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Gisch DL, Brennan M, Lake BB, Basta J, Keller MS, Melo Ferreira R, Akilesh S, Ghag R, Lu C, Cheng YH, Collins KS, Parikh SV, Rovin BH, Robbins L, Stout L, Conklin KY, Diep D, Zhang B, Knoten A, Barwinska D, Asghari M, Sabo AR, Ferkowicz MJ, Sutton TA, Kelly KJ, De Boer IH, Rosas SE, Kiryluk K, Hodgin JB, Alakwaa F, Winfree S, Jefferson N, Türkmen A, Gaut JP, Gehlenborg N, Phillips CL, El-Achkar TM, Dagher PC, Hato T, Zhang K, Himmelfarb J, Kretzler M, Mollah S, Jain S, Rauchman M, Eadon MT. The chromatin landscape of healthy and injured cell types in the human kidney. Nat Commun 2024; 15:433. [PMID: 38199997 PMCID: PMC10781985 DOI: 10.1038/s41467-023-44467-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024] Open
Abstract
There is a need to define regions of gene activation or repression that control human kidney cells in states of health, injury, and repair to understand the molecular pathogenesis of kidney disease and design therapeutic strategies. Comprehensive integration of gene expression with epigenetic features that define regulatory elements remains a significant challenge. We measure dual single nucleus RNA expression and chromatin accessibility, DNA methylation, and H3K27ac, H3K4me1, H3K4me3, and H3K27me3 histone modifications to decipher the chromatin landscape and gene regulation of the kidney in reference and adaptive injury states. We establish a spatially-anchored epigenomic atlas to define the kidney's active, silent, and regulatory accessible chromatin regions across the genome. Using this atlas, we note distinct control of adaptive injury in different epithelial cell types. A proximal tubule cell transcription factor network of ELF3, KLF6, and KLF10 regulates the transition between health and injury, while in thick ascending limb cells this transition is regulated by NR2F1. Further, combined perturbation of ELF3, KLF6, and KLF10 distinguishes two adaptive proximal tubular cell subtypes, one of which manifested a repair trajectory after knockout. This atlas will serve as a foundation to facilitate targeted cell-specific therapeutics by reprogramming gene regulatory networks.
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Affiliation(s)
- Debora L Gisch
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Blue B Lake
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Jeannine Basta
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | | | | | | | - Reetika Ghag
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Charles Lu
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Ying-Hua Cheng
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Samir V Parikh
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Brad H Rovin
- Ohio State University Wexner Medical Center, Columbus, OH, 43210, USA
| | - Lynn Robbins
- St. Louis Veteran Affairs Medical Center, St. Louis, MO, 63106, USA
| | - Lisa Stout
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Kimberly Y Conklin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Dinh Diep
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Bo Zhang
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Amanda Knoten
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Daria Barwinska
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Mahla Asghari
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela R Sabo
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | - Timothy A Sutton
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | | | | | - Sylvia E Rosas
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | | | | | | | - Seth Winfree
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Nichole Jefferson
- Kidney Precision Medicine Project Community Engagement Committee, Dallas, TX, USA
| | - Aydın Türkmen
- Istanbul School of Medicine, Division of Nephrology, Istanbul, Turkey
| | - Joseph P Gaut
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | - Pierre C Dagher
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Takashi Hato
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kun Zhang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Shamim Mollah
- Washington University in Saint Louis, St. Louis, MO, 63103, USA
| | - Sanjay Jain
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael Rauchman
- Washington University in Saint Louis, St. Louis, MO, 63103, USA.
| | - Michael T Eadon
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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Lea WA, Winklhofer T, Zelenchuk L, Sharma M, Rossol-Allison J, Fields TA, Reif G, Calvet JP, Bakeberg JL, Wallace DP, Ward CJ. Polycystin-1 Interacting Protein-1 (CU062) Interacts with the Ectodomain of Polycystin-1 (PC1). Cells 2023; 12:2166. [PMID: 37681898 PMCID: PMC10487028 DOI: 10.3390/cells12172166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/07/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
The PKD1 gene, encoding protein polycystin-1 (PC1), is responsible for 85% of cases of autosomal dominant polycystic kidney disease (ADPKD). PC1 has been shown to be present in urinary exosome-like vesicles (PKD-ELVs) and lowered in individuals with germline PKD1 mutations. A label-free mass spectrometry comparison of urinary PKD-ELVs from normal individuals and those with PKD1 mutations showed that several proteins were reduced to a degree that matched the decrease observed in PC1 levels. Some of these proteins, such as polycystin-2 (PC2), may be present in a higher-order multi-protein assembly with PC1-the polycystin complex (PCC). CU062 (Q9NYP8) is decreased in ADPKD PKD-ELVs and, thus, is a candidate PCC component. CU062 is a small glycoprotein with a signal peptide but no transmembrane domain and can oligomerize with itself and interact with PC1. We investigated the localization of CU062 together with PC1 and PC2 using immunofluorescence (IF). In nonconfluent cells, all three proteins were localized in close proximity to focal adhesions (FAs), retraction fibers (RFs), and RF-associated extracellular vesicles (migrasomes). In confluent cells, primary cilia had PC1/PC2/CU062 + extracellular vesicles adherent to their plasma membrane. In cells exposed to mitochondrion-decoupling agents, we detected the development of novel PC1/CU062 + ring-like structures that entrained swollen mitochondria. In contact-inhibited cells under mitochondrial stress, PC1, PC2, and CU062 were observed on large, apically budding extracellular vesicles, where the proteins formed a reticular network on the membrane. CU062 interacts with PC1 and may have a role in the identification of senescent mitochondria and their extrusion in extracellular vesicles.
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Affiliation(s)
- Wendy A. Lea
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - Thomas Winklhofer
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - Lesya Zelenchuk
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - Madhulika Sharma
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | | | - Timothy A. Fields
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, 3901 Rainbow Blvd., Mail Stop 3062, Kansas City, KS 66160, USA
| | - Gail Reif
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - James P. Calvet
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - Jason L. Bakeberg
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - Darren P. Wallace
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
| | - Christopher J. Ward
- Department of Nephrology and Hypertension, The Jared Grantham Kidney Institute, University of Kansas Medical Center, Kansas City, 3901 Rainbow Blvd., Mail Stop 3018, KS 66160, USA (D.P.W.)
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Kim H, Sung J, Kim H, Ryu H, Cho Park H, Oh YK, Lee HS, Oh KH, Ahn C. Expression and secretion of CXCL12 are enhanced in autosomal dominant polycystic kidney disease. BMB Rep 2020. [PMID: 31186083 PMCID: PMC6675246 DOI: 10.5483/bmbrep.2019.52.7.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD), one of the most common human monogenic diseases (frequency of 1/1000-1/400), is characterized by numerous fluid-filled renal cysts (RCs). Inactivation of the PKD1 or PKD2 gene by germline and somatic mutations is necessary for cyst formation in ADPKD. To mechanistically understand cyst formation and growth, we isolated RCs from Korean patients with ADPKD and immortalized them with human telomerase reverse transcriptase (hTERT). Three hTERT-immortalized RC cell lines were characterized as proximal epithelial cells with germline and somatic PKD1 mutations. Thus, we first established hTERT-immortalized proximal cyst cells with somatic PKD1 mutations. Through transcriptome sequencing and Gene Ontology (GO) analysis, we found that upregulated genes were related to cell division and that downregulated genes were related to cell differentiation. We wondered whether the upregulated gene for the chemokine CXCL12 is related to the mTOR signaling pathway in cyst growth in ADPKD. CXCL12 mRNA expression and secretion were increased in RC cell lines. We then examined CXCL12 levels in RC fluids from patients with ADPKD and found increased CXCL12 levels. The CXCL12 receptor CXC chemokine receptor 4 (CXCR4) was upregulated, and the mTOR signaling pathway, which is downstream of the CXCL12/CXCR4 axis, was activated in ADPKD kidney tissue. To confirm activation of the mTOR signaling pathway by CXCL12 via CXCR4, we treated the RC cell lines with recombinant CXCL12 and the CXCR4 antagonist AMD3100; CXCL12 induced the mTOR signaling pathway, but the CXCR4 antagonist AMD3100 blocked the mTOR signaling pathway. Taken together, these results suggest that enhanced CXCL12 in RC fluids activates the mTOR signaling pathway via CXCR4 in ADPKD cyst growth.
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Affiliation(s)
- Hyunho Kim
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Korea
| | - Jinmo Sung
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Korea
| | - Hyunsuk Kim
- Internal Medicine, Hallym University Medical Center, Chuncheon Sacred Heart Hospital, Chuncheon 24253, Korea
| | - Hyunjin Ryu
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Hayne Cho Park
- Department of Internal Medicine, Hallym University Medical Center, Kangnam Sacred Heart Hospital, Seoul 07441, Korea
| | - Yun Kyu Oh
- Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul 07061, Korea
| | - Hyun-Seob Lee
- Genomics Core Facility, Department of Transdisciplinary Research and Collaboration, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Korea
| | - Kook-Hwan Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Curie Ahn
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Korea
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Weydert C, Decuypere JP, De Smedt H, Janssens P, Vennekens R, Mekahli D. Fundamental insights into autosomal dominant polycystic kidney disease from human-based cell models. Pediatr Nephrol 2019; 34:1697-1715. [PMID: 30215095 DOI: 10.1007/s00467-018-4057-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 07/23/2018] [Accepted: 08/13/2018] [Indexed: 12/17/2022]
Abstract
Several animal- and human-derived models are used in autosomal dominant polycystic kidney disease (ADPKD) research to gain insight in the disease mechanism. However, a consistent correlation between animal and human ADPKD models is lacking. Therefore, established human-derived models are relevant to affirm research results and translate findings into a clinical set-up. In this review, we give an extensive overview of the existing human-based cell models. We discuss their source (urine, nephrectomy and stem cell), immortalisation procedures, genetic engineering, kidney segmental origin and characterisation with nephron segment markers. We summarise the most studied pathways and lessons learned from these different ADPKD models. Finally, we issue recommendations for the derivation of human-derived cell lines and for experimental set-ups with these cell lines.
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Affiliation(s)
- Caroline Weydert
- PKD Research Group, Laboratory of Pediatrics, Department of Development and Regeneration, GPURE, KU Leuven, Leuven, Belgium
| | - Jean-Paul Decuypere
- PKD Research Group, Laboratory of Pediatrics, Department of Development and Regeneration, GPURE, KU Leuven, Leuven, Belgium
| | - Humbert De Smedt
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Peter Janssens
- PKD Research Group, Laboratory of Pediatrics, Department of Development and Regeneration, GPURE, KU Leuven, Leuven, Belgium
- Department of Nephrology, University Hospitals Brussels, Brussels, Belgium
| | - Rudi Vennekens
- VIB Center for Brain and Disease Research, Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Djalila Mekahli
- PKD Research Group, Laboratory of Pediatrics, Department of Development and Regeneration, GPURE, KU Leuven, Leuven, Belgium.
- Department of Pediatric Nephrology, University Hospitals Leuven, Herestraat 49, 3000, Leuven, Belgium.
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Gufford BT, Robarge JD, Eadon MT, Gao H, Lin H, Liu Y, Desta Z, Skaar TC. Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes. Pharmacol Res Perspect 2018; 6:e00386. [PMID: 29610665 PMCID: PMC5869567 DOI: 10.1002/prp2.386] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/12/2018] [Indexed: 01/06/2023] Open
Abstract
Rifampin is a pleiotropic inducer of multiple drug metabolizing enzymes and transporters. This work utilized a global approach to evaluate rifampin effects on conjugating enzyme gene expression with relevance to human xeno‐ and endo‐biotic metabolism. Primary human hepatocytes from 7 subjects were treated with rifampin (10 μmol/L, 24 hours). Standard methods for RNA‐seq library construction, EZBead preparation, and NextGen sequencing were used to measure UDP‐glucuronosyl transferase UGT, sulfonyltransferase SULT, N acetyltransferase NAT, and glutathione‐S‐transferase GST mRNA expression compared to vehicle control (0.01% MeOH). Rifampin‐induced (>1.25‐fold) mRNA expression of 13 clinically important phase II drug metabolizing genes and repressed (>1.25‐fold) the expression of 3 genes (P < .05). Rifampin‐induced miRNA expression changes correlated with mRNA changes and miRNAs were identified that may modulate conjugating enzyme expression. NAT2 gene expression was most strongly repressed (1.3‐fold) by rifampin while UGT1A4 and UGT1A1 genes were most strongly induced (7.9‐ and 4.8‐fold, respectively). Physiologically based pharmacokinetic modeling (PBPK) was used to simulate the clinical consequences of rifampin induction of CYP3A4‐ and UGT1A4‐mediated midazolam metabolism. Simulations evaluating isolated UGT1A4 induction predicted increased midazolam N‐glucuronide exposure (~4‐fold) with minimal reductions in parent midazolam exposure (~10%). Simulations accounting for simultaneous induction of both CYP3A4 and UGT1A4 predicted a ~10‐fold decrease in parent midazolam exposure with only a ~2‐fold decrease in midazolam N‐glucuronide metabolite exposure. These data reveal differential effects of rifampin on the human conjugating enzyme transcriptome and potential associations with miRNAs that form the basis for future mechanistic studies to elucidate the interplay of conjugating enzyme regulatory elements.
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Affiliation(s)
- Brandon T Gufford
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis IN
| | - Jason D Robarge
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis IN
| | - Michael T Eadon
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis IN
| | - Hongyu Gao
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Hai Lin
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Yunlong Liu
- Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN
| | - Zeruesenay Desta
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis IN
| | - Todd C Skaar
- Department of Medicine Division of Clinical Pharmacology Indiana University School of Medicine Indianapolis IN
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Genetic Variants Contributing to Colistin Cytotoxicity: Identification of TGIF1 and HOXD10 Using a Population Genomics Approach. Int J Mol Sci 2017; 18:ijms18030661. [PMID: 28335481 PMCID: PMC5372673 DOI: 10.3390/ijms18030661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/27/2022] Open
Abstract
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines. To this end, we employed International HapMap lymphoblastoid cell lines (LCLs) of Yoruban ancestry with known genetic information to perform a genome-wide association study (GWAS) with cellular sensitivity to colistin. Further association studies revealed that single nucleotide polymorphisms (SNPs) associated with gene expression and protein expression were significantly enriched in SNPs associated with cytotoxicity (p ≤ 0.001 for gene and p = 0.015 for protein expression). The most highly associated SNP, chr18:3417240 (p = 6.49 × 10−8), was nominally a cis-expression quantitative trait locus (eQTL) of the gene TGIF1 (transforming growth factor β (TGFβ)-induced factor-1; p = 0.021) and was associated with expression of the protein HOXD10 (homeobox protein D10; p = 7.17 × 10−5). To demonstrate functional relevance in a murine colistin nephrotoxicity model, HOXD10 immunohistochemistry revealed upregulated protein expression independent of mRNA expression in response to colistin administration. Knockdown of TGIF1 resulted in decreased protein expression of HOXD10 and increased resistance to colistin cytotoxicity. Furthermore, knockdown of HOXD10 in renal cells also resulted in increased resistance to colistin cytotoxicity, supporting the physiological relevance of the initial genomic associations.
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de Almeida RMC, Clendenon SG, Richards WG, Boedigheimer M, Damore M, Rossetti S, Harris PC, Herbert BS, Xu WM, Wandinger-Ness A, Ward HH, Glazier JA, Bacallao RL. Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. Hum Genomics 2016; 10:37. [PMID: 27871310 PMCID: PMC5117508 DOI: 10.1186/s40246-016-0095-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 11/04/2016] [Indexed: 12/18/2022] Open
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD) causes progressive loss of renal function in adults as a consequence of the accumulation of cysts. ADPKD is the most common genetic cause of end-stage renal disease. Mutations in polycystin-1 occur in 87% of cases of ADPKD and mutations in polycystin-2 are found in 12% of ADPKD patients. The complexity of ADPKD has hampered efforts to identify the mechanisms underlying its pathogenesis. No current FDA (Federal Drug Administration)-approved therapies ameliorate ADPKD progression. Results We used the de Almeida laboratory’s sensitive new transcriptogram method for whole-genome gene expression data analysis to analyze microarray data from cell lines developed from cell isolates of normal kidney and of both non-cystic nephrons and cysts from the kidney of a patient with ADPKD. We compared results obtained using standard Ingenuity Volcano plot analysis, Gene Set Enrichment Analysis (GSEA) and transcriptogram analysis. Transcriptogram analysis confirmed the findings of Ingenuity, GSEA, and published analysis of ADPKD kidney data and also identified multiple new expression changes in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways related to cell growth, cell death, genetic information processing, nucleotide metabolism, signal transduction, immune response, response to stimulus, cellular processes, ion homeostasis and transport and cofactors, vitamins, amino acids, energy, carbohydrates, drugs, lipids, and glycans. Transcriptogram analysis also provides significance metrics which allow us to prioritize further study of these pathways. Conclusions Transcriptogram analysis identifies novel pathways altered in ADPKD, providing new avenues to identify both ADPKD’s mechanisms of pathogenesis and pharmaceutical targets to ameliorate the progression of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0095-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rita M C de Almeida
- Biocomplexity Institute and Department of Physics, Indiana University, Bloomington, IN, 47405, USA.,Instituto de Física and Instituto Nacional de Ciência e Tecnologia, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Sherry G Clendenon
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47405, USA
| | | | | | - Michael Damore
- AMGEN Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320-1799, USA
| | - Sandro Rossetti
- Division of Nephrology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Peter C Harris
- Division of Nephrology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Britney-Shea Herbert
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Wei Min Xu
- Division of Nephrology, Department of Medicine, Richard Roudebush VAMC and Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela Wandinger-Ness
- Department of Pathology MSC08-4640 and Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Heather H Ward
- Division of Nephrology, Department of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - James A Glazier
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47405, USA
| | - Robert L Bacallao
- Division of Nephrology, Department of Medicine, Richard Roudebush VAMC and Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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Peda JD, Salah SM, Wallace DP, Fields PE, Grantham CJ, Fields TA, Swenson-Fields KI. Autocrine IL-10 activation of the STAT3 pathway is required for pathological macrophage differentiation in polycystic kidney disease. Dis Model Mech 2016; 9:1051-61. [PMID: 27491076 PMCID: PMC5047688 DOI: 10.1242/dmm.024745] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/14/2016] [Indexed: 12/16/2022] Open
Abstract
Polycystic kidney disease (PKD) is characterized by slow expansion of fluid-filled cysts derived from tubules within the kidney. Cystic expansion results in injury to surrounding parenchyma and leads to inflammation, scarring and ultimately loss of renal function. Macrophages are a key element in this process, promoting cyst epithelial cell proliferation, cyst expansion and disease progression. Previously, we have shown that the microenvironment established by cystic epithelial cells can ‘program’ macrophages, inducing M2-like macrophage polarization that is characterized by expression of markers that include Arg1 and Il10. Here, we functionally characterize these macrophages, demonstrating that their differentiation enhances their ability to promote cyst cell proliferation. This observation indicates a model of reciprocal pathological interactions between cysts and the innate immune system: cyst epithelial cells promote macrophage polarization to a phenotype that, in turn, is especially efficient in promoting cyst cell proliferation and cyst growth. To better understand the genesis of this macrophage phenotype, we examined the role of IL-10, a regulatory cytokine shown to be important for macrophage-stimulated tissue repair in other settings. Herein, we show that the acquisition of the pathological macrophage phenotype requires IL-10 secretion by the macrophages. Further, we demonstrate a requirement for IL-10-dependent autocrine activation of the STAT3 pathway. These data suggest that the IL-10 pathway in macrophages plays an essential role in the pathological relationship between cysts and the innate immune system in PKD, and thus could be a potential therapeutic target. Summary: Macrophages in polycystic kidney disease are induced by cyst epithelial cell factors to perform pathological pro-proliferative functions through stimulation of an autocrine IL-10–STAT3 pathway.
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Affiliation(s)
- Jacqueline D Peda
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sally M Salah
- Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Darren P Wallace
- Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Patrick E Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Connor J Grantham
- Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Timothy A Fields
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Katherine I Swenson-Fields
- Kidney Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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Belmonte JM, Clendenon SG, Oliveira GM, Swat MH, Greene EV, Jeyaraman S, Glazier JA, Bacallao RL. Virtual-tissue computer simulations define the roles of cell adhesion and proliferation in the onset of kidney cystic disease. Mol Biol Cell 2016; 27:3673-3685. [PMID: 27193300 PMCID: PMC5221598 DOI: 10.1091/mbc.e16-01-0059] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/10/2016] [Indexed: 12/15/2022] Open
Abstract
Virtual-tissue modeling is used to model emergent cyst growth in polycystic kidney disease. Model predictions, confirmed experimentally, show that decreased cell adhesion is necessary to produce stalk cysts, and loss of contact inhibition causes saccular cysts. Virtual-tissue modeling can be used to fully explore cell- and tissue-based behaviors. In autosomal dominant polycystic kidney disease (ADPKD), cysts accumulate and progressively impair renal function. Mutations in PKD1 and PKD2 genes are causally linked to ADPKD, but how these mutations drive cell behaviors that underlie ADPKD pathogenesis is unknown. Human ADPKD cysts frequently express cadherin-8 (cad8), and expression of cad8 ectopically in vitro suffices to initiate cystogenesis. To explore cell behavioral mechanisms of cad8-driven cyst initiation, we developed a virtual-tissue computer model. Our simulations predicted that either reduced cell–cell adhesion or reduced contact inhibition of proliferation triggers cyst induction. To reproduce the full range of cyst morphologies observed in vivo, changes in both cell adhesion and proliferation are required. However, only loss-of-adhesion simulations produced morphologies matching in vitro cad8-induced cysts. Conversely, the saccular cysts described by others arise predominantly by decreased contact inhibition, that is, increased proliferation. In vitro experiments confirmed that cell–cell adhesion was reduced and proliferation was increased by ectopic cad8 expression. We conclude that adhesion loss due to cadherin type switching in ADPKD suffices to drive cystogenesis. Thus, control of cadherin type switching provides a new target for therapeutic intervention.
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Affiliation(s)
- Julio M Belmonte
- Biocomplexity Institute, Physics Department, Indiana University, Bloomington, IN 47405
| | - Sherry G Clendenon
- Biocomplexity Institute, Physics Department, Indiana University, Bloomington, IN 47405
| | - Guilherme M Oliveira
- Biocomplexity Institute, Physics Department, Indiana University, Bloomington, IN 47405
| | - Maciej H Swat
- Biocomplexity Institute, Physics Department, Indiana University, Bloomington, IN 47405
| | - Evan V Greene
- Division of Nephrology, Richard L. Roudebush VA Medical Center, and Indiana University School of Medicine, Indianapolis, IN 46202
| | - Srividhya Jeyaraman
- Biocomplexity Institute, Physics Department, Indiana University, Bloomington, IN 47405
| | - James A Glazier
- Biocomplexity Institute, Physics Department, Indiana University, Bloomington, IN 47405
| | - Robert L Bacallao
- Division of Nephrology, Richard L. Roudebush VA Medical Center, and Indiana University School of Medicine, Indianapolis, IN 46202
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10
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Benson EA, Eadon MT, Desta Z, Liu Y, Lin H, Burgess KS, Segar MW, Gaedigk A, Skaar TC. Rifampin Regulation of Drug Transporters Gene Expression and the Association of MicroRNAs in Human Hepatocytes. Front Pharmacol 2016; 7:111. [PMID: 27199754 PMCID: PMC4845040 DOI: 10.3389/fphar.2016.00111] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/12/2016] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Membrane drug transporters contribute to the disposition of many drugs. In human liver, drug transport is controlled by two main superfamilies of transporters, the solute carrier transporters (SLC) and the ATP Binding Cassette transporters (ABC). Altered expression of these transporters due to drug-drug interactions can contribute to differences in drug exposure and possibly effect. In this study, we determined the effect of rifampin on gene expression of hundreds of membrane transporters along with all clinically relevant drug transporters. METHODS In this study, primary human hepatocytes (n = 7 donors) were cultured and treated for 24 h with rifampin and vehicle control. RNA was isolated from the hepatocytes, mRNA expression was measured by RNA-seq, and miRNA expression was analyzed by Taqman OpenArray. The effect of rifampin on the expression of selected transporters was also tested in kidney cell lines. The impact of rifampin on the expression of 410 transporter genes from 19 different transporter gene families was compared with vehicle control. RESULTS Expression patterns of 12 clinically relevant drug transporter genes were changed by rifampin (FDR < 0.05). For example, the expressions of ABCC2, ABCB1, and ABCC3 were increased 1.9-, 1.7-, and 1.2-fold, respectively. The effects of rifampin on four uptake drug transporters (SLCO1B3, SLC47A1, SLC29A1, SLC22A9) were negatively correlated with the rifampin effects on specific microRNA expression (SLCO1B3/miR-92a, SLC47A1/miR-95, SLC29A1/miR-30d#, and SLC22A9/miR-20; r < -0.79; p < 0.05). Seven hepatic drug transporter genes (SLC22A1, SLC22A5, SLC15A1, SLC29A1, SLCO4C1, ABCC2, and ABCC4), whose expression was altered by rifampin in hepatocytes, were also present in a renal proximal tubular cell line, but in renal cells rifampin did not alter their gene expression. PXR expression was very low in the kidney cells; this may explain why rifampin induces gene expression in a tissue-specific manner. CONCLUSION Rifampin alters the expression of many of the clinically relevant hepatic drug transporters, which may provide a rational basis for understanding rifampin-induced drug-drug interactions reported in vivo. The relevance of its effect on many other transporters remains to be studied.
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Affiliation(s)
- Eric A Benson
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
| | - Michael T Eadon
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
| | - Zeruesenay Desta
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Hai Lin
- Department of Medical and Molecular Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Kimberly S Burgess
- Department of Pharmacology and Toxicology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Matthew W Segar
- Department of Medical and Molecular Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City and School of Medicine, University of Missouri-Kansas City Kansas City, MO, USA
| | - Todd C Skaar
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
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11
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Jerman S, Ward HH, Lee R, Lopes CAM, Fry AM, MacDougall M, Wandinger-Ness A. OFD1 and flotillins are integral components of a ciliary signaling protein complex organized by polycystins in renal epithelia and odontoblasts. PLoS One 2014; 9:e106330. [PMID: 25180832 PMCID: PMC4152239 DOI: 10.1371/journal.pone.0106330] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/31/2014] [Indexed: 12/16/2022] Open
Abstract
Mutation of the X-linked oral-facial-digital syndrome type 1 (OFD1) gene is embryonic lethal in males and results in craniofacial malformations and adult onset polycystic kidney disease in females. While the OFD1 protein localizes to centriolar satellites, centrosomes and basal bodies, its cellular function and how it relates to cystic kidney disease is largely unknown. Here, we demonstrate that OFD1 is assembled into a protein complex that is localized to the primary cilium and contains the epidermal growth factor receptor (EGFR) and domain organizing flotillin proteins. This protein complex, which has similarity to a basolateral adhesion domain formed during cell polarization, also contains the polycystin proteins that when mutant cause autosomal dominant polycystic kidney disease (ADPKD). Importantly, in human ADPKD cells where mutant polycystin-1 fails to localize to cilia, there is a concomitant loss of localization of polycystin-2, OFD1, EGFR and flotillin-1 to cilia. Together, these data suggest that polycystins are necessary for assembly of a novel flotillin-containing ciliary signaling complex and provide a molecular rationale for the common renal pathologies caused by OFD1 and PKD mutations.
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Affiliation(s)
- Stephanie Jerman
- Department of Pathology MSC08-4640 and Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Heather H. Ward
- Department of Internal Medicine, Division of Nephrology MSC10-5550, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Rebecca Lee
- Department of Pathology MSC08-4640 and Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Carla A. M. Lopes
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Andrew M. Fry
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Mary MacDougall
- Institute of Oral Health Research & Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama, Birmingham, Alabama, United States of America
| | - Angela Wandinger-Ness
- Department of Pathology MSC08-4640 and Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America
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