Cell Reports Methods最新文献

Optimized full-spectrum flow cytometry panel for deep immunophenotyping of murine lungs. 用于小鼠肺部深度免疫分型的全谱流式细胞仪优化面板。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-24 DOI: 10.1016/j.crmeth.2024.100885

Zora Baumann, Carsten Wiethe, Cinja M Vecchi, Veronica Richina, Telma Lopes, Mohamed Bentires-Alj

引用次数: 0

Recovering single-cell expression profiles from spatial transcriptomics with scResolve. 利用 scResolve 从空间转录组学中恢复单细胞表达谱。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-09-25 DOI: 10.1016/j.crmeth.2024.100864

Hao Chen, Young Je Lee, Jose A Ovando-Ricardez, Lorena Rosas, Mauricio Rojas, Ana L Mora, Ziv Bar-Joseph, Jose Lugo-Martinez

引用次数: 0

Computationally guided high-throughput engineering of an anti-CRISPR protein for precise genome editing in human cells. 计算引导下的高通量抗 CRISPR 蛋白工程，用于在人类细胞中进行精确的基因组编辑。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 DOI: 10.1016/j.crmeth.2024.100882

Julia Marsiglia, Kia Vaalavirta, Estefany Knight, Muneaki Nakamura, Le Cong, Nicholas W Hughes

{"title":"Computationally guided high-throughput engineering of an anti-CRISPR protein for precise genome editing in human cells.","authors":"Julia Marsiglia, Kia Vaalavirta, Estefany Knight, Muneaki Nakamura, Le Cong, Nicholas W Hughes","doi":"10.1016/j.crmeth.2024.100882","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100882","url":null,"abstract":"The application of CRISPR-Cas systems to genome editing has revolutionized experimental biology and is an emerging gene and cell therapy modality. CRISPR-Cas systems target off-target regions within the human genome, which is a challenge that must be addressed. Phages have evolved anti-CRISPR proteins (Acrs) to evade CRISPR-Cas-based immunity. Here, we engineer an Acr (AcrIIA4) to increase the precision of CRISPR-Cas-based genome targeting. We developed an approach that leveraged (1) computational guidance, (2) deep mutational scanning, and (3) highly parallel DNA repair measurements within human cells. In a single experiment, ∼10,000 Acr variants were tested. Variants that improved editing precision were tested in additional validation experiments that revealed robust enhancement of gene editing precision and synergy with a high-fidelity version of Cas9. This scalable high-throughput screening framework is a promising methodology to engineer Acrs to increase gene editing precision, which could be used to improve the safety of gene editing-based therapeutics.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509372","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

Transgenic sensors reveal compartment-specific effects of aggregation-prone proteins on subcellular proteostasis during aging. 转基因传感器揭示了易聚集蛋白在衰老过程中对亚细胞蛋白稳态的特异性影响。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-10-08 DOI: 10.1016/j.crmeth.2024.100875

Michelle Curley, Mamta Rai, Chia-Lung Chuang, Vishwajeeth Pagala, Anna Stephan, Zane Coleman, Maricela Robles-Murguia, Yong-Dong Wang, Junmin Peng, Fabio Demontis

{"title":"Transgenic sensors reveal compartment-specific effects of aggregation-prone proteins on subcellular proteostasis during aging.","authors":"Michelle Curley, Mamta Rai, Chia-Lung Chuang, Vishwajeeth Pagala, Anna Stephan, Zane Coleman, Maricela Robles-Murguia, Yong-Dong Wang, Junmin Peng, Fabio Demontis","doi":"10.1016/j.crmeth.2024.100875","DOIUrl":"10.1016/j.crmeth.2024.100875","url":null,"abstract":"Loss of proteostasis is a hallmark of aging that underlies many age-related diseases. Different cell compartments experience distinctive challenges in maintaining protein quality control, but how aging regulates subcellular proteostasis remains underexplored. Here, by targeting the misfolding-prone FlucDM luciferase to the cytoplasm, mitochondria, and nucleus, we established transgenic sensors to examine subcellular proteostasis in Drosophila. Analysis of detergent-insoluble and -soluble levels of compartment-targeted FlucDM variants indicates that thermal stress, cold shock, and pro-longevity inter-organ signaling differentially affect subcellular proteostasis during aging. Moreover, aggregation-prone proteins that cause different neurodegenerative diseases induce a diverse range of outcomes on FlucDM insolubility, suggesting that subcellular proteostasis is impaired in a disease-specific manner. Further analyses with FlucDM and mass spectrometry indicate that pathogenic tauV337M produces an unexpectedly complex regulation of solubility for different FlucDM variants and protein subsets. Altogether, compartment-targeted FlucDM sensors pinpoint a diverse modulation of subcellular proteostasis by aging regulators.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142393923","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

An accelerated Parkinson's disease monkey model using AAV-α-synuclein plus poly(ADP-ribose). 使用 AAV-α-synuclein 加聚（ADP-核糖）的加速帕金森病猴模型。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-10-15 DOI: 10.1016/j.crmeth.2024.100876

Shuyi Liu, Naixue Yang, Yaping Yan, Shaobo Wang, Jialing Chen, Yichao Wang, Xue Gan, Jiawen Zhou, Guoqing Xie, Hong Wang, Tianzhuang Huang, Weizhi Ji, Zhengbo Wang, Wei Si

引用次数: 0

Accurate and sensitive interactome profiling using a quantitative protein-fragment complementation assay. 利用定量蛋白质片段互补测定法进行准确而灵敏的相互作用组分析。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 DOI: 10.1016/j.crmeth.2024.100880

Natalia Lazarewicz, Gaëlle Le Dez, Romina Cerjani, Lunelys Runeshaw, Matthias Meurer, Michael Knop, Robert Wysocki, Gwenaël Rabut

引用次数: 0

Generation, expansion, gene delivery, and single-cell profiling in rhesus macaque plasma B cells. 猕猴血浆 B 细胞的生成、扩增、基因传递和单细胞分析。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-10-14 DOI: 10.1016/j.crmeth.2024.100878

Rene Yu-Hong Cheng, Anna E Helmers, Shannon Kreuser, Noelle Dahl, Yuchi Honaker, Christina Lopez, David J Rawlings, Richard G James

{"title":"Generation, expansion, gene delivery, and single-cell profiling in rhesus macaque plasma B cells.","authors":"Rene Yu-Hong Cheng, Anna E Helmers, Shannon Kreuser, Noelle Dahl, Yuchi Honaker, Christina Lopez, David J Rawlings, Richard G James","doi":"10.1016/j.crmeth.2024.100878","DOIUrl":"10.1016/j.crmeth.2024.100878","url":null,"abstract":"A key step in developing engineered B cells for therapeutic purposes is evaluation in immunocompetent, large-animal models. Therefore, we developed methods to purify, expand, and differentiate non-human primate (NHP; rhesus macaque) B cells. After 7 days in culture, B cells expanded 10-fold, differentiated into a plasma cell phenotype (CD38, CD138), and secreted immunoglobulin G. Using single-cell sequencing and flow cytometry, we verified the presence of plasma cell genes in differentiated NHP B cells and unearthed less-recognized markers, such as CD59 and CD79A. In contrast with human cells, we found that the immune checkpoint molecule CD274 (PD-L1) and major histocompatibility complex (MHC) class I molecules were upregulated in NHP plasma cells in the transcriptional data. Lastly, we established the conditions for efficient transduction of NHP B cells with adeno-associated virus (AAV) vectors, achieving a delivery rate of approximately 60%. We envision that this work will accelerate proof-of-concept studies using engineered B cells in NHPs.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476380","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

Mimicking and analyzing the tumor microenvironment. 模拟和分析肿瘤微环境。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-09-30 DOI: 10.1016/j.crmeth.2024.100866

Roxane Crouigneau, Yan-Fang Li, Jamie Auxillos, Eliana Goncalves-Alves, Rodolphe Marie, Albin Sandelin, Stine Falsig Pedersen

引用次数: 0

Cell-free DNA end characteristics enable accurate and sensitive cancer diagnosis. 无细胞 DNA 末端特征可实现准确、灵敏的癌症诊断。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-10-14 DOI: 10.1016/j.crmeth.2024.100877

Jia Ju, Xin Zhao, Yunyun An, Mengqi Yang, Ziteng Zhang, Xiaoyi Liu, Dingxue Hu, Wanqiu Wang, Yuqi Pan, Zhaohua Xia, Fei Fan, Xuetong Shen, Kun Sun

{"title":"Cell-free DNA end characteristics enable accurate and sensitive cancer diagnosis.","authors":"Jia Ju, Xin Zhao, Yunyun An, Mengqi Yang, Ziteng Zhang, Xiaoyi Liu, Dingxue Hu, Wanqiu Wang, Yuqi Pan, Zhaohua Xia, Fei Fan, Xuetong Shen, Kun Sun","doi":"10.1016/j.crmeth.2024.100877","DOIUrl":"10.1016/j.crmeth.2024.100877","url":null,"abstract":"The fragmentation patterns of cell-free DNA (cfDNA) in plasma can potentially be utilized as diagnostic biomarkers in liquid biopsy. However, our knowledge of this biological process and the information encoded in fragmentation patterns remains preliminary. Here, we investigated the cfDNA fragmentomic characteristics against nucleosome positioning patterns in hematopoietic cells. cfDNA molecules with ends located within nucleosomes were relatively shorter with altered end motif patterns, demonstrating the feasibility of enriching tumor-derived cfDNA in patients with cancer through the selection of molecules possessing such ends. We then developed three cfDNA fragmentomic metrics after end selection, which showed significant alterations in patients with cancer and enabled cancer diagnosis. By incorporating machine learning, we further built high-performance diagnostic models, which achieved an overall area under the curve of 0.95 and 85.1% sensitivity at 95% specificity. Hence, our investigations explored the end characteristics of cfDNA fragmentomics and their merits in building accurate and sensitive cancer diagnostic models.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476378","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

Cryosectioning and immunofluorescence of C. elegans reveals endogenous polyphosphate in intestinal endo-lysosomal organelles. 冷冻切片和免疫荧光揭示了线虫肠道内溶酶体细胞器中的内源性多聚磷酸盐。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-10-15 DOI: 10.1016/j.crmeth.2024.100879

Ellen Quarles, Lauren Petreanu, Anjali Narain, Aanchal Jain, Akash Rai, Joyful Wang, Bryndon Oleson, Ursula Jakob

{"title":"Cryosectioning and immunofluorescence of C. elegans reveals endogenous polyphosphate in intestinal endo-lysosomal organelles.","authors":"Ellen Quarles, Lauren Petreanu, Anjali Narain, Aanchal Jain, Akash Rai, Joyful Wang, Bryndon Oleson, Ursula Jakob","doi":"10.1016/j.crmeth.2024.100879","DOIUrl":"10.1016/j.crmeth.2024.100879","url":null,"abstract":"Polyphosphate (polyP) is a ubiquitous polyanion present throughout the tree of life. While polyP's widely varied functions have been interrogated in single-celled organisms, little is known about the cellular distribution and function of polyP in multicellular organisms. To study polyP in metazoans, we developed the nematode Caenorhabditis elegans as a model system. We designed a high-throughput, longitudinal-orientation cryosectioning method that allowed us to scrutinize the intracellular localization of polyP in fixed C. elegans using fluorescent polyP probes and co-immunostaining targeting appropriate marker proteins. We discovered that the vast majority of polyP is localized within the endo-lysosomal compartments of the intestinal cells and is highly sensitive toward the disruption of endo-lysosomal compartment generation and food availability. This study lays the groundwork for further mechanistic research of polyPs in multicellular organisms and provides a reliable method for immunostaining hundreds of fixed worms in a single experiment.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476379","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