Spatial transcriptomics defines injury-specific microenvironments in the adult mouse kidney and novel cellular interactions in regeneration and disease

Creators: Polonsky, Michal¹; Gerhardt, Louisa M. S.²; Yun, Jina¹; Koppitch, Kari²; Colón, Katsuya Lex¹; Amrhein, Henry¹; Zheng, Shiwei³; Yuan, Guo-Cheng³; Thomson, Matt¹; Cai, Long¹; McMahon, Andrew P.²

1. California Institute of Technology
2. University of Southern California
3. Icahn School of Medicine at Mount Sinai

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.

Copyright and License

The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.

Acknowledgement

We thank Inna-Marie Strazhnik for help with figure illustration and design.

Funding

Work in APM’s and LC’s laboratory was supported by a Broad Innovation Grant from the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at the University of Southern California and a grant from the NIH to APM (NIDDK UC2DK126024). Additional support from the German Research Foundation grant GE 3179/1-1 (LMSG) and German Society of Internal Medicine (DGIM) Clinician Scientist grant (LMSG).

Contributions

MP, LMSG, APM and LC conceptualized the study. JY and MP designed the probes with input from LMSG. LMSG and KK performed surgeries, tissue collection and validation experiments. JY performed seqFISH experiments. KLC and MP wrote image processing scripts. MP, LMSG and SZ analyzed data with input from GC MT, APM and LC. MP, LMSG and HL were responsible for visualization. MP and LMSG wrote the initial draft of the manuscript. MP, LMSG, APM and LC edited and reviewed the manuscript. APM and LC supervised all aspects of the project.

Data Availability

The source data and processed data from this study will be available https://datadryad.org/stash after completion of the review process. The codebook is available in Table S3. Processed data can be browsed at https://woldlab.caltech.edu/celltiles/mouse_kidney_fibrosis/.

Code Availability

Scripts used for pre-processing seqFISH images can be found at https://github.com/CaiGroup/pyfish_tools.

Conflict of Interest

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