1
|
Kasprzyk-Pawelec A, Tan M, Phua YL, Rahhal R, McIntosh A, Fernandez H, Mosaoa R, Girgis M, Cheema A, Jiang L, Kroemer LF, Popratiloff A, Clarkson C, Kirmsa BM, Pearson GW, Glasgow E, Albanese C, Vockley J, Avantaggiati ML. Loss of the mitochondrial citrate carrier, Slc25a1/CIC disrupts embryogenesis via 2-Hydroxyglutarate. bioRxiv 2024:2023.07.18.549409. [PMID: 37503155 PMCID: PMC10370133 DOI: 10.1101/2023.07.18.549409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Biallelic germline mutations in the SLC25A1 gene lead to combined D/L-2-hydroxyglutaric aciduria (D/L-2HGA), a fatal systemic disease uniquely characterized by the accumulation of both enantiomers of 2-hydroxyglutaric acid (2HG). How SLC25A1 deficiency contributes to D/L-2HGA and the role played by 2HG is unclear and no therapy exists. Both enantiomers act as oncometabolites, but their activities in normal tissues remain understudied. Here we show that mice lacking both SLC25A1 alleles exhibit developmental abnormalities that mirror human D/L-2HGA. SLC25A1 deficient cells undergo premature senescence, suggesting that loss of proliferative capacity underlies the pathogenesis of D/L-2HGA. Remarkably, D- and L-2HG directly induce senescence and treatment of zebrafish embryos with the combination of D- and L-2HG phenocopies SLC25A1 loss, leading to developmental abnormalities in an additive fashion relative to either enantiomer alone. Metabolic analyses further demonstrate that cells with dysfunctional SLC25A1 undergo mitochondrial respiratory deficit and remodeling of the metabolism and we propose several strategies to correct these defects. These results reveal for the first time pathogenic and growth suppressive activities of 2HG in the context of SLC25A1 deficiency and suggest that targeting the 2HG pathway may be beneficial for the treatment of D/L-2HGA.
Collapse
|
2
|
Airik M, Arbore H, Childs E, Huynh AB, Phua YL, Chen CW, Aird K, Bharathi S, Zhang B, Conlon P, Kmoch S, Kidd K, Bleyer AJ, Vockley J, Goetzman E, Wipf P, Airik R. Mitochondrial ROS Triggers KIN Pathogenesis in FAN1-Deficient Kidneys. Antioxidants (Basel) 2023; 12:900. [PMID: 37107275 PMCID: PMC10135478 DOI: 10.3390/antiox12040900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/02/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
Karyomegalic interstitial nephritis (KIN) is a genetic adult-onset chronic kidney disease (CKD) characterized by genomic instability and mitotic abnormalities in the tubular epithelial cells. KIN is caused by recessive mutations in the FAN1 DNA repair enzyme. However, the endogenous source of DNA damage in FAN1/KIN kidneys has not been identified. Here we show, using FAN1-deficient human renal tubular epithelial cells (hRTECs) and FAN1-null mice as a model of KIN, that FAN1 kidney pathophysiology is triggered by hypersensitivity to endogenous reactive oxygen species (ROS), which cause chronic oxidative and double-strand DNA damage in the kidney tubular epithelial cells, accompanied by an intrinsic failure to repair DNA damage. Furthermore, persistent oxidative stress in FAN1-deficient RTECs and FAN1 kidneys caused mitochondrial deficiencies in oxidative phosphorylation and fatty acid oxidation. The administration of subclinical, low-dose cisplatin increased oxidative stress and aggravated mitochondrial dysfunction in FAN1-deficient kidneys, thereby exacerbating KIN pathophysiology. In contrast, treatment of FAN1 mice with a mitochondria-targeted ROS scavenger, JP4-039, attenuated oxidative stress and accumulation of DNA damage, mitigated tubular injury, and preserved kidney function in cisplatin-treated FAN1-null mice, demonstrating that endogenous oxygen stress is an important source of DNA damage in FAN1-deficient kidneys and a driver of KIN pathogenesis. Our findings indicate that therapeutic modulation of kidney oxidative stress may be a promising avenue to mitigate FAN1/KIN kidney pathophysiology and disease progression in patients.
Collapse
Affiliation(s)
- Merlin Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Haley Arbore
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Elizabeth Childs
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Amy B. Huynh
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Yu Leng Phua
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Chi Wei Chen
- Department of Pharmacology & Chemical Biology and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Katherine Aird
- Department of Pharmacology & Chemical Biology and UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Sivakama Bharathi
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Bob Zhang
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Peter Conlon
- Nephrology Department, Beaumont Hospital, D09 V2N0 Dublin, Ireland
| | - Stanislav Kmoch
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Kendrah Kidd
- Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | | | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Eric Goetzman
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Peter Wipf
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rannar Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15224, USA
| |
Collapse
|
3
|
Phua YL, D’Annibale OM, Karunanidhi A, Mohsen AW, Kirmse B, Dobrowolski SF, Vockley J. A multiomics approach to understanding pathology of Combined D,L-2- Hydroxyglutaric Aciduria and phenylbutyrate as potential treatment. bioRxiv 2023:2023.02.02.526527. [PMID: 36778323 PMCID: PMC9915603 DOI: 10.1101/2023.02.02.526527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Combined D, L-2-Hydroxyglutaric Aciduria (D,L-2HGA) is a rare genetic disorder caused by recessive mutations in the SLC25A1 gene that encodes the mitochondrial citrate carrier protein (CIC). SLC25A1 deficiency leads to a secondary increase in mitochondrial 2-ketoglutarate that, in turn, is reduced to neurotoxic 2-hydroxyglutarate. Clinical symptoms of Combined D,L-2HGA include neonatal encephalopathy, respiratory insufficiency and often with death in infancy. No current therapies exist, although replenishing cytosolic stores by citrate supplementation to replenish cytosolic stores has been proposed. In this study, we demonstrated that patient derived fibroblasts exhibited impaired cellular bioenergetics that were worsened with citrate supplementation. We hypothesized treating patient cells with phenylbutyrate, an FDA approved pharmaceutical drug, would reduce mitochondrial 2-ketoglutarate, leading to improved cellular bioenergetics including oxygen consumption and fatty acid oxidation. Metabolomic and RNA-seq analyses demonstrated a significant decrease in intracellular 2-ketoglutarate, 2-hydroxyglutarate, and in levels of mRNA coding for citrate synthase and isocitrate dehydrogenase. Consistent with the known action of phenylbutyrate, detected levels of phenylacetylglutamine was consistent with the drug acting as 2-ketoglutarate sink in patient cells. Our pre-clinical studies suggest citrate supplementation is unlikely to be an effective treatment of the disorder. However, cellular bioenergetics suggests phenylbutyrate may have interventional utility for this rare disease.
Collapse
Affiliation(s)
- Yu Leng Phua
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Olivia M D’Annibale
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Anuradha Karunanidhi
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Al-Walid Mohsen
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Brian Kirmse
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Steven F Dobrowolski
- Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Genetic and Genomic Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| |
Collapse
|
4
|
Airik M, Phua YL, Huynh AB, McCourt BT, Rush BM, Tan RJ, Vockley J, Murray SL, Dorman A, Conlon PJ, Airik R. Persistent DNA damage underlies tubular cell polyploidization and progression to chronic kidney disease in kidneys deficient in the DNA repair protein FAN1. Kidney Int 2022; 102:1042-1056. [PMID: 35931300 PMCID: PMC9588672 DOI: 10.1016/j.kint.2022.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 12/14/2022]
Abstract
Defective DNA repair pathways contribute to the development of chronic kidney disease (CKD) in humans. However, the molecular mechanisms underlying DNA damage-induced CKD pathogenesis are not well understood. Here, we investigated the role of tubular cell DNA damage in the pathogenesis of CKD using mice in which the DNA repair protein Fan1 was knocked out. The phenotype of these mice is orthologous to the human DNA damage syndrome, karyomegalic interstitial nephritis (KIN). Inactivation of Fan1 in kidney proximal tubule cells sensitized the kidneys to genotoxic and obstructive injury characterized by replication stress and persistent DNA damage response activity. Accumulation of DNA damage in Fan1 tubular cells induced epithelial dedifferentiation and tubular injury. Characteristic to KIN, cells with chronic DNA damage failed to complete mitosis and underwent polyploidization. In vitro and in vivo studies showed that polyploidization was caused by the overexpression of DNA replication factors CDT1 and CDC6 in FAN1 deficient cells. Mechanistically, inhibiting DNA replication with Roscovitine reduced tubular injury, blocked the development of KIN and mitigated kidney function in these Fan1 knockout mice. Thus, our data delineate a mechanistic pathway by which persistent DNA damage in the kidney tubular cells leads to kidney injury and development of CKD. Furthermore, therapeutic modulation of cell cycle activity may provide an opportunity to mitigate the DNA damage response induced CKD progression.
Collapse
Affiliation(s)
- Merlin Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yu Leng Phua
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amy B Huynh
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Blake T McCourt
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brittney M Rush
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Roderick J Tan
- Renal-Electrolyte Division, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jerry Vockley
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Susan L Murray
- Department of Nephrology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Anthony Dorman
- Department of Nephrology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter J Conlon
- Department of Nephrology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Rannar Airik
- Division of Nephrology, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA; Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
| |
Collapse
|
5
|
Dobrowolski SF, Phua YL, Tourkova IL, Sudano C, Vockley J, Larrouture QC, Blair HC. Glutamine energy substrate anaplerosis increases bone density in the Pah enu2 classical PKU mouse in the absence of phenylalanine restriction. JIMD Rep 2022; 63:446-452. [PMID: 36101821 PMCID: PMC9458609 DOI: 10.1002/jmd2.12308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/09/2022] Open
Abstract
Osteopenia is an under-investigated clinical presentation of phenylalanine hydroxylase (PAH)-deficient phenylketonuria (PKU). While osteopenia is not fully penetrant in human PKU, the Pahenu2 mouse is universally osteopenic and ideal to study the phenotype. We determined Pahenu2 mesenchymal stem cells (MSCs) are developmentally impaired in the osteoblast lineage. Moreover, we determined energy dysregulation and oxidative stress contribute to the osteoblast developmental deficit. The MSC preferred substrate glutamine (Gln) was applied to enhance energy homeostasis. In vitro Pahenu2 MSCs, in the context of 1200 μM Phe, respond to Gln with increased in situ alkaline phosphatase activity indicating augmented osteoblast differentiation. Oximetry applied to Pahenu2 MSCs in osteoblast differentiation show Gln energy substrate increases oxygen consumption, specifically maximum respiration and respiratory reserve. For 60 days post-weaning, Pahenu2 animals received either no intervention (standard lab chow), amino acid defined chow maintaining plasma Phe at ~200 μM, or standard lab chow where ad libitum water was a 2% Gln solution. Bone density was assessed by microcomputed tomography and bone growth assessed by dye labeling. Bone density and dye labeling in Phe-restricted Pahenu2 was indistinguishable from untreated Pahenu2. Gln energy substrate provided to Pahenu2, in the context of uncontrolled hyperphenylalaninemia, present increased bone density and dye labeling. These data provide further evidence that Pahenu2 MSCs experience a secondary energy deficit that is responsive both in vitro and in vivo to Gln energy substrate and independent of hyperphenylalaninemia. Energy support may have effect to treat human PKU osteopenia and elements of PKU neurologic disease resistant to standard of care systemic Phe reduction. Glutamine energy substrate anaplerosis increased Pahenu2 bone density and improved in vitro MSC function in the context of hyperphenylalaninemia in the classical PKU range.
Collapse
Affiliation(s)
- Steven F. Dobrowolski
- Department of PathologyUniversity of Pittsburgh, School of MedicinePittsburghPennsylvaniaUSA
| | - Yu Leng Phua
- Division of Medical Genetics and GenomicsChildren's Hospital of PittsburghPittsburghPennsylvaniaUSA
- Present address:
Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkUSA
| | - Irina L. Tourkova
- Department of PathologyUniversity of Pittsburgh, School of MedicinePittsburghPennsylvaniaUSA
- Pittsburgh Veteran's Affairs Medical CenterPittsburghPennsylvaniaUSA
| | - Cayla Sudano
- Department of PathologyUniversity of Pittsburgh, School of MedicinePittsburghPennsylvaniaUSA
| | - Jerry Vockley
- Division of Medical Genetics and GenomicsChildren's Hospital of PittsburghPittsburghPennsylvaniaUSA
| | - Quitterie C. Larrouture
- Department of PathologyUniversity of Pittsburgh, School of MedicinePittsburghPennsylvaniaUSA
- Pittsburgh Veteran's Affairs Medical CenterPittsburghPennsylvaniaUSA
| | - Harry C. Blair
- Department of PathologyUniversity of Pittsburgh, School of MedicinePittsburghPennsylvaniaUSA
- Pittsburgh Veteran's Affairs Medical CenterPittsburghPennsylvaniaUSA
| |
Collapse
|
6
|
Dobrowolski SF, Phua YL, Vockley J, Goetzman E, Blair HC. Phenylketonuria oxidative stress and energy dysregulation: Emerging pathophysiological elements provide interventional opportunity. Mol Genet Metab 2022; 136:111-117. [PMID: 35379539 PMCID: PMC9832337 DOI: 10.1016/j.ymgme.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 01/13/2023]
Abstract
Phenylalanine hydroxylase (PAH) deficient phenylketonuria (PKU) is rightfully considered the paradigm treatable metabolic disease. Dietary substrate restriction (i.e. phenylalanine (Phe) restriction) was applied >60 years ago and remains the primary PKU management means. The traditional model of PKU neuropathophysiology dictates blood Phe over-representation directs asymmetric blood:brain barrier amino acid transport through the LAT1 transporter with subsequent increased cerebral Phe concentration and low concentrations of tyrosine (Tyr), tryptophan (Trp), leucine (Leu), valine (Val), and isoleucine (Ile). Low Tyr and Trp concentrations generate secondary serotonergic and dopaminergic neurotransmitter paucities, widely attributed as drivers of PKU neurologic phenotypes. White matter disease, a central PKU characteristic, is ascribed to Phe-mediated tissue toxicity. Impaired cerebral protein synthesis, by reduced concentrations of non-Phe large neutral amino acids, is another cited pathological mechanism. The PKU amino acid transport model suggests Phe management should be more efficacious than is realized, as even early identified, continuously treated patients that retain therapy compliance into adulthood, demonstrate neurologic disease elements. Reduced cerebral metabolism was an early-recognized element of PKU pathology. Legacy data (late 1960's to mid-1970's) determined the Phe catabolite phenylpyruvate inhibits mitochondrial pyruvate transport. Respirometry of Pahenu2 cerebral mitochondria have attenuated respiratory chain complex 1 induction in response to pyruvate substrate, indicating reduced energy metabolism. Oxidative stress is intrinsic to PKU and Pahenu2 brain tissue presents increased reactive oxygen species. Phenylpyruvate inhibits glucose-6-phosphate dehydrogenase that generates reduced niacinamide adenine dinucleotide phosphate the obligatory cofactor of glutathione reductase. Pahenu2 brain tissue metabolomics identified increased oxidized glutathione and glutathione disulfide. Over-represented glutathione disulfide argues for reduced glutathione reductase activity secondary to reduced NADPH. Herein, we review evidence of energy and oxidative stress involvement in PKU pathology. Data suggests energy deficit and oxidative stress are features of PKU pathophysiology, providing intervention-amenable therapeutic targets to ameliorate disease elements refractory to standard of care.
Collapse
Affiliation(s)
- Steven F Dobrowolski
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America.
| | - Yu Leng Phua
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Jerry Vockley
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Eric Goetzman
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Harry C Blair
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America; Veteran's Affairs Medical Center, Pittsburgh, PA, United States of America
| |
Collapse
|
7
|
Dobrowolski SF, Phua YL, Sudano C, Spridik K, Zinn PO, Wang Y, Bharathi S, Vockley J, Goetzman E. Comparative metabolomics in the Pah enu2 classical PKU mouse identifies cerebral energy pathway disruption and oxidative stress. Mol Genet Metab 2022; 136:38-45. [PMID: 35367142 PMCID: PMC9759961 DOI: 10.1016/j.ymgme.2022.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/06/2023]
Abstract
Classical phenylketonuria (PKU, OMIM 261600) owes to hepatic deficiency of phenylalanine hydroxylase (PAH) that enzymatically converts phenylalanine (Phe) to tyrosine (Tyr). PKU neurologic phenotypes include impaired brain development, decreased myelination, early onset mental retardation, seizures, and late-onset features (neuropsychiatric, Parkinsonism). Phe over-representation is systemic; however, tissue response to hyperphenylalaninemia is not consistent. To characterize hyperphenylalaninemia tissue response, metabolomics was applied to Pahenu2 classical PKU mouse blood, liver, and brain. In blood and liver over-represented analytes were principally Phe, Phe catabolites, and Phe-related analytes (Phe-conjugates, Phe-containing dipeptides). In addition to Phe and Phe-related analytes, the metabolomic profile of Pahenu2 brain tissue evidenced oxidative stress responses and energy dysregulation. Glutathione and homocarnosine anti-oxidative responses are apparent Pahenu2 brain. Oxidative stress in Pahenu2 brain was further evidenced by increased reactive oxygen species. Pahenu2 brain presents an increased NADH/NAD ratio suggesting respiratory chain complex 1 dysfunction. Respirometry in Pahenu2 brain mitochondria functionally confirmed reduced respiratory chain activity with an attenuated response to pyruvate substrate. Glycolysis pathway analytes are over-represented in Pahenu2 brain tissue. PKU pathologies owe to liver metabolic deficiency; yet, Pahenu2 liver tissue shows neither energy disruption nor anti-oxidative response. Unique aspects of metabolomic homeostasis in PKU brain tissue along with increased reactive oxygen species and respiratory chain deficit provide insight to neurologic disease mechanisms. While some elements of assumed, long standing PKU neuropathology are enforced by metabolomic data (e.g. reduced tryptophan and serotonin representation), energy dysregulation and tissue oxidative stress expand mechanisms underlying neuropathology.
Collapse
Affiliation(s)
- Steven F Dobrowolski
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America.
| | - Yu Leng Phua
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Cayla Sudano
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Kayla Spridik
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Pascal O Zinn
- Department of Neurological Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Yudong Wang
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Sivakama Bharathi
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Jerry Vockley
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Eric Goetzman
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States of America
| |
Collapse
|
8
|
Clugston A, Bodnar A, Cerqueira DM, Phua YL, Lawler A, Boggs K, Pfenning A, Ho J, Kostka D. Chromatin accessibility and microRNA expression in nephron progenitor cells during kidney development. Genomics 2022; 114:278-291. [PMID: 34942352 PMCID: PMC8792369 DOI: 10.1016/j.ygeno.2021.12.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 01/03/2023]
Abstract
Mammalian nephrons originate from a population of nephron progenitor cells, and changes in these cells' transcriptomes contribute to the cessation of nephrogenesis, an important determinant of nephron number. To characterize microRNA (miRNA) expression and identify putative cis-regulatory regions, we collected nephron progenitor cells from mouse kidneys at embryonic day 14.5 and postnatal day zero and assayed small RNA expression and transposase-accessible chromatin. We detect expression of 1104 miRNA (114 with expression changes), and 46,374 chromatin accessible regions (2103 with changes in accessibility). Genome-wide, our data highlight processes like cellular differentiation, cell migration, extracellular matrix interactions, and developmental signaling pathways. Furthermore, they identify new candidate cis-regulatory elements for Eya1 and Pax8, both genes with a role in nephron progenitor cell differentiation. Finally, we associate expression-changing miRNAs, including let-7-5p, miR-125b-5p, miR-181a-2-3p, and miR-9-3p, with candidate cis-regulatory elements and target genes. These analyses highlight new putative cis-regulatory loci for miRNA in nephron progenitors.
Collapse
Affiliation(s)
- Andrew Clugston
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Andrew Bodnar
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Débora Malta Cerqueira
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Yu Leng Phua
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Genetic and Genomic Medicine, Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pathology, Clinical Biochemical Genetics Laboratory, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Alyssa Lawler
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA,Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kristy Boggs
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Andreas Pfenning
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA,Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jacqueline Ho
- Rangos Research Center, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA,Co-Corresponding authors:Dr. Dennis Kostka, Rangos Research Center 8117, Department of Developmental Biology, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-9905, ; Dr. Jacqueline Ho, Rangos Research Center 5127, Department of Pediatrics, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-5303,
| | - Dennis Kostka
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Computational & Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Co-Corresponding authors:Dr. Dennis Kostka, Rangos Research Center 8117, Department of Developmental Biology, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-9905, ; Dr. Jacqueline Ho, Rangos Research Center 5127, Department of Pediatrics, 530 45th St., Pittsburgh, Pennsylvania 15224, USA, Phone: 412-692-5303,
| |
Collapse
|
9
|
Phua YL, Dobrowolski SF. An Infant with a Constellation of Biochemical Abnormalities. Clin Chem 2021; 67:1035-1036. [PMID: 34229345 DOI: 10.1093/clinchem/hvab028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/28/2021] [Indexed: 11/14/2022]
Affiliation(s)
- Yu Leng Phua
- Division of Medical Genetics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Steven F Dobrowolski
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
10
|
Dobrowolski SF, Phua YL, Sudano C, Spridik K, Zinn PO, Wang Y, Bharathi S, Vockley J, Goetzman E. Phenylalanine hydroxylase deficient phenylketonuria comparative metabolomics identifies energy pathway disruption and oxidative stress. Mol Genet Metab 2021:S1096-7192(21)00686-7. [PMID: 33846068 DOI: 10.1016/j.ymgme.2021.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/02/2021] [Accepted: 04/02/2021] [Indexed: 11/15/2022]
Abstract
Classical phenylketonuria (PKU, OMIM 261600) owes to hepatic deficiency of phenylalanine hydroxylase (PAH) that enzymatically converts phenylalanine (Phe) to tyrosine (Tyr). PKU neurologic phenotypes include impaired brain development, decreased myelination, early onset mental retardation, seizures, and late-onset features (neuropsychiatric, Parkinsonism). PAH deficiency leads to systemic hyperphenylalaninemia; however, the impact of Phe varies between tissues. To characterize tissue response to hyperphenylalaninemia, metabolomics was applied to tissue from therapy noncompliant classical PKU patients (blood, liver), the Pahenu2 classical PKU mouse (blood, liver, brain) and the PAH deficient pig (blood, liver, brain, cerebrospinal fluid). In blood, liver, and CSF from both patients and animal models over-represented analytes were principally Phe, Phe catabolites, and Phe-related analytes (conjugates, Phe-containing dipeptides). In addition to Phe and Phe-related analytes, the metabolomic profile of PKU brain tissue (mouse, pig) evidenced oxidative stress responses and energy dysregulation. In Pahenu2 and PKU pig brain tissues, anti-oxidative response by glutathione and homocarnosine is apparent. Oxidative stress in Pahenu2 brain was further demonstrated by increased reactive oxygen species. In Pahenu2 and PKU pig brain, an increased NADH/NAD ratio suggests a respiratory chain dysfunction. Respirometry in PKU brain mitochondria (mouse, pig) functionally confirmed reduced respiratory chain activity. Glycolysis pathway analytes are over-represented in PKU brain tissue (mouse, pig). PKU pathologies owe to liver metabolic deficiency; yet, PKU liver tissue (mouse, pig, human) shows neither energy disruption nor anti-oxidative response. Unique aspects of metabolomic homeostasis in PKU brain tissue along with increased reactive oxygen species and respiratory chain deficit provide insight to neurologic disease mechanisms. While some elements of assumed, long standing PKU neuropathology are enforced by metabolomic data (e.g. reduced tryptophan and serotonin representation), energy dysregulation and tissue oxidative stress expand mechanisms underlying neuropathology.
Collapse
Affiliation(s)
- Steven F Dobrowolski
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States.
| | - Yu Leng Phua
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Cayla Sudano
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Kayla Spridik
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Pascal O Zinn
- Department of Neurological Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Yudong Wang
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Sivakama Bharathi
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Jerry Vockley
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| | - Eric Goetzman
- Division of Medical Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15224, United States
| |
Collapse
|
11
|
Chiba T, Cerqueira DM, Li Y, Bodnar AJ, Mukherjee E, Pfister K, Phua YL, Shaikh K, Sanders BT, Hemker SL, Pagano PJ, Wu YL, Ho J, Sims-Lucas S. Endothelial-Derived miR-17∼92 Promotes Angiogenesis to Protect against Renal Ischemia-Reperfusion Injury. J Am Soc Nephrol 2021; 32:553-562. [PMID: 33514560 PMCID: PMC7920169 DOI: 10.1681/asn.2020050717] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 11/21/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Damage to the renal microvasculature is a hallmark of renal ischemia-reperfusion injury (IRI)-mediated AKI. The miR-17∼92 miRNA cluster (encoding miR-17, -18a, -19a, -20a, -19b-1, and -92a-1) regulates angiogenesis in multiple settings, but no definitive role in renal endothelium during AKI pathogenesis has been established. METHODS Antibodies bound to magnetic beads were utilized to selectively enrich for renal endothelial cells from mice. Endothelial-specific miR-17∼92 knockout (miR-17∼92endo-/- ) mice were generated and given renal IRI. Mice were monitored for the development of AKI using serum chemistries and histology and for renal blood flow using magnetic resonance imaging (MRI) and laser Doppler imaging. Mice were treated with miRNA mimics during renal IRI, and therapeutic efficacies were evaluated. RESULTS miR-17, -18a, -20a, -19b, and pri-miR-17∼92 are dynamically regulated in renal endothelial cells after renal IRI. miR-17∼92endo-/- exacerbates renal IRI in male and female mice. Specifically, miR-17∼92endo-/- promotes renal tubular injury, reduces renal blood flow, promotes microvascular rarefaction, increases renal oxidative stress, and promotes macrophage infiltration to injured kidneys. The potent antiangiogenic factor thrombospondin 1 (TSP1) is highly expressed in renal endothelium in miR-17∼92endo-/- after renal IRI and is a target of miR-18a and miR-19a/b. miR-17∼92 is critical in the angiogenic response after renal IRI, which treatment with miR-18a and miR-19b mimics can mitigate. CONCLUSIONS These data suggest that endothelial-derived miR-17∼92 stimulates a reparative response in damaged renal vasculature during renal IRI by regulating angiogenic pathways.
Collapse
Affiliation(s)
- Takuto Chiba
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Débora M. Cerqueira
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yao Li
- Heart, Lung, Blood and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Andrew J. Bodnar
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Elina Mukherjee
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Katherine Pfister
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yu Leng Phua
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kai Shaikh
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Brandon T. Sanders
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Shelby L. Hemker
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Patrick J. Pagano
- Heart, Lung, Blood and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Yijen L. Wu
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Sunder Sims-Lucas
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
- Heart, Lung, Blood and Vascular Medicine Institute, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| |
Collapse
|
12
|
Dobrowolski SF, Sudano C, Phua YL, Tourkova IL, Spridik K, Goetzman ES, Vockley J, Blair HC. Mesenchymal stem cell energy deficit and oxidative stress contribute to osteopenia in the Pah enu2 classical PKU mouse. Mol Genet Metab 2021; 132:173-179. [PMID: 33602601 PMCID: PMC9795491 DOI: 10.1016/j.ymgme.2021.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/31/2022]
Abstract
Osteopenia occurs in a subset of phenylalanine hydroxylase (PAH) deficient phenylketonuria (PKU) patients. While osteopenia is not fully penetrant in patients, the Pahenu2 classical PKU mouse is universally osteopenic, making it an ideal model of the phenotype. Pahenu2 Phe management, with a Phe-fee amino acid defined diet, does not improve bone density as histomorphometry metrics remain indistinguishable from untreated animals. Previously, we demonstrated Pahenu2 mesenchymal stem cells (MSCs) display impaired osteoblast differentiation. Oxidative stress is recognized in PKU patients and PKU animal models. Pahenu2 MSCs experience oxidative stress determined by intracellular superoxide over-representation. The deleterious impact of oxidative stress on mitochondria is recognized. Oximetry applied to Pahenu2 MSCs identified mitochondrial stress by increased basal respiration with concurrently reduced maximal respiration and respiratory reserve. Proton leak secondary to mitochondrial complex 1 dysfunction is a recognized superoxide source. Respirometry applied to Pahenu2 MSCs, in the course of osteoblast differentiation, identified a partial complex 1 deficit. Pahenu2 MSCs treated with the antioxidant resveratrol demonstrated increased mitochondrial mass by MitoTracker green labeling. In hyperphenylalaninemic conditions, resveratrol increased in situ alkaline phosphatase activity suggesting partial recovery of Pahenu2 MSCs osteoblast differentiation. Up-regulation of oxidative energy production is required for osteoblasts differentiation. Our data suggests impaired Pahenu2 MSC developmental competence involves an energy deficit. We posit energy support and oxidative stress reduction will enable Pahenu2 MSC differentiation in the osteoblast lineage to subsequently increase bone density.
Collapse
Affiliation(s)
- Steven F Dobrowolski
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America.
| | - Cayla Sudano
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America
| | - Yu Leng Phua
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Irina L Tourkova
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America; Pittsburgh Veteran's Affairs Medical Center, Pittsburgh, PA 15261, United States of America
| | - Kayla Spridik
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America
| | - Eric S Goetzman
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Jerry Vockley
- Division of Medical Genetics, Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, United States of America
| | - Harry C Blair
- Department of Pathology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15224, United States of America; Pittsburgh Veteran's Affairs Medical Center, Pittsburgh, PA 15261, United States of America
| |
Collapse
|
13
|
Phua YL, Chen KH, Hemker SL, Marrone AK, Bodnar AJ, Liu X, Clugston A, Kostka D, Butterworth MB, Ho J. Loss of miR-17~92 results in dysregulation of Cftr in nephron progenitors. Am J Physiol Renal Physiol 2019; 316:F993-F1005. [PMID: 30838872 DOI: 10.1152/ajprenal.00450.2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We have previously demonstrated that loss of miR-17~92 in nephron progenitors in a mouse model results in renal hypodysplasia and chronic kidney disease. Clinically, decreased congenital nephron endowment because of renal hypodysplasia is associated with an increased risk of hypertension and chronic kidney disease, and this is at least partly dependent on the self-renewal of nephron progenitors. Here, we present evidence for a novel molecular mechanism regulating the self-renewal of nephron progenitors and congenital nephron endowment by the highly conserved miR-17~92 cluster. Whole transcriptome sequencing revealed that nephron progenitors lacking this cluster demonstrated increased Cftr expression. We showed that one member of the cluster, miR-19b, is sufficient to repress Cftr expression in vitro and that perturbation of Cftr activity in nephron progenitors results in impaired proliferation. Together, these data suggest that miR-19b regulates Cftr expression in nephron progenitors, with this interaction playing a role in appropriate nephron progenitor self-renewal during kidney development to generate normal nephron endowment.
Collapse
Affiliation(s)
- Yu Leng Phua
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Kevin Hong Chen
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Department of Biological Sciences, Carnegie Mellon University , Pittsburgh, Pennsylvania
| | - Shelby L Hemker
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - April K Marrone
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Andrew J Bodnar
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Xiaoning Liu
- Department of Cell Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Andrew Clugston
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania.,Department of Developmental Biology and Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Dennis Kostka
- Department of Developmental Biology and Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Michael B Butterworth
- Department of Cell Biology, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| | - Jacqueline Ho
- Rangos Research Center, UPMC Children's Hospital of Pittsburgh , Pittsburgh, Pennsylvania.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine , Pittsburgh, Pennsylvania
| |
Collapse
|
14
|
Phua YL, Clugston A, Chen KH, Kostka D, Ho J. Small non-coding RNA expression in mouse nephrogenic mesenchymal progenitors. Sci Data 2018; 5:180218. [PMID: 30422124 PMCID: PMC6233257 DOI: 10.1038/sdata.2018.218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 08/15/2018] [Indexed: 01/02/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that are essential for the regulation of gene expression and play critical roles in human health and disease. Here we present comprehensive miRNA profiling data for mouse nephrogenic mesenchymal progenitors, a population of cells enriched for nephron progenitors that give rise to most cell-types of the nephron, the functional unit of the kidney. We describe a miRNA expression in nephrogenic mesenchymal progenitors, with 162 miRNAs differentially expressed in progenitors when compared to whole kidney. We also annotated 49 novel miRNAs in the developing kidney and experimentally validated 4 of them. Our data are available as a public resource, so that it can be integrated into future studies and analyzed in the context of other functional and epigenomic data in kidney development. Specifically, it will be useful in the effort to shed light on molecular mechanisms underlying processes essential for normal kidney development, like nephron progenitor specification, self-renewal and differentiation.
Collapse
Affiliation(s)
- Yu Leng Phua
- Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Andrew Clugston
- Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA.,Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kevin Hong Chen
- Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| | - Dennis Kostka
- Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Computational & Systems Biology and Pittsburgh Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jacqueline Ho
- Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,Department of Pediatrics, Division of Nephrology, University of Pittsburgh School of Medicine, PA, USA
| |
Collapse
|
15
|
Espiritu EB, Crunk AE, Bais A, Hochbaum D, Cervino AS, Phua YL, Butterworth MB, Goto T, Ho J, Hukriede NA, Cirio MC. The Lhx1-Ldb1 complex interacts with Furry to regulate microRNA expression during pronephric kidney development. Sci Rep 2018; 8:16029. [PMID: 30375416 PMCID: PMC6207768 DOI: 10.1038/s41598-018-34038-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022] Open
Abstract
The molecular events driving specification of the kidney have been well characterized. However, how the initial kidney field size is established, patterned, and proportioned is not well characterized. Lhx1 is a transcription factor expressed in pronephric progenitors and is required for specification of the kidney, but few Lhx1 interacting proteins or downstream targets have been identified. By tandem-affinity purification, we isolated FRY like transcriptional coactivator (Fryl), one of two paralogous genes, fryl and furry (fry), have been described in vertebrates. Both proteins were found to interact with the Ldb1-Lhx1 complex, but our studies focused on Lhx1/Fry functional roles, as they are expressed in overlapping domains. We found that Xenopus embryos depleted of fry exhibit loss of pronephric mesoderm, phenocopying the Lhx1-depleted animals. In addition, we demonstrated a synergism between Fry and Lhx1, identified candidate microRNAs regulated by the pair, and confirmed these microRNA clusters influence specification of the kidney. Therefore, our data shows that a constitutively-active Ldb1-Lhx1 complex interacts with a broadly expressed microRNA repressor, Fry, to establish the kidney field.
Collapse
Affiliation(s)
- Eugenel B Espiritu
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amanda E Crunk
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Abha Bais
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel Hochbaum
- Universidad de Buenos Aires, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
| | - Ailen S Cervino
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina.,CONICET- Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina
| | - Yu Leng Phua
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Toshiyasu Goto
- Department of Molecular Cell Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA.,Center for Critical Care Nephrology, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Cecilia Cirio
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Buenos Aires, Argentina. .,CONICET- Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Buenos Aires, Argentina.
| |
Collapse
|
16
|
Phua YL, Ho J. Insights into the Regulation of Collecting Duct Homeostasis by Small Noncoding RNAs. J Am Soc Nephrol 2017; 29:349-350. [PMID: 29222396 DOI: 10.1681/asn.2017101072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
- Yu Leng Phua
- Division of Nephrology, Department of Pediatrics, Rangos Research Center, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; and.,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pennsylvania
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, Rangos Research Center, Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; and .,Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pennsylvania
| |
Collapse
|
17
|
Cerqueira DM, Bodnar AJ, Phua YL, Freer R, Hemker SL, Walensky LD, Hukriede NA, Ho J. Bim gene dosage is critical in modulating nephron progenitor survival in the absence of microRNAs during kidney development. FASEB J 2017; 31:3540-3554. [PMID: 28446592 DOI: 10.1096/fj.201700010r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/11/2017] [Indexed: 12/18/2022]
Abstract
Low nephron endowment at birth has been associated with an increased risk for developing hypertension and chronic kidney disease. We demonstrated in an earlier study that conditional deletion of the microRNA (miRNA)-processing enzyme Dicer from nephron progenitors results in premature depletion of the progenitors and increased expression of the proapoptotic protein Bim (also known as Bcl-2L11). In this study, we generated a compound mouse model with conditional deletion of both Dicer and Bim, to determine the biologic significance of increased Bim expression in Dicer-deficient nephron progenitors. The loss of Bim partially restored the number of nephron progenitors and improved nephron formation. The number of progenitors undergoing apoptosis was significantly reduced in kidneys with loss of a single allele, or both alleles, of Bim compared to mutant kidneys. Furthermore, 2 miRNAs expressed in nephron progenitors (miR-17 and miR-106b) regulated Bim levels in vitro and in vivo Together, these data suggest that miRNA-mediated regulation of Bim controls nephron progenitor survival during nephrogenesis, as one potential means of regulating nephron endowment.-Cerqueira, D. M., Bodnar, A. J., Phua, Y. L., Freer, R., Hemker, S. L., Walensky, L. D., Hukriede, N. A., Ho, J. Bim gene dosage is critical in modulating nephron progenitor survival in the absence of microRNAs during kidney development.
Collapse
Affiliation(s)
- Débora M Cerqueira
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Andrew J Bodnar
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yu Leng Phua
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rachel Freer
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Shelby L Hemker
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Loren D Walensky
- Department of Pediatric Oncology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Neil A Hukriede
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jacqueline Ho
- Division of Nephrology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA;
| |
Collapse
|
18
|
Phua YL, Gilbert T, Combes A, Wilkinson L, Little MH. Neonatal vascularization and oxygen tension regulate appropriate perinatal renal medulla/papilla maturation. J Pathol 2016; 238:665-76. [PMID: 26800422 DOI: 10.1002/path.4690] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/21/2015] [Accepted: 01/11/2016] [Indexed: 11/11/2022]
Abstract
Congenital medullary dysplasia with obstructive nephropathy is a common congenital disorder observed in paediatric patients and represents the foremost cause of renal failure. However, the molecular processes regulating normal papillary outgrowth during the postnatal period are unclear. In this study, transcriptional profiling of the renal medulla across postnatal development revealed enrichment of non-canonical Wnt signalling, vascular development, and planar cell polarity genes, all of which may contribute to perinatal medulla/papilla maturation. These pathways were investigated in a model of papillary hypoplasia with functional obstruction, the Crim1(KST264/KST264) transgenic mouse. Postnatal elongation of the renal papilla via convergent extension was unaffected in the Crim1(KST264/KST264) hypoplastic renal papilla. In contrast, these mice displayed a disorganized papillary vascular network, tissue hypoxia, and elevated Vegfa expression. In addition, we demonstrate the involvement of accompanying systemic hypoxia arising from placental insufficiency, in appropriate papillary maturation. In conclusion, this study highlights the requirement for normal vascular development in collecting duct patterning, development of appropriate nephron architecture, and perinatal papillary maturation, such that disturbances contribute to obstructive nephropathy.
Collapse
Affiliation(s)
- Yu Leng Phua
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Rangos Research Center, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA.,School of Medicine, Department of Pediatrics, Division of Nephrology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Thierry Gilbert
- Centre for Developmental Biology, University Paul Sabatier, Toulouse, France
| | - Alexander Combes
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, VIC, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Lorine Wilkinson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Melissa H Little
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.,Department of Pediatrics, University of Melbourne, Melbourne, VIC, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| |
Collapse
|
19
|
Phua YL, Chu JYS, Marrone AK, Bodnar AJ, Sims-Lucas S, Ho J. Renal stromal miRNAs are required for normal nephrogenesis and glomerular mesangial survival. Physiol Rep 2015; 3:3/10/e12537. [PMID: 26438731 PMCID: PMC4632944 DOI: 10.14814/phy2.12537] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small noncoding RNAs that post-transcriptionally regulate mRNA levels. While previous studies have demonstrated that miRNAs are indispensable in the nephron progenitor and ureteric bud lineage, little is understood about stromal miRNAs during kidney development. The renal stroma (marked by expression of FoxD1) gives rise to the renal interstitium, a subset of peritubular capillaries, and multiple supportive vascular cell types including pericytes and the glomerular mesangium. In this study, we generated FoxD1GC;Dicerfl/fl transgenic mice that lack miRNA biogenesis in the FoxD1 lineage. Loss of Dicer activity resulted in multifaceted renal anomalies including perturbed nephrogenesis, expansion of nephron progenitors, decreased renin-expressing cells, fewer smooth muscle afferent arterioles, and progressive mesangial cell loss in mature glomeruli. Although the initial lineage specification of FoxD1+ stroma was not perturbed, both the glomerular mesangium and renal interstitium exhibited ectopic apoptosis, which was associated with increased expression of Bcl2l11 (Bim) and p53 effector genes (Bax, Trp53inp1, Jun, Cdkn1a, Mmp2, and Arid3a). Using a combination of high-throughput miRNA profiling of the FoxD1+-derived cells and mRNA profiling of differentially expressed transcripts in FoxD1GC;Dicerfl/fl kidneys, at least 72 miRNA:mRNA target interactions were identified to be suppressive of the apoptotic program. Together, the results support an indispensable role for stromal miRNAs in the regulation of apoptosis during kidney development.
Collapse
Affiliation(s)
- Yu Leng Phua
- Rangos Research Center, School of Medicine, Children's Hospital of Pittsburgh of UPMC University of Pittsburgh, Pittsburgh, Pennsylvania Department of Pediatrics, Division of Nephrology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jessica Y S Chu
- Rangos Research Center, School of Medicine, Children's Hospital of Pittsburgh of UPMC University of Pittsburgh, Pittsburgh, Pennsylvania Department of Pediatrics, Division of Nephrology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - April K Marrone
- Rangos Research Center, School of Medicine, Children's Hospital of Pittsburgh of UPMC University of Pittsburgh, Pittsburgh, Pennsylvania Department of Pediatrics, Division of Nephrology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Andrew J Bodnar
- Rangos Research Center, School of Medicine, Children's Hospital of Pittsburgh of UPMC University of Pittsburgh, Pittsburgh, Pennsylvania Department of Pediatrics, Division of Nephrology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sunder Sims-Lucas
- Rangos Research Center, School of Medicine, Children's Hospital of Pittsburgh of UPMC University of Pittsburgh, Pittsburgh, Pennsylvania Department of Pediatrics, Division of Nephrology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jacqueline Ho
- Rangos Research Center, School of Medicine, Children's Hospital of Pittsburgh of UPMC University of Pittsburgh, Pittsburgh, Pennsylvania Department of Pediatrics, Division of Nephrology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
20
|
Phua YL, Martel N, Pennisi DJ, Little MH, Wilkinson L. Distinct sites of renal fibrosis inCrim1mutant mice arise from multiple cellular origins. J Pathol 2013; 229:685-96. [DOI: 10.1002/path.4155] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 11/16/2012] [Accepted: 12/03/2012] [Indexed: 01/08/2023]
Affiliation(s)
- Yu Leng Phua
- Institute for Molecular Bioscience; University of Queensland; Australia
| | - Nick Martel
- Institute for Molecular Bioscience; University of Queensland; Australia
| | - David J Pennisi
- School of Biomedical Sciences; University of Queensland; Australia
| | - Melissa H Little
- Institute for Molecular Bioscience; University of Queensland; Australia
| | - Lorine Wilkinson
- Institute for Molecular Bioscience; University of Queensland; Australia
| |
Collapse
|
21
|
Wilkinson L, Kurniawan ND, Phua YL, Nguyen MJ, Li J, Galloway GJ, Hashitani H, Lang RJ, Little MH. Association between congenital defects in papillary outgrowth and functional obstruction in Crim1 mutant mice. J Pathol 2012; 227:499-510. [PMID: 22488641 DOI: 10.1002/path.4036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 03/09/2012] [Accepted: 03/29/2012] [Indexed: 12/25/2022]
Abstract
Crim1 hypomorphic (Crim1(KST264/KST264)) mice display progressive renal disease characterized by glomerular defects, leaky peritubular vasculature, and progressive interstitial fibrosis. Here we show that 27% of these mice also present with hydronephrosis, suggesting obstructive nephropathy. Dynamic magnetic resonance imaging using Magnevist showed fast development of hypo-intense signal in the kidneys of Crim1(KST264/KST264) mice, suggesting pooling of filtrate within the renal parenchyma. Rhodamine dextran (10 kDa) clearance was also delayed in Crim1(KST264/KST264) mice. Pyeloureteric peristalsis, while present, was less co-ordinated in Crim1(KST264/KST264) mice. However, isolated renal pelvis preparations suggest normal pelvic smooth muscle contractile responses. An analysis of maturation during the immediate postnatal period [postnatal day (P) 0-15] revealed defects in papillary extension in Crim1({KST264/KST264) mice. While Crim1 expression is weak in pelvic smooth muscle, strong expression is seen in the interstitium and loops of Henle of the extending papilla, commencing at the tip of the P1 papilla and disseminating throughout the papilla by P15. These results, as well as implicating Crim1 in papillary extension and pelvic smooth muscle contractility, highlight the previously unrecognized association between defects in papillary development and progression to chronic kidney disease later in life.
Collapse
Affiliation(s)
- Lorine Wilkinson
- Institute for Molecular Bioscience, The University of Queensland, QLD 4072, Australia
| | | | | | | | | | | | | | | | | |
Collapse
|