in real time. In a recent issue of Cell, Zhu et al. introduce Oligo-LiveFISH,<sup>1</sup> a high-resolution live-cell imaging platform that tracks non-repetitive loci without genome engineering. By assembling fluorescent guide RNA pools with dCas9, this method enables 20-nm, 50-ms resolution imaging, offering insights into dynamic genome organization across cell lines and primary cells.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101079"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267479","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}
{"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":"https://doi.org/10.1016/j.crmeth.2025.101076","url":null,"abstract":"<p><p>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.</p>","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":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318150","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-06-09DOI: 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":"<p><p>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.</p>","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-05-27DOI: 10.1016/j.crmeth.2025.101053
Qi-Xin Zhang, Dovini Jayasinghe, Zhe Zhang, Sang Hong Lee, Hai-Ming Xu, Guo-Bo Chen
{"title":"Precise estimation of in-depth relatedness in biobank-scale datasets using deepKin.","authors":"Qi-Xin Zhang, Dovini Jayasinghe, Zhe Zhang, Sang Hong Lee, Hai-Ming Xu, Guo-Bo Chen","doi":"10.1016/j.crmeth.2025.101053","DOIUrl":"10.1016/j.crmeth.2025.101053","url":null,"abstract":"<p><p>Accurate relatedness estimation is essential in biobank-scale genetic studies. We present deepKin, a method-of-moments framework that accounts for sampling variance to enable statistical inference and classification of relatedness. Unlike traditional methods using fixed thresholds, deepKin computes data-specific significance thresholds, determines the minimum effective number of markers, and estimates the statistical power to detect distant relatives. Through simulations, we demonstrate that deepKin accurately infers both unrelated pairs and relatives by leveraging sampling variance. In the UK Biobank (UKB), analysis of the 3K Oxford subset showed that SNP sets with a larger effective number of markers provided greater power for detecting distant relatives. In the White British subset, deepKin identified over 212,000 significant relative pairs, categorized into six degrees, and revealed their geographic patterns across 19 UKB assessment centers through within-cohort and cross-cohort relatedness estimation. An R package (deepKin) is available at GitHub.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101053"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144175102","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-06-09DOI: 10.1016/j.crmeth.2025.101073
Michael Burger, Finn Brigger, Valeria Mantella, Jean-Christophe Leroux
{"title":"Encapsulation of protein/DNA complexes into unilamellar liposomes via annexin-mediated membrane recruitment and sonication.","authors":"Michael Burger, Finn Brigger, Valeria Mantella, Jean-Christophe Leroux","doi":"10.1016/j.crmeth.2025.101073","DOIUrl":"10.1016/j.crmeth.2025.101073","url":null,"abstract":"<p><p>This paper reports an effective protocol to encapsulate native protein/DNA complexes into unilamellar vesicles composed of natural lipids without the use of organic solvents, in physiological buffers, and at low protein/DNA concentrations. DNA compaction is achieved with the human mitochondrial transcription factor A (TFAM), which forms complexes (TFAMoplexes) when mixed with plasmid DNA (pDNA). The complexes are recruited to the surface of preformed giant unilamellar vesicles (GUVs) with the help of human annexin A4 and thereby concentrated at the membranes. This is followed by transforming the TFAMoplex-coated GUVs into small vesicles using short sonication pulses. This method results in the encapsulation of around 40% of the TFAMoplexes into unilamellar liposomes with an average hydrodynamic diameter of 121 nm. By harnessing the functions of human proteins, this approach enables the creation of complex molecular assemblies that will pave the way for a wide array of biochemical and biomedical applications.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101073"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267476","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-05-21DOI: 10.1016/j.crmeth.2025.101054
Wenhao Cao, Zhiqun Tan, Bereket T Berackey, Jason K Nguyen, Sara R Brown, Shiyang Du, Bin Lin, Qiao Ye, Magdalene Seiler, Todd C Holmes, Xiangmin Xu
{"title":"An AAV capsid proposed as microglia-targeting directs genetic expression in forebrain excitatory neurons.","authors":"Wenhao Cao, Zhiqun Tan, Bereket T Berackey, Jason K Nguyen, Sara R Brown, Shiyang Du, Bin Lin, Qiao Ye, Magdalene Seiler, Todd C Holmes, Xiangmin Xu","doi":"10.1016/j.crmeth.2025.101054","DOIUrl":"10.1016/j.crmeth.2025.101054","url":null,"abstract":"<p><p>A newly developed capsid AAV-MG1.2 was reported to mediate specific microglial transduction. However, we find that AAV-MG1.2 actually enables specific genetic access to excitatory neurons in forebrain regions including hippocampal formation and visual cortex but does not confer expression in microglia or astrocytes in vivo. Furthermore, we find that AAV-MG1.2 specifically labels the deep layer of the CA1 pyramidal layer in a titer-dependent manner. We show that AAV-MG1.2-Cre can be used to genetically target excitatory neurons for cell-type-specific neural circuit mapping studies. We also find that AAV-MG1.2 conserves specificity for excitatory neurons in rat hippocampus. Thus, the AAV-MG1.2 presents a useful viral-genetic tool for targeting excitatory neurons in the forebrain across different species.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101054"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144128854","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-05-28DOI: 10.1016/j.crmeth.2025.101055
Juliana Gutschow Gameiro, Constantin A Hintschich, Agnès Dekeyser, Valérie Hox, James E Schwob, Eric H Holbrook, Marco Aurélio Fornazieri, Brian Lin
{"title":"Quiescent horizontal basal stem cells act as a niche for olfactory neurogenesis in a mouse 3D organoid model.","authors":"Juliana Gutschow Gameiro, Constantin A Hintschich, Agnès Dekeyser, Valérie Hox, James E Schwob, Eric H Holbrook, Marco Aurélio Fornazieri, Brian Lin","doi":"10.1016/j.crmeth.2025.101055","DOIUrl":"10.1016/j.crmeth.2025.101055","url":null,"abstract":"<p><p>The olfactory epithelium contains two basal stem cell populations that facilitate the usually life-long ability for neuronal regeneration that is required for maintaining our sense of smell. Horizontal basal cells (HBCs) are generally quiescent and only become active after direct injury to the epithelium that eliminates more than just the olfactory sensory neurons (OSNs). Globose basal cells (GBCs) lie apical to HBCs and are solely responsible for the generation of olfactory neurons in the undamaged epithelium. Understanding how these two neurogenic stem cell populations are regulated as OSNs are replenished is hampered by a lack of robust culture models. Here, we report the development of a 3D mouse organoid model that recapitulates the neurogenic cascade, forming immature OSNs while maintaining both HBCs and GBCs in culture. We use this model to demonstrate that, despite their relative quiescence, HBCs form a critical niche for the emergence and composition of the organoid.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101055"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144181936","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}
Elena N Waidmann, Victor H Y Yang, Erica Luo, William C Doyle, Erich D Jarvis
{"title":"Mountable miniature microphones to identify and assign mouse ultrasonic vocalizations.","authors":"Elena N Waidmann, Victor H Y Yang, Erica Luo, William C Doyle, Erich D Jarvis","doi":"10.1016/j.crmeth.2025.101081","DOIUrl":"https://doi.org/10.1016/j.crmeth.2025.101081","url":null,"abstract":"<p><p>Mouse ultrasonic vocalizations (USVs) are a promising model for studying vocal production. Although, in courtship interactions, males emit the majority of the USVs, female mice also produce USVs. In order to study the mechanisms of vocal production in freely behaving mice, it is necessary to identify the individual responsible for each syllable. Prior studies have used microphone arrays, but these are costly and require complex analyses to pinpoint the vocalizer. Here, we developed an inexpensive, ultrasound-sensitive wearable microphone to identify USVs from individual mice in socializing pairs. We reliably detected USVs and assigned 90% to a specific animal in a pair based on relative amplitude differences. When paired with video tracking, we increased the assigned percentage (97%) and described the courtship behavioral landscape in which USVs occur. These results offer a low-cost, simple method to study social communication between pairs of mice and other ultrasonically vocalizing animals.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 6","pages":"101081"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144318152","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}
Cell Reports MethodsPub Date : 2025-06-16Epub Date: 2025-06-09DOI: 10.1016/j.crmeth.2025.101075
André Forjaz, Eduarda Vaz, Valentina Matos Romero, Saurabh Joshi, Vasco Queiroga, Alicia M Braxton, Ann C Jiang, Kohei Fujikura, Toby Cornish, Seung-Mo Hong, Ralph H Hruban, Pei-Hsun Wu, Laura D Wood, Ashley L Kiemen, Denis Wirtz
{"title":"Three-dimensional assessments are necessary to determine the true, spatially resolved composition of tissues.","authors":"André Forjaz, Eduarda Vaz, Valentina Matos Romero, Saurabh Joshi, Vasco Queiroga, Alicia M Braxton, Ann C Jiang, Kohei Fujikura, Toby Cornish, Seung-Mo Hong, Ralph H Hruban, Pei-Hsun Wu, Laura D Wood, Ashley L Kiemen, Denis Wirtz","doi":"10.1016/j.crmeth.2025.101075","DOIUrl":"10.1016/j.crmeth.2025.101075","url":null,"abstract":"<p><p>Methods for spatially resolved cellular profiling of tissue sections enable in-depth study of inter- and intra-sample heterogeneity but often profile small regions, requiring evaluation of many samples to compensate for limited assessment. Recent advances in three-dimensional (3D) tissue mapping offer deeper insights; however, attempts to quantify the information gained in transitioning to 3D remains limited. Here, to compare inter- and intra-sample tissue heterogeneity, we analyze >100 pancreas samples as cores, whole-slide images (WSIs), and cm<sup>3</sup>-sized 3D samples. We show that tens of WSIs and hundreds of tissue microarrays are needed to approximate the compositional tissue heterogeneity of tumors. Additionally, spatial correlations of pancreatic structures decay significantly within microns, demonstrating that isolated two-dimensional (2D) sections poorly represent their surroundings. Through 3D simulations, we determined the number of slides necessary to accurately measure tumor burden. These results quantify the power of 3D mapping and establish sampling methods for biological studies prioritizing composition or incidence.</p>","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"101075"},"PeriodicalIF":4.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267478","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}