Cell Reports Methods最新文献_第5页

A probabilistic modeling framework for genomic networks incorporating sample heterogeneity. 包含样本异质性的基因组网络的概率建模框架。

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-14 DOI: 10.1016/j.crmeth.2025.100984

Liying Chen, Satwik Acharyya, Chunyu Luo, Yang Ni, Veerabhadran Baladandayuthapani

{"title":"A probabilistic modeling framework for genomic networks incorporating sample heterogeneity.","authors":"Liying Chen, Satwik Acharyya, Chunyu Luo, Yang Ni, Veerabhadran Baladandayuthapani","doi":"10.1016/j.crmeth.2025.100984","DOIUrl":"10.1016/j.crmeth.2025.100984","url":null,"abstract":"Probabilistic graphical models are powerful tools to quantify, visualize, and interpret network dependencies in complex biological systems such as high-throughput -omics. However, many graphical models assume sample homogeneity, limiting their effectiveness. We propose a flexible Bayesian approach called graphical regression (GraphR), which (1) incorporates sample heterogeneity at different scales through a regression-based formulation, (2) enables sparse sample-specific network estimation, (3) identifies and quantifies potential effects of heterogeneity on network structures, and (4) achieves computational efficiency via variational Bayes algorithms. We illustrate the comparative efficiency of GraphR against existing state-of-the-art methods in terms of network structure recovery and computational cost across multiple settings. We use GraphR to analyze three multi-omic and spatial transcriptomic datasets to investigate inter- and intra-sample molecular networks and delineate biological discoveries that otherwise cannot be revealed by existing approaches. We have developed a GraphR R package along with an accompanying Shiny App that provides comprehensive analysis and dynamic visualization functions.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100984"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955270/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426267","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

Refined culture conditions with increased physiological relevance uncover oncogene-dependent metabolic signatures in Ewing sarcoma spheroids. 精细化的培养条件与增加的生理相关性揭示了尤因肉瘤球状体中癌基因依赖的代谢特征。

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-07 DOI: 10.1016/j.crmeth.2025.100966

A Katharina Ceranski, Martha J Carreño-Gonzalez, Anna C Ehlers, Kimberley M Hanssen, Nadine Gmelin, Florian H Geyer, Zuzanna Kolodynska, Endrit Vinca, Tobias Faehling, Philipp Poeller, Shunya Ohmura, Florencia Cidre-Aranaz, Almut Schulze, Thomas G P Grünewald

{"title":"Refined culture conditions with increased physiological relevance uncover oncogene-dependent metabolic signatures in Ewing sarcoma spheroids.","authors":"A Katharina Ceranski, Martha J Carreño-Gonzalez, Anna C Ehlers, Kimberley M Hanssen, Nadine Gmelin, Florian H Geyer, Zuzanna Kolodynska, Endrit Vinca, Tobias Faehling, Philipp Poeller, Shunya Ohmura, Florencia Cidre-Aranaz, Almut Schulze, Thomas G P Grünewald","doi":"10.1016/j.crmeth.2025.100966","DOIUrl":"10.1016/j.crmeth.2025.100966","url":null,"abstract":"Ewing sarcoma (EwS) cell line culture largely relies on standard techniques, which do not recapitulate physiological conditions. Here, we report on a feasible and cost-efficient EwS cell culture technique with increased physiological relevance employing an advanced medium composition, reduced fetal calf serum, and spheroidal growth. Improved reflection of the transcriptional activity related to proliferation, hypoxia, and differentiation in EwS patient tumors was detected in EwS cells grown in this refined in vitro condition. Moreover, transcriptional signatures associated with the oncogenic activity of the EwS-specific FET::ETS fusion transcription factors in the refined culture condition were shifted from proliferative toward metabolic gene signatures. The herein-presented EwS cell culture technique with increased physiological relevance provides a broadly applicable approach for enhanced in vitro modeling relevant to advancing EwS research and the validity of experimental results.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100966"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955266/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143374773","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

Comparative prospects of imaging methods for whole-brain mammalian connectomics. 哺乳动物全脑连接组学成像方法的比较展望。

IF 4.3

Cell Reports Methods Pub Date : 2025-02-24 Epub Date: 2025-02-18 DOI: 10.1016/j.crmeth.2025.100988

Logan Thrasher Collins, Todd Huffman, Randal Koene

{"title":"Comparative prospects of imaging methods for whole-brain mammalian connectomics.","authors":"Logan Thrasher Collins, Todd Huffman, Randal Koene","doi":"10.1016/j.crmeth.2025.100988","DOIUrl":"10.1016/j.crmeth.2025.100988","url":null,"abstract":"Mammalian whole-brain connectomes are a foundational ingredient for a holistic understanding of brains. Indeed, imaging connectomes at sufficient resolution to densely reconstruct cellular morphology and synapses represents a long-standing goal in neuroscience. Mouse connectomes could soon come within reach, while human connectomes remain a more distant yet still worthy goal. Though the technologies needed to reconstruct whole-brain connectomes have not yet reached full maturity, they are advancing rapidly. Close examination of these technologies may help plan connectomics projects. Here, we quantitatively compare imaging technologies that have the potential to enable whole-brain mammalian connectomics. We perform calculations on electron microscopy (EM) techniques and expansion light-sheet fluorescence microscopy (ExLSFM) methods. We consider techniques that have sufficient resolution to identify all synapses and sufficient speed to be relevant for whole mammalian brains. We offer this analysis as a resource for those considering how to organize efforts toward imaging whole-brain mammalian connectomes.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100988"},"PeriodicalIF":4.3,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143459778","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 thermoplastic chip for 2D and 3D correlative assays combining screening and high-resolution imaging of immune cell responses. 一种用于二维和三维相关分析的热塑性芯片，结合免疫细胞反应的筛选和高分辨率成像。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2025-01-17 DOI: 10.1016/j.crmeth.2025.100965

Hanna van Ooijen, Quentin Verron, Hanqing Zhang, Patrick A Sandoz, Thomas W Frisk, Valentina Carannante, Karl Olofsson, Arnika K Wagner, Niklas Sandström, Björn Önfelt

{"title":"A thermoplastic chip for 2D and 3D correlative assays combining screening and high-resolution imaging of immune cell responses.","authors":"Hanna van Ooijen, Quentin Verron, Hanqing Zhang, Patrick A Sandoz, Thomas W Frisk, Valentina Carannante, Karl Olofsson, Arnika K Wagner, Niklas Sandström, Björn Önfelt","doi":"10.1016/j.crmeth.2025.100965","DOIUrl":"10.1016/j.crmeth.2025.100965","url":null,"abstract":"We present an easy-to-use, disposable, thermoplastic microwell chip designed to support screening and high-resolution imaging of single-cell behavior in two- and three-dimensional (2D and 3D) cell cultures. We show that the chip has excellent optical properties and provide simple protocols for efficient long-term cell culture of suspension and adherent cells, the latter grown either as monolayers or as hundreds of single, uniformly sized spheroids. We then demonstrate the applicability of the system for single-cell analysis by correlating the dynamic cytotoxic response of single immune cells grown under different metabolic conditions to their intracellular cytolytic load at the end of the assay. Additionally, we illustrate highly multiplex cytotoxicity screening of tumor spheroids in the chip, comparing the effect of environment cues characteristic of the tumor microenvironment on natural killer (NK)-cell-induced killing. Following the functional screening, we perform high-resolution 3D immunofluorescent imaging of infiltrating NK cells within the spheroid volumes.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100965"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11841093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013077","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

Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA. 通过AtaCNA检测单细胞染色质测序数据的拷贝数改变。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2025-01-14 DOI: 10.1016/j.crmeth.2024.100939

Xiaochen Wang, Zijie Jin, Yang Shi, Ruibin Xi

{"title":"Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA.","authors":"Xiaochen Wang, Zijie Jin, Yang Shi, Ruibin Xi","doi":"10.1016/j.crmeth.2024.100939","DOIUrl":"10.1016/j.crmeth.2024.100939","url":null,"abstract":"Single-cell assay of transposase-accessible chromatin sequencing (scATAC-seq) unbiasedly profiles genome-wide chromatin accessibility in single cells. In single-cell tumor studies, identification of normal cells or tumor clonal structures often relies on copy-number alterations (CNAs). However, CNA detection from scATAC-seq is difficult due to the high noise, sparsity, and confounding factors. Here, we describe AtaCNA, a computational algorithm that accurately detects high-resolution CNAs from scATAC-seq data. We benchmark AtaCNA using simulation and real data and find AtaCNA's superior performance. Analyses of 10 scATAC-seq datasets show that AtaCNA could effectively distinguish malignant from non-malignant cells. In glioblastoma, endometrial, and ovarian cancer samples, AtaCNA identifies subclones at distinct cellular states, suggesting an important interplay between genetic and epigenetic plasticity. Some tumor subclones only differ in small-scale (10-20 Mb) CNAs, demonstrating the importance of high-resolution CNA detection. These data show that AtaCNA can aid in integrative analysis to understand the complex heterogeneity in cancer.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100939"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013080","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

Selective activation of mesoscale functional circuits via multichannel infrared stimulation of cortical columns in ultra-high-field 7T MRI. 在超高场7T MRI中，多通道红外刺激皮质柱选择性激活中尺度功能回路。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 DOI: 10.1016/j.crmeth.2024.100961

Feiyan Tian, Yipeng Liu, Meixuan Chen, Kenneth Edward Schriver, Anna Wang Roe

{"title":"Selective activation of mesoscale functional circuits via multichannel infrared stimulation of cortical columns in ultra-high-field 7T MRI.","authors":"Feiyan Tian, Yipeng Liu, Meixuan Chen, Kenneth Edward Schriver, Anna Wang Roe","doi":"10.1016/j.crmeth.2024.100961","DOIUrl":"10.1016/j.crmeth.2024.100961","url":null,"abstract":"To restore vision in the blind, advances in visual cortical prosthetics (VCPs) have offered high-channel-count electrical interfaces. Here, we design a 100-fiber optical bundle interface apposed to known feature-specific (color, shape, motion, and depth) functional columns that populate the visual cortex in humans, primates, and cats. Based on a non-viral optical stimulation method (INS, infrared neural stimulation; 1,875 nm), it can deliver dynamic patterns of stimulation, is non-penetrating and non-damaging to tissue, and is movable and removable. In addition, its magnetic resonance (MR) compatibility (INS-fMRI) permits systematic mapping of brain-wide circuits. In the MRI, we illustrate (1) the single-point activation of functionally specific networks, (2) shifting cortical networks activated via shifting points of stimulation, and (3) \"moving dot\" stimulation-evoked activation of higher-order motion-selective areas. We suggest that, by mimicking patterns of columnar activation normally activated by visual stimuli, a columnar VCP opens doors for the planned activation of feature-specific circuits and their associated visual percepts.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 1","pages":"100961"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059417","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 network-enabled pipeline for gene discovery and validation in non-model plant species. 非模式植物物种基因发现和验证的网络管道。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 DOI: 10.1016/j.crmeth.2024.100963

Dae Kwan Ko, Federica Brandizzi

引用次数: 0

Generation of super-resolution images from barcode-based spatial transcriptomics by deep image prior. 基于条形码的空间转录组学的深度图像先验生成超分辨率图像。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2024-12-26 DOI: 10.1016/j.crmeth.2024.100937

Jeongbin Park, Seungho Cook, Dongjoo Lee, Jinyeong Choi, Seongjin Yoo, Sungwoo Bae, Hyung-Jun Im, Daeseung Lee, Hongyoon Choi

{"title":"Generation of super-resolution images from barcode-based spatial transcriptomics by deep image prior.","authors":"Jeongbin Park, Seungho Cook, Dongjoo Lee, Jinyeong Choi, Seongjin Yoo, Sungwoo Bae, Hyung-Jun Im, Daeseung Lee, Hongyoon Choi","doi":"10.1016/j.crmeth.2024.100937","DOIUrl":"10.1016/j.crmeth.2024.100937","url":null,"abstract":"Spatially resolved transcriptomics (ST) has revolutionized the field of biology by providing a powerful tool for analyzing gene expression in situ. However, current ST methods, particularly barcode-based methods, have limitations in reconstructing high-resolution images from barcodes sparsely distributed in slides. Here, we present SuperST, an algorithm that enables the reconstruction of dense matrices (higher-resolution and non-zero-inflated matrices) from low-resolution ST libraries. SuperST is based on deep image prior, which reconstructs spatial gene expression patterns as image matrices. Compared with previous methods, SuperST generated output images that more closely resembled immunofluorescence images for given gene expression maps. Furthermore, we demonstrated how one can combine images created by SuperST with computer vision algorithms. In this context, we proposed a method for extracting features from the images, which can aid in spatial clustering of genes. By providing a dense matrix for each gene in situ, SuperST can successfully address the resolution and zero-inflation issue.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100937"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840945/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142898681","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

Analysis of TEM micrographs with deep learning reveals APOE genotype-specific associations between HDL particle diameter and Alzheimer's dementia. 用深度学习分析TEM显微图揭示APOE基因型特异性HDL颗粒直径与阿尔茨海默氏痴呆症之间的关联。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 DOI: 10.1016/j.crmeth.2024.100962

Jack Jingyuan Zheng, Brian Vannak Hong, Joanne K Agus, Xinyu Tang, Fei Guo, Carlito B Lebrilla, Izumi Maezawa, Lee-Way Jin, Wyatt N Vreeland, Dean C Ripple, Angela M Zivkovic

{"title":"Analysis of TEM micrographs with deep learning reveals APOE genotype-specific associations between HDL particle diameter and Alzheimer's dementia.","authors":"Jack Jingyuan Zheng, Brian Vannak Hong, Joanne K Agus, Xinyu Tang, Fei Guo, Carlito B Lebrilla, Izumi Maezawa, Lee-Way Jin, Wyatt N Vreeland, Dean C Ripple, Angela M Zivkovic","doi":"10.1016/j.crmeth.2024.100962","DOIUrl":"10.1016/j.crmeth.2024.100962","url":null,"abstract":"High-density lipoprotein (HDL) particle diameter distribution is informative in the diagnosis of many conditions, including Alzheimer's disease (AD). However, obtaining an accurate HDL size measurement is challenging. We demonstrated the utility of measuring the diameter of more than 1,800,000 HDL particles with the deep learning model YOLOv7 (you only look once) from micrographs of 183 HDL samples, including patients with dementia or normal cognition (controls). This method was shown to be more efficient and accurate than conventional image analysis software. Using this method, we found a higher abundance of small HDLs in participants with dementia compared to controls in patients with the apolipoprotein E (APOE) ε3ε4 genotype, whereas patients with the APOE ε3ε3 genotype had higher variability in the abundance of different HDL subclasses. Our results show an example of accurate individual HDL particle diameter measurement for large-scale clinical samples, which can be expanded to characterize the relationship between disease risk and other nanoparticles in the sub-20-nm diameter size range.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"5 1","pages":"100962"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840948/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143059114","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

Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. CITE-seq数据的多模式分层分类描绘了跨谱系和组织的免疫细胞状态。

IF 4.3

Cell Reports Methods Pub Date : 2025-01-27 Epub Date: 2025-01-14 DOI: 10.1016/j.crmeth.2024.100938

Daniel P Caron, William L Specht, David Chen, Steven B Wells, Peter A Szabo, Isaac J Jensen, Donna L Farber, Peter A Sims

{"title":"Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues.","authors":"Daniel P Caron, William L Specht, David Chen, Steven B Wells, Peter A Szabo, Isaac J Jensen, Donna L Farber, Peter A Sims","doi":"10.1016/j.crmeth.2024.100938","DOIUrl":"10.1016/j.crmeth.2024.100938","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) is invaluable for profiling cellular heterogeneity and transcriptional states, but transcriptomic profiles do not always delineate subsets defined by surface proteins. Cellular indexing of transcriptomes and epitopes (CITE-seq) enables simultaneous profiling of single-cell transcriptomes and surface proteomes; however, accurate cell-type annotation requires a classifier that integrates multimodal data. Here, we describe multimodal classifier hierarchy (MMoCHi), a marker-based approach for accurate cell-type classification across multiple single-cell modalities that does not rely on reference atlases. We benchmark MMoCHi using sorted T lymphocyte subsets and annotate a cross-tissue human immune cell dataset. MMoCHi outperforms leading transcriptome-based classifiers and multimodal unsupervised clustering in its ability to identify immune cell subsets that are not readily resolved and to reveal subset markers. MMoCHi is designed for adaptability and can integrate annotation of cell types and developmental states across diverse lineages, samples, or modalities.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100938"},"PeriodicalIF":4.3,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013083","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