Cell Reports Methods最新文献_第8页

Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO. 利用 dSILO 系统分析胰腺癌类器官模型中蛋白质组的周转。

IF 3.8

Cell Reports Methods Pub Date : 2024-05-20 Epub Date: 2024-04-26 DOI: 10.1016/j.crmeth.2024.100760

Alison B Ross, Darvesh Gorhe, Jenny Kim Kim, Stefanie Hodapp, Lela DeVine, Karina M Chan, Iok In Christine Chio, Marko Jovanovic, Marina Ayres Pereira

{"title":"Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO.","authors":"Alison B Ross, Darvesh Gorhe, Jenny Kim Kim, Stefanie Hodapp, Lela DeVine, Karina M Chan, Iok In Christine Chio, Marko Jovanovic, Marina Ayres Pereira","doi":"10.1016/j.crmeth.2024.100760","DOIUrl":"10.1016/j.crmeth.2024.100760","url":null,"abstract":"The role of protein turnover in pancreatic ductal adenocarcinoma (PDA) metastasis has not been previously investigated. We introduce dynamic stable-isotope labeling of organoids (dSILO): a dynamic SILAC derivative that combines a pulse of isotopically labeled amino acids with isobaric tandem mass-tag (TMT) labeling to measure proteome-wide protein turnover rates in organoids. We applied it to a PDA model and discovered that metastatic organoids exhibit an accelerated global proteome turnover compared to primary tumor organoids. Globally, most turnover changes are not reflected at the level of protein abundance. Interestingly, the group of proteins that show the highest turnover increase in metastatic PDA compared to tumor is involved in mitochondrial respiration. This indicates that metastatic PDA may adopt alternative respiratory chain functionality that is controlled by the rate at which proteins are turned over. Collectively, our analysis of proteome turnover in PDA organoids offers insights into the mechanisms underlying PDA metastasis.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11133751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874809","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

Optimizing the conversion of phosphoenolpyruvate to lactate by enzymatic channeling with mixed nanoparticle display. 通过混合纳米粒子显示的酶通道优化磷酸烯醇丙酮酸到乳酸的转化。

IF 3.8

Cell Reports Methods Pub Date : 2024-05-20 Epub Date: 2024-05-06 DOI: 10.1016/j.crmeth.2024.100764

Shelby L Hooe, Christopher M Green, Kimihiro Susumu, Michael H Stewart, Joyce C Breger, Igor L Medintz

{"title":"Optimizing the conversion of phosphoenolpyruvate to lactate by enzymatic channeling with mixed nanoparticle display.","authors":"Shelby L Hooe, Christopher M Green, Kimihiro Susumu, Michael H Stewart, Joyce C Breger, Igor L Medintz","doi":"10.1016/j.crmeth.2024.100764","DOIUrl":"10.1016/j.crmeth.2024.100764","url":null,"abstract":"Co-assembling enzymes with nanoparticles (NPs) into nanoclusters allows them to access channeling, a highly efficient form of multienzyme catalysis. Using pyruvate kinase (PykA) and lactate dehydrogenase (LDH) to convert phosphoenolpyruvic acid to lactic acid with semiconductor quantum dots (QDs) confirms how enzyme cluster formation dictates the rate of coupled catalytic flux (kflux) across a series of differentially sized/shaped QDs and 2D nanoplatelets (NPLs). Enzyme kinetics and coupled flux were used to demonstrate that by mixing different NP systems into clusters, a >10× improvement in kflux is observed relative to free enzymes, which is also ≥2× greater than enhancement on individual NPs. Cluster formation was characterized with gel electrophoresis and transmission electron microscopy (TEM) imaging. The generalizability of this mixed-NP approach to improving flux is confirmed by application to a seven-enzyme system. This represents a powerful approach for accessing channeling with almost any choice of enzymes constituting a multienzyme cascade.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11133815/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140877466","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

Analyzing the functional effects of DNA variants with gene editing. 通过基因编辑分析 DNA 变异的功能效应。

IF 3.8

Cell Reports Methods Pub Date : 2024-05-20 Epub Date: 2024-05-13 DOI: 10.1016/j.crmeth.2024.100776

Sarah Cooper, Sofia Obolenski, Andrew J Waters, Andrew R Bassett, Matthew A Coelho

引用次数: 0

Methods for making and observing model lipid droplets. 制作和观察模型脂滴的方法。

IF 3.8

Cell Reports Methods Pub Date : 2024-05-20 Epub Date: 2024-05-14 DOI: 10.1016/j.crmeth.2024.100774

Sonali A Gandhi, Shahnaz Parveen, Munirah Alduhailan, Ramesh Tripathi, Nasser Junedi, Mohammad Saqallah, Matthew A Sanders, Peter M Hoffmann, Katherine Truex, James G Granneman, Christopher V Kelly

引用次数: 0

Subtype-WGME enables whole-genome-wide multi-omics cancer subtyping 亚型-WGME 实现了全基因组多组学癌症亚型分析

IF 3.8

Cell Reports Methods Pub Date : 2024-05-01 DOI: 10.1016/j.crmeth.2024.100781

Hai Yang, Liang Zhao, Dongdong Li, Congcong An, Xiaoyang Fang, Yiwen Chen, Jingping Liu, Ting Xiao, Zhe Wang

引用次数: 0

Bioengineering methods for vascularizing organoids. 血管化器官组织的生物工程方法。

IF 3.8

Cell Reports Methods Pub Date : 2024-05-01 DOI: 10.1016/j.crmeth.2024.100779

Peter N Nwokoye, O. Abilez

引用次数: 0

Modular dual-color BiAD sensors for locus-specific readout of epigenome modifications in single cells. 模块化双色 BiAD 传感器，用于读取单细胞中表观基因组修饰的特异性位点。

IF 3.8

Cell Reports Methods Pub Date : 2024-04-22 Epub Date: 2024-03-29 DOI: 10.1016/j.crmeth.2024.100739

Anja R Köhler, Johannes Haußer, Annika Harsch, Steffen Bernhardt, Lilia Häußermann, Lisa-Marie Brenner, Cristiana Lungu, Monilola A Olayioye, Pavel Bashtrykov, Albert Jeltsch

{"title":"Modular dual-color BiAD sensors for locus-specific readout of epigenome modifications in single cells.","authors":"Anja R Köhler, Johannes Haußer, Annika Harsch, Steffen Bernhardt, Lilia Häußermann, Lisa-Marie Brenner, Cristiana Lungu, Monilola A Olayioye, Pavel Bashtrykov, Albert Jeltsch","doi":"10.1016/j.crmeth.2024.100739","DOIUrl":"10.1016/j.crmeth.2024.100739","url":null,"abstract":"Dynamic changes in the epigenome at defined genomic loci play crucial roles during cellular differentiation and disease development. Here, we developed dual-color bimolecular anchor detector (BiAD) sensors for high-sensitivity readout of locus-specific epigenome modifications by fluorescence microscopy. Our BiAD sensors comprise an sgRNA/dCas9 complex as anchor and double chromatin reader domains as detector modules, both fused to complementary parts of a split IFP2.0 fluorophore, enabling its reconstitution upon binding of both parts in close proximity. In addition, a YPet fluorophore is recruited to the sgRNA to mark the genomic locus of interest. With these dual-color BiAD sensors, we detected H3K9me2/3 and DNA methylation and their dynamic changes upon RNAi or inhibitor treatment with high sensitivity at endogenous genomic regions. Furthermore, we showcased locus-specific H3K36me2/3 readout as well as H3K27me3 and H3K9me2/3 enrichment on the inactive X chromosome, highlighting the broad applicability of our dual-color BiAD sensors for single-cell epigenome studies.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11045877/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140330147","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

Single-cell biclustering for cell-specific transcriptomic perturbation detection in AD progression. 单细胞双聚类用于检测注意力缺失症进展过程中细胞特异性转录组扰动。

IF 3.8

Cell Reports Methods Pub Date : 2024-04-22 Epub Date: 2024-03-29 DOI: 10.1016/j.crmeth.2024.100742

Yuqiao Gong, Jingsi Xu, Maoying Wu, Ruitian Gao, Jianle Sun, Zhangsheng Yu, Yue Zhang

{"title":"Single-cell biclustering for cell-specific transcriptomic perturbation detection in AD progression.","authors":"Yuqiao Gong, Jingsi Xu, Maoying Wu, Ruitian Gao, Jianle Sun, Zhangsheng Yu, Yue Zhang","doi":"10.1016/j.crmeth.2024.100742","DOIUrl":"10.1016/j.crmeth.2024.100742","url":null,"abstract":"The pathogenesis of Alzheimer disease (AD) involves complex gene regulatory changes across different cell types. To help decipher this complexity, we introduce single-cell Bayesian biclustering (scBC), a framework for identifying cell-specific gene network biomarkers in scRNA and snRNA-seq data. Through biclustering, scBC enables the analysis of perturbations in functional gene modules at the single-cell level. Applying the scBC framework to AD snRNA-seq data reveals the perturbations within gene modules across distinct cell groups and sheds light on gene-cell correlations during AD progression. Notably, our method helps to overcome common challenges in single-cell data analysis, including batch effects and dropout events. Incorporating prior knowledge further enables the framework to yield more biologically interpretable results. Comparative analyses on simulated and real-world datasets demonstrate the precision and robustness of our approach compared to other state-of-the-art biclustering methods. scBC holds potential for unraveling the mechanisms underlying polygenic diseases characterized by intricate gene coexpression patterns.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11045878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140330149","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

An engineering strategy to target activated EGFR with CAR T cells. 利用 CAR T 细胞靶向活化表皮生长因子受体的工程策略。

IF 3.8

Cell Reports Methods Pub Date : 2024-04-22 Epub Date: 2024-03-15 DOI: 10.1016/j.crmeth.2024.100728

Markus Dobersberger, Delia Sumesgutner, Charlotte U Zajc, Benjamin Salzer, Elisabeth Laurent, Dominik Emminger, Elise Sylvander, Elisabeth Lehner, Magdalena Teufl, Jacqueline Seigner, Madhusudhan Reddy Bobbili, Renate Kunert, Manfred Lehner, Michael W Traxlmayr

{"title":"An engineering strategy to target activated EGFR with CAR T cells.","authors":"Markus Dobersberger, Delia Sumesgutner, Charlotte U Zajc, Benjamin Salzer, Elisabeth Laurent, Dominik Emminger, Elise Sylvander, Elisabeth Lehner, Magdalena Teufl, Jacqueline Seigner, Madhusudhan Reddy Bobbili, Renate Kunert, Manfred Lehner, Michael W Traxlmayr","doi":"10.1016/j.crmeth.2024.100728","DOIUrl":"10.1016/j.crmeth.2024.100728","url":null,"abstract":"Chimeric antigen receptor (CAR) T cells have shown remarkable response rates in hematological malignancies. In contrast, CAR T cell treatment of solid tumors is associated with several challenges, in particular the expression of most tumor-associated antigens at lower levels in vital organs, resulting in on-target/off-tumor toxicities. Thus, innovative approaches to improve the tumor specificity of CAR T cells are urgently needed. Based on the observation that many human solid tumors activate epidermal growth factor receptor (EGFR) on their surface through secretion of EGFR ligands, we developed an engineering strategy for CAR-binding domains specifically directed against the ligand-activated conformation of EGFR. We show, in several experimental systems, that the generated binding domains indeed enable CAR T cells to distinguish between active and inactive EGFR. We anticipate that this engineering concept will be an important step forward to improve the tumor specificity of CAR T cells directed against EGFR-positive solid cancers.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":3.8,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11045874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140902","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

Single-cell adhesive profiling in an optofluidic device elucidates CD8⁺ T lymphocyte phenotypes in inflamed vasculature-like microenvironments. 光流体设备中的单细胞粘附谱分析阐明了发炎血管样微环境中的 CD8+ T 淋巴细胞表型。

IF 4.3

Cell Reports Methods Pub Date : 2024-04-22 Epub Date: 2024-03-29 DOI: 10.1016/j.crmeth.2024.100743

Camila P Camargo, Yunus Alapan, Abir K Muhuri, Samuel N Lucas, Susan N Thomas

{"title":"Single-cell adhesive profiling in an optofluidic device elucidates CD8+ T lymphocyte phenotypes in inflamed vasculature-like microenvironments.","authors":"Camila P Camargo, Yunus Alapan, Abir K Muhuri, Samuel N Lucas, Susan N Thomas","doi":"10.1016/j.crmeth.2024.100743","DOIUrl":"10.1016/j.crmeth.2024.100743","url":null,"abstract":"Tissue infiltration by circulating leukocytes occurs via adhesive interactions with the local vasculature, but how the adhesive quality of circulating cells guides the homing of specific phenotypes to different vascular microenvironments remains undefined. We developed an optofluidic system enabling fluorescent labeling of photoactivatable cells based on their adhesive rolling velocity in an inflamed vasculature-mimicking microfluidic device under physiological fluid flow. In so doing, single-cell level multidimensional profiling of cellular characteristics could be characterized and related to the associated adhesive phenotype. When applied to CD8+ T cells, ligand/receptor expression profiles and subtypes associated with adhesion were revealed, providing insight into inflamed tissue infiltration capabilities of specific CD8+ T lymphocyte subsets and how local vascular microenvironmental features may regulate the quality of cellular infiltration. This methodology facilitates rapid screening of cell populations for enhanced homing capabilities under defined biochemical and biophysical microenvironments, relevant to leukocyte homing modulation in multiple pathologies.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11046032/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140330148","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