Cell Reports Methods最新文献_第2页

Controlled aggregative assembly to form self-organizing macroscopic human intestine from induced pluripotent stem cells.

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-10 DOI: 10.1016/j.crmeth.2024.100930

Junichi Takahashi, Hady Yuki Sugihara, Shu Kato, Sho Kawasaki, Sayaka Nagata, Ryuichi Okamoto, Tomohiro Mizutani

{"title":"Controlled aggregative assembly to form self-organizing macroscopic human intestine from induced pluripotent stem cells.","authors":"Junichi Takahashi, Hady Yuki Sugihara, Shu Kato, Sho Kawasaki, Sayaka Nagata, Ryuichi Okamoto, Tomohiro Mizutani","doi":"10.1016/j.crmeth.2024.100930","DOIUrl":"10.1016/j.crmeth.2024.100930","url":null,"abstract":"Human intestinal organoids (HIOs) derived from human pluripotent stem cells (hPSCs) are promising resources for intestinal regenerative therapy as they recapitulate both endodermal and mesodermal components of the intestine. However, due to their hPSC-line-dependent mesenchymal development and spherical morphology, HIOs have limited applicability beyond basic research and development. Here, we demonstrate the incorporation of separately differentiated mesodermal and mid/hindgut cells into assembled spheroids to stabilize mesenchymal growth in HIOs. In parallel, we generate tubular intestinal constructs (assembled human intestinal tubules [a-HITs]) by leveraging the high aggregative property of assembled spheroids. Through rotational culture in a bioreactor, a-HITs self-organize to develop epithelium and supportive mesenchyme. Upon mesenteric transplantation, a-HITs mature into centimeter-scale tubular intestinal tissue with complex architectures. Our aggregation- and suspension-based approach offers basic technology for engineering tubular intestinal tissue from hPSCs, which could be ultimately applied to the generation of the human intestine for clinical application.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100930"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814496","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

A statistical approach for systematic identification of transition cells from scRNA-seq data.

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-06 DOI: 10.1016/j.crmeth.2024.100913

Yuanxin Wang, Merve Dede, Vakul Mohanty, Jinzhuang Dou, Ziyi Li, Ken Chen

引用次数: 0

Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state. 完整的蛋白质条形码可以一次性识别 CRISPRi 菌株及其代谢状态。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-11-26 DOI: 10.1016/j.crmeth.2024.100908

Vanessa Pahl, Paul Lubrano, Felicia Troßmann, Daniel Petras, Hannes Link

{"title":"Intact protein barcoding enables one-shot identification of CRISPRi strains and their metabolic state.","authors":"Vanessa Pahl, Paul Lubrano, Felicia Troßmann, Daniel Petras, Hannes Link","doi":"10.1016/j.crmeth.2024.100908","DOIUrl":"10.1016/j.crmeth.2024.100908","url":null,"abstract":"Detecting strain-specific barcodes with mass spectrometry can facilitate the screening of genetically engineered bacterial libraries. Here, we introduce intact protein barcoding, a method to measure protein-based library barcodes and metabolites using flow injection mass spectrometry (FI-MS). Protein barcodes are based on ubiquitin with N-terminal tags of six amino acids. We demonstrate that FI-MS detects intact ubiquitin proteins and identifies the mass of N-terminal barcodes. In the same analysis, we measured relative concentrations of primary metabolites. We constructed six ubiquitin-barcoded CRISPR interference (CRISPRi) strains targeting metabolic enzymes and analyzed their metabolic profiles and ubiquitin barcodes. FI-MS detected barcodes and distinct metabolome changes in CRISPRi-targeted pathways. We demonstrate the scalability of intact protein barcoding by measuring 132 ubiquitin barcodes in microtiter plates. These results show that intact protein barcoding enables fast and simultaneous detection of library barcodes and intracellular metabolites, opening up new possibilities for mass spectrometry-based barcoding.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100908"},"PeriodicalIF":4.3,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740797","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

A programmable, open-source robot that scratches cultured tissues to investigate cell migration, healing, and tissue sculpting.

IF 4.3

Cell Reports Methods Pub Date : 2024-12-16 Epub Date: 2024-12-09 DOI: 10.1016/j.crmeth.2024.100915

Yubin Lin, Alexander Silverman-Dultz, Madeline Bailey, Daniel J Cohen

引用次数: 0

A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex. 针对普通包柔氏包虫病的核心基因组多基因组测序技术（MLST）方案有助于深入了解该物种复合体的进化历史。

IF 4.3

Cell Reports Methods Pub Date : 2024-12-12 DOI: 10.1016/j.crmeth.2024.100935

Sabrina Hepner, Keith A Jolley, Santiago Castillo-Ramirez, Evangelos Mourkas, Alexandra Dangel, Andreas Wieser, Johannes Hübner, Andreas Sing, Volker Fingerle, Gabriele Margos

{"title":"A core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex.","authors":"Sabrina Hepner, Keith A Jolley, Santiago Castillo-Ramirez, Evangelos Mourkas, Alexandra Dangel, Andreas Wieser, Johannes Hübner, Andreas Sing, Volker Fingerle, Gabriele Margos","doi":"10.1016/j.crmeth.2024.100935","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100935","url":null,"abstract":"Multi-locus sequence typing (MLST) based on eight genes has become the method of choice for Borrelia typing and is extensively used for population studies. Whole-genome sequencing enables studies to scale up to genomic levels but necessitates extended schemes. We have developed a 639-loci core genome MLST (cgMLST) scheme for Borrelia burgdorferi sensu lato (s.l.) that enables unambiguous genotyping and improves the robustness of phylogenies and lineage resolution within species. Notably, all inner nodes of the cgMLST phylogenies had consistently high statistical support. Analyses of the genetically homogeneous European B. bavariensis population support the notion that cgMLST provides high discriminatory power even for closely related isolates. While isolates differed maximally in one MLST locus, there were up to 179 cgMLST loci differences. Thus, the developed cgMLST scheme for B. burgdorferi s.l. resolves lineages at a finer resolution than MLST and improves insights into the evolutionary history of the species complex.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100935"},"PeriodicalIF":4.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142865597","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

WEST is an ensemble method for spatial transcriptomics analysis. WEST 是一种用于空间转录组学分析的集合方法。

IF 4.3

Cell Reports Methods Pub Date : 2024-11-18 Epub Date: 2024-11-07 DOI: 10.1016/j.crmeth.2024.100886

Jiazhang Cai, Huimin Cheng, Shushan Wu, Wenxuan Zhong, Guo-Cheng Yuan, Ping Ma

引用次数: 0

Scalable log-ratio lasso regression for enhanced microbial feature selection with FLORAL. 利用 FLORAL 增强微生物特征选择的可扩展对数比率套索回归。

IF 4.3

Cell Reports Methods Pub Date : 2024-11-18 Epub Date: 2024-11-07 DOI: 10.1016/j.crmeth.2024.100899

Teng Fei, Tyler Funnell, Nicholas R Waters, Sandeep S Raj, Mirae Baichoo, Keimya Sadeghi, Anqi Dai, Oriana Miltiadous, Roni Shouval, Meng Lv, Jonathan U Peled, Doris M Ponce, Miguel-Angel Perales, Mithat Gönen, Marcel R M van den Brink

{"title":"Scalable log-ratio lasso regression for enhanced microbial feature selection with FLORAL.","authors":"Teng Fei, Tyler Funnell, Nicholas R Waters, Sandeep S Raj, Mirae Baichoo, Keimya Sadeghi, Anqi Dai, Oriana Miltiadous, Roni Shouval, Meng Lv, Jonathan U Peled, Doris M Ponce, Miguel-Angel Perales, Mithat Gönen, Marcel R M van den Brink","doi":"10.1016/j.crmeth.2024.100899","DOIUrl":"10.1016/j.crmeth.2024.100899","url":null,"abstract":"Identifying predictive biomarkers of patient outcomes from high-throughput microbiome data is of high interest, while existing computational methods do not satisfactorily account for complex survival endpoints, longitudinal samples, and taxa-specific sequencing biases. We present FLORAL, an open-source tool to perform scalable log-ratio lasso regression and microbial feature selection for continuous, binary, time-to-event, and competing risk outcomes, with compatibility for longitudinal microbiome data as time-dependent covariates. The proposed method adapts the augmented Lagrangian algorithm for a zero-sum constraint optimization problem while enabling a two-stage screening process for enhanced false-positive control. In extensive simulation and real-data analyses, FLORAL achieved consistently better false-positive control compared to other lasso-based approaches and better sensitivity over popular differential abundance testing methods for datasets with smaller sample sizes. In a survival analysis of allogeneic hematopoietic cell transplant recipients, FLORAL demonstrated considerable improvement in microbial feature selection by utilizing longitudinal microbiome data over solely using baseline microbiome data.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100899"},"PeriodicalIF":4.3,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606500","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

Accelerated production of human epithelial organoids in a miniaturized spinning bioreactor. 在微型旋转生物反应器中加速生产人类上皮细胞器官组织。

IF 4.3

Cell Reports Methods Pub Date : 2024-11-18 DOI: 10.1016/j.crmeth.2024.100903

Shicheng Ye, Ary Marsee, Gilles S van Tienderen, Mohammad Rezaeimoghaddam, Hafsah Sheikh, Roos-Anne Samsom, Eelco J P de Koning, Sabine Fuchs, Monique M A Verstegen, Luc J W van der Laan, Frans van de Vosse, Jos Malda, Keita Ito, Bart Spee, Kerstin Schneeberger

{"title":"Accelerated production of human epithelial organoids in a miniaturized spinning bioreactor.","authors":"Shicheng Ye, Ary Marsee, Gilles S van Tienderen, Mohammad Rezaeimoghaddam, Hafsah Sheikh, Roos-Anne Samsom, Eelco J P de Koning, Sabine Fuchs, Monique M A Verstegen, Luc J W van der Laan, Frans van de Vosse, Jos Malda, Keita Ito, Bart Spee, Kerstin Schneeberger","doi":"10.1016/j.crmeth.2024.100903","DOIUrl":"https://doi.org/10.1016/j.crmeth.2024.100903","url":null,"abstract":"Conventional static culture of organoids necessitates weekly manual passaging and results in nonhomogeneous exposure of organoids to nutrients, oxygen, and toxic metabolites. Here, we developed a miniaturized spinning bioreactor, RPMotion, specifically optimized for accelerated and cost-effective culture of epithelial organoids under homogeneous conditions. We established tissue-specific RPMotion settings and standard operating protocols for the expansion of human epithelial organoids derived from the liver, intestine, and pancreas. All organoid types proliferated faster in the bioreactor (5.2-fold, 3-fold, and 4-fold, respectively) compared to static culture while keeping their organ-specific phenotypes. We confirmed that the bioreactor is suitable for organoid establishment directly from biopsies and for long-term expansion of liver organoids. Furthermore, we showed that after accelerated expansion, liver organoids can be differentiated into hepatocyte-like cells in the RPMotion bioreactor. In conclusion, this miniaturized bioreactor enables work-, time-, and cost-efficient organoid culture, holding great promise for organoid-based fundamental and translational research and development.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":"4 11","pages":"100903"},"PeriodicalIF":4.3,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677130","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

Generation of self-renewing neuromesodermal progenitors with neuronal and skeletal muscle bipotential from human embryonic stem cells. 从人类胚胎干细胞中产生具有神经元和骨骼肌双潜能的自我更新神经表皮祖细胞。

IF 4.3

Cell Reports Methods Pub Date : 2024-11-18 Epub Date: 2024-11-07 DOI: 10.1016/j.crmeth.2024.100897

Pingxin Sun, Yuan Yuan, Zhuman Lv, Xinlu Yu, Haoxin Ma, Shulong Liang, Jiqianzhu Zhang, Jiangbo Zhu, Junyu Lu, Chunyan Wang, Le Huan, Caixia Jin, Chao Wang, Wenlin Li

{"title":"Generation of self-renewing neuromesodermal progenitors with neuronal and skeletal muscle bipotential from human embryonic stem cells.","authors":"Pingxin Sun, Yuan Yuan, Zhuman Lv, Xinlu Yu, Haoxin Ma, Shulong Liang, Jiqianzhu Zhang, Jiangbo Zhu, Junyu Lu, Chunyan Wang, Le Huan, Caixia Jin, Chao Wang, Wenlin Li","doi":"10.1016/j.crmeth.2024.100897","DOIUrl":"10.1016/j.crmeth.2024.100897","url":null,"abstract":"Progress has been made in generating spinal cord and trunk derivatives from neuromesodermal progenitors (NMPs). However, maintaining the self-renewal of NMPs in vitro remains a challenge. In this study, we developed a cocktail of small molecules and growth factors that induces human embryonic stem cells to produce self-renewing NMPs (srNMPs) under chemically defined conditions. These srNMPs maintain the state of neuromesodermal progenitors in prolonged culture and have the potential to generate mesodermal cells and neurons, even at the single-cell level. Additionally, suspended srNMP aggregates can spontaneously differentiate into all tissue types of early embryonic trunks. Furthermore, transplanted srNMP-derived muscle satellite cells or progenitors of motor neurons were integrated into skeletal muscle or the spinal cord, respectively, and contributed to regeneration in mouse models. In summary, srNMPs hold great promise for applications in developmental biology and as renewable cell sources for cell therapy for trunk and spinal cord injuries.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100897"},"PeriodicalIF":4.3,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606449","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

iSubGen generates integrative disease subtypes by pairwise similarity assessment. iSubGen 通过成对相似性评估生成综合疾病亚型。

IF 4.3

Cell Reports Methods Pub Date : 2024-11-18 Epub Date: 2024-10-23 DOI: 10.1016/j.crmeth.2024.100884

Natalie S Fox, Mao Tian, Alexander L Markowitz, Syed Haider, Constance H Li, Paul C Boutros

{"title":"iSubGen generates integrative disease subtypes by pairwise similarity assessment.","authors":"Natalie S Fox, Mao Tian, Alexander L Markowitz, Syed Haider, Constance H Li, Paul C Boutros","doi":"10.1016/j.crmeth.2024.100884","DOIUrl":"10.1016/j.crmeth.2024.100884","url":null,"abstract":"There are myriad types of biomedical data-molecular, clinical images, and others. When a group of patients with the same underlying disease exhibits similarities across multiple types of data, this is called a subtype. Existing subtyping approaches struggle to handle diverse data types with missing information. To improve subtype discovery, we exploited changes in the correlation-structure between different data types to create iSubGen, an algorithm for integrative subtype generation. iSubGen can accommodate any feature that can be compared with a similarity metric to create subtypes versatilely. It can combine arbitrary data types for subtype discovery, such as merging genetic, transcriptomic, proteomic, and pathway data. iSubGen recapitulates known subtypes across multiple cancers even with substantial missing data and identifies subtypes with distinct clinical behaviors. It performs equally with or superior to other subtyping methods, offering greater stability and robustness to missing data and flexibility to new data types. It is available at https://cran.r-project.org/web/packages/iSubGen.","PeriodicalId":29773,"journal":{"name":"Cell Reports Methods","volume":" ","pages":"100884"},"PeriodicalIF":4.3,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142509369","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