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Poll BG, Leo KT, Deshpande V, Jayatissa N, Pisitkun T, Park E, Yang CR, Raghuram V, Knepper MA. A resource database for protein kinase substrate sequence-preference motifs based on large-scale mass spectrometry data. Cell Commun Signal 2024; 22:137. [PMID: 38374071 PMCID: PMC10875805 DOI: 10.1186/s12964-023-01436-2] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/12/2023] [Indexed: 02/21/2024] Open
Abstract
BACKGROUND Protein phosphorylation is one of the most prevalent posttranslational modifications involved in molecular control of cellular processes, and is mediated by over 520 protein kinases in humans and other mammals. Identification of the protein kinases responsible for phosphorylation events is key to understanding signaling pathways. Unbiased phosphoproteomics experiments have generated a wealth of data that can be used to identify protein kinase targets and their preferred substrate sequences. METHODS This study utilized prior data from mass spectrometry-based studies identifying sites of protein phosphorylation after in vitro incubation of protein mixtures with recombinant protein kinases. PTM-Logo software was used with these data to generate position-dependent Shannon information matrices and sequence motif 'logos'. Webpages were constructed for facile access to logos for each kinase and a new stand-alone application was written in Python that uses the position-dependent Shannon information matrices to identify kinases most likely to phosphorylate a particular phosphorylation site. RESULTS A database of kinase substrate target preference logos allows browsing, searching, or downloading target motif data for each protein kinase ( https://esbl.nhlbi.nih.gov/Databases/Kinase_Logos/ ). These logos were combined with phylogenetic analysis of protein kinase catalytic sequences to reveal substrate preference patterns specific to particular groups of kinases ( https://esbl.nhlbi.nih.gov/Databases/Kinase_Logos/KinaseTree.html ). A stand-alone program, KinasePredictor, is provided ( https://esbl.nhlbi.nih.gov/Databases/Kinase_Logos/KinasePredictor.html ). It takes as input, amino-acid sequences surrounding a given phosphorylation site and generates a ranked list of protein kinases most likely to phosphorylate that site. CONCLUSIONS This study provides three new resources for protein kinase characterization. It provides a tool for prediction of kinase-substrate interactions, which in combination with other types of data (co-localization, etc.), can predict which kinases are likely responsible for a given phosphorylation event in a given tissue. Video Abstract.
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Affiliation(s)
- Brian G Poll
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Kirby T Leo
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Venky Deshpande
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Nipun Jayatissa
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Trairak Pisitkun
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Euijung Park
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, 10 Center Drive, National Institutes of Health, Bethesda, MD, 20892-1603, USA.
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Bingham MA, Neijman K, Yang CR, Aponte A, Mak A, Kikuchi H, Jung HJ, Poll BG, Raghuram V, Park E, Chou CL, Chen L, Leipziger J, Knepper MA, Dona M. Circadian gene expression in mouse renal proximal tubule. Am J Physiol Renal Physiol 2023; 324:F301-F314. [PMID: 36727945 PMCID: PMC9988533 DOI: 10.1152/ajprenal.00231.2022] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/03/2023] Open
Abstract
Circadian variability in kidney function is well recognized but is often ignored as a potential confounding variable in physiological experiments. Here, we have created a data resource consisting of expression levels for mRNA transcripts in microdissected proximal tubule segments from mice as a function of the time of day. Small-sample RNA sequencing was applied to microdissected S1 proximal convoluted tubules and S2 proximal straight tubules. After stringent filtering, the data were analyzed using JTK-Cycle to detect periodicity. The data set is provided as a user-friendly webpage at https://esbl.nhlbi.nih.gov/Databases/Circadian-Prox2/. In proximal convoluted tubules, 234 transcripts varied in a circadian manner (4.0% of the total). In proximal straight tubules, 334 transcripts varied in a circadian manner (5.3%). Transcripts previously known to be associated with corticosteroid action and with increased flow were found to be overrepresented among circadian transcripts peaking during the "dark" portion of the day [zeitgeber time (ZT)14-22], corresponding to peak levels of corticosterone and glomerular filtration rate in mice. To ask whether there is a time-of-day dependence of protein abundances in the kidney, we carried out LC-MS/MS-based proteomics in whole mouse kidneys at ZT12 and ZT0. The full data set (n = 6,546 proteins) is available at https://esbl.nhlbi.nih.gov/Databases/Circadian-Proteome/. Overall, 293 proteins were differentially expressed between ZT12 and ZT0 (197 proteins greater at ZT12 and 96 proteins greater at ZT0). Among the regulated proteins, only nine proteins were found to be periodic in the RNA-sequencing analysis, suggesting a high level of posttranscriptional regulation of protein abundances.NEW & NOTEWORTHY Circadian variation in gene expression can be an important determinant in the regulation of kidney function. The authors used RNA-sequencing transcriptomics and LC-MS/MS-based proteomics to identify gene products expressed in a periodic manner. The data were used to construct user-friendly web resources.
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Affiliation(s)
- Molly A Bingham
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Kim Neijman
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Chin-Rang Yang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Angel Aponte
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Angela Mak
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hiroaki Kikuchi
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Hyun Jun Jung
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Brian G Poll
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Viswanathan Raghuram
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Euijung Park
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Chung-Lin Chou
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Lihe Chen
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Jens Leipziger
- Department of Biomedicine, Physiology, Aarhus University, Aarhus, Denmark
| | - Mark A Knepper
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Margo Dona
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
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Park E, Yang CR, Raghuram V, Deshpande V, Datta A, Poll BG, Leo KT, Kikuchi H, Chen L, Chou CL, Knepper MA. Data resource: vasopressin-regulated protein phosphorylation sites in the collecting duct. Am J Physiol Renal Physiol 2023; 324:F43-F55. [PMID: 36264882 PMCID: PMC9762968 DOI: 10.1152/ajprenal.00229.2022] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/04/2022] [Accepted: 10/17/2022] [Indexed: 02/04/2023] Open
Abstract
Vasopressin controls renal water excretion through actions to regulate aquaporin-2 (AQP2) trafficking, transcription, and degradation. These actions are in part dependent on vasopressin-induced phosphorylation changes in collecting duct cells. Although most efforts have focused on the phosphorylation of AQP2 itself, phosphoproteomic studies have identified many vasopressin-regulated phosphorylation sites in proteins other than AQP2. The goal of this bioinformatics-based review is to create a compendium of vasopressin-regulated phosphorylation sites with a focus on those that are seen in both native rat inner medullary collecting ducts and cultured collecting duct cells from the mouse (mpkCCD), arguing that these sites are the best candidates for roles in AQP2 regulation. This analysis identified 51 vasopressin-regulated phosphorylation sites in 45 proteins. We provide resource web pages at https://esbl.nhlbi.nih.gov/Databases/AVP-Phos/ and https://esbl.nhlbi.nih.gov/AVP-Network/, listing the phosphorylation sites and describing annotated functions of each of the vasopressin-targeted phosphoproteins. Among these sites are 23 consensus protein kinase A (PKA) sites that are increased in response to vasopressin, consistent with a central role for PKA in vasopressin signaling. The remaining sites are predicted to be phosphorylated by other kinases, most notably ERK1/2, which accounts for decreased phosphorylation at sites with a X-p(S/T)-P-X motif. Additional protein kinases that undergo vasopressin-induced changes in phosphorylation are Camkk2, Cdk18, Erbb3, Mink1, and Src, which also may be activated directly or indirectly by PKA. The regulated phosphoproteins are mapped to processes that hypothetically can account for vasopressin-mediated control of AQP2 trafficking, cytoskeletal alterations, and Aqp2 gene expression, providing grist for future studies.NEW & NOTEWORTHY Vasopressin regulates renal water excretion through control of the aquaporin-2 water channel in collecting duct cells. Studies of vasopressin-induced protein phosphorylation have focused mainly on the phosphorylation of aquaporin-2. This study describes 44 phosphoproteins other than aquaporin-2 that undergo vasopressin-mediated phosphorylation changes and summarizes potential physiological roles of each.
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Affiliation(s)
- Euijung Park
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Venkatesh Deshpande
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Arnab Datta
- Laboratory of Translational Neuroscience, Division of Neuroscience, Yenepoya Research Center, Yenepoya (Deemed to be University), Mangalore, India
| | - Brian G Poll
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Kirby T Leo
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Hiroaki Kikuchi
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Sung CC, Poll BG, Lin SH, Murillo-de-Ozores AR, Chou CL, Chen L, Yang CR, Chen MH, Hsu YJ, Knepper MA. Early Molecular Events Mediating Loss of Aquaporin-2 during Ureteral Obstruction in Rats. J Am Soc Nephrol 2022; 33:2040-2058. [PMID: 35918145 PMCID: PMC9678028 DOI: 10.1681/asn.2022050601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Ureteral obstruction is marked by disappearance of the vasopressin-dependent water channel aquaporin-2 (AQP2) in the renal collecting duct and polyuria upon reversal. Most studies of unilateral ureteral obstruction (UUO) models have examined late time points, obscuring the early signals that trigger loss of AQP2. METHODS We performed RNA-Seq on microdissected rat cortical collecting ducts (CCDs) to identify early signaling pathways after establishment of UUO. RESULTS Vasopressin V2 receptor (AVPR2) mRNA was decreased 3 hours after UUO, identifying one cause of AQP2 loss. Collecting duct principal cell differentiation markers were lost, including many not regulated by vasopressin. Immediate early genes in CCDs were widely induced 3 hours after UUO, including Myc, Atf3, and Fos (confirmed at the protein level). Simultaneously, expression of NF-κB signaling response genes known to repress Aqp2 increased. RNA-Seq for CCDs at an even earlier time point (30 minutes) showed widespread mRNA loss, indicating a "stunned" profile. Immunocytochemical labeling of markers of mRNA-degrading P-bodies DDX6 and 4E-T indicated an increase in P-body formation within 30 minutes. CONCLUSIONS Immediately after establishment of UUO, collecting ducts manifest a stunned state with broad disappearance of mRNAs. Within 3 hours, there is upregulation of immediate early and inflammatory genes and disappearance of the V2 vasopressin receptor, resulting in loss of AQP2 (confirmed by lipopolysaccharide administration). The inflammatory response seen rapidly after UUO establishment may be relevant to both UUO-induced polyuria and long-term development of fibrosis in UUO kidneys.
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Affiliation(s)
- Chih-Chien Sung
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Brian G. Poll
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Shih-Hua Lin
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Adrian R. Murillo-de-Ozores
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Min-Hsiu Chen
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Juei Hsu
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Mark A. Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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Chen L, Jung HJ, Datta A, Park E, Poll BG, Kikuchi H, Leo KT, Mehta Y, Lewis S, Khundmiri SJ, Khan S, Chou CL, Raghuram V, Yang CR, Knepper MA. Systems Biology of the Vasopressin V2 Receptor: New Tools for Discovery of Molecular Actions of a GPCR. Annu Rev Pharmacol Toxicol 2022; 62:595-616. [PMID: 34579536 PMCID: PMC10676752 DOI: 10.1146/annurev-pharmtox-052120-011012] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Indexed: 11/09/2022]
Abstract
Systems biology can be defined as the study of a biological process in which all of the relevant components are investigated together in parallel to discover the mechanism. Although the approach is not new, it has come to the forefront as a result of genome sequencing projects completed in the first few years of the current century. It has elements of large-scale data acquisition (chiefly next-generation sequencing-based methods and protein mass spectrometry) and large-scale data analysis (big data integration and Bayesian modeling). Here we discuss these methodologies and show how they can be applied to understand the downstream effects of GPCR signaling, specifically looking at how the neurohypophyseal peptide hormone vasopressin, working through the V2 receptor and PKA activation, regulates the water channel aquaporin-2. The emerging picture provides a detailedframework for understanding the molecular mechanisms involved in water balance disorders, pointing the way to improved treatment of both polyuric disorders and water-retention disorders causing dilutional hyponatremia.
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Affiliation(s)
- Lihe Chen
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Hyun Jun Jung
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
- Division of Nephrology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Arnab Datta
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
- Yenepoya Research Center, Yenepoya, Mangalore 575018, Karnataka, India
| | - Euijung Park
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Brian G Poll
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Hiroaki Kikuchi
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Kirby T Leo
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Yash Mehta
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Spencer Lewis
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Syed J Khundmiri
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Shaza Khan
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20814, USA;
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Mehta YR, Lewis SA, Leo KT, Chen L, Park E, Raghuram V, Chou CL, Yang CR, Kikuchi H, Khundmiri S, Poll BG, Knepper MA. "ADPKD-omics": determinants of cyclic AMP levels in renal epithelial cells. Kidney Int 2022; 101:47-62. [PMID: 34757121 PMCID: PMC10671900 DOI: 10.1016/j.kint.2021.10.014] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022]
Abstract
The regulation of cyclic adenosine monophosphate (cAMP) levels in kidney epithelial cells is important in at least 2 groups of disorders, namely water balance disorders and autosomal dominant polycystic kidney disease. Focusing on the latter, we review genes that code for proteins that are determinants of cAMP levels in cells. We identify which of these determinants are expressed in the 14 kidney tubule segments using recently published RNA-sequencing and protein mass spectrometry data ("autosomal dominant polycystic kidney disease-omics"). This includes G protein-coupled receptors, adenylyl cyclases, cyclic nucleotide phosphodiesterases, cAMP transporters, cAMP-binding proteins, regulator of G protein-signaling proteins, G protein-coupled receptor kinases, arrestins, calcium transporters, and calcium-binding proteins. In addition, compartmentalized cAMP signaling in the primary cilium is discussed, and a specialized database of the proteome of the primary cilium of cultured "IMCD3" cells is provided as an online resource (https://esbl.nhlbi.nih.gov/Databases/CiliumProteome/). Overall, this article provides a general resource in the form of a curated list of proteins likely to play roles in determination of cAMP levels in kidney epithelial cells and, therefore, likely to be determinants of progression of autosomal dominant polycystic kidney disease.
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Affiliation(s)
- Yash R Mehta
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Spencer A Lewis
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kirby T Leo
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Euijung Park
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chin-Rang Yang
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hiroaki Kikuchi
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Syed Khundmiri
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Brian G Poll
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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Poll BG, Xu J, Gupta K, Shubitowski TB, Pluznick JL. Olfactory receptor 78 modulates renin but not baseline blood pressure. Physiol Rep 2021; 9:e15017. [PMID: 34549531 PMCID: PMC8455973 DOI: 10.14814/phy2.15017] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/11/2023] Open
Abstract
Olfactory receptor 78 (Olfr78) is a G protein-coupled receptor (GPCR) that is expressed in the juxtaglomerular apparatus (JGA) of the kidney as well as the peripheral vasculature, and is activated by gut microbial metabolites. We previously reported that Olfr78 plays a role in renin secretion in isolated glomeruli, and that Olfr78 knockout (KO) mice have lower plasma renin activity. We also noted that in anesthetized mice, Olfr78KO appeared to be hypotensive. In this study, we used radiotelemetry to determine the role of Olfr78 in chronic blood pressure regulation. We found that the blood pressure of Olfr78KO mice is not significantly different than that of their WT counterparts at baseline, or on high- or low-salt diets. However, Olfr78KO mice have depressed heart rates on high-salt diets. We also report that Olfr78KO mice have lower renin protein levels associated with glomeruli. Finally, we developed a mouse where Olfr78 was selectively knocked out in the JGA, which phenocopied the lower renin association findings. In sum, these experiments suggest that Olfr78 modulates renin, but does not play an active role in blood pressure regulation at baseline, and is more likely activated by high levels of short chain fatty acids or hypotensive events. This study provides important context to our knowledge of Olfr78 in BP regulation.
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Affiliation(s)
- Brian G. Poll
- Department of PhysiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Jiaojiao Xu
- Department of PhysiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Kunal Gupta
- Department of PhysiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Tyler B. Shubitowski
- Department of PhysiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Oakland University William Beaumont School of MedicineRochesterMichiganUSA
| | - Jennifer L. Pluznick
- Department of PhysiologyJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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Poll BG, Chen L, Chou CL, Raghuram V, Knepper MA. Landscape of GPCR expression along the mouse nephron. Am J Physiol Renal Physiol 2021; 321:F50-F68. [PMID: 34029142 PMCID: PMC8321805 DOI: 10.1152/ajprenal.00077.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 12/11/2022] Open
Abstract
Kidney transport and other renal functions are regulated by multiple G protein-coupled receptors (GPCRs) expressed along the renal tubule. The rapid, recent appearance of comprehensive unbiased gene expression data in the various renal tubule segments, chiefly RNA sequencing and protein mass spectrometry data, has provided a means of identifying patterns of GPCR expression along the renal tubule. To allow for comprehensive mapping, we first curated a comprehensive list of GPCRs in the genomes of mice, rats, and humans (https://hpcwebapps.cit.nih.gov/ESBL/Database/GPCRs/) using multiple online data sources. We used this list to mine segment-specific and cell type-specific expression data from RNA-sequencing studies in microdissected mouse tubule segments to identify GPCRs that are selectively expressed in discrete tubule segments. Comparisons of these mapped mouse GPCRs with other omics datasets as well as functional data from isolated perfused tubule and micropuncture studies confirmed patterns of expression for well-known receptors and identified poorly studied GPCRs that are likely to play roles in the regulation of renal tubule function. Thus, we provide data resources for GPCR expression across the renal tubule, highlighting both well-known GPCRs and understudied receptors to provide guidance for future studies.
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Affiliation(s)
- Brian G Poll
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Lihe Chen
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Chung-Lin Chou
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Viswanathan Raghuram
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Mark A Knepper
- Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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9
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Abstract
Shifts in the gut microbiome play a key role in blood pressure regulation, and changes in the production of gut microbial metabolites are likely to be a key mechanism. Known gut microbial metabolites include short-chain fatty acids, which can signal via G-protein-coupled receptors, and trimethylamine-N oxide. In this review, we provide an overview of gut microbial metabolites documented thus far to play a role in blood pressure regulation.
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Affiliation(s)
- Brian G Poll
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Muhammad Umar Cheema
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jennifer L Pluznick
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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10
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Poll BG, Xu J, Jun S, Sanchez J, Zaidman NA, He X, Lester L, Berkowitz DE, Paolocci N, Gao WD, Pluznick JL. Acetate, a Short-Chain Fatty Acid, Acutely Lowers Heart Rate and Cardiac Contractility Along with Blood Pressure. J Pharmacol Exp Ther 2021; 377:39-50. [PMID: 33414131 DOI: 10.1124/jpet.120.000187] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Short-chain fatty acids (SCFAs) are metabolites produced almost exclusively by the gut microbiota and are an essential mechanism by which gut microbes influence host physiology. Given that SCFAs induce vasodilation, we hypothesized that they might have additional cardiovascular effects. In this study, novel mechanisms of SCFA action were uncovered by examining the acute effects of SCFAs on cardiovascular physiology in vivo and ex vivo. Acute delivery of SCFAs in conscious radiotelemetry-implanted mice results in a simultaneous decrease in both mean arterial pressure and heart rate (HR). Inhibition of sympathetic tone by the selective β-1 adrenergic receptor antagonist atenolol blocks the acute drop in HR seen with acetate administration, yet the decrease in mean arterial pressure persists. Treatment with tyramine, an indirect sympathomimetic, also blocks the acetate-induced acute drop in HR. Langendorff preparations show that acetate lowers HR only after long-term exposure and at a smaller magnitude than seen in vivo. Pressure-volume loops after acetate injection show a decrease in load-independent measures of cardiac contractility. Isolated trabecular muscle preparations also show a reduction in force generation upon SCFA treatment, though only at supraphysiological concentrations. These experiments demonstrate a direct cardiac component of the SCFA cardiovascular response. These data show that acetate affects blood pressure and cardiac function through parallel mechanisms and establish a role for SCFAs in modulating sympathetic tone and cardiac contractility, further advancing our understanding of the role of SCFAs in blood pressure regulation. SIGNIFICANCE STATEMENT: Acetate, a short-chain fatty acid, acutely lowers heart rate (HR) as well as mean arterial pressure in vivo in radiotelemetry-implanted mice. Acetate is acting in a sympatholytic manner on HR and exerts negative inotropic effects in vivo. This work has implications for potential short-chain fatty acid therapeutics as well as gut dysbiosis-related disease states.
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Affiliation(s)
- Brian G Poll
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Jiaojiao Xu
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Seungho Jun
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Jason Sanchez
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Nathan A Zaidman
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Xiaojun He
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Laeben Lester
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Dan E Berkowitz
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Nazareno Paolocci
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Wei Dong Gao
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
| | - Jennifer L Pluznick
- Department of Physiology (B.G.P., J.X., J.S., N.Z., J.L.P.), Division of Cardiology (S.J., N.P.), Department of Anesthesiology and Critical Care Medicine (X.H., L.L., W.D.G.), Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Anesthesiology and Perioperative Medicine, The University of Alabama at Birmingham (D.B.); and Department of Biomedical Sciences, University of Padova, Padova, Italy (N.P.)
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11
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Jacob JT, Nair RR, Poll BG, Pineda CM, Hobbs RP, Matunis MJ, Coulombe PA. Keratin 17 regulates nuclear morphology and chromatin organization. J Cell Sci 2020; 133:jcs254094. [PMID: 33008845 PMCID: PMC7648610 DOI: 10.1242/jcs.254094] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022] Open
Abstract
Keratin 17 (KRT17; K17), a non-lamin intermediate filament protein, was recently found to occur in the nucleus. We report here on K17-dependent differences in nuclear morphology, chromatin organization, and cell proliferation. Human tumor keratinocyte cell lines lacking K17 exhibit flatter nuclei relative to normal. Re-expression of wild-type K17, but not a mutant form lacking an intact nuclear localization signal (NLS), rescues nuclear morphology in KRT17-null cells. Analyses of primary cultures of skin keratinocytes from a mouse strain expressing K17 with a mutated NLS corroborated these findings. Proteomics screens identified K17-interacting nuclear proteins with known roles in gene expression, chromatin organization and RNA processing. Key histone modifications and LAP2β (an isoform encoded by TMPO) localization within the nucleus are altered in the absence of K17, correlating with decreased cell proliferation and suppression of GLI1 target genes. Nuclear K17 thus impacts nuclear morphology with an associated impact on chromatin organization, gene expression, and proliferation in epithelial cells.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Justin T Jacob
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Raji R Nair
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brian G Poll
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Christopher M Pineda
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ryan P Hobbs
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Cell Biology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pierre A Coulombe
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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12
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Zieman AG, Poll BG, Ma J, Coulombe PA. Altered keratinocyte differentiation is an early driver of keratin mutation-based palmoplantar keratoderma. Hum Mol Genet 2020; 28:2255-2270. [PMID: 31220272 DOI: 10.1093/hmg/ddz050] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/08/2019] [Accepted: 03/04/2019] [Indexed: 12/15/2022] Open
Abstract
The type I intermediate filament keratin 16 (KRT16 gene; K16 protein) is constitutively expressed in ectoderm-derived appendages and in palmar/plantar epidermis and is robustly induced when the epidermis experiences chemical, mechanical or environmental stress. Missense mutations at the KRT16 locus can cause pachyonychia congenita (PC, OMIM:167200) or focal non-epidermolytic palmoplantar keratoderma (FNEPPK, OMIM:613000), which each entail painful calluses on palmar and plantar skin. Krt16-null mice develop footpad lesions that mimic PC-associated PPK, providing an opportunity to decipher its pathophysiology, and develop therapies. We report on insight gained from a genome-wide analysis of gene expression in PPK-like lesions of Krt16-null mice. Comparison of this data set with publicly available microarray data of PPK lesions from individuals with PC revealed significant synergies in gene expression profiles. Keratin 9 (Krt9/K9), the most robustly expressed gene in differentiating volar keratinocytes, is markedly downregulated in Krt16-null paw skin, well-ahead of lesion onset, and is paralleled by pleiotropic defects in terminal differentiation. Effective prevention of PPK-like lesions in Krt16-null paw skin (via topical delivery of the Nrf2 inducer sulforaphane) involves the stimulation of Krt9 expression. These findings highlight a role for defective terminal differentiation and loss of Krt9/K9 expression as additional drivers of PC-associated PPK and highlight restoration of KRT9 expression as a worthy target for therapy. Further, we report on the novel observation that keratin 16 can localize to the nucleus of epithelial cells, implying a potential nuclear function that may be relevant to PC and FNEPPK.
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Affiliation(s)
- Abigail G Zieman
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Brian G Poll
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Physiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Jingqun Ma
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Pierre A Coulombe
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
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13
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Shubitowski TB, Poll BG, Natarajan N, Pluznick JL. Short-chain fatty acid delivery: assessing exogenous administration of the microbiome metabolite acetate in mice. Physiol Rep 2019; 7:e14005. [PMID: 30810289 PMCID: PMC6391713 DOI: 10.14814/phy2.14005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 02/06/2023] Open
Abstract
Short-chain fatty acids (SCFAs) are fermentation by-products of gut microbes which have been linked to positive effects on host physiology; the most abundant SCFA is acetate. Exogenous administration of acetate alters host metabolism, immune function, and blood pressure, making it a biologic of interest. The effects of acetate have been attributed to activation of G-protein-coupled receptors and other proteins (i.e., HDACs), often occurring at locations distant from the gut such as the pancreas or the kidney. However, due to technical difficulties and costs, studies have often delivered exogenous acetate without determining if systemic plasma acetate levels are altered. Thus, it is unclear to what extent each method of acetate delivery may alter systemic plasma acetate levels. In this study, we aimed to determine if acetate is elevated after exogenous administration by drinking water (DW), oral gavage (OG), or intraperitoneal (IP) injection, and if so, over what timecourse, to best inform future studies. Using a commercially available kit, we demonstrated that sodium acetate delivered over 21 days in DW does not elicit a measurable change in systemic acetate over baseline. However, when acetate is delivered by OG or IP injection, there are rapid, reproducible, and dose-dependent changes in plasma acetate. These studies report, for the first time, the timecourse of changes in plasma acetate following acetate administration by three common methods, and thus inform the best practices for exogenous acetate delivery.
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Affiliation(s)
| | - Brian G. Poll
- Department of PhysiologyJohns Hopkins School of MedicineBaltimoreMaryland
| | - Niranjana Natarajan
- Department of Stem Cell and Regenerative BiologyHarvard Stem Cell InstituteHarvard UniversityCambridgeMassachusetts
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14
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Hobbs RP, DePianto DJ, Jacob JT, Han MC, Chung BM, Batazzi AS, Poll BG, Guo Y, Han J, Ong S, Zheng W, Taube JM, Čiháková D, Wan F, Coulombe PA. Keratin-dependent regulation of Aire and gene expression in skin tumor keratinocytes. Nat Genet 2015; 47:933-8. [PMID: 26168014 PMCID: PMC4520766 DOI: 10.1038/ng.3355] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 06/19/2015] [Indexed: 12/20/2022]
Abstract
Expression of the intermediate filament protein keratin 17 (K17) is robustly upregulated in inflammatory skin diseases and in many tumors originating in stratified and pseudostratified epithelia. We report that autoimmune regulator (Aire), a transcriptional regulator, is inducibly expressed in human and mouse tumor keratinocytes in a K17-dependent manner and is required for timely onset of Gli2-induced skin tumorigenesis in mice. The induction of Aire mRNA in keratinocytes depends on a functional interaction between K17 and the heterogeneous nuclear ribonucleoprotein hnRNP K. Further, K17 colocalizes with Aire protein in the nucleus of tumor-prone keratinocytes, and each factor is bound to a specific promoter region featuring an NF-κB consensus sequence in a relevant subset of K17- and Aire-dependent proinflammatory genes. These findings provide radically new insight into keratin intermediate filament and Aire function, along with a molecular basis for the K17-dependent amplification of inflammatory and immune responses in diseased epithelia.
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Affiliation(s)
- Ryan P. Hobbs
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daryle J. DePianto
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Justin T. Jacob
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Minerva C. Han
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Byung-Min Chung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Adriana S. Batazzi
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Brian G. Poll
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yajuan Guo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jingnan Han
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - SuFey Ong
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Wenxin Zheng
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Janis M. Taube
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Dermatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Čiháková
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Pathology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Fengyi Wan
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore MD 21205, USA
| | - Pierre A. Coulombe
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Dermatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore MD 21205, USA
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