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Nanamatsu A, de Araújo L, LaFavers KA, El-Achkar TM. Advances in uromodulin biology and potential clinical applications. Nat Rev Nephrol 2024:10.1038/s41581-024-00881-7. [PMID: 39160319 DOI: 10.1038/s41581-024-00881-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2024] [Indexed: 08/21/2024]
Abstract
Uromodulin (also known as Tamm-Horsfall protein) is a kidney-specific glycoprotein secreted bidirectionally into urine and into the circulation, and it is the most abundant protein in normal urine. Although the discovery of uromodulin predates modern medicine, its significance in health and disease has been rather enigmatic. Research studies have gradually revealed that uromodulin exists in multiple forms and has important roles in urinary and systemic homeostasis. Most uromodulin in urine is polymerized into highly organized filaments, whereas non-polymeric uromodulin is detected both in urine and in the circulation, and can have distinct roles. The interactions of uromodulin with the immune system, which were initially reported to be a key role of this protein, are now better understood. Moreover, the discovery that uromodulin is associated with a spectrum of kidney diseases, including acute kidney injury, chronic kidney disease and autosomal-dominant tubulointerstitial kidney disease, has further accelerated investigations into the role of this protein. These discoveries have prompted new questions and ushered in a new era in uromodulin research. Here, we delineate the latest discoveries in uromodulin biology and its emerging roles in modulating kidney and systemic diseases, and consider future directions, including its potential clinical applications.
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Affiliation(s)
- Azuma Nanamatsu
- Department of Medicine, Division of Nephrology and Hypertension, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Larissa de Araújo
- Department of Medicine, Division of Nephrology and Hypertension, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kaice A LaFavers
- Department of Medicine, Division of Nephrology and Hypertension, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tarek M El-Achkar
- Department of Medicine, Division of Nephrology and Hypertension, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA.
- Roudebush VA Medical Center, Indianapolis, IN, USA.
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2
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Vivante A. Genetics of Chronic Kidney Disease. N Engl J Med 2024; 391:627-639. [PMID: 39141855 DOI: 10.1056/nejmra2308577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Affiliation(s)
- Asaf Vivante
- From the Department of Pediatrics and the Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, and the Nephro-Genetics Clinic and Genetic Kidney Disease Research Laboratory, Sheba Medical Center, Tel Hashomer, and the Faculty of Medicine, Tel Aviv University, Tel Aviv - all in Israel
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3
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Harita Y. Urinary extracellular vesicles in childhood kidney diseases. Pediatr Nephrol 2024; 39:2293-2300. [PMID: 38093081 PMCID: PMC11199279 DOI: 10.1007/s00467-023-06243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 06/26/2024]
Abstract
Most biological fluids contain extracellular vesicles (EVs). EVs are surrounded by a lipid bilayer and contain biological macromolecules such as proteins, lipids, RNA, and DNA. They lack a functioning nucleus and are incapable of replicating. The physiological characteristics and molecular composition of EVs in body fluids provide valuable information about the status of originating cells. Consequently, they could be effectively utilized for diagnostic and prognostic applications. Urine contains a heterogeneous population of EVs. To date, these urinary extracellular vesicles (uEVs) have been ignored in the standard urinalysis. In recent years, knowledge has accumulated on how uEVs should be separated and analyzed. It has become clear how uEVs reflect the expression of each molecule in cells in nephron segments and how they are altered in disease states such as glomerular/tubular disorders, rare congenital diseases, acute kidney injury (AKI), and chronic kidney disease (CKD). Significant promise exists for the molecular expression signature of uEVs detected by simple techniques such as enzyme-linked immunosorbent assay (ELISA), making them more applicable in clinical settings. This review presents the current understanding regarding uEVs, emphasizing the potential for non-invasive diagnostics, especially for childhood kidney diseases.
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Affiliation(s)
- Yutaka Harita
- Department of Pediatrics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
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4
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Ng MSY, Kaur G, Francis RS, Hawley CM, Johnson DW. Drug repurposing for glomerular diseases: an underutilized resource. Nat Rev Nephrol 2024:10.1038/s41581-024-00864-8. [PMID: 39085415 DOI: 10.1038/s41581-024-00864-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2024] [Indexed: 08/02/2024]
Abstract
Drug repurposing in glomerular disease can deliver opportunities for steroid-free regimens, enable personalized multi-target options for resistant or relapsing disease and enhance treatment options for understudied populations (for example, children) and in resource-limited settings. Identification of drug-repurposing candidates can be data driven, which utilizes existing data on disease pathobiology, drug features and clinical outcomes, or experimental, which involves high-throughput drug screens. Information from databases of approved drugs, clinical trials and PubMed registries suggests that at least 96 drugs on the market cover 49 targets with immunosuppressive potential that could be candidates for drug repurposing in glomerular disease. Furthermore, evidence to support drug repurposing is available for 191 immune drug target-glomerular disease pairs. Non-immunological drug repurposing includes strategies to reduce haemodynamic overload, podocyte injury and kidney fibrosis. Recommended strategies to expand drug-repurposing capacity in glomerular disease include enriching drug databases with glomeruli-specific information, enhancing the accessibility of primary clinical trial data, biomarker discovery to improve participant selection into clinical trials and improve surrogate outcomes and initiatives to reduce patent, regulatory and organizational hurdles.
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Affiliation(s)
- Monica Suet Ying Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia.
| | - Gursimran Kaur
- Department of Rheumatology, Saint Vincent's Hospital, Sydney, New South Wales, Australia
- Saint Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Rheumatology Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Ross S Francis
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Carmel M Hawley
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Centre for Kidney Disease Research, University of Queensland, Brisbane, Queensland, Australia
| | - David W Johnson
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Centre for Kidney Disease Research, University of Queensland, Brisbane, Queensland, Australia
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5
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Mashouf P, Tabibzadeh N, Kuraoka S, Oishi H, Morizane R. Cryopreservation of human kidney organoids. Cell Mol Life Sci 2024; 81:306. [PMID: 39023560 DOI: 10.1007/s00018-024-05352-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/21/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
Recent advances in stem cell research have led to the creation of organoids, miniature replicas of human organs, offering innovative avenues for studying diseases. Kidney organoids, with their ability to replicate complex renal structures, provide a novel platform for investigating kidney diseases and assessing drug efficacy, albeit hindered by labor-intensive generation and batch variations, highlighting the need for tailored cryopreservation methods to enable widespread utilization. Here, we evaluated cryopreservation strategies for kidney organoids by contrasting slow-freezing and vitrification methods. 118 kidney organoids were categorized into five conditions. Control organoids followed standard culture, while two slow-freezing groups used 10% DMSO (SF1) or commercial freezing media (SF2). Vitrification involved V1 (20% DMSO, 20% Ethylene Glycol with sucrose) and V2 (15% DMSO, 15% Ethylene Glycol). Assessment of viability, functionality, and structural integrity post-thawing revealed notable differences. Vitrification, particularly V1, exhibited superior viability (91% for V1, 26% for V2, 79% for SF1, and 83% for SF2 compared to 99.4% in controls). 3D imaging highlighted distinct nephron segments among groups, emphasizing V1's efficacy in preserving both podocytes and tubules in kidney organoids. Cisplatin-induced injury revealed a significant reduction in regenerative capacities in organoids cryopreserved by flow-freezing methods, while the V1 method did not show statistical significance compared to the unfrozen controls. This study underscores vitrification, especially with high concentrations of cryoprotectants, as an effective approach for maintaining kidney organoid viability and structure during cryopreservation, offering practical approaches for kidney organoid research.
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Affiliation(s)
- Parham Mashouf
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, 149 13th Street, Boston, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
| | - Nahid Tabibzadeh
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, 149 13th Street, Boston, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
| | - Shohei Kuraoka
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, 149 13th Street, Boston, MA, 02129, USA
- Harvard Medical School, Boston, MA, USA
| | - Haruka Oishi
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, 149 13th Street, Boston, MA, 02129, USA
| | - Ryuji Morizane
- Nephrology Division, Department of Medicine, Massachusetts General Hospital, 149 13th Street, Boston, MA, 02129, USA.
- Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA.
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6
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Na DH, Cui S, Fang X, Lee H, Eum SH, Shin YJ, Lim SW, Yang CW, Chung BH. Advancements in Research on Genetic Kidney Diseases Using Human-Induced Pluripotent Stem Cell-Derived Kidney Organoids. Cells 2024; 13:1190. [PMID: 39056771 PMCID: PMC11274677 DOI: 10.3390/cells13141190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/09/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Genetic or hereditary kidney disease stands as a pivotal cause of chronic kidney disease (CKD). The proliferation and widespread utilization of DNA testing in clinical settings have notably eased the diagnosis of genetic kidney diseases, which were once elusive but are now increasingly identified in cases previously deemed CKD of unknown etiology. However, despite these diagnostic strides, research into disease pathogenesis and novel drug development faces significant hurdles, chiefly due to the dearth of appropriate animal models and the challenges posed by limited patient cohorts in clinical studies. Conversely, the advent and utilization of human-induced pluripotent stem cells (hiPSCs) offer a promising avenue for genetic kidney disease research. Particularly, the development of hiPSC-derived kidney organoid systems presents a novel platform for investigating various forms of genetic kidney diseases. Moreover, the integration of the CRISPR/Cas9 technique into this system holds immense potential for efficient research on genetic kidney diseases. This review aims to explore the applications of in vitro kidney organoids generated from hiPSCs in the study of diverse genetic kidney diseases. Additionally, it will delve into the limitations of this research platform and outline future perspectives for advancing research in this crucial area.
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Affiliation(s)
- Do Hyun Na
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sheng Cui
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
| | - Xianying Fang
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
| | - Hanbi Lee
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sang Hun Eum
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
- Division of Nephrology, Department of Internal Medicine, Incheon St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, Incheon 21431, Republic of Korea
| | - Yoo Jin Shin
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
| | - Sun Woo Lim
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
| | - Chul Woo Yang
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Byung Ha Chung
- Transplantation Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (D.H.N.); (S.C.); (X.F.); (H.L.); (S.H.E.); (Y.J.S.); (S.W.L.); (C.W.Y.)
- Division of Nephrology, Department of Internal Medicine, Seoul St. Mary’s Hospital, The College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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7
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Kidd KO, Williams AH, Taylor A, Martin L, Robins V, Sayer JA, Olinger E, Mabillard HR, Papagregoriou G, Deltas C, Stavrou C, Conlon PJ, Hogan RE, Elhassan EAE, Springer D, Zima T, Izzi C, Vrbacká A, Piherová L, Pohludka M, Radina M, Vylet'al P, Hodanova K, Zivna M, Kmoch S, Bleyer AJ. Eight-Fold Increased COVID-19 Mortality in Autosomal Dominant Tubulointerstitial Kidney Disease due to MUC1 Mutations: An Observational Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.03.24309887. [PMID: 39006416 PMCID: PMC11245082 DOI: 10.1101/2024.07.03.24309887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background MUC1 and UMOD pathogenic variants cause autosomal dominant tubulointerstitial kidney disease (ADTKD). MUC1 is expressed in kidney, nasal mucosa and respiratory tract, while UMOD is expressed only in kidney. Due to haplo-insufficiency ADTKD- MUC1 patients produce approximately 50% of normal mucin-1. Methods To determine whether decreased mucin-1 production was associated with an increased COVID-19 risk, we sent a survey to members of an ADTKD registry in September 2021, after the initial, severe wave of COVID-19. We linked results to previously obtained ADTKD genotype and plasma CA15-3 (mucin-1) levels and created a longitudinal registry of COVID-19 related deaths. Results Surveys were emailed to 637 individuals, with responses from 89 ADTKD- MUC1 and 132 ADTKD- UMOD individuals. 19/83 (23%) ADTKD- MUC1 survey respondents reported a prior COVID-19 infection vs. 14/125 (11%) ADTKD- UMOD respondents (odds ratio (OR) 2.35 (95%CI 1.60-3.11, P = 0.0260). Including additional familial cases reported from survey respondents, 10/41 (24%) ADTKD- MUC1 individuals died of COVID-19 vs. 1/30 (3%) with ADTKD- UMOD , with OR 9.21 (95%CI 1.22-69.32), P = 0.03. The mean plasma mucin-1 level prior to infection in 14 infected and 27 uninfected ADTKD- MUC1 individuals was 7.06±4.12 vs. 10.21±4.02 U/mL ( P = 0.035). Over three years duration, our longitudinal registry identified 19 COVID-19 deaths in 360 ADTKD- MUC1 individuals (5%) vs. 3 deaths in 478 ADTKD- UMOD individuals (0.6%) ( P = 0.0007). Multivariate logistic regression revealed the following odds ratios (95% confidence interval) for COVID-19 deaths: ADTKD- MUC1 8.4 (2.9-29.5), kidney transplant 5.5 (1.6-9.1), body mass index (kg/m 2 ) 1.1 (1.0-1.2), age (y) 1.04 (1.0-1.1). Conclusions Individuals with ADTKD- MUC1 are at an eight-fold increased risk of COVID-19 mortality vs. ADTKD- UMOD individuals. Haplo-insufficient production of mucin-1 may be responsible.
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8
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Elhassan EA, Kmochová T, Benson KA, Fennelly NK, Barešová V, Kidd K, Doyle B, Dorman A, Morrin MM, Kyne NC, Vyleťal P, Hartmannová H, Hodaňová K, Sovová J, Mušálková D, Vrbacká A, Přistoupilová A, Živný J, Svojšová K, Radina M, Stránecký V, Loginov D, Pompach P, Novák P, Vaníčková Z, Hansíková H, Rajnochová-Bloudíčková S, Viklický O, Hůlková H, Cavalleri GL, Hnízda A, Bleyer AJ, Kmoch S, Conlon PJ, Živná M. A Novel Monoallelic ALG5 Variant Causing Late-Onset ADPKD and Tubulointerstitial Fibrosis. Kidney Int Rep 2024; 9:2209-2226. [PMID: 39081747 PMCID: PMC11284371 DOI: 10.1016/j.ekir.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 08/02/2024] Open
Abstract
Introduction Monoallelic variants in the ALG5 gene encoding asparagine-linked glycosylation protein 5 homolog (ALG5) have been recently shown to disrupt polycystin-1 (PC1) maturation and trafficking via underglycosylation, causing an autosomal dominant polycystic kidney disease-like (ADPKD-like) phenotype and interstitial fibrosis. In this report, we present clinical, genetic, histopathologic, and protein structure and functional correlates of a new ALG5 variant, p.R79W, that we identified in 2 distant genetically related Irish families displaying an atypical late-onset ADPKD phenotype combined with tubulointerstitial damage. Methods Whole exome and targeted sequencing were used for segregation analysis of available relatives. This was followed by immunohistochemistry examinations of kidney biopsies, and targeted (UMOD, MUC1) and untargeted plasma proteome and N-glycomic studies. Results We identified a monoallelic ALG5 variant [GRCh37 (NM_013338.5): g.37569565G>A, c.235C>T; p.R79W] that cosegregates in 23 individuals, of whom 18 were clinically affected. We detected abnormal localization of ALG5 in the Golgi apparatus of renal tubular cells in patients' kidney specimens. Further, we detected the pathological accumulation of uromodulin, an N-glycosylated glycosylphosphatidylinositol (GPI)-anchored protein, in the endoplasmic reticulum (ER), but not mucin-1, an O- and N-glycosylated protein. Biochemical investigation revealed decreased plasma and urinary uromodulin levels in clinically affected individuals. Proteomic and glycoproteomic profiling revealed the dysregulation of chronic kidney disease (CKD)-associated proteins. Conclusion ALG5 dysfunction adversely affects maturation and trafficking of N-glycosylated and GPI anchored protein uromodulin, leading to structural and functional changes in the kidney. Our findings confirm ALG5 as a cause of late-onset ADPKD and provide additional insight into the molecular mechanisms of ADPKD-ALG5.
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Affiliation(s)
- Elhussein A.E. Elhassan
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Tereza Kmochová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Katherine A. Benson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | | | - Veronika Barešová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Kendrah Kidd
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Brendan Doyle
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Anthony Dorman
- Department of Pathology, Beaumont Hospital, Dublin, Ireland
| | - Martina M. Morrin
- Department of Radiology, Beaumont Hospital and Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Niamh C. Kyne
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
| | - Petr Vyleťal
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jana Sovová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Alena Vrbacká
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Jan Živný
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Klára Svojšová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Martin Radina
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Dmitry Loginov
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Pompach
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Novák
- Institute of Microbiology, The Czech Academy of Sciences, Vestec, Czech Republic
| | - Zdislava Vaníčková
- Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital and of The First Faculty of medicine of Charles University in Prague, Prague, Czech Republic
| | - Hana Hansíková
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Silvie Rajnochová-Bloudíčková
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ondřej Viklický
- Department of Nephrology, Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Helena Hůlková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons, Dublin, Ireland
| | - Aleš Hnízda
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Peter J. Conlon
- Department of Nephrology and Transplantation, Beaumont Hospital, Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Martina Živná
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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9
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Yang K, Feng Z, Pastor-Pareja JC. p24-Tango1 interactions ensure ER-Golgi interface stability and efficient transport. J Cell Biol 2024; 223:e202309045. [PMID: 38470362 PMCID: PMC10932740 DOI: 10.1083/jcb.202309045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/07/2024] [Accepted: 02/05/2024] [Indexed: 03/13/2024] Open
Abstract
The eukaryotic p24 family, consisting of α-, β-, γ- and δ-p24 subfamilies, has long been known to be involved in regulating secretion. Despite increasing interest in these proteins, fundamental questions remain about their role. Here, we systematically investigated Drosophila p24 proteins. We discovered that members of all four p24 subfamilies are required for general secretion and that their localizations between ER exit site (ERES) and Golgi are interdependent in an α→βδ→γ sequence. We also found that localization of p24 proteins and ERES determinant Tango1 requires interaction through their respective GOLD and SH3 lumenal domains, with Tango1 loss sending p24 proteins to the plasma membrane and vice versa. Finally, we show that p24 loss expands the COPII zone at ERES and increases the number of ER-Golgi vesicles, supporting a restrictive role of p24 proteins on vesicle budding for efficient transport. Our results reveal Tango1-p24 interplay as central to the generation of a stable ER-Golgi interface.
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Affiliation(s)
- Ke Yang
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi Feng
- School of Life Sciences, Tsinghua University, Beijing, China
| | - José Carlos Pastor-Pareja
- School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- Institute of Neurosciences, Consejo Superior de Investigaciones Científicas-Universidad Miguel Hernández, San Juan de Alicante, Spain
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10
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Fages V, Bourre F, Larrue R, Wenzel A, Gibier JB, Bonte F, Dhaenens CM, Kidd K, Kmoch S, Bleyer A, Glowacki F, Grunewald O. Description of a New Simple and Cost-Effective Molecular Testing That Could Simplify MUC1 Variant Detection. Kidney Int Rep 2024; 9:1451-1457. [PMID: 38707821 PMCID: PMC11068942 DOI: 10.1016/j.ekir.2024.01.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Patients with autosomal dominant tubulointerstitial kidney disease (ADTKD) usually present with nonspecific progressive chronic kidney disease (CKD) with mild to negative proteinuria and a family history. ADTKD-MUC1 leads to the formation of a frameshift protein that accumulates in the cytoplasm, leading to tubulointerstitial damage. ADTKD-MUC1 prevalence remains unclear because MUC1 variants are not routinely detected by standard next-generation sequencing (NGS) techniques. Methods We developed a bioinformatic counting script that can detect specific genetic sequences and count the number of occurrences. We used DNA samples from 27 patients for validation, 11 of them were patients from the Lille University Hospital in France and 16 were from the Wake Forest Hospital, NC. All patients from Lille were tested with an NGS gene panel with our script and all patients from Wake Forest Hospital were tested with the snapshot reference technique. Between January 2018 and February 2023, we collected data on all patients diagnosed with MUC1 variants with this script. Results A total of 27 samples were tested anonymously by the BROAD Institute reference technique for confirmation and we were able to get a 100% concordance for MUC1 diagnosis. Clinico-biologic characteristics in our cohort were similar to those previously described in ADTKD-MUC1. Conclusion We describe a new simple and cost-effective method for molecular testing of ADTKD-MUC1. Genetic analyses in our cohort suggest that MUC1 might be the first cause of ADTKD. Increasing the availability of MUC1 diagnosis tools will contribute to a better understanding of the disease and to the development of specific treatments.
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Affiliation(s)
- Victor Fages
- Nephrology, Centre Hospitalier Regional Universitaire de Lille, Lille, France
| | - Florentin Bourre
- Nephrology, Centre Hospitalier Regional Universitaire de Lille, Lille, France
| | - Romain Larrue
- Service de Toxicologie et Génopathies, CHU Lille, Lille, France
| | - Andrea Wenzel
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Cologne, Germany
| | | | - Fabrice Bonte
- Functional and Structural Platform, Université de Lille, Lille, France
| | - Claire-Marie Dhaenens
- Department of Biochemistry and Molecular Biology, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Kendrah Kidd
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stanislav Kmoch
- First Faculty of Medicine, Charles University, Nové Město, Czechia
| | - Anthony Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - François Glowacki
- Nephrology, Centre Hospitalier Regional Universitaire de Lille, Lille, France
| | - Olivier Grunewald
- Neuroscience and Cognition, University Lille, Inserm, CHU Lille, Lille, France
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11
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Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, Ferracane MJ, Weaver VM, Läubli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nat Biotechnol 2024; 42:597-607. [PMID: 37537499 PMCID: PMC11018308 DOI: 10.1038/s41587-023-01840-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand the landscape of targetable substrates, we designed degraders that achieve substrate selectivity via recognition of a discrete peptide and glycan motif and achieve cell-type selectivity via antigen-driven cell-surface binding. We applied this approach to mucins, O-glycosylated proteins that drive cancer progression through biophysical and immunological mechanisms. Engineering of a bacterial mucin-selective protease yielded a variant for fusion to a cancer antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cancer cells, promoted cell death in culture models of mucin-driven growth and survival, and reduced tumor growth in mouse models of breast cancer progression. This work establishes a blueprint for the development of biologics that degrade specific protein glycoforms on target cells.
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Affiliation(s)
- Kayvon Pedram
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Gabrielle S Tender
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Natalia R Mantuano
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kevin J Metcalf
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Simon P Wisnovsky
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Giovanni C Forcina
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Angel Kuo
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Caitlyn L Miller
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Departments of Radiation Oncology and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Heinz Läubli
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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12
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Dilmen E, Orhon I, Jansen J, Hoenderop JGJ. Advancements in kidney organoids and tubuloids to study (dys)function. Trends Cell Biol 2024; 34:299-311. [PMID: 37865608 DOI: 10.1016/j.tcb.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/14/2023] [Accepted: 09/27/2023] [Indexed: 10/23/2023]
Abstract
The rising prevalence of kidney diseases urges the need for novel therapies. Kidney organoids and tubuloids are advanced in vitro models and have recently been described as promising tools to study kidney (patho)physiology. Recent developments have shown their application in disease modeling, drug screening, and nephrotoxicity. These applications rely on their ability to mimic (dys)function in vitro including endocrine activity and drug, electrolyte, and water transport. This review provides an overview of these emerging kidney models and focuses on the most recent developments that utilize their functional capabilities. In addition, we cover current limitations and provide future perspectives for this rapidly evolving field, including what these functional properties mean for translational and personalized medicine now and in the future.
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Affiliation(s)
- E Dilmen
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I Orhon
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J Jansen
- Department of Internal Medicine, Nephrology, and Transplantation, Erasmus Medical Center, Rotterdam, The Netherlands; Institute of Experimental Medicine and Systems Biology, University Hospital RWTH Aachen, Aachen, Germany
| | - J G J Hoenderop
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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13
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Roberts BS, Mitra D, Abishek S, Beher R, Satpute-Krishnan P. The p24-family and COPII subunit SEC24C facilitate the clearance of alpha1-antitrypsin Z from the endoplasmic reticulum to lysosomes. Mol Biol Cell 2024; 35:ar45. [PMID: 38294851 PMCID: PMC10916869 DOI: 10.1091/mbc.e23-06-0257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 01/16/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024] Open
Abstract
A subpopulation of the alpha-1-antitrypsin misfolding Z mutant (ATZ) is cleared from the endoplasmic reticulum (ER) via an ER-to-lysosome-associated degradation (ERLAD) pathway. Here, we report that the COPII subunit SEC24C and the p24-family of proteins facilitate the clearance of ATZ via ERLAD. In addition to the previously reported ERLAD components calnexin and FAM134B, we discovered that ATZ coimmunoprecipitates with the p24-family members TMP21 and TMED9. This contrasts with wild type alpha1-antitrypsin, which did not coimmunoprecipitate with FAM134B, calnexin or the p24-family members. Live-cell imaging revealed that ATZ and the p24-family members traffic together from the ER to lysosomes. Using chemical inhibitors to block ER exit or autophagy, we demonstrated that p24-family members and ATZ co-accumulate at SEC24C marked ER-exit sites or in ER-derived compartments, respectively. Furthermore, depletion of SEC24C, TMP21, or TMED9 inhibited lysosomal trafficking of ATZ and resulted in the increase of intracellular ATZ levels. Conversely, overexpression of these p24-family members resulted in the reduction of ATZ levels. Intriguingly, the p24-family members coimmunoprecipitate with ATZ, FAM134B, and SEC24C. Thus, we propose a model in which the p24-family functions in an adaptor complex linking SEC24C with the ERLAD machinery for the clearance of ATZ.
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Affiliation(s)
| | - Debashree Mitra
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Sudhanshu Abishek
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814
| | - Richa Beher
- Uniformed Services University of the Health Sciences, Bethesda, MD 20814
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14
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Jefferis J, Mallett AJ. Exploring the impact and utility of genomic sequencing in established CKD. Clin Kidney J 2024; 17:sfae043. [PMID: 38464959 PMCID: PMC10921391 DOI: 10.1093/ckj/sfae043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Indexed: 03/12/2024] Open
Abstract
Clinical genetics is increasingly recognized as an important area within nephrology care. Clinicians require awareness of genetic kidney disease to recognize clinical phenotypes, consider use of genomics to aid diagnosis, and inform treatment decisions. Understanding the broad spectrum of clinical phenotypes and principles of genomic sequencing is becoming increasingly required in clinical nephrology, with nephrologists requiring education and support to achieve meaningful patient outcomes. Establishment of effective clinical resources, multi-disciplinary teams and education is important to increase application of genomics in clinical care, for the benefit of patients and their families. Novel applications of genomics in chronic kidney disease include pharmacogenomics and clinical translation of polygenic risk scores. This review explores established and emerging impacts and utility of genomics in kidney disease.
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Affiliation(s)
- Julia Jefferis
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Brisbane, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Andrew J Mallett
- Faculty of Medicine, The University of Queensland, Brisbane, Australia
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Department of Renal Medicine, Townsville University Hospital, Douglas, Australia
- College of Medicine and Dentistry, James Cook University, Douglas, Australia
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15
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Long HY, Qian ZP, Lan Q, Xu YJ, Da JJ, Yu FX, Zha Y. Human pluripotent stem cell-derived kidney organoids: Current progress and challenges. World J Stem Cells 2024; 16:114-125. [PMID: 38455108 PMCID: PMC10915962 DOI: 10.4252/wjsc.v16.i2.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/18/2023] [Accepted: 01/29/2024] [Indexed: 02/26/2024] Open
Abstract
Human pluripotent stem cell (hPSC)-derived kidney organoids share similarities with the fetal kidney. However, the current hPSC-derived kidney organoids have some limitations, including the inability to perform nephrogenesis and lack of a corticomedullary definition, uniform vascular system, and coordinated exit pathway for urinary filtrate. Therefore, further studies are required to produce hPSC-derived kidney organoids that accurately mimic human kidneys to facilitate research on kidney development, regeneration, disease modeling, and drug screening. In this review, we discussed recent advances in the generation of hPSC-derived kidney organoids, how these organoids contribute to the understanding of human kidney development and research in disease modeling. Additionally, the limitations, future research focus, and applications of hPSC-derived kidney organoids were highlighted.
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Affiliation(s)
- Hong-Yan Long
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Zu-Ping Qian
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Qin Lan
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
| | - Yong-Jie Xu
- Department of Laboratory Medicine, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Jing-Jing Da
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Fu-Xun Yu
- Key Laboratory of Diagnosis and Treatment of Pulmonary Immune Diseases, National Health Commission, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China
| | - Yan Zha
- Graduate School, Zunyi Medical University, Zunyi 563000, Guizhou Province, China
- Department of Nephrology, Guizhou Provincial People's Hospital, Guiyang 550002, Guizhou Province, China.
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16
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Pahuja A, Goux Corredera I, Moya-Rull D, Garreta E, Montserrat N. Engineering physiological environments to advance kidney organoid models from human pluripotent stem cells. Curr Opin Cell Biol 2024; 86:102306. [PMID: 38194750 DOI: 10.1016/j.ceb.2023.102306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
During embryogenesis, the mammalian kidney arises because of reciprocal interactions between the ureteric bud (UB) and the metanephric mesenchyme (MM), driving UB branching and nephron induction. These morphogenetic processes involve a series of cellular rearrangements that are tightly controlled by gene regulatory networks and signaling cascades. Here, we discuss how kidney developmental studies have informed the definition of procedures to obtain kidney organoids from human pluripotent stem cells (hPSCs). Moreover, bioengineering techniques have emerged as potential solutions to externally impose controlled microenvironments for organoid generation from hPSCs. Next, we summarize some of these advances with major focus On recent works merging hPSC-derived kidney organoids (hPSC-kidney organoids) with organ-on-chip to develop robust models for drug discovery and disease modeling applications. We foresee that, in the near future, coupling of different organoid models through bioengineering approaches will help advancing to recreate organ-to-organ crosstalk to increase our understanding on kidney disease progression in the human context and search for new therapeutics.
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Affiliation(s)
- Anisha Pahuja
- Pluripotency for Organ Regeneration. Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Iphigénie Goux Corredera
- Pluripotency for Organ Regeneration. Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Daniel Moya-Rull
- Pluripotency for Organ Regeneration. Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Elena Garreta
- Pluripotency for Organ Regeneration. Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; University of Barcelona, 08028 Barcelona, Spain.
| | - Nuria Montserrat
- Pluripotency for Organ Regeneration. Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain; University of Barcelona, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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17
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Kishi S, Nagasu H, Kidokoro K, Kashihara N. Oxidative stress and the role of redox signalling in chronic kidney disease. Nat Rev Nephrol 2024; 20:101-119. [PMID: 37857763 DOI: 10.1038/s41581-023-00775-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
Chronic kidney disease (CKD) is a major public health concern, underscoring a need to identify pathogenic mechanisms and potential therapeutic targets. Reactive oxygen species (ROS) are derivatives of oxygen molecules that are generated during aerobic metabolism and are involved in a variety of cellular functions that are governed by redox conditions. Low levels of ROS are required for diverse processes, including intracellular signal transduction, metabolism, immune and hypoxic responses, and transcriptional regulation. However, excess ROS can be pathological, and contribute to the development and progression of chronic diseases. Despite evidence linking elevated levels of ROS to CKD development and progression, the use of low-molecular-weight antioxidants to remove ROS has not been successful in preventing or slowing disease progression. More recent advances have enabled evaluation of the molecular interactions between specific ROS and their targets in redox signalling pathways. Such studies may pave the way for the development of sophisticated treatments that allow the selective control of specific ROS-mediated signalling pathways.
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Affiliation(s)
- Seiji Kishi
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Hajime Nagasu
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Kengo Kidokoro
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Naoki Kashihara
- Department of Nephrology and Hypertension, Kawasaki Medical School, Kurashiki, Okayama, Japan.
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18
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Guo X, Zhou W, Jin J, Lin J, Zhang W, Zhang L, Luan X. Integrative Multi-Omics Analysis Identifies Transmembrane p24 Trafficking Protein 1 (TMED1) as a Potential Prognostic Marker in Colorectal Cancer. BIOLOGY 2024; 13:83. [PMID: 38392302 PMCID: PMC10886729 DOI: 10.3390/biology13020083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Several TMED protein family members are overexpressed in malignant tumors and associated with tumor progression. TMED1 belongs to the TMED protein family and is involved in protein vesicular trafficking. However, the expression level and biological role of TMED1 in colorectal cancer (CRC) have yet to be fully elucidated. In this study, the integration of patient survival and multi-omics data (immunohistochemical staining, transcriptomics, and proteomics) revealed that the highly expressed TMED1 was related to the poor prognosis in CRC. Crystal violet staining indicated the cell growth was reduced after knocking down TMED1. Moreover, the flow cytometry results showed that TMED1 knockdown could increase cell apoptosis. The expression of TMED1 was positively correlated with other TMED family members (TMED2, TMED4, TMED9, and TMED10) in CRC, and the protein-protein interaction network suggested its potential impact on immune regulation. Furthermore, TMED1 expression was positively associated with the infiltration levels of regulatory T cells (Tregs), cancer-associated fibroblasts (CAFs), and endothelial cells and negatively correlated with the infiltration levels of CD4+ T cells, CD8+ T cells, and B cells. At last, the CTRP and GDSC datasets on the GSCA platform were used to analyze the relationship between TMED1 expression and drug sensitivity (IC50). The result found that the elevation of TMED1 was positively correlated with IC50 and implied it could increase the drug resistance of cancer cells. This research revealed that TMED1 is a novel prognostic biomarker in CRC and provided a valuable strategy for analyzing potential therapeutic targets of malignant tumors.
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Affiliation(s)
- Xin Guo
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai 201203, China
| | - Wei Zhou
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jinmei Jin
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiayi Lin
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Weidong Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Shanghai Institute of Pharmaceutical Industry, China State Institute of Pharmaceutical Industry, Shanghai 201203, China
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lijun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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19
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Satariano M, Ghose S, Raina R. The Pathophysiology of Inherited Renal Cystic Diseases. Genes (Basel) 2024; 15:91. [PMID: 38254980 PMCID: PMC10815569 DOI: 10.3390/genes15010091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Renal cystic diseases (RCDs) can arise from utero to early adulthood and present with a variety of symptoms including renal, hepatic, and cardiovascular manifestations. It is well known that common RCDs such as autosomal polycystic kidney disease and autosomal recessive kidney disease are linked to genes such as PKD1 and PKHD1, respectively. However, it is important to investigate the genetic pathophysiology of how these gene mutations lead to clinical symptoms and include some of the less-studied RCDs, such as autosomal dominant tubulointerstitial kidney disease, multicystic dysplastic kidney, Zellweger syndrome, calyceal diverticula, and more. We plan to take a thorough look into the genetic involvement and clinical sequalae of a number of RCDs with the goal of helping to guide diagnosis, counseling, and treatment.
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Affiliation(s)
- Matthew Satariano
- Department of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (M.S.); (S.G.)
| | - Shaarav Ghose
- Department of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA; (M.S.); (S.G.)
| | - Rupesh Raina
- Akron Nephrology Associates, Cleveland Clinic Akron General Medical Center, Akron, OH 44307, USA
- Department of Nephrology, Akron Children’s Hospital, Akron, OH 44308, USA
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20
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Schiano G, Lake J, Mariniello M, Schaeffer C, Harvent M, Rampoldi L, Olinger E, Devuyst O. Allelic effects on uromodulin aggregates drive autosomal dominant tubulointerstitial kidney disease. EMBO Mol Med 2023; 15:e18242. [PMID: 37885358 PMCID: PMC10701617 DOI: 10.15252/emmm.202318242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/29/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Missense mutations in the uromodulin (UMOD) gene cause autosomal dominant tubulointerstitial kidney disease (ADTKD), one of the most common monogenic kidney diseases. The unknown impact of the allelic and gene dosage effects and fate of mutant uromodulin leaves open the gap between postulated gain-of-function mutations, end-organ damage and disease progression in ADTKD. Based on two prevalent missense UMOD mutations with divergent disease progression, we generated UmodC171Y and UmodR186S knock-in mice that showed strong allelic and gene dosage effects on uromodulin aggregates and activation of ER stress and unfolded protein and immune responses, leading to variable kidney damage. Deletion of the wild-type Umod allele in heterozygous UmodR186S mice increased the formation of uromodulin aggregates and ER stress. Studies in kidney tubular cells confirmed differences in uromodulin aggregates, with activation of mutation-specific quality control and clearance mechanisms. Enhancement of autophagy by starvation and mTORC1 inhibition decreased uromodulin aggregates. These studies substantiate the role of toxic aggregates as driving progression of ADTKD-UMOD, relevant for therapeutic strategies to improve clearance of mutant uromodulin.
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Affiliation(s)
- Guglielmo Schiano
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
| | - Jennifer Lake
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
| | - Marta Mariniello
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
| | - Céline Schaeffer
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Marianne Harvent
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
- Institut de Recherche Expérimentale et CliniqueUCLouvainBrusselsBelgium
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell BiologyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Eric Olinger
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
- Translational and Clinical Research InstituteNewcastle UniversityNewcastle upon TyneUK
- Center for Human GeneticsCliniques Universitaires Saint‐Luc, UCLouvainBrusselsBelgium
| | - Olivier Devuyst
- Mechanisms of Inherited Kidney Disorders, Institute of PhysiologyUniversity of ZurichZurichSwitzerland
- Institut de Recherche Expérimentale et CliniqueUCLouvainBrusselsBelgium
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21
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Ghosh S, Villacorta-Martin C, Lindstrom-Vautrin J, Kenney D, Golden CS, Edwards CV, Sanchorawala V, Connors LH, Giadone RM, Murphy GJ. Mapping cellular response to destabilized transthyretin reveals cell- and amyloidogenic protein-specific signatures. Amyloid 2023; 30:379-393. [PMID: 37439769 DOI: 10.1080/13506129.2023.2224494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/04/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND In ATTR amyloidosis, transthyretin (TTR) protein is secreted from the liver and deposited as toxic aggregates at downstream target tissues. Despite recent advancements in treatments for ATTR amyloidosis, the mechanisms underlying misfolded TTR-mediated cellular damage remain elusive. METHODS In an effort to define early events of TTR-associated stress, we exposed neuronal (SH-SY5Y) and cardiac (AC16) cells to wild-type and destabilized TTR variants (TTRV122I (p.V142I) and TTRL55P (p.L70P)) and performed transcriptional (RNAseq) and epigenetic (ATACseq) profiling. We subsequently compared TTR-responsive signatures to cells exposed to destabilized antibody light chain protein associated with AL amyloidosis as well as ER stressors (thapsigargin, heat shock). RESULTS In doing so, we observed overlapping, yet distinct cell type- and amyloidogenic protein-specific signatures, suggesting unique responses to each amyloidogenic variant. Moreover, we identified chromatin level changes in AC16 cells exposed to mutant TTR that resolved upon pre-incubation with kinetic stabilizer tafamidis. CONCLUSIONS Collectively, these data provide insight into the mechanisms underlying destabilized protein-mediated cellular damage and provide a robust resource representing cellular responses to aggregation-prone proteins and ER stress.
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Affiliation(s)
- Sabrina Ghosh
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
| | | | | | - Devin Kenney
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Carly S Golden
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Camille V Edwards
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Vaishali Sanchorawala
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Lawreen H Connors
- Amyloidosis Center, Alan and Sandra Gerry Amyloid Research Laboratory, Boston University School of Medicine, Boston, MA, USA
| | - Richard M Giadone
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
| | - George J Murphy
- Center for Regenerative Medicine, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Section of Hematology and Oncology, Boston University School of Medicine, Boston, MA, USA
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22
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Fistrek Prlic M, Huljev Frkovic S, Beck B, Tonkovic Durisevic I, Bulimbasic S, Coric M, Lamot L, Ivandic E, Vukovic Brinar I. Two sides of the same coin: a complex presentation of autosomal dominant tubulointerstitial kidney diseases: a literature review and case reports. Front Pediatr 2023; 11:1283325. [PMID: 38027261 PMCID: PMC10667683 DOI: 10.3389/fped.2023.1283325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Genetic kidney diseases are underdiagnosed; namely, from 7% to 40% of patients suffering from chronic kidney disease (CKD) can carry a pathogenic variant, depending on population characteristics. Hereditary tubulointerstitial kidney diseases, including autosomal dominant tubulointerstitial kidney diseases (ADTKD), are even more challenging to diagnose. ADTKD is a rare form of genetic kidney disease resulting from pathogenic variants in the MUC1, UMOD, HNF1B, REN, SEC61A1, and DNAJB11 genes. There is no typical clinical or histopathological sign of ADTKD, it is characterized by progressive CKD, an autosomal dominant inheritance pattern, and tubular atrophy with interstitial fibrosis on kidney biopsy. There is no significant proteinuria, and the urinary sediment is bland. The patients usually do not have severe arterial hypertension. There can be a history of early gout, especially when compared to the UMOD gene variants. Children can have enuresis due to a loss of renal concentration. On ultrasound, the kidneys can appear normal or small in size. Renal cysts are not pathognomonic for any of the named diseases. End-stage renal disease (ESRD) develops at the average age of 45, but this can be very variable. Family history that suggests autosomal dominant inheritance and CKD fulfilling the aforementioned characteristics of tubulointerstitial kidney disease should raise suspicion of ADTKD. In the setting of a negative family history for CKD, clinical suspicion should be raised based on clinical characteristics, including early onset of hyperuricemia or gout and compatible histology on the kidney biopsy. Contrary to the aforementioned characteristics of ADTKD, in the case of HNF1B-related disease, there is a more complex clinical presentation with extrarenal manifestations of the disease (diabetes mellitus, hypomagnesemia, neurologic and psychiatric disturbances, etc.). The diagnosis of ADTKD is based on a positive family history and a detection of the pathogenic variant in one of the genes in an affected individual. Aim The aim of our study is to present two case reports of ADTKD with different characteristics (slowly progressive CKD vs. complex clinical presentation with an extrarenal manifestation of the disease) with a literature review. Methods A 34-year-old patient with CKD and a positive family history of CKD in whom kidney biopsy showed nonspecific chronic changes, with only genetic analysis confirming the diagnosis of MUC1-related ADTKD. Our second case is of a 17-year-old patient with an unremarkable family history who was initially referred to genetic counseling due to cognitive and motor impairment with long-lasting epilepsy. Extensive workup revealed increased serum creatinine levels with no proteinuria and bland urinary sediment, along with hypomagnesemia. His genetic analysis revealed 17q12 deletion syndrome, causing the loss of one copy of the HNF1B gene, the AATF, and the LHX1 gene. Conclusion Autosomal dominant tubulointerstitial kidney diseases are challenging to diagnose due to a lack of typical clinical or histopathological signs as well as an uncharacteristic and versatile clinical presentation. Increased clinical awareness is crucial for the detection of these diseases.
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Affiliation(s)
- Margareta Fistrek Prlic
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, Zagreb, Croatia
| | - Sanda Huljev Frkovic
- Department of Pediatrics, Division of Genetics and Metabolism, University Hospital Center Zagreb, Zagreb, Croatia
- University of Zagreb, School of Medicine, Zagreb, Croatia
| | - Bodo Beck
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Ivana Tonkovic Durisevic
- Department of Laboratory Diagnostics, Division of Cytogenetics, University Hospital Center Zagreb, Zagreb, Croatia
| | - Stela Bulimbasic
- University of Zagreb, School of Medicine, Zagreb, Croatia
- Department of Pathology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Marijana Coric
- University of Zagreb, School of Medicine, Zagreb, Croatia
- Department of Pathology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Lovro Lamot
- University of Zagreb, School of Medicine, Zagreb, Croatia
- Department of Pediatrics, Division of Nephrology, Dialysis and Transplantation, University Hospital Center Zagreb, Zagreb, Croatia
| | - Ema Ivandic
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, Zagreb, Croatia
| | - Ivana Vukovic Brinar
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, Zagreb, Croatia
- University of Zagreb, School of Medicine, Zagreb, Croatia
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23
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Huang HJ, Chou CL, Sandar TT, Liu WC, Yang HC, Lin YC, Zheng CM, Chiu HW. Currently Used Methods to Evaluate the Efficacy of Therapeutic Drugs and Kidney Safety. Biomolecules 2023; 13:1581. [PMID: 38002263 PMCID: PMC10669823 DOI: 10.3390/biom13111581] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
Kidney diseases with kidney failure or damage, such as chronic kidney disease (CKD) and acute kidney injury (AKI), are common clinical problems worldwide and have rapidly increased in prevalence, affecting millions of people in recent decades. A series of novel diagnostic or predictive biomarkers have been discovered over the past decade, enhancing the investigation of renal dysfunction in preclinical studies and clinical risk assessment for humans. Since multiple causes lead to renal failure, animal studies have been extensively used to identify specific disease biomarkers for understanding the potential targets and nephropathy events in therapeutic insights into disease progression. Mice are the most commonly used model to investigate the mechanism of human nephropathy, and the current alternative methods, including in vitro and in silico models, can offer quicker, cheaper, and more effective methods to avoid or reduce the unethical procedures of animal usage. This review provides modern approaches, including animal and nonanimal assays, that can be applied to study chronic nonclinical safety. These specific situations could be utilized in nonclinical or clinical drug development to provide information on kidney disease.
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Affiliation(s)
- Hung-Jin Huang
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan (C.-L.C.)
| | - Chu-Lin Chou
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan (C.-L.C.)
- Division of Nephrology, Department of Internal Medicine, Hsin Kuo Min Hospital, Taipei Medical University, Taoyuan City 320, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 110, Taiwan
| | - Tin Tin Sandar
- Cancer Epidemiology Unit, Oxford Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Wen-Chih Liu
- Department of Biology and Anatomy, National Defense Medical Center, Taipei 114, Taiwan
- Section of Nephrology, Department of Medicine, Antai Medical Care Corporation Antai Tian-Sheng Memorial Hospital, Pingtung 928, Taiwan
| | - Hsiu-Chien Yang
- Division of Nephrology, Department of Internal Medicine, Zuoying Branch of Kaohsiung Armed Forces General Hospital, Kaohsiung 813, Taiwan
- Division of Nephrology, Department of Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Yen-Chung Lin
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan (C.-L.C.)
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 110, Taiwan
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei 110, Taiwan
| | - Cai-Mei Zheng
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan (C.-L.C.)
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 110, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
| | - Hui-Wen Chiu
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei 110, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City 235, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
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24
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Kim Y, Li C, Gu C, Fang Y, Tycksen E, Puri A, Pietka TA, Sivapackiam J, Kidd K, Park SJ, Johnson BG, Kmoch S, Duffield JS, Bleyer AJ, Jackrel ME, Urano F, Sharma V, Lindahl M, Chen YM. MANF stimulates autophagy and restores mitochondrial homeostasis to treat autosomal dominant tubulointerstitial kidney disease in mice. Nat Commun 2023; 14:6493. [PMID: 37838725 PMCID: PMC10576802 DOI: 10.1038/s41467-023-42154-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
Misfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD-UMOD), a leading hereditary kidney disease. There are no targeted therapies. In our generated mouse model recapitulating human ADTKD-UMOD carrying a leading UMOD mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are impaired, leading to cGAS-STING activation and tubular injury. Moreover, we demonstrate that inducible tubular overexpression of mesencephalic astrocyte-derived neurotrophic factor (MANF), a secreted endoplasmic reticulum protein, after the onset of disease stimulates autophagy/mitophagy, clears mutant UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, thus protecting kidney function in our ADTKD mouse model. Conversely, genetic ablation of MANF in the mutant thick ascending limb tubular cells worsens autophagy suppression and kidney fibrosis. Together, we have discovered MANF as a biotherapeutic protein and elucidated previously unknown mechanisms of MANF in the regulation of organelle homeostasis, which may have broad therapeutic applications to treat various proteinopathies.
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Affiliation(s)
- Yeawon Kim
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Chuang Li
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Chenjian Gu
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Yili Fang
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Eric Tycksen
- Genome Technology Access Center, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Anuradhika Puri
- Department of Chemistry, Washington University, St. Louis, MO, USA
| | - Terri A Pietka
- Nutrition and Geriatrics Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Jothilingam Sivapackiam
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kendrah Kidd
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Sun-Ji Park
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bryce G Johnson
- Pfizer Worldwide Research and Development, Inflammation & Immunology, Cambridge, MA, USA
| | - Stanislav Kmoch
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Anthony J Bleyer
- Section of Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Research Unit of Rare Diseases, Department of Pediatric and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Fumihiko Urano
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Vijay Sharma
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biomedical Engineering, School of Engineering & Applied Science, Washington University, St. Louis, MO, USA
| | - Maria Lindahl
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ying Maggie Chen
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, MO, USA.
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25
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Naas S, Krüger R, Knaup KX, Naas J, Grampp S, Schiffer M, Wiesener M, Schödel J. Hypoxia controls expression of kidney-pathogenic MUC1 variants. Life Sci Alliance 2023; 6:e202302078. [PMID: 37316299 PMCID: PMC10267510 DOI: 10.26508/lsa.202302078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
The interplay between genetic and environmental factors influences the course of chronic kidney disease (CKD). In this context, genetic alterations in the kidney disease gene MUC1 (Mucin1) predispose to the development of CKD. These variations comprise the polymorphism rs4072037, which alters splicing of MUC1 mRNA, the length of a region with variable number of tandem repeats (VNTR), and rare autosomal-dominant inherited dominant-negative mutations in or 5' to the VNTR that causes autosomal dominant tubulointerstitial kidney disease (ADTKD-MUC1). As hypoxia plays a pivotal role in states of acute and chronic kidney injury, we explored the effects of hypoxia-inducible transcription factors (HIF) on the expression of MUC1 and its pathogenic variants in isolated primary human renal tubular cells. We defined a HIF-binding DNA regulatory element in the promoter-proximal region of MUC1 from which hypoxia or treatment with HIF stabilizers, which were recently approved for an anti-anemic therapy in CKD patients, increased levels of wild-type MUC1 and the disease-associated variants. Thus, application of these compounds might exert unfavorable effects in patients carrying MUC1 risk variants.
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Affiliation(s)
- Stephanie Naas
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - René Krüger
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karl Xaver Knaup
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Julia Naas
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Wien, Austria
| | - Steffen Grampp
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mario Schiffer
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Wiesener
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Schödel
- Department of Nephrology and Hypertension, Uniklinikum Erlangen und Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Ghosh Roy S, Li Z, Guo Z, Long KT, Rehrl S, Tian X, Dong K, Besse W. Dnajb11-Kidney Disease Develops from Reduced Polycystin-1 Dosage but not Unfolded Protein Response in Mice. J Am Soc Nephrol 2023; 34:1521-1534. [PMID: 37332102 PMCID: PMC10482070 DOI: 10.1681/asn.0000000000000164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/18/2023] [Indexed: 06/20/2023] Open
Abstract
SIGNIFICANCE STATEMENT Heterozygous DNAJB11 mutation carriers manifest with small cystic kidneys and renal failure in adulthood. Recessive cases with prenatal cystic kidney dysplasia were recently described. Our in vitro and mouse model studies investigate the proposed disease mechanism as an overlap of autosomal-dominant polycystic kidney disease and autosomal-dominant tubulointerstitial kidney disease pathogenesis. We find that DNAJB11 loss impairs cleavage and maturation of the autosomal-dominant polycystic kidney disease protein polycystin-1 (PC1) and results in dosage-dependent cyst formation in mice. We find that Dnajb11 loss does not activate the unfolded protein response, drawing a fundamental contrast with the pathogenesis of autosomal-dominant tubulointerstitial kidney disease. We instead propose that fibrosis in DNAJB11 -kidney disease may represent an exaggerated response to polycystin-dependent cysts. BACKGROUND Patients with heterozygous inactivating mutations in DNAJB11 manifest with cystic but not enlarged kidneys and renal failure in adulthood. Pathogenesis is proposed to resemble an overlap of autosomal-dominant polycystic kidney disease (ADPKD) and autosomal-dominant tubulointerstitial kidney disease (ADTKD), but this phenotype has never been modeled in vivo . DNAJB11 encodes an Hsp40 cochaperone in the endoplasmic reticulum: the site of maturation of the ADPKD polycystin-1 (PC1) protein and of unfolded protein response (UPR) activation in ADTKD. We hypothesized that investigation of DNAJB11 would shed light on mechanisms for both diseases. METHODS We used germline and conditional alleles to model Dnajb11 -kidney disease in mice. In complementary experiments, we generated two novel Dnajb11-/- cell lines that allow assessment of PC1 C-terminal fragment and its ratio to the immature full-length protein. RESULTS Dnajb11 loss results in a profound defect in PC1 cleavage but with no effect on other cystoproteins assayed. Dnajb11-/- mice are live-born at below the expected Mendelian ratio and die at a weaning age with cystic kidneys. Conditional loss of Dnajb11 in renal tubular epithelium results in PC1 dosage-dependent kidney cysts, thus defining a shared mechanism with ADPKD. Dnajb11 mouse models show no evidence of UPR activation or cyst-independent fibrosis, which is a fundamental distinction from typical ADTKD pathogenesis. CONCLUSIONS DNAJB11 -kidney disease is on the spectrum of ADPKD phenotypes with a PC1-dependent pathomechanism. The absence of UPR across multiple models suggests that alternative mechanisms, which may be cyst-dependent, explain the renal failure in the absence of kidney enlargement.
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Affiliation(s)
- Sounak Ghosh Roy
- Section of Nephrology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
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27
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Nishinakamura R. Advances and challenges toward developing kidney organoids for clinical applications. Cell Stem Cell 2023; 30:1017-1027. [PMID: 37541208 DOI: 10.1016/j.stem.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 08/06/2023]
Abstract
Kidney organoids have enabled modeling of human development and disease. While methods of generating the nephron lineage are well established, new protocols to induce another lineage, the ureteric bud/collecting duct, have been reported in the past 5 years. Many reports have described modeling of various hereditary kidney diseases, with polycystic kidney disease serving as the archetypal disease, by using patient-derived or genome-edited kidney organoids. The generation of more organotypic kidneys is also becoming feasible. In this review, I also discuss the significant challenges for more sophisticated disease modeling and for realizing the ambitious goal of generating transplantable synthetic kidneys.
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Affiliation(s)
- Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan.
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28
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Sun S, Hu K, Wang L, Liu M, Zhang Y, Dong N, Wu Q. Spatial position is a key determinant of N-glycan functionality of the scavenger receptor cysteine-rich domain of human hepsin. FEBS J 2023; 290:3966-3982. [PMID: 36802168 DOI: 10.1111/febs.16757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 02/03/2023] [Accepted: 02/17/2023] [Indexed: 02/21/2023]
Abstract
The scavenger receptor cysteine-rich (SRCR) domain is a key constituent in diverse proteins. N-glycosylation is important in protein expression and function. In the SRCR domain of different proteins, N-glycosylation sites and functionality vary substantially. In this study, we examined the importance of N-glycosylation site positions in the SRCR domain of hepsin, a type II transmembrane serine protease involved in many pathophysiological processes. We analysed hepsin mutants with alternative N-glycosylation sites in the SRCR and protease domains using three-dimensional modelling, site-directed mutagenesis, HepG2 cell expression, immunostaining, and western blotting. We found that the N-glycan function in the SRCR domain in promoting hepsin expression and activation on the cell surface cannot be replaced by alternatively created N-glycans in the protease domain. Within the SRCR domain, the presence of an N-glycan in a confined surface area was essential for calnexin-assisted protein folding, endoplasmic reticulum (ER) exiting, and zymogen activation of hepsin on the cell surface. Hepsin mutants with alternative N-glycosylation sites on the opposite side of the SRCR domain were trapped by ER chaperones, resulting in the activation of the unfolded protein response in HepG2 cells. These results indicate that the spatial N-glycan positioning in the SRCR domain is a key determinant in the interaction with calnexin and subsequent cell surface expression of hepsin. These findings may help to understand the conservation and functionality of N-glycosylation sites in the SRCR domains of different proteins.
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Affiliation(s)
- Shijin Sun
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
- NHC Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Kaixuan Hu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
- NHC Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lina Wang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
| | - Meng Liu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
| | - Yikai Zhang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
- NHC Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ningzheng Dong
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
- NHC Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qingyu Wu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Suzhou Medical College, Soochow University, Suzhou, China
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29
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Wu D, Huang LF, Chen XC, Huang XR, Li HY, An N, Tang JX, Liu HF, Yang C. Research progress on endoplasmic reticulum homeostasis in kidney diseases. Cell Death Dis 2023; 14:473. [PMID: 37500613 PMCID: PMC10374544 DOI: 10.1038/s41419-023-05905-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/10/2023] [Accepted: 06/19/2023] [Indexed: 07/29/2023]
Abstract
The endoplasmic reticulum (ER) plays important roles in biosynthetic and metabolic processes, including protein and lipid synthesis, Ca2+ homeostasis regulation, and subcellular organelle crosstalk. Dysregulation of ER homeostasis can cause toxic protein accumulation, lipid accumulation, and Ca2+ homeostasis disturbance, leading to cell injury and even death. Accumulating evidence indicates that the dysregulation of ER homeostasis promotes the onset and progression of kidney diseases. However, maintaining ER homeostasis through unfolded protein response, ER-associated protein degradation, autophagy or ER-phagy, and crosstalk with other organelles may be potential therapeutic strategies for kidney disorders. In this review, we summarize the recent research progress on the relationship and molecular mechanisms of ER dysfunction in kidney pathologies. In addition, the endogenous protective strategies for ER homeostasis and their potential application for kidney diseases have been discussed.
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Affiliation(s)
- Dan Wu
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Li-Feng Huang
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Xiao-Cui Chen
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Xiao-Rong Huang
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Hui-Yuan Li
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Ning An
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Ji-Xin Tang
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China
| | - Hua-Feng Liu
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China.
| | - Chen Yang
- Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Non-communicable Diseases, Key Laboratory of Prevention and Management of Chronic Kidney Disease of Zhanjiang City, Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, 524001, Zhanjiang, Guangdong, China.
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30
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Saei H, Morinière V, Heidet L, Gribouval O, Lebbah S, Tores F, Mautret-Godefroy M, Knebelmann B, Burtey S, Vuiblet V, Antignac C, Nitschké P, Dorval G. VNtyper enables accurate alignment-free genotyping of MUC1 coding VNTR using short-read sequencing data in autosomal dominant tubulointerstitial kidney disease. iScience 2023; 26:107171. [PMID: 37456840 PMCID: PMC10338300 DOI: 10.1016/j.isci.2023.107171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
The human genome comprises approximately 3% of tandem repeats with variable length (VNTR), a few of which have been linked to human rare diseases. Autosomal dominant tubulointerstitial kidney disease-MUC1 (ADTKD-MUC1) is caused by specific frameshift variants in the coding VNTR of the MUC1 gene. Calling variants from VNTR using short-read sequencing (SRS) is challenging due to poor read mappability. We developed a computational pipeline, VNtyper, for reliable detection of MUC1 VNTR pathogenic variants and demonstrated its clinical utility in two distinct cohorts: (1) a historical cohort including 108 families with ADTKD and (2) a replication naive cohort comprising 2,910 patients previously tested on a panel of genes involved in monogenic renal diseases. In the historical cohort all cases known to carry pathogenic MUC1 variants were re-identified, and a new 25bp-frameshift insertion in an additional mislaid family was detected. In the replication cohort, we discovered and validated 30 new patients.
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Affiliation(s)
- Hassan Saei
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Vincent Morinière
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Laurence Heidet
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Néphrologie Pédiatrique, Centre de Référence MARHEA, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Olivier Gribouval
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Said Lebbah
- Département de Santé Publique, Unité de Recherche Clinique, Hôpital Pitié-Salpêtrière, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Frederic Tores
- Plateforme Bio-informatique, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Manon Mautret-Godefroy
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Bertrand Knebelmann
- Service de Néphrologie, Centre de Référence MARHEA, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Stéphane Burtey
- Inserm, C2VN, INRAE, C2VN, Aix-Marseille Université, Marseille, France
- Centre de Néphrologie et Transplantation Rénale, AP-HM Hôpital de la Conception, Marseille, France
| | - Vincent Vuiblet
- Service de Néphrologie, CHU de Reims, Reims, France
- Service de Pathologie, CHU De Reims, Reims, France
- Institut d'Intelligence Artificielle en Santé, Université de Reims Champagne-Ardenne et CHU de Reims, Reims, France
| | - Corinne Antignac
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
| | - Patrick Nitschké
- Plateforme Bio-informatique, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
| | - Guillaume Dorval
- Laboratoire des Maladies Rénales Héréditaires, Inserm UMR 1163, Institut Imagine, Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Assistance publique, Hôpitaux de Paris (AP-HP), Paris, France
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31
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Schlosser P, Zhang J, Liu H, Surapaneni AL, Rhee EP, Arking DE, Yu B, Boerwinkle E, Welling PA, Chatterjee N, Susztak K, Coresh J, Grams ME. Transcriptome- and proteome-wide association studies nominate determinants of kidney function and damage. Genome Biol 2023; 24:150. [PMID: 37365616 DOI: 10.1186/s13059-023-02993-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND The pathophysiological causes of kidney disease are not fully understood. Here we show that the integration of genome-wide genetic, transcriptomic, and proteomic association studies can nominate causal determinants of kidney function and damage. RESULTS Through transcriptome-wide association studies (TWAS) in kidney cortex, kidney tubule, liver, and whole blood and proteome-wide association studies (PWAS) in plasma, we assess for effects of 12,893 genes and 1342 proteins on kidney filtration (glomerular filtration rate (GFR) estimated by creatinine; GFR estimated by cystatin C; and blood urea nitrogen) and kidney damage (albuminuria). We find 1561 associations distributed among 260 genomic regions that are supported as putatively causal. We then prioritize 153 of these genomic regions using additional colocalization analyses. Our genome-wide findings are supported by existing knowledge (animal models for MANBA, DACH1, SH3YL1, INHBB), exceed the underlying GWAS signals (28 region-trait combinations without significant GWAS hit), identify independent gene/protein-trait associations within the same genomic region (INHBC, SPRYD4), nominate tissues underlying the associations (tubule expression of NRBP1), and distinguish markers of kidney filtration from those with a role in creatinine and cystatin C metabolism. Furthermore, we follow up on members of the TGF-beta superfamily of proteins and find a prognostic value of INHBC for kidney disease progression even after adjustment for measured glomerular filtration rate (GFR). CONCLUSION In summary, this study combines multimodal, genome-wide association studies to generate a catalog of putatively causal target genes and proteins relevant to kidney function and damage which can guide follow-up studies in physiology, basic science, and clinical medicine.
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Affiliation(s)
- Pascal Schlosser
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Jingning Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongbo Liu
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya L Surapaneni
- Welch Center for Prevention Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD, USA
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bing Yu
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Eric Boerwinkle
- Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Paul A Welling
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Katalin Susztak
- Department of Medicine and Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Morgan E Grams
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Division of Precision Medicine, New York University Grossman School of Medicine, New York, NY, USA
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32
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Jensen KB, Little MH. Organoids are not organs: Sources of variation and misinformation in organoid biology. Stem Cell Reports 2023; 18:1255-1270. [PMID: 37315519 DOI: 10.1016/j.stemcr.2023.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023] Open
Abstract
In the past decade, the term organoid has moved from obscurity to common use to describe a 3D in vitro cellular model of a tissue that recapitulates structural and functional elements of the in vivo organ it models. The term organoid is now applied to structures formed as a result of two distinct processes: the capacity for adult epithelial stem cells to re-create a tissue niche in vitro and the ability to direct the differentiation of pluripotent stem cells to a 3D self-organizing multicellular model of organogenesis. While these two organoid fields rely upon different stem cell types and recapitulate different processes, both share common challenges around robustness, accuracy, and reproducibility. Critically, organoids are not organs. This commentary serves to discuss these challenges, how they impact genuine utility, and shine a light on the need to improve the standards applied to all organoid approaches.
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Affiliation(s)
- Kim Bak Jensen
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Melissa Helen Little
- Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; Novo Nordisk Foundation Centre for Stem Cell Medicine, Murdoch Children's Research Institute, Parkville, Melbourne, VIC 3052, Australia.
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33
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Kang HM. Kidney Organoid Derived from Human Pluripotent and Adult Stem Cells for Disease Modeling. Dev Reprod 2023; 27:57-65. [PMID: 37529017 PMCID: PMC10390101 DOI: 10.12717/dr.2023.27.2.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/27/2023] [Accepted: 05/26/2023] [Indexed: 08/03/2023]
Abstract
Kidney disease affects a significant portion of the global population, yet effective therapies are lacking despite advancements in identifying genetic causes. This limitation can be attributed to the absence of adequate in vitro models that accurately mimic human kidney disease, hindering targeted therapeutic development. However, the emergence of human induced pluripotent stem cells (PSCs) and the development of organoids using them have opened up a way to model kidney development and disease in humans, as well as validate the effects of new drugs. To fully leverage their capabilities in these fields, it is crucial for kidney organoids to closely resemble the structure and functionality of adult human kidneys. In this review, we aim to discuss the potential of using human PSCs or adult kidney stem cell-derived kidney organoids to model genetic kidney disease and renal cancer.
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Affiliation(s)
- Hyun Mi Kang
- Korea Research Institute of Bioscience
and Biotechnology (KRIBB), Daejeon 34141,
Korea
- Department of Functional Genomics, Korea
University of Science and Technology (UST), Daejeon
34113, Korea
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34
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Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, Rutter JC, Therrien M, Yoon H, Lai ZW, Baublis A, Subramanian R, Devkota R, Small J, Sreekanth V, Han M, Lim D, Carpenter AE, Flannick J, Finucane H, Haigis MC, Claussnitzer M, Sheu E, Stevens B, Wagner BK, Choudhary A, Shaw JL, Pablo JL, Greka A. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. Cell Metab 2023; 35:887-905.e11. [PMID: 37075753 PMCID: PMC10257950 DOI: 10.1016/j.cmet.2023.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/21/2023] [Accepted: 03/27/2023] [Indexed: 04/21/2023]
Abstract
Cellular exposure to free fatty acids (FFAs) is implicated in the pathogenesis of obesity-associated diseases. However, there are no scalable approaches to comprehensively assess the diverse FFAs circulating in human plasma. Furthermore, assessing how FFA-mediated processes interact with genetic risk for disease remains elusive. Here, we report the design and implementation of fatty acid library for comprehensive ontologies (FALCON), an unbiased, scalable, and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids associated with decreased membrane fluidity. Furthermore, we prioritized genes that reflect the combined effects of harmful FFA exposure and genetic risk for type 2 diabetes (T2D). We found that c-MAF-inducing protein (CMIP) protects cells from FFA exposure by modulating Akt signaling. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism.
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Affiliation(s)
- Nicolas Wieder
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Department of Neurology with Experimental Neurology and Berlin Institute of Health, Charité, 10117 Berlin, Germany
| | - Juliana Coraor Fried
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Choah Kim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Eriene-Heidi Sidhom
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Matthew R Brown
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Carlos Arevalo
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Moran Dvela-Levitt
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | | | - Jonas Sieber
- Department of Endocrinology, Metabolism and Cardiovascular Systems, University of Fribourg, Fribourg, Switzerland
| | | | - Julian Pacheco
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Shantanu Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justine C Rutter
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | - Haejin Yoon
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Zon Weng Lai
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Aaron Baublis
- Harvard Chan Advanced Multiomics Platform, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Renuka Subramanian
- Laboratory for Surgical and Metabolic Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ranjan Devkota
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonnell Small
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vedagopuram Sreekanth
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Myeonghoon Han
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Donghyun Lim
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Jason Flannick
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Hilary Finucane
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Analytic and Translational Genetics Unit, Mass General Hospital, Boston, MA 02114, USA
| | - Marcia C Haigis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Ludwig Center for Cancer Research at Harvard, Boston, MA 02115, USA
| | - Melina Claussnitzer
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric Sheu
- Laboratory for Surgical and Metabolic Research, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Beth Stevens
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Boston Children's Hospital, F.M. Kirby Neurobiology Center, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Bridget K Wagner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Amit Choudhary
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jillian L Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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35
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Zou W, Lai M, Jiang Y, Mao L, Zhou W, Zhang S, Lai P, Guo B, Wei T, Nie C, Zheng L, Zhang J, Gao X, Zhao X, Xia L, Zou Z, Liu A, Liu S, Cui Z, Bai X. Exosome Release Delays Senescence by Disposing of Obsolete Biomolecules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2204826. [PMID: 36683247 PMCID: PMC10015858 DOI: 10.1002/advs.202204826] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Accumulation of obsolete biomolecules can accelerate cell senescence and organism aging. The two efficient intracellular systems, namely the ubiquitin-proteasome system and the autophagy-lysosome system, play important roles in dealing with cellular wastes. However, how multicellular organisms orchestrate the processing of obsolete molecules and delay aging remains unclear. Herein, it is shown that prevention of exosome release by GW4869 or Rab27a-/- accelerated senescence in various cells and mice, while stimulating exosome release by nutrient restriction delays aging. Interestingly, exosomes isolate from serum-deprived cells or diet-restricted human plasma, enriched with garbage biomolecules, including misfolded proteins, oxidized lipids, and proteins. These cellular wastes can be englobed by macrophages, eventually, for disintegration in vivo. Inhibition of nutrient-sensing mTORC1 signaling increases exosome release and delays senescence, while constitutive activation of mTORC1 reduces exosome secretion and exacerbates senescence in vitro and in mice. Notably, inhibition of exosome release attenuates nutrient restriction- or rapamycin-delayed senescence, supporting a key role for exosome secretion in this process. This study reveals a potential mechanism by which stimulated exosome release delays aging in multicellular organisms, by orchestrating the harmful biomolecules disposal via exosomes and macrophages.
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Affiliation(s)
- Wenchong Zou
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative DiseasesThe Third Affiliated Hospital of Southern Medical UniversityGuangzhou510630China
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Mingqiang Lai
- The Fifth Affiliated HospitalSouthern Medical UniversityGuangzhouGuangdong510900China
| | - Yuanjun Jiang
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Linlin Mao
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Wu Zhou
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Sheng Zhang
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Pinglin Lai
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative DiseasesThe Third Affiliated Hospital of Southern Medical UniversityGuangzhou510630China
| | - Bin Guo
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Tiantian Wei
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Chengtao Nie
- Department of Laboratory MedicineNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Lei Zheng
- Department of Laboratory MedicineNanfang HospitalSouthern Medical UniversityGuangzhou510515China
| | - Jiahuan Zhang
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Xuefei Gao
- Department of PhysiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Xiaoyang Zhao
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Laixin Xia
- Department of Developmental BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Zhipeng Zou
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Anling Liu
- Department of BiochemistrySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
| | - Shiming Liu
- Department of CardiologyGuangzhou Institute of Cardiovascular DiseaseGuangdong Key Laboratory of Vascular DiseasesThe Second Affiliated HospitalGuangzhou Medical UniversityGuangzhou510260China
| | - Zhong‐Kai Cui
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
- Department of Spine SurgeryGanzhou People's HospitalGanzhou342800China
| | - Xiaochun Bai
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative DiseasesThe Third Affiliated Hospital of Southern Medical UniversityGuangzhou510630China
- State Key Laboratory of Organ Failure ResearchDepartment of Cell BiologySchool of Basic Medical SciencesSouthern Medical UniversityGuangzhou510515China
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36
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Yang C, Guo J, Ni K, Wen K, Qin Y, Gu R, Wang C, Liu L, Pan Y, Li J, Luo M, Deng L. Mechanical Ventilation-Related High Stretch Mainly Induces Endoplasmic Reticulum Stress and Thus Mediates Inflammation Response in Cultured Human Primary Airway Smooth Muscle Cells. Int J Mol Sci 2023; 24:ijms24043811. [PMID: 36835223 PMCID: PMC9958795 DOI: 10.3390/ijms24043811] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/29/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Ventilator-induced lung injury (VILI) occurs in mechanically ventilated patients of respiratory disease and is typically characterized by airway inflammation. However, recent studies increasingly indicate that a major cause of VILI may be the excessive mechanical loading such as high stretch (>10% strain) on airway smooth muscle cells (ASMCs) due to mechanical ventilation (MV). Although ASMCs are the primary mechanosensitive cells in airways and contribute to various airway inflammation diseases, it is still unclear how they respond to high stretch and what mediates such a response. Therefore, we used whole genome-wide mRNA-sequencing (mRNA-Seq), bioinformatics, and functional identification to systematically analyze the mRNA expression profiles and signaling pathway enrichment of cultured human ASMCs exposed to high stretch (13% strain), aiming to screen the susceptible signaling pathway through which cells respond to high stretch. The data revealed that in response to high stretch, 111 mRNAs with count ≥100 in ASMCs were significantly differentially expressed (defined as DE-mRNAs). These DE-mRNAs are mainly enriched in endoplasmic reticulum (ER) stress-related signaling pathways. ER stress inhibitor (TUDCA) abolished high-stretch-enhanced mRNA expression of genes associated with ER stress, downstream inflammation signaling, and major inflammatory cytokines. These results demonstrate in a data-driven approach that in ASMCs, high stretch mainly induced ER stress and activated ER stress-related signaling and downstream inflammation response. Therefore, it suggests that ER stress and related signaling pathways in ASMCs may be potential targets for timely diagnosis and intervention of MV-related pulmonary airway diseases such as VILI.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Mingzhi Luo
- Correspondence: (M.L.); (L.D.); Tel.: +86-136-1611-9565 (M.L.); +86-136-8520-7009 (L.D.)
| | - Linhong Deng
- Correspondence: (M.L.); (L.D.); Tel.: +86-136-1611-9565 (M.L.); +86-136-8520-7009 (L.D.)
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Shaw JL, Pablo JL, Greka A. Mechanisms of Protein Trafficking and Quality Control in the Kidney and Beyond. Annu Rev Physiol 2023; 85:407-423. [PMID: 36763970 DOI: 10.1146/annurev-physiol-031522-100639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Numerous trafficking and quality control pathways evolved to handle the diversity of proteins made by eukaryotic cells. However, at every step along the biosynthetic pathway, there is the potential for quality control system failure. This review focuses on the mechanisms of disrupted proteostasis. Inspired by diseases caused by misfolded proteins in the kidney (mucin 1 and uromodulin), we outline the general principles of protein biosynthesis, delineate the recognition and degradation pathways targeting misfolded proteins, and discuss the role of cargo receptors in protein trafficking and lipid homeostasis. We also discuss technical approaches including live-cell fluorescent microscopy, chemical screens to elucidate trafficking mechanisms, multiplexed single-cell CRISPR screening platforms to systematically delineate mechanisms of proteostasis, and the advancement of novel tools to degrade secretory and membrane-associated proteins. By focusing on components of trafficking that go awry, we highlight ongoing efforts to understand fundamental mechanisms of disrupted proteostasis and implications for the treatment of human proteinopathies.
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Affiliation(s)
- Jillian L Shaw
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; .,Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Juan Lorenzo Pablo
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; .,Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Anna Greka
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; .,Kidney Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
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Kuo TC, Cabrera-Barragan DN, Lopez-Marfil M, Lopez-Cantu DO, Lemos DR. Can Kidney Organoid Xenografts Accelerate Therapeutic Development for Genetic Kidney Disorders? J Am Soc Nephrol 2023; 34:184-190. [PMID: 36344066 PMCID: PMC10103095 DOI: 10.1681/asn.2022080862] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
A number of genetic kidney diseases can now be replicated experimentally, using kidney organoids generated from human pluripotent stem cells. This methodology holds great potential for drug discovery. Under in vitro conditions, however, kidney organoids remain developmentally immature, develop scarce vasculature, and may contain undesired off-target cell types. Those critical deficiencies limit their potential as disease-modeling tools. Orthotopic transplantation under the kidney capsule improves the anatomic maturity and vascularization of kidney organoids, while reducing off-target cell content. The improvements can translate into more accurate representations of disease phenotypes and mechanisms in vivo . Recent studies using kidney organoid xenografts highlighted the unique potential of this novel methodology for elucidating molecular mechanisms driving monogenic kidney disorders and for the development ofnovel pharmacotherapies.
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Affiliation(s)
- Ting-Chun Kuo
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Dalia N. Cabrera-Barragan
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Marta Lopez-Marfil
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Universitat de Barcelona, Barcelona, Spain
| | - Diana O. Lopez-Cantu
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Dario R. Lemos
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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Urinary Extracellular Vesicles in Chronic Kidney Disease: From Bench to Bedside? Diagnostics (Basel) 2023; 13:diagnostics13030443. [PMID: 36766548 PMCID: PMC9913975 DOI: 10.3390/diagnostics13030443] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
Extracellular vesicles are a diverse group of particles that include exosomes, microvesicles, and apoptotic bodies and are defined by size, composition, site of origin, and density. They incorporate various bioactive molecules from their cell of origin during formation, such as soluble proteins, membrane receptors, nucleic acids (mRNAs and miRNAs), and lipids, which can then be transferred to target cells. Extracellular vesicles/exosomes have been extensively studied as a critical factor in pathophysiological processes of human diseases. Urinary extracellular vesicles could be a promising liquid biopsy for determining the pattern and/or severity of kidney histologic injury. The signature of urinary extracellular vesicles may pave the way for noninvasive methods to supplement existing testing methods for diagnosing kidney diseases. We discuss the potential role of urinary extracellular vesicles in various chronic kidney diseases in this review, highlighting open questions and discussing the potential for future research.
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Roberts BS, Satpute-Krishnan P. The many hats of transmembrane emp24 domain protein TMED9 in secretory pathway homeostasis. Front Cell Dev Biol 2023; 10:1096899. [PMID: 36733337 PMCID: PMC9888432 DOI: 10.3389/fcell.2022.1096899] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The secretory pathway is an intracellular highway for the vesicular transport of newly synthesized proteins that spans the endoplasmic reticulum (ER), Golgi, lysosomes and the cell surface. A variety of cargo receptors, chaperones, and quality control proteins maintain the smooth flow of cargo along this route. Among these is vesicular transport protein TMED9, which belongs to the p24/transmembrane emp24 domain (TMED) family of proteins, and is expressed across vertebrate species. The TMED family is comprised of structurally-related type I transmembrane proteins with a luminal N-terminal Golgi-dynamics domain, a luminal coiled-coil domain, a transmembrane domain and a short cytosolic C-terminal tail that binds COPI and COPII coat proteins. TMED9, like other members of the TMED family, was first identified as an abundant constituent of the COPI and COPII coated vesicles that mediate traffic between the ER and the Golgi. TMED9 is typically purified in hetero-oligomers together with TMED family members, suggesting that it may function as part of a complex. Recently, TMED family members have been discovered to play various roles in secretory pathway homeostasis including secreted protein processing, quality control and degradation of misfolded proteins, and post-Golgi trafficking. In particular, TMED9 has been implicated in autophagy, lysosomal sorting, viral replication and cancer, which we will discuss in this Mini-Review.
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Kim Y, Li C, Gu C, Tycksen E, Puri A, Pietka TA, Sivapackiam J, Fang Y, Kidd K, Park SJ, Johnson BG, Kmoch S, Duffield JS, Bleyer AJ, Jackrel ME, Urano F, Sharma V, Lindahl M, Chen YM. MANF stimulates autophagy and restores mitochondrial homeostasis to treat toxic proteinopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.10.523171. [PMID: 36711449 PMCID: PMC9882049 DOI: 10.1101/2023.01.10.523171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Misfolded protein aggregates may cause toxic proteinopathy, including autosomal dominant tubulointerstitial kidney disease due to uromodulin mutations (ADTKD- UMOD ), one of the leading hereditary kidney diseases, and Alzheimer’s disease etc. There are no targeted therapies. ADTKD is also a genetic form of renal fibrosis and chronic kidney disease, which affects 500 million people worldwide. For the first time, in our newly generated mouse model recapitulating human ADTKD- UMOD carrying a leading UMOD deletion mutation, we show that autophagy/mitophagy and mitochondrial biogenesis are severely impaired, leading to cGAS- STING activation and tubular injury. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a novel endoplasmic reticulum stress-regulated secreted protein. We provide the first study that inducible tubular overexpression of MANF after the onset of disease stimulates autophagy/mitophagy and clearance of the misfolded UMOD, and promotes mitochondrial biogenesis through p-AMPK enhancement, resulting in protection of kidney function. Conversely, genetic ablation of endogenous MANF upregulated in the mutant mouse and human tubular cells worsens autophagy suppression and kidney fibrosis. Together, we discover MANF as a novel biotherapeutic protein and elucidate previously unknown mechanisms of MANF in regulating organelle homeostasis to treat ADTKD, which may have broad therapeutic application to treat various proteinopathies.
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Lausecker F, Lennon R, Randles MJ. The kidney matrisome in health, aging, and disease. Kidney Int 2022; 102:1000-1012. [PMID: 35870643 DOI: 10.1016/j.kint.2022.06.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]
Abstract
Dysregulated extracellular matrix is the hallmark of fibrosis, and it has a profound impact on kidney function in disease. Furthermore, perturbation of matrix homeostasis is a feature of aging and is associated with declining kidney function. Understanding these dynamic processes, in the hope of developing therapies to combat matrix dysregulation, requires the integration of data acquired by both well-established and novel technologies. Owing to its complexity, the extracellular proteome, or matrisome, still holds many secrets and has great potential for the identification of clinical biomarkers and drug targets. The molecular resolution of matrix composition during aging and disease has been illuminated by cutting-edge mass spectrometry-based proteomics in recent years, but there remain key questions about the mechanisms that drive altered matrix composition. Basement membrane components are particularly important in the context of kidney function; and data from proteomic studies suggest that switches between basement membrane and interstitial matrix proteins are likely to contribute to organ dysfunction during aging and disease. Understanding the impact of such changes on physical properties of the matrix, and the subsequent cellular response to altered stiffness and viscoelasticity, is of critical importance. Likewise, the comparison of proteomic data sets from multiple organs is required to identify common matrix biomarkers and shared pathways for therapeutic intervention. Coupled with single-cell transcriptomics, there is the potential to identify the cellular origin of matrix changes, which could enable cell-targeted therapy. This review provides a contemporary perspective of the complex kidney matrisome and draws comparison to altered matrix in heart and liver disease.
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Affiliation(s)
- Franziska Lausecker
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK; Department of Paediatric Nephrology, Royal Manchester Children's Hospital, Manchester University Hospitals National Health Service (NHS) Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Michael J Randles
- Chester Medical School, Faculty of Medicine and Life Sciences, University of Chester, Chester, UK.
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Dorison A, Forbes TA, Little MH. What can we learn from kidney organoids? Kidney Int 2022; 102:1013-1029. [PMID: 35970244 DOI: 10.1016/j.kint.2022.06.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/15/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022]
Abstract
The ability to generate 3-dimensional models of the developing human kidney via the directed differentiation of pluripotent stem cells-termed kidney organoids-has been hailed as a major advance in experimental nephrology. Although these provide an opportunity to interrogate human development, model-specific kidney diseases facilitate drug screening and even deliver bioengineered tissue; most of these prophetic end points remain to be realized. Indeed, at present we are still finding out what we can learn and what we cannot learn from this approach. In this review, we will summarize the approaches available to generate models of the human kidney from stem cells, the existing successful applications of kidney organoids, their limitations, and remaining challenges.
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Affiliation(s)
- Aude Dorison
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia; Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas A Forbes
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia; Department of Nephrology, Royal Children's Hospital, Parkville, Melbourne, Australia
| | - Melissa H Little
- Murdoch Children's Research Institute, Parkville, Melbourne, Australia; Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Melbourne, Australia; Novo Nordisk Foundation Centre for Stem Cell Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.
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Takizawa K, Ueda K, Sekiguchi M, Nakano E, Nishimura T, Kajiho Y, Kanda S, Miura K, Hattori M, Hashimoto J, Hamasaki Y, Hisano M, Omori T, Okamoto T, Kitayama H, Fujita N, Kuramochi H, Ichiki T, Oka A, Harita Y. Urinary extracellular vesicles signature for diagnosis of kidney disease. iScience 2022; 25:105416. [PMID: 36439984 PMCID: PMC9684058 DOI: 10.1016/j.isci.2022.105416] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/07/2022] [Accepted: 10/17/2022] [Indexed: 11/09/2022] Open
Abstract
Congenital disorders characterized by the quantitative and qualitative reduction in the number of functional nephrons are the primary cause of chronic kidney disease (CKD) in children. We aimed to describe the alteration of urinary extracellular vesicles (uEVs) associated with decreased renal function during childhood. By nanoparticle tracking analysis and quantitative proteomics, we identified differentially expressed proteins in uEVs in bilateral renal hypoplasia, which is characterized by a congenitally reduced number of nephrons. This expression signature of uEVs reflected decreased renal function in CKD patients by congenital anomalies of the kidney and urinary tract or ciliopathy. As a proof-of-concept, we constructed a prototype ELISA system that enabled the isolation of uEVs and quantitation of expression of molecules representing the signature. The system identified decreased renal function even in its early stage. The uEVs signature could pave the way for non-invasive methods that can complement existing testing methods for diagnosing kidney diseases. Urinary extracellular vesicles (uEVs) are altered in chronic kidney disease (CKD) Characteristic expression signatures associated with childhood CKD are identified An ELISA utilizing the signature detected decreased renal function uEVs signature has potential in diagnosing kidney diseases
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Affiliation(s)
- Keiichi Takizawa
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Koji Ueda
- Project for Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Masahiro Sekiguchi
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Eiji Nakano
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Tatsuya Nishimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yuko Kajiho
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Shoichiro Kanda
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Kenichiro Miura
- Department of Pediatric Nephrology, Tokyo Women’s Medical University, Tokyo 162-8666, Japan
| | - Motoshi Hattori
- Department of Pediatric Nephrology, Tokyo Women’s Medical University, Tokyo 162-8666, Japan
| | - Junya Hashimoto
- Department of Nephrology, Faculty of Medicine, Toho University, Tokyo 143-8541, Japan
| | - Yuko Hamasaki
- Department of Nephrology, Faculty of Medicine, Toho University, Tokyo 143-8541, Japan
| | - Masataka Hisano
- Department of Nephrology, Chiba Children’s Hospital, Chiba 266-0007, Japan
| | - Tae Omori
- Department of Pediatrics, Tokyo Metropolitan Bokutoh Hospital, Tokyo 130-8575, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Graduate School of Medicine, Hokkaido 060-8648, Japan
| | - Hirotsugu Kitayama
- Department of Nephrology, Shizuoka Children’s Hospital, Shizuoka, 420-8660, Japan
| | - Naoya Fujita
- Department of Nephrology, Aichi Children’s Health and Medical Center, Aichi 474-8710, Japan
| | - Hiromi Kuramochi
- Department of Materials Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Takanori Ichiki
- Department of Materials Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yutaka Harita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
- Corresponding author
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45
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Kalejaiye TD, Barreto AD, Musah S. Translating Organoids into Artificial Kidneys. CURRENT TRANSPLANTATION REPORTS 2022; 9:276-286. [PMID: 36311696 PMCID: PMC9592871 DOI: 10.1007/s40472-022-00383-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/21/2022]
Abstract
Purpose of Review
Kidney disease affects more than 13% of the world population, and current treatment options are limited to dialysis and organ transplantation. The generation of kidney organoids from human-induced pluripotent stem (hiPS) cells could be harnessed to engineer artificial organs and help overcome the challenges associated with the limited supply of transplantable kidneys. The purpose of this article is to review the progress in kidney organoid generation and transplantation and highlight some existing challenges in the field. We also examined possible improvements that could help realize the potential of organoids as artificial organs or alternatives for kidney transplantation therapy. Recent Findings Organoids are useful for understanding the mechanisms of kidney development, and they provide robust platforms for drug screening, disease modeling, and generation of tissues for organ replacement therapies. Efforts to design organoids rely on the ability of cells to self-assemble and pattern themselves into recognizable tissues. While existing protocols for generating organoids result in multicellular structures reminiscent of the developing kidney, many do not yet fully recapitulate the complex cellular composition, structure, and functions of the intact kidney. Recent advances toward achieving these goals include identifying cell culture conditions that produce organoids with improved vasculature and cell maturation and functional states. Still, additional improvements are needed to enhance tissue patterning, specialization, and function, and avoid tumorigenicity after transplantation. Summary This report focuses on kidney organoid studies, advancements and limitations, and future directions for improvements towards transplantation.
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Affiliation(s)
- Titilola D. Kalejaiye
- grid.26009.3d0000 0004 1936 7961Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC USA
| | - Amanda D. Barreto
- grid.26009.3d0000 0004 1936 7961Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC USA
| | - Samira Musah
- grid.26009.3d0000 0004 1936 7961Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC USA ,grid.26009.3d0000 0004 1936 7961Department of Cell Biology, Duke University, Durham, NC USA ,Affiliate Faculty of the Developmental and Stem Cell Biology Program, Duke Regeneration Center, and Duke MEDx Initiative, Durham, NC USA
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Kagan M, Pleniceanu O, Vivante A. The genetic basis of congenital anomalies of the kidney and urinary tract. Pediatr Nephrol 2022; 37:2231-2243. [PMID: 35122119 DOI: 10.1007/s00467-021-05420-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
During the past decades, remarkable progress has been made in our understanding of the molecular basis of kidney diseases, as well as in the ability to pinpoint disease-causing genetic changes. Congenital anomalies of the kidney and urinary tract (CAKUT) are remarkably diverse, and may be either isolated to the kidney or involve other systems, and are notorious in their variable genotype-phenotype correlations. Genetic conditions underlying CAKUT are individually rare, but collectively contribute to disease etiology in ~ 16% of children with CAKUT. In this review, we will discuss basic concepts of kidney development and genetics, common causes of monogenic CAKUT, and the approach to diagnosing and managing a patient with suspected monogenic CAKUT. Altogether, the concepts presented herein represent an introduction to the emergence of nephrogenetics, a fast-growing multi-disciplinary field that is focused on deciphering the causes and manifestations of genetic kidney diseases as well as providing the framework for managing patients with genetic forms of CAKUT.
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Affiliation(s)
- Maayan Kagan
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Pleniceanu
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Asaf Vivante
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Talpiot Medical Leadership Program, Tel HaShomer, Ramat Gan, Israel.
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Hiratsuka K, Miyoshi T, Kroll KT, Gupta NR, Valerius MT, Ferrante T, Yamashita M, Lewis JA, Morizane R. Organoid-on-a-chip model of human ARPKD reveals mechanosensing pathomechanisms for drug discovery. SCIENCE ADVANCES 2022; 8:eabq0866. [PMID: 36129975 PMCID: PMC9491724 DOI: 10.1126/sciadv.abq0866] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/03/2022] [Indexed: 05/23/2023]
Abstract
Organoids serve as a novel tool for disease modeling in three-dimensional multicellular contexts. Static organoids, however, lack the requisite biophysical microenvironment such as fluid flow, limiting their ability to faithfully recapitulate disease pathology. Here, we unite organoids with organ-on-a-chip technology to unravel disease pathology and develop therapies for autosomal recessive polycystic kidney disease. PKHD1-mutant organoids-on-a-chip are subjected to flow that induces clinically relevant phenotypes of distal nephron dilatation. Transcriptomics discover 229 signal pathways that are not identified by static models. Mechanosensing molecules, RAC1 and FOS, are identified as potential therapeutic targets and validated by patient kidney samples. On the basis of this insight, we tested two U.S. Food and Drug Administration-approved and one investigational new drugs that target RAC1 and FOS in our organoid-on-a-chip model, which suppressed cyst formation. Our observations highlight the vast potential of organoid-on-a-chip models to elucidate complex disease mechanisms for therapeutic testing and discovery.
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Affiliation(s)
- Ken Hiratsuka
- Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Tomoya Miyoshi
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Katharina T. Kroll
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Navin R. Gupta
- Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
| | - M. Todd Valerius
- Harvard Medical School, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
| | - Thomas Ferrante
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Michifumi Yamashita
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jennifer A. Lewis
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
| | - Ryuji Morizane
- Nephrology Division, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- John A. Paulson School of Engineering and Applied Sciences and Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Division of Renal Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute (HSCI), Cambridge, MA, USA
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Gao L, Jin N, Ye Z, Ma T, Huang Y, Li H, Du J, Li Z. A possible connection between reactive oxygen species and the unfolded protein response in lens development: From insight to foresight. Front Cell Dev Biol 2022; 10:820949. [PMID: 36211466 PMCID: PMC9535091 DOI: 10.3389/fcell.2022.820949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 08/31/2022] [Indexed: 11/28/2022] Open
Abstract
The lens is a relatively special and simple organ. It has become an ideal model to study the common developmental characteristics among different organic systems. Lens development is a complex process influenced by numerous factors, including signals from the intracellular and extracellular environment. Reactive oxygen species (ROS) are a group of highly reactive and oxygen-containing molecules that can cause endoplasmic reticulum stress in lens cells. As an adaptive response to ER stress, lens cells initiate the unfolded protein response (UPR) to maintain normal protein synthesis by selectively increasing/decreasing protein synthesis and increasing the degradation of misfolded proteins. Generally, the UPR signaling pathways have been well characterized in the context of many pathological conditions. However, recent studies have also confirmed that all three UPR signaling pathways participate in a variety of developmental processes, including those of the lens. In this review, we first briefly summarize the three stages of lens development and present the basic profiles of ROS and the UPR. We then discuss the interconnections between lens development and these two mechanisms. Additionally, the potential adoption of human pluripotent stem-cell-based lentoids in lens development research is proposed to provide a novel perspective on future developmental studies.
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Affiliation(s)
- Lixiong Gao
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Ni Jin
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
- Department of Endocrinology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, The Chinese PLA General Hospital, Beijing, China
| | - Zi Ye
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Tianju Ma
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yang Huang
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Hongyu Li
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jinlin Du
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhaohui Li
- Senior Department of Ophthalmology, The Third Medical Center of Chinese PLA General Hospital, Beijing, China
- *Correspondence: Zhaohui Li,
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Živná M, Kidd KO, Barešová V, Hůlková H, Kmoch S, Bleyer AJ. Autosomal dominant tubulointerstitial kidney disease: A review. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:309-324. [PMID: 36250282 PMCID: PMC9619361 DOI: 10.1002/ajmg.c.32008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 09/29/2022] [Indexed: 01/11/2023]
Abstract
The clinical characteristics of autosomal dominant tubulointerstitial kidney disease (ADTKD) include bland urinary sediment, slowly progressive chronic kidney disease (CKD) with many patients reaching end stage renal disease (ESRD) between age 20 and 70 years, and autosomal dominant inheritance. Due to advances in genetic diagnosis, ADTKD is becoming increasingly recognized as a cause of CKD. Pathogenic variants in UMOD, MUC1, and REN are the most common causes of ADTKD. ADTKD-UMOD is also associated with hyperuricemia and gout. ADTKD-REN often presents in childhood with mild hypotension, CKD, hyperkalemia, acidosis, and anemia. ADTKD-MUC1 patients present only with CKD. This review describes the pathophysiology, genetics, clinical manifestation, and diagnosis for ADTKD, with an emphasis on genetic testing and genetic counseling suggestions for patients.
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Affiliation(s)
- Martina Živná
- Research Unit of Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Kendrah O. Kidd
- Research Unit of Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles UniversityPragueCzech Republic,Wake Forest University School of MedicineSection on NephrologyWinston‐SalemNorth CarolinaUSA
| | - Veronika Barešová
- Research Unit of Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Helena Hůlková
- Research Unit of Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles UniversityPragueCzech Republic
| | - Stanislav Kmoch
- Research Unit of Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles UniversityPragueCzech Republic,Wake Forest University School of MedicineSection on NephrologyWinston‐SalemNorth CarolinaUSA
| | - Anthony J. Bleyer
- Research Unit of Rare Diseases, Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles UniversityPragueCzech Republic,Wake Forest University School of MedicineSection on NephrologyWinston‐SalemNorth CarolinaUSA
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50
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Olinger E, Schaeffer C, Kidd K, Elhassan EAE, Cheng Y, Dufour I, Schiano G, Mabillard H, Pasqualetto E, Hofmann P, Fuster DG, Kistler AD, Wilson IJ, Kmoch S, Raymond L, Robert T, Eckardt KU, Bleyer AJ, Köttgen A, Conlon PJ, Wiesener M, Sayer JA, Rampoldi L, Devuyst O. An intermediate-effect size variant in UMOD confers risk for chronic kidney disease. Proc Natl Acad Sci U S A 2022; 119:e2114734119. [PMID: 35947615 PMCID: PMC9388113 DOI: 10.1073/pnas.2114734119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 05/04/2022] [Indexed: 12/12/2022] Open
Abstract
The kidney-specific gene UMOD encodes for uromodulin, the most abundant protein excreted in normal urine. Rare large-effect variants in UMOD cause autosomal dominant tubulointerstitial kidney disease (ADTKD), while common low-impact variants strongly associate with kidney function and the risk of chronic kidney disease (CKD) in the general population. It is unknown whether intermediate-effect variants in UMOD contribute to CKD. Here, candidate intermediate-effect UMOD variants were identified using large-population and ADTKD cohorts. Biological and phenotypical effects were investigated using cell models, in silico simulations, patient samples, and international databases and biobanks. Eight UMOD missense variants reported in ADTKD are present in the Genome Aggregation Database (gnomAD), with minor allele frequency (MAF) ranging from 10-5 to 10-3. Among them, the missense variant p.Thr62Pro is detected in ∼1/1,000 individuals of European ancestry, shows incomplete penetrance but a high genetic load in familial clusters of CKD, and is associated with kidney failure in the 100,000 Genomes Project (odds ratio [OR] = 3.99 [1.84 to 8.98]) and the UK Biobank (OR = 4.12 [1.32 to 12.85). Compared with canonical ADTKD mutations, the p.Thr62Pro carriers displayed reduced disease severity, with slower progression of CKD and an intermediate reduction of urinary uromodulin levels, in line with an intermediate trafficking defect in vitro and modest induction of endoplasmic reticulum (ER) stress. Identification of an intermediate-effect UMOD variant completes the spectrum of UMOD-associated kidney diseases and provides insights into the mechanisms of ADTKD and the genetic architecture of CKD.
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Affiliation(s)
- Eric Olinger
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Céline Schaeffer
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, 20132 Italy
| | - Kendrah Kidd
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Elhussein A. E. Elhassan
- Division of Nephrology, Beaumont General Hospital, 1297 Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, 1297 Dublin, Ireland
| | - Yurong Cheng
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, D-79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, D-79106 Freiburg, Germany
| | - Inès Dufour
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
- Division of Nephrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Guglielmo Schiano
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Holly Mabillard
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals National Health Service Trust, Newcastle upon Tyne NE7 7DN, United Kingdom
| | - Elena Pasqualetto
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, 20132 Italy
| | - Patrick Hofmann
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
| | - Daniel G. Fuster
- Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Andreas D. Kistler
- Department of Medicine, Cantonal Hospital Frauenfeld, 8501 Frauenfeld, Switzerland
| | - Ian J. Wilson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
| | - Stanislav Kmoch
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Laure Raymond
- Genetics Department, Laboratoire Eurofins Biomnis, Lyon, 69007 France
| | - Thomas Robert
- Centre de Néphrologie et Transplantation Rénale, Centre Hospitalier Universitaire (CHU) la Conception, Assistance Publique - Hôpitaux de Marseille (AP-HM), Marseille, 13005 France
- Marseille Medical Genetics, Bioinformatics & Genetics, Unité Mixte de Recherche (UMR)_S910, Aix-Marseille Université, Marseille, 13005 France
| | | | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Anthony J. Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, 128 08 Prague, Czech Republic
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, D-79106 Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, D-79106 Freiburg, Germany
| | - Peter J. Conlon
- Division of Nephrology, Beaumont General Hospital, 1297 Dublin, Ireland
- Department of Medicine, Royal College of Surgeons in Ireland, 1297 Dublin, Ireland
| | - Michael Wiesener
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - John A. Sayer
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE1 3BZ, United Kingdom
- Renal Services, Newcastle Upon Tyne Hospitals National Health Service Trust, Newcastle upon Tyne NE7 7DN, United Kingdom
- National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle upon Tyne NE4 5PL, United Kingdom
| | - Luca Rampoldi
- Molecular Genetics of Renal Disorders, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Milan, 20132 Italy
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, CH-8057 Zurich, Switzerland
- Division of Nephrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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