[ { "id": "authors:hx122-ds441", "collection": "authors", "collection_id": "hx122-ds441", "cite_using_url": "https://authors.library.caltech.edu/records/hx122-ds441", "type": "monograph", "title": "Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease", "author": [ { "family_name": "Polonsky", "given_name": "Michal", "orcid": "0000-0003-3871-460X", "clpid": "Polonsky-Michal" }, { "family_name": "Gerhardt", "given_name": "Louisa M. S.", "orcid": "0000-0003-3052-1563", "clpid": "Gerhardt-Louisa-M-S" }, { "family_name": "Yun", "given_name": "Jina", "clpid": "Yun-Jina" }, { "family_name": "Koppitch", "given_name": "Kari", "clpid": "Koppitch-Kari" }, { "family_name": "Col\u00f3n", "given_name": "Katsuya Lex", "orcid": "0000-0002-7347-6128", "clpid": "Col\u00f3n-Katsuya-Lex" }, { "family_name": "Amrhein", "given_name": "Henry", "orcid": "0000-0002-4264-140X", "clpid": "Amrhein-H" }, { "family_name": "Zheng", "given_name": "Shiwei", "orcid": "0000-0001-6682-6743", "clpid": "Zheng-Shiwei" }, { "family_name": "Yuan", "given_name": "Guo-Cheng", "clpid": "Yuan-Guo-Cheng" }, { "family_name": "Thomson", "given_name": "Matt", "orcid": "0000-0003-1021-1234", "clpid": "Thomson-M-W" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" }, { "family_name": "McMahon", "given_name": "Andrew P.", "orcid": "0000-0002-3779-1729", "clpid": "McMahon-Andrew-P" } ], "abstract": "

Kidney injury disrupts the intricate renal architecture and triggers limited regeneration, and injury-invoked inflammation and fibrosis. Deciphering molecular pathways and cellular interactions driving these processes is challenging due to the complex renal architecture. Here, we applied single cell spatial transcriptomics to examine ischemia-reperfusion injury in the mouse kidney. Spatial transcriptomics revealed injury-specific and spatially-dependent gene expression patterns in distinct cellular microenvironments within the kidney and predicted Clcf1-Crfl1 in a molecular interplay between persistently injured proximal tubule cells and neighboring fibroblasts. Immune cell types play a critical role in organ repair. Spatial analysis revealed cellular microenvironments resembling early tertiary lymphoid structures and identified associated molecular pathways. Collectively, this study supports a focus on molecular interactions in cellular microenvironments to enhance understanding of injury, repair and disease.

", "doi": "10.1101/2023.11.22.568217", "issn": "2692-8205", "publisher": "BioRxiv", "publication": "bioRxiv", "publication_date": "2023-11-22" }, { "id": "authors:sr2rf-e0549", "collection": "authors", "collection_id": "sr2rf-e0549", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20210430-091508303", "type": "monograph", "title": "Integrated spatial genomics in tissues reveals invariant and cell type dependent nuclear architecture", "author": [ { "family_name": "Takei", "given_name": "Yodai", "clpid": "Takei-Yodai" }, { "family_name": "Zheng", "given_name": "Shiwei", "orcid": "0000-0001-6682-6743", "clpid": "Zheng-Shiwei" }, { "family_name": "Yun", "given_name": "Jina", "clpid": "Yun-Jina" }, { "family_name": "Shah", "given_name": "Sheel", "clpid": "Shah-Sheel" }, { "family_name": "Pierson", "given_name": "Nico", "orcid": "0000-0002-2451-0633", "clpid": "Pierson-Nico-G" }, { "family_name": "White", "given_name": "Jonathan", "orcid": "0000-0002-7009-3332", "clpid": "White-Joanthan-A" }, { "family_name": "Schindler", "given_name": "Simone", "clpid": "Schindler-Simone" }, { "family_name": "Tischbirek", "given_name": "Carsten", "clpid": "Tischbirek-Carsten" }, { "family_name": "Yuan", "given_name": "Guo-Cheng", "orcid": "0000-0002-2283-4714", "clpid": "Yuan-Guo-Cheng" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" } ], "abstract": "Nuclear architecture in tissues can arise from cell-type specific organization of nuclear bodies, chromatin states and chromosome structures. However, the lack of genome-wide measurements to interrelate such modalities within single cells limits our overall understanding of nuclear architecture. Here, we demonstrate integrated spatial genomics in the mouse brain cortex, imaging thousands of genomic loci along with RNAs and subnuclear markers simultaneously in individual cells. We revealed chromatin fixed points, combined with cell-type specific organization of nuclear bodies, arrange the interchromosomal organization and radial positioning of chromosomes in diverse cell types. At the sub-megabase level, we uncovered a collection of single-cell chromosome domain structures, including those for the active and inactive X chromosomes. These results advance our understanding of single-cell nuclear architecture in complex tissues.", "doi": "10.1101/2021.04.26.441547", "publication_date": "2021-04-27" }, { "id": "authors:ah4qa-qnq68", "collection": "authors", "collection_id": "ah4qa-qnq68", "cite_using_url": "https://resolver.caltech.edu/CaltechAUTHORS:20180822-140737502", "type": "monograph", "title": "Decomposing spatially dependent and cell type specific contributions to cellular heterogeneity", "author": [ { "family_name": "Zhu", "given_name": "Qian", "clpid": "Zhu-Qian" }, { "family_name": "Shah", "given_name": "Sheel", "clpid": "Shah-Sheel" }, { "family_name": "Dries", "given_name": "Ruben", "clpid": "Dries-R" }, { "family_name": "Cai", "given_name": "Long", "orcid": "0000-0002-7154-5361", "clpid": "Cai-Long" }, { "family_name": "Yuan", "given_name": "Guo-Cheng", "orcid": "0000-0002-2283-4714", "clpid": "Yuan-Guo-Cheng" } ], "abstract": "Both the intrinsic regulatory network and spatial environment are contributors of cellular identity and result in cell state variations. However, their individual contributions remain poorly understood. Here we present a systematic approach to integrate both sequencing- and imaging-based single-cell transcriptomic profiles, thereby combining whole-transcriptomic and spatial information from these assays. We applied this approach to dissect the cell-type and spatial domain associated heterogeneity within the mouse visual cortex region. Our analysis identified distinct spatially associated signatures within glutamatergic and astrocyte cell compartments, indicating strong interactions between cells and their surrounding environment. Using these signatures as a guide to analyze single cell RNAseq data, we identified previously unknown, but spatially associated subpopulations. As such, our integrated approach provides a powerful tool for dissecting the roles of intrinsic regulatory networks and spatial environment in the maintenance of cellular states.", "doi": "10.1101/275156", "publication_date": "2018-03-02" } ]