Cell Reports Methods最新文献_第7页

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":" ","pages":"100875"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142393923","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 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

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":" ","pages":"100878"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476380","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

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

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":" ","pages":"100877"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476378","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

Size-reduced DREADD derivatives for AAV-assisted multimodal chemogenetic control of neuronal activity and behavior. 减小尺寸的 DREADD 衍生物，用于 AAV 辅助的神经元活动和行为的多模式化学遗传控制。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 DOI: 10.1016/j.crmeth.2024.100881

Takahito Miyake, Kaho Tanaka, Yutsuki Inoue, Yuji Nagai, Reo Nishimura, Takehito Seta, Shumpei Nakagawa, Ken-Ichi Inoue, Emi Hasegawa, Takafumi Minamimoto, Masao Doi

{"title":"Size-reduced DREADD derivatives for AAV-assisted multimodal chemogenetic control of neuronal activity and behavior.","authors":"Takahito Miyake, Kaho Tanaka, Yutsuki Inoue, Yuji Nagai, Reo Nishimura, Takehito Seta, Shumpei Nakagawa, Ken-Ichi Inoue, Emi Hasegawa, Takafumi Minamimoto, Masao Doi","doi":"10.1016/j.crmeth.2024.100881","DOIUrl":"10.1016/j.crmeth.2024.100881","url":null,"abstract":"Designer receptors exclusively activated by designer drugs (DREADDs) are engineered G-protein-coupled receptors that afford reversible manipulation of neuronal activity in vivo. Here, we introduce size-reduced DREADD derivatives miniDq and miniDi, which inherit the basic receptor properties from the Gq-coupled excitatory receptor hM3Dq and the Gi-coupled inhibitory receptor hM4Di, respectively, while being approximately 30% smaller in size. Taking advantage of the compact size of the receptors, we generated an adeno-associated virus (AAV) vector carrying both miniDq and the other DREADD family receptor (κ-opioid receptor-based inhibitory DREADD [KORD]) within the maximum AAV capacity (4.7 kb), allowing us to modulate neuronal activity and animal behavior in both excitatory and inhibitory directions using a single viral vector. We confirmed that expressing miniDq, but not miniDi, allowed activation of striatum activity in the cynomolgus monkey (Macaca fascicularis). The compact DREADDs may thus widen the opportunity for multiplexed interrogation and/or intervention in neuronal regulation in mice and non-human primates.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"4 10","pages":"100881"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573748/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509373","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

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":" ","pages":"100879"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573743/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142476379","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

Adult zebrafish can learn Morris water maze-like tasks in a two-dimensional virtual reality system. 成年斑马鱼可以在二维虚拟现实系统中学习类似莫里斯水迷宫的任务。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 Epub Date: 2024-09-23 DOI: 10.1016/j.crmeth.2024.100863

Tanvir Islam, Makio Torigoe, Yuki Tanimoto, Hitoshi Okamoto

引用次数: 0

CENCAT enables immunometabolic profiling by measuring protein synthesis via bioorthogonal noncanonical amino acid tagging. CENCAT 可通过生物正交非对称氨基酸标记测量蛋白质合成，从而进行免疫代谢分析。

IF 4.3

Cell Reports Methods Pub Date : 2024-10-21 DOI: 10.1016/j.crmeth.2024.100883

Frank Vrieling, Hendrik J P van der Zande, Britta Naus, Lisa Smeehuijzen, Julia I P van Heck, Bob J Ignacio, Kimberly M Bonger, Jan Van den Bossche, Sander Kersten, Rinke Stienstra

{"title":"CENCAT enables immunometabolic profiling by measuring protein synthesis via bioorthogonal noncanonical amino acid tagging.","authors":"Frank Vrieling, Hendrik J P van der Zande, Britta Naus, Lisa Smeehuijzen, Julia I P van Heck, Bob J Ignacio, Kimberly M Bonger, Jan Van den Bossche, Sander Kersten, Rinke Stienstra","doi":"10.1016/j.crmeth.2024.100883","DOIUrl":"10.1016/j.crmeth.2024.100883","url":null,"abstract":"Cellular energy metabolism significantly contributes to immune cell function. To further advance immunometabolic research, novel methods to study the metabolism of immune cells in complex samples are required. Here, we introduce CENCAT (cellular energetics through noncanonical amino acid tagging). This technique utilizes click labeling of alkyne-bearing noncanonical amino acids to measure protein synthesis inhibition as a proxy for metabolic activity. CENCAT successfully reproduced known metabolic signatures of lipopolysaccharide (LPS)/interferon (IFN)γ and interleukin (IL)-4 activation in human primary macrophages. Application of CENCAT in peripheral blood mononuclear cells revealed diverse metabolic rewiring upon stimulation with different activators. Finally, CENCAT was used to analyze the cellular metabolism of murine tissue-resident immune cells from various organs. Tissue-specific clustering was observed based on metabolic profiles, likely driven by microenvironmental priming. In conclusion, CENCAT offers valuable insights into immune cell metabolic responses, presenting a powerful platform for studying cellular metabolism in complex samples and tissues in both humans and mice.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"4 10","pages":"100883"},"PeriodicalIF":4.3,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11573747/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509371","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