@article{3ecb0adeddf74b0c8ecb348df69c8dee,
title = "Transcriptomic Analysis of Human Podocytes In Vitro: Effects of Differentiation and APOL1 Genotype",
abstract = "Introduction: The mechanisms in podocytes that mediate the pathologic effects of the APOL1 high-risk (HR) variants remain incompletely understood, although various molecular and cellular mechanisms have been proposed. We previously established conditionally immortalized human urine-derived podocyte-like epithelial cell (HUPEC) lines to investigate APOL1 HR variant–induced podocytopathy. Methods: We conducted comprehensive transcriptomic analysis, including mRNA, microRNA (miRNA), and transfer RNA fragments (tRFs), to characterize the transcriptional profiles in undifferentiated and differentiated HUPEC with APOL1 HR (G1/G2, 2 cell lines) and APOL1 low-risk (LR) (G0/G0, 2 cell lines) genotypes. We reanalyzed single-cell RNA-seq data from urinary podocytes from focal segmental glomerulosclerosis (FSGS) subjects to characterize the effect of APOL1 genotypes on podocyte transcriptomes. Results: Differential expression analysis showed that the ribosomal pathway was one of the most enriched pathways, suggesting that altered function of the translation initiation machinery may contribute to APOL1 variant–induced podocyte injury. Expression of genes related to the elongation initiation factor 2 pathway was also enriched in the APOL1 HR urinary podocytes from single-cell RNA-seq, supporting a prior report on the role of this pathway in APOL1-associated cell injury. Expression of microRNA and tRFs were analyzed, and the profile of small RNAs differed by both differentiation status and APOL1 genotype. Conclusion: We have profiled the transcriptomic landscape of human podocytes, including mRNA, miRNA, and tRF, to characterize the effects of differentiation and of different APOL1 genotypes. The candidate pathways, miRNAs, and tRFs described here expand understanding of APOL1-associated podocytopathies.",
keywords = "APOL1, RNA-seq, differentiation, miRNA, podocytes, tRNA fragments",
author = "Teruhiko Yoshida and Latt, {Khun Zaw} and Rosenberg, {Avi Z.} and Shashi Shrivastav and Jurgen Heymann and Halushka, {Marc K.} and Winkler, {Cheryl A.} and Kopp, {Jeffrey B.}",
note = "Funding Information: This work was supported by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland (institutional review board protocols: 94-DK-0127, Pathogenesis of Glomerulosclerosis; 94-DK-0133, Focal Segmental Glomerulosclerosis Genetics) (principal investigator JBK). We thank Drs. Sanga Mitra, Pavol Genzor, and Astrid D. Haase (NIDDK, NIH) for technical support in small RNA-seq; Tsai-Wei Shen, Yongmei Zhao, Sequencing Facility and Bioinformatics Group (Frederick National Laboratory for Cancer Research (FNLCR), National Cancer Institute, NIH) for total RNA-seq support; and Peter Yuen (NIDDK, NIH) for critical manuscript review. This work used the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov). The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government. This project has been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract 75N91019D00024. This research was supported by the Intramural Research Program of the NIH, including the National Cancer Institute, Center for Cancer Research, and the NIDDK. Original data files and count tables are deposited in GEO (GSE194337). Data are available from the authors upon request. TY, SS, JH, CAW, and JBK conceived the study design. TY and SS cultured HUPECs. TY analyzed HUPECs data with support by MKH and AZR. KZL and TY analyzed urinary single-cell data. TY, KZL, JBK drafted the manuscript, and all the authors edited the manuscript. Funding Information: This work was supported by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, Maryland (institutional review board protocols: 94-DK-0127, Pathogenesis of Glomerulosclerosis; 94-DK-0133, Focal Segmental Glomerulosclerosis Genetics) (principal investigator JBK). We thank Drs. Sanga Mitra, Pavol Genzor, and Astrid D. Haase (NIDDK, NIH) for technical support in small RNA-seq; Tsai-Wei Shen, Yongmei Zhao, Sequencing Facility and Bioinformatics Group (Frederick National Laboratory for Cancer Research (FNLCR), National Cancer Institute, NIH) for total RNA-seq support; and Peter Yuen (NIDDK, NIH) for critical manuscript review. This work used the computational resources of the NIH HPC Biowulf cluster ( http://hpc.nih.gov ). The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government. Funding Information: This project has been funded in part with federal funds from the National Cancer Institute, National Institutes of Health, under contract 75N91019D00024. This research was supported by the Intramural Research Program of the NIH, including the National Cancer Institute, Center for Cancer Research, and the NIDDK. Publisher Copyright: {\textcopyright} 2022",
year = "2023",
month = jan,
doi = "10.1016/j.ekir.2022.10.011",
language = "English (US)",
volume = "8",
pages = "164--178",
journal = "Kidney International Reports",
issn = "2468-0249",
publisher = "Elsevier Inc.",
number = "1",
}