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Wang L, Wang J, Zhang Y, Zhang H. Current perspectives and trends of the research on hypertensive nephropathy: a bibliometric analysis from 2000 to 2023. Ren Fail 2024; 46:2310122. [PMID: 38345042 PMCID: PMC10863539 DOI: 10.1080/0886022x.2024.2310122] [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: 10/31/2023] [Accepted: 01/21/2024] [Indexed: 02/15/2024] Open
Abstract
Hypertensive nephropathy continues to be a major cause of end-stage renal disease and poses a significant global health burden. Despite the staggering development of research in hypertensive nephropathy, scientists and clinicians can only seek out useful information through articles and reviews, it remains a hurdle for them to quickly track the trend in this field. This study uses the bibliometric method to identify the evolutionary development and recent hotspots of hypertensive nephropathy. The Web of Science Core Collection database was used to extract publications on hypertensive nephropathy from January 2000 to November 2023. CiteSpace was used to capture the patterns and trends from multi-perspectives, including countries/regions, institutions, keywords, and references. In total, 557 publications on hypertensive nephropathy were eligible for inclusion. China (n = 208, 37.34%) was the most influential contributor among all the countries. Veterans Health Administration (n = 19, 3.41%) was found to be the most productive institution. Keyword bursting till now are renal fibrosis, outcomes, and mechanisms which are predicted to be the potential frontiers and hotspots in the future. The top seven references were listed, and their burst strength was shown. A comprehensive overview of the current status and research frontiers of hypertensive nephropathy has been provided through the bibliometric perspective. Recent advancements and challenges in hypertensive nephropathy have been discussed. These findings can offer informative instructions for researchers and scholars.
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Affiliation(s)
- Lan Wang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
- Institute of Nephrology, Peking University, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
| | - Jingyu Wang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
- Institute of Nephrology, Peking University, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
| | - Yuemiao Zhang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
- Institute of Nephrology, Peking University, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
| | - Hong Zhang
- Renal Division, Department of Medicine, Peking University First Hospital, Beijing, China
- Institute of Nephrology, Peking University, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
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2
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Gumber RI, Doshi MD. Is It Time To Drop the Use of Race From Kidney Donor Risk Index Calculator? Transplantation 2024; 108:1643-1646. [PMID: 38548698 PMCID: PMC11265987 DOI: 10.1097/tp.0000000000004998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Affiliation(s)
| | - Mona D Doshi
- Department of Medicine, University of Michigan, Ann Arbor, MI
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3
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Locke JE. Donation-Attributable Risk-A Call to Action. JAMA Surg 2024:2821592. [PMID: 39046768 DOI: 10.1001/jamasurg.2024.2417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Affiliation(s)
- Jayme E Locke
- University of Alabama at Birmingham Heersink School of Medicine, Birmingham
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4
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Tsokos GC. The immunology of systemic lupus erythematosus. Nat Immunol 2024:10.1038/s41590-024-01898-7. [PMID: 39009839 DOI: 10.1038/s41590-024-01898-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/17/2024] [Indexed: 07/17/2024]
Abstract
Understanding the pathogenesis and clinical manifestations of systemic lupus erythematosus (SLE) has been a great challenge. Reductionist approaches to understand the nature of the disease have identified many pathogenetic contributors that parallel clinical heterogeneity. This Review outlines the immunological control of SLE and looks to experimental tools and approaches that are improving our understanding of the complex contribution of interacting genetics, environment, sex and immunoregulatory factors and their interface with processes inherent to tissue parenchymal cells. Efforts to advance precision medicine in the care of patients with SLE along with treatment strategies to correct the immune system hold hope and are also examined.
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Affiliation(s)
- George C Tsokos
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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5
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Rodríguez RD, Alarcón-Riquelme ME. Exploring the contribution of genetics on the clinical manifestations of systemic lupus erythematosus. Best Pract Res Clin Rheumatol 2024:101971. [PMID: 39013664 DOI: 10.1016/j.berh.2024.101971] [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: 06/06/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/18/2024]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by diverse clinical manifestations affecting multiple organs and systems. The understanding of genetic factors underlying the various manifestations of SLE has evolved considerably in recent years. This review provides an overview of the genetic implications in some of the most prevalent manifestations of SLE, including renal involvement, neuropsychiatric, cutaneous, constitutional, musculoskeletal, and cardiovascular manifestations. We discuss the current state of knowledge regarding the genetic basis of these manifestations, highlighting key genetic variants and pathways implicated in their pathogenesis. Additionally, we explore the clinical implications of genetic findings, including their potential role in risk stratification, prognosis, and personalized treatment approaches for patients with SLE. Through a comprehensive examination of the genetic landscape of SLE manifestations, this review aims to provide insights into the underlying mechanisms driving disease heterogeneity and inform future research directions in this field.
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Affiliation(s)
- Ruth D Rodríguez
- Center for Genomics and Oncological Research (GENyO). Pfizer/ University of Granada/ Andalusian Government, Spain
| | - Marta E Alarcón-Riquelme
- Center for Genomics and Oncological Research (GENyO). Pfizer/ University of Granada/ Andalusian Government, Spain; Institute for Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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6
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Pelchen-Matthews A, Mocroft A, Ryom L, Ross MJ, Sharma S, Coca S, Achhra A, Cornell E, Tracy R, Phillips A, Alonso MM, Toulomi G, Agan BK, Medland N, Wyatt CM. Long-term impact of immediate versus deferred antiretroviral therapy on kidney health in people with HIV. Kidney Int 2024; 106:136-144. [PMID: 38697479 PMCID: PMC11193627 DOI: 10.1016/j.kint.2024.04.010] [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: 01/05/2024] [Revised: 03/20/2024] [Accepted: 04/01/2024] [Indexed: 05/05/2024]
Abstract
People with human immunodeficiency virus (HIV) are at risk for chronic kidney disease (CKD) due to HIV and antiretroviral therapy (ART) nephrotoxicity. Immediate ART initiation reduces mortality and is now the standard of care, but the long-term impact of prolonged ART exposure on CKD is unknown. To evaluate this, the Strategic Timing of Antiretroviral Treatment (START) trial randomized 4,684 ART-naïve adults with CD4 cell count under 500 cells/mm3 to immediate versus deferred ART. We previously reported a small but statistically significantly greater decline in estimated glomerular filtration rate (eGFR) over a median of 2.1 years in participants randomized to deferred versus immediate ART. Here, we compare the incidence of CKD events and changes in eGFR and urine albumin/creatinine ratio (UACR) in participants randomized to immediate versus deferred ART during extended follow-up. Over a median of 9.3 years, eight participants experienced kidney failure or kidney-related death, three in the immediate and five in the deferred ART arms, respectively. Over a median of five years of more comprehensive follow-up, the annual rate of eGFR decline was 1.19 mL/min/1.73m2/year, with no significant difference between treatment arms (difference deferred - immediate arm 0.055; 95% confidence interval -0.106, 0.217 mL/min/1.73m2). Results were similar in models adjusted for baseline covariates associated with CKD, including UACR and APOL1 genotype. Similarly, there was no significant difference between treatment arms in incidence of confirmed UACR 30 mg/g or more (odds ratio 1.13; 95% confidence interval 0.85, 1.51). Thus, our findings provide the most definitive evidence to date in support of the long-term safety of early ART with respect to kidney health.
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Affiliation(s)
- Annegret Pelchen-Matthews
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London, London, UK
| | - Amanda Mocroft
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London, London, UK; CHIP, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lene Ryom
- CHIP, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Infectious Diseases 144, Hvidovre University Hospital, Copenhagen, Denmark
| | - Michael J Ross
- Department of Medicine, Division of Nephrology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Shweta Sharma
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Steven Coca
- Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Amit Achhra
- Department of Medicine, Division of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Russell Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont, Burlington, Vermont, USA
| | - Andrew Phillips
- Centre for Clinical Research, Epidemiology, Modelling and Evaluation (CREME), Institute for Global Health, University College London, London, UK
| | - Marta Montero Alonso
- Infectious Diseases Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Giota Toulomi
- Department of Hygiene, Epidemiology & Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Brian K Agan
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA; The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicholas Medland
- Kirby Institute, University of New South Wales, Sydney, Australia
| | - Christina M Wyatt
- Department of Medicine, Division of Nephrology, Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina, USA.
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7
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Tabachnikov O, Skorecki K, Kruzel-Davila E. APOL1 nephropathy - a population genetics success story. Curr Opin Nephrol Hypertens 2024; 33:447-455. [PMID: 38415700 PMCID: PMC11139250 DOI: 10.1097/mnh.0000000000000977] [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] [Indexed: 02/29/2024]
Abstract
PURPOSE OF REVIEW More than a decade ago, apolipoprotein L1 ( APOL1 ) risk alleles designated G1 and G2, were discovered to be causally associated with markedly increased risk for progressive kidney disease in individuals of recent African ancestry. Gratifying progress has been made during the intervening years, extending to the development and clinical testing of genomically precise small molecule therapy accompanied by emergence of RNA medicine platforms and clinical testing within just over a decade. RECENT FINDINGS Given the plethora of excellent prior review articles, we will focus on new findings regarding unresolved questions relating mechanism of cell injury with mode of inheritance, regulation and modulation of APOL1 activity, modifiers and triggers for APOL1 kidney risk penetrance, the pleiotropic spectrum of APOL1 related disease beyond the kidney - all within the context of relevance to therapeutic advances. SUMMARY Notwithstanding remaining controversies and uncertainties, promising genomically precise therapies targeted at APOL1 mRNA using antisense oligonucleotides (ASO), inhibitors of APOL1 expression, and small molecules that specifically bind and inhibit APOL1 cation flux are emerging, many already at the clinical trial stage. These therapies hold great promise for mitigating APOL1 kidney injury and possibly other systemic phenotypes as well. A challenge will be to develop guidelines for appropriate use in susceptible individuals who will derive the greatest benefit.
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Affiliation(s)
- Orly Tabachnikov
- Department of Nephrology, Rambam Healthcare Campus, Haifa, Israel
| | - Karl Skorecki
- Department of Nephrology, Rambam Healthcare Campus, Haifa, Israel
- Departments of Genetics and Developmental Biology and Rappaport Faculty of Medicine and Research Institute, Technion—Israel Institute of Technology, Haifa, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Etty Kruzel-Davila
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
- Department of Nephrology, Galilee Medical Center, Nahariya, Israel
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8
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Zoccali C, Mallamaci F, Lightstone L, Jha V, Pollock C, Tuttle K, Kotanko P, Wiecek A, Anders HJ, Remuzzi G, Kalantar-Zadeh K, Levin A, Vanholder R. A new era in the science and care of kidney diseases. Nat Rev Nephrol 2024; 20:460-472. [PMID: 38575770 DOI: 10.1038/s41581-024-00828-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
Notable progress in basic, translational and clinical nephrology research has been made over the past five decades. Nonetheless, many challenges remain, including obstacles to the early detection of kidney disease, disparities in access to care and variability in responses to existing and emerging therapies. Innovations in drug development, research technologies, tissue engineering and regenerative medicine have the potential to improve patient outcomes. Exciting prospects include the availability of new drugs to slow or halt the progression of chronic kidney disease, the development of bioartificial kidneys that mimic healthy kidney functions, and tissue engineering techniques that could enable transplantable kidneys to be created from the cells of the recipient, removing the risk of rejection. Cell and gene therapies have the potential to be applied for kidney tissue regeneration and repair. In addition, about 30% of kidney disease cases are monogenic and could potentially be treated using these genetic medicine approaches. Systemic diseases that involve the kidney, such as diabetes mellitus and hypertension, might also be amenable to these treatments. Continued investment, communication, collaboration and translation of innovations are crucial to realize their full potential. In addition, increasing sophistication in exploring large datasets, implementation science, and qualitative methodologies will improve the ability to deliver transformational kidney health strategies.
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Affiliation(s)
- Carmine Zoccali
- Kidney Research Institute, New York City, NY, USA.
- Institute of Molecular Biology and Genetics (Biogem), Ariano Irpino, Italy.
- Associazione Ipertensione Nefrologia Trapianto Kidney (IPNET), c/o Nefrologia, Grande Ospedale Metropolitano, Reggio Calabria, Italy.
| | - Francesca Mallamaci
- Nephrology, Dialysis and Transplantation Unit Azienda Ospedaliera "Bianchi-Melacrino-Morelli", Reggio Calabria, Italy
- CNR-IFC, Institute of Clinical Physiology, Research Unit of Clinical Epidemiology and Physiopathology of Kidney Diseases and Hypertension of Reggio Calabria, Reggio Calabria, Italy
| | - Liz Lightstone
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Vivek Jha
- George Institute for Global Health, UNSW, New Delhi, India
- School of Public Health, Imperial College, London, UK
- Prasanna School of Public Health, Manipal Academy of Medical Education, Manipal, India
| | - Carol Pollock
- Kolling Institute, Royal North Shore Hospital University of Sydney, Sydney, NSW, Australia
| | - Katherine Tuttle
- Providence Medical Research Center, Providence Inland Northwest, Spokane, Washington, USA
- Department of Medicine, University of Washington, Seattle, Spokane, Washington, USA
- Kidney Research Institute, Institute of Translational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Peter Kotanko
- Kidney Research Institute, New York, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrzej Wiecek
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, 40-027, Katowice, Poland
| | - Hans Joachim Anders
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig Maximilians University Munich, Munich, Germany
| | - Giuseppe Remuzzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCSS, Bergamo, Italy
| | - Kamyar Kalantar-Zadeh
- Harold Simmons Center for Kidney Disease Research and Epidemiology, California, USA
- Division of Nephrology and Hypertension, University of California Irvine, School of Medicine, Orange, Irvine, USA
- Veterans Affairs Healthcare System, Division of Nephrology, Long Beach, California, USA
| | - Adeera Levin
- University of British Columbia, Vancouver General Hospital, Division of Nephrology, Vancouver, British Columbia, Canada
- British Columbia, Provincial Kidney Agency, Vancouver, British Columbia, Canada
| | - Raymond Vanholder
- European Kidney Health Alliance, Brussels, Belgium
- Nephrology Section, Department of Internal Medicine and Paediatrics, University Hospital Ghent, Ghent, Belgium
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9
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Itoku A, Isaac J, Wilson S, Reidy K, Kaskel F. APOL1 Nephropathy Risk Variants Through the Life Course: A Review. Am J Kidney Dis 2024; 84:102-110. [PMID: 38341125 DOI: 10.1053/j.ajkd.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 02/12/2024]
Abstract
Two variant alleles of the gene apolipoprotein L1 (APOL1), known as risk variants (RVs), are a major contributor to kidney disease burden in those of African descent. The APOL1 protein contributes to innate immunity and may protect against Trypanosoma, HIV, Salmonella, and leishmaniasis. However, the effects of carrying 1 or more RVs contribute to a variety of disease processes starting as early as in utero and can be exacerbated by other factors (or "second hits"). Indeed, these genetic variations interact with environmental exposures, infections, and systemic disease to modify health outcomes across the life span. This review focuses on APOL1-associated diseases through the life-course perspective and discusses how early exposure to second hits can impact long-term outcomes. APOL1-related kidney disease typically presents in adolescents to young adults, and individuals harboring RVs are more likely to progress to kidney failure than are those with kidney disease who lack APOL-1 RVs. Ongoing research is aimed at elucidating the association of APOL1 RV effects with adverse donor and recipient kidney transplant outcomes. Unfortunately, there is currently no established treatment for APOL1-associated nephropathy. Long-term research is needed to evaluate the risk and protective factors associated with APOL1 RVs at different stages of life.
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Affiliation(s)
- Ai Itoku
- Division of Pediatric Nephrology, Children's Hospital at Montefiore, Bronx, New York
| | - Jaya Isaac
- Division of Pediatric Nephrology, Children's Hospital at Montefiore, Bronx, New York
| | - Scott Wilson
- Albert Einstein College of Medicine, Bronx, New York.
| | - Kimberly Reidy
- Division of Pediatric Nephrology, Children's Hospital at Montefiore, Bronx, New York
| | - Frederick Kaskel
- Division of Pediatric Nephrology, Children's Hospital at Montefiore, Bronx, New York
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10
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Olono A, Mitesser V, Happi A, Happi C. Building genomic capacity for precision health in Africa. Nat Med 2024; 30:1856-1864. [PMID: 38961224 DOI: 10.1038/s41591-024-03081-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/21/2024] [Indexed: 07/05/2024]
Abstract
The African continent is poised to have a pivotal role in the global population landscape, with the United Nations projecting a population of 2.5 billion (more than 25% of the global population) by 2050. Amid this demographic shift, Africa faces a unique healthcare challenge-navigating a complex landscape of infectious and non-communicable diseases. This necessitates a departure from the conventional 'one-size-fits-all' medical model toward precision approaches that are efficient and sustainable. Genomic capacity is a pillar of precision health; however, access to up-to-date genetic testing in African countries is limited, compounded by a startling lack of representation of data from populations of African descent in gene discovery studies. In this Review, we delve into the challenges impeding the development of genomic capacity in Africa, such as the lack of electronic clinical and epidemiological records, infrastructural challenges, high supply chain costs and the 'dependency trap' that jeopardizes long-term sustainability. We emphasize the need for strategies hinged on true partnerships, robust infrastructure, workforce development and well-crafted policies. Finally, we outline recent progress and existing initiatives that should be considered as role models for future capacity-building initiatives.
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Affiliation(s)
- Alhaji Olono
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria
| | - Vera Mitesser
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria
| | - Anise Happi
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria
| | - Christian Happi
- The African Centre of Excellence for Genomics and Infectious Diseases, ACEGID, Ede, Nigeria.
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11
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Tory K. The dominant findings of a recessive man: from Mendel's kid pea to kidney. Pediatr Nephrol 2024; 39:2049-2059. [PMID: 38051388 PMCID: PMC11147900 DOI: 10.1007/s00467-023-06238-9] [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: 08/21/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
The research of Mendel, born two centuries ago, still has many direct implications for our everyday clinical work. He introduced the terms "dominant" and "recessive" characters and determined their 3:1 ratio in the offspring of heterozygous "hybrid" plants. This distribution allowed calculation of the number of the phenotype-determining "elements," i.e., the alleles, and has been used ever since to prove the monogenic origin of a disorder. The Mendelian inheritance of monogenic kidney disorders is still of great help in distinguishing them from those with multifactorial origin in clinical practice. Inheritance of most monogenic kidney disorders fits to Mendel's observations: the equal contribution of the two parents and the complete penetrance or the direct correlation between the frequency of the recessive character and the degree of inbreeding. Nevertheless, beyond the truth of these basic concepts, several observations have expanded their genetic characteristics. The extreme genetic heterogeneity, the pleiotropy of the causal genes and the role of modifiers in ciliopathies, the digenic inheritance and parental imprinting in some tubulopathies, and the incomplete penetrance and eventual interallelic interactions in podocytopathies, reflect this expansion. For all these reasons, the transmission pattern in a natural setting may depend not only on the "character" but also on the causal gene and the variant. Mendel's passion for research combined with his modest personality and meticulous approach can still serve as an example in the work required to understand the non-Mendelian universe of genetics.
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Affiliation(s)
- Kálmán Tory
- MTA-SE Lendület Nephrogenetic Laboratory, Hungarian Academy of Sciences, Budapest, Hungary.
- Pediatric Center, MTA Center of Excellence, Semmelweis University, Budapest, Hungary.
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12
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Juliar BA, Stanaway IB, Sano F, Fu H, Smith KD, Akilesh S, Scales SJ, El Saghir J, Bhatraju PK, Liu E, Yang J, Lin J, Eddy S, Kretzler M, Zheng Y, Himmelfarb J, Harder JL, Freedman BS. Interferon-γ induces combined pyroptotic angiopathy and APOL1 expression in human kidney disease. Cell Rep 2024; 43:114310. [PMID: 38838223 PMCID: PMC11216883 DOI: 10.1016/j.celrep.2024.114310] [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: 09/27/2023] [Revised: 03/18/2024] [Accepted: 05/16/2024] [Indexed: 06/07/2024] Open
Abstract
Elevated interferon (IFN) signaling is associated with kidney diseases including COVID-19, HIV, and apolipoprotein-L1 (APOL1) nephropathy, but whether IFNs directly contribute to nephrotoxicity remains unclear. Using human kidney organoids, primary endothelial cells, and patient samples, we demonstrate that IFN-γ induces pyroptotic angiopathy in combination with APOL1 expression. Single-cell RNA sequencing, immunoblotting, and quantitative fluorescence-based assays reveal that IFN-γ-mediated expression of APOL1 is accompanied by pyroptotic endothelial network degradation in organoids. Pharmacological blockade of IFN-γ signaling inhibits APOL1 expression, prevents upregulation of pyroptosis-associated genes, and rescues vascular networks. Multiomic analyses in patients with COVID-19, proteinuric kidney disease, and collapsing glomerulopathy similarly demonstrate increased IFN signaling and pyroptosis-associated gene expression correlating with accelerated renal disease progression. Our results reveal that IFN-γ signaling simultaneously induces endothelial injury and primes renal cells for pyroptosis, suggesting a combinatorial mechanism for APOL1-mediated collapsing glomerulopathy, which can be targeted therapeutically.
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Affiliation(s)
- Benjamin A Juliar
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Ian B Stanaway
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Fumika Sano
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Hongxia Fu
- Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Division of Hematology, Department of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington School of Medicine, Seattle, WA 98109, USA; Bloodworks Northwest Research Institute, Seattle, WA 98102, USA; Plurexa, Seattle, WA 98109, USA
| | - Kelly D Smith
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Shreeram Akilesh
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Suzie J Scales
- Department of Immunology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jamal El Saghir
- Division of Nephrology, Department of Internal Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pavan K Bhatraju
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Esther Liu
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Johnson Yang
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jennie Lin
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sean Eddy
- Division of Nephrology, Department of Internal Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Matthias Kretzler
- Division of Nephrology, Department of Internal Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ying Zheng
- Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Jennifer L Harder
- Division of Nephrology, Department of Internal Medicine, and Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Benjamin S Freedman
- Division of Nephrology, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Kidney Research Institute, University of Washington School of Medicine, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington School of Medicine, Seattle, WA 98109, USA; Plurexa, Seattle, WA 98109, USA.
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13
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Breeyear JH, Hellwege JN, Schroeder PH, House JS, Poisner HM, Mitchell SL, Charest B, Khakharia A, Basnet TB, Halladay CW, Reaven PD, Meigs JB, Rhee MK, Sun Y, Lynch MG, Bick AG, Wilson OD, Hung AM, Nealon CL, Iyengar SK, Rotroff DM, Buse JB, Leong A, Mercader JM, Sobrin L, Brantley MA, Peachey NS, Motsinger-Reif AA, Wilson PW, Sun YV, Giri A, Phillips LS, Edwards TL. Adaptive selection at G6PD and disparities in diabetes complications. Nat Med 2024:10.1038/s41591-024-03089-1. [PMID: 38918629 DOI: 10.1038/s41591-024-03089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Diabetes complications occur at higher rates in individuals of African ancestry. Glucose-6-phosphate dehydrogenase deficiency (G6PDdef), common in some African populations, confers malaria resistance, and reduces hemoglobin A1c (HbA1c) levels by shortening erythrocyte lifespan. In a combined-ancestry genome-wide association study of diabetic retinopathy, we identified nine loci including a G6PDdef causal variant, rs1050828 -T (Val98Met), which was also associated with increased risk of other diabetes complications. The effect of rs1050828 -T on retinopathy was fully mediated by glucose levels. In the years preceding diabetes diagnosis and insulin prescription, glucose levels were significantly higher and HbA1c significantly lower in those with versus without G6PDdef. In the Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial, participants with G6PDdef had significantly higher hazards of incident retinopathy and neuropathy. At the same HbA1c levels, G6PDdef participants in both ACCORD and the Million Veteran Program had significantly increased risk of retinopathy. We estimate that 12% and 9% of diabetic retinopathy and neuropathy cases, respectively, in participants of African ancestry are due to this exposure. Across continentally defined ancestral populations, the differences in frequency of rs1050828 -T and other G6PDdef alleles contribute to disparities in diabetes complications. Diabetes management guided by glucose or potentially genotype-adjusted HbA1c levels could lead to more timely diagnoses and appropriate intensification of therapy, decreasing the risk of diabetes complications in patients with G6PDdef alleles.
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Affiliation(s)
- Joseph H Breeyear
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA
| | - Jacklyn N Hellwege
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Philip H Schroeder
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - John S House
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Hannah M Poisner
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Sabrina L Mitchell
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian Charest
- Massachusetts Veterans Epidemiology Research and Information Center, Boston, MA, USA
| | - Anjali Khakharia
- Atlanta VA Medical Center, Decatur, GA, USA
- Department of Medicine and Geriatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Til B Basnet
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, USA
- College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mary K Rhee
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Yang Sun
- Department of Ophthalmology, Stanford University School of Medicine, Palo Alto, CA, USA
- Veterans Administration Palo Alto Health Care System, Palo Alto, California, USA
| | | | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Otis D Wilson
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA
| | - Adriana M Hung
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA
| | - Cari L Nealon
- Eye Clinic, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Department of Ophthalmology & Visual Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Sudha K Iyengar
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Department of Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Daniel M Rotroff
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Endocrinology and Metabolism Institute, Cleveland Clinic, Cleveland, OH, USA
- Center for Quantitative Metabolic Research, Cleveland Clinic, Cleveland, OH, USA
| | - John B Buse
- Division of Endocrinology & Metabolism, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Aaron Leong
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M Mercader
- Program in Metabolism, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Endocrine Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lucia Sobrin
- Department of Ophthalmology, Mass Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Milam A Brantley
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA
- Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Neal S Peachey
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, USA
- Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Alison A Motsinger-Reif
- Biostatistics and Computational Biology Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Peter W Wilson
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Cardiology, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Yan V Sun
- Atlanta VA Medical Center, Decatur, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ayush Giri
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA.
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA.
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Lawrence S Phillips
- Atlanta VA Medical Center, Decatur, GA, USA
- Division of Endocrinology, Metabolism, and Lipids, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- VA Tennessee Valley Healthcare System (626), Nashville, TN, USA.
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Abdulhamid A, Shepherd BE, Wudil UJ, Van Wyk C, Dankishiya FS, Hussaini N, Wester CW, Aliyu MH. Sickle cell trait, APOL1 risk allele status and chronic kidney disease among ART-experienced adults living with HIV in northern Nigeria. Int J STD AIDS 2024:9564624241262397. [PMID: 38915133 DOI: 10.1177/09564624241262397] [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: 06/26/2024]
Abstract
BACKGROUND We sought to determine the prevalence of sickle cell trait (SCT) and apolipoprotein-1 (APOL1) risk variants in people living with HIV (PLWH) in Nigeria, and to establish if SCT and APOL1 high-risk status correlate with estimated glomerular filtration rate (eGFR) and/or prevalent chronic kidney disease (CKD). METHODS Baseline demographic and clinical data were obtained during three cross-sectional visits. CKD was defined as having an eGFR<60 mL/min/1.73 m2. We collected urine specimens to determine urine albumin-creatine ratio and blood samples for sickle cell genotyping, APOL1 testing, and for creatinine/cystatin C assessment. The associations between SCT, APOL1 genotype, and eGFR/CKD stages/CKD were investigated using linear/ordinal logistic/logistic regression models, respectively. RESULTS Of 2443 participants, 599 (24.5%) had SCT, and 2291 (93.8%) had a low-risk APOL1 genotype (0 or 1 risk variant), while 152 (6.2%) had high-risk genotype (2 allele copies). In total, 108 participants (4.4%) were diagnosed with CKD. In adjusted analyses, SCT was associated with lower eGFR (adjusted mean difference [aMD]= -2.33, 95% CI -4.25, -0.42), but not with worse CKD stages, or increased odds of developing CKD. Participants with the APOL1 high risk genotype were more likely to have lower eGFR (aMD= -5.45, 95% CI -8.87, -2.03), to develop CKD (adjusted odds ratio [aOR] = 1.97, 95% CI: 1.03, 3.75), and to be in worse CKD stages (aOR = 1.60, 95% CI: 1.12, 2.29) than those with the low-risk genotype. There was no evidence of interaction between SCT and APOL1 genotype on eGFR or risk of CKD. CONCLUSION Our findings highlight the multifaceted interplay of genetic factors in the pathogenesis of CKD in PLWH.
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Affiliation(s)
- Abdurrahman Abdulhamid
- Department of Statistics, School of Technology, Kano State Polytechnic, Kano, Nigeria
- Department of Mathematical Sciences, Bayero University, Kano, Nigeria
| | - Bryan E Shepherd
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Usman J Wudil
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Chelsea Van Wyk
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Nafiu Hussaini
- Department of Mathematical Sciences, Bayero University, Kano, Nigeria
| | - C William Wester
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Muktar H Aliyu
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
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15
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Mitrotti A, Giliberti M, Di Leo V, di Bari I, Pontrelli P, Gesualdo L. Hidden genetics behind glomerular scars: an opportunity to understand the heterogeneity of focal segmental glomerulosclerosis? Pediatr Nephrol 2024; 39:1685-1707. [PMID: 37728640 PMCID: PMC11026212 DOI: 10.1007/s00467-023-06046-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/02/2023] [Accepted: 05/30/2023] [Indexed: 09/21/2023]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a complex disease which describes different kinds of kidney defects, not exclusively linked with podocyte defects. Since nephrin mutation was first described in association with early-onset nephrotic syndrome (NS), many advancements have been made in understanding genetic patterns associated with FSGS. New genetic causes of FSGS have been discovered, displaying unexpected genotypes, and recognizing possible site of damage. Many recent large-scale sequencing analyses on patients affected by idiopathic chronic kidney disease (CKD), kidney failure (KF) of unknown origin, or classified as FSGS, have revealed collagen alpha IV genes, as one of the most frequent sites of pathogenic mutations. Also, recent interest in complex and systemic lysosomal storage diseases, such as Fabry disease, has highlighted GLA mutations as possible causes of FSGS. Tubulointerstitial disease, recently classified by KDIGO based on genetic subtypes, when associated with UMOD variants, may phenotypically gain FSGS features, as well as ciliopathy genes or others, otherwise leading to completely different phenotypes, but found carrying pathogenic variants with associated FSGS phenotype. Thus, glomerulosclerosis may conceal different heterogeneous conditions. When a kidney biopsy is performed, the principal objective is to provide an accurate diagnosis. The broad spectrum of phenotypic expression and genetic complexity is demonstrating that a combined path of management needs to be applied. Genetic investigation should not be reserved only to selected cases, but rather part of medical management, integrating with clinical and renal pathology records. FSGS heterogeneity should be interpreted as an interesting opportunity to discover new pathways of CKD, requiring prompt genotype-phenotype correlation. In this review, we aim to highlight how FSGS represents a peculiar kidney condition, demanding multidisciplinary management, and in which genetic analysis may solve some otherwise unrevealed idiopathic cases. Unfortunately there is not a uniform correlation between specific mutations and FSGS morphological classes, as the same variants may be identified in familial cases or sporadic FSGS/NS or manifest a variable spectrum of the same disease. These non-specific features make diagnosis challenging. The complexity of FSGS genotypes requires new directions. Old morphological classification does not provide much information about the responsible cause of disease and misdiagnoses may expose patients to immunosuppressive therapy side effects, mistaken genetic counseling, and misguided kidney transplant programs.
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Affiliation(s)
- Adele Mitrotti
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy.
| | - Marica Giliberti
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Vincenzo Di Leo
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Ighli di Bari
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Paola Pontrelli
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
| | - Loreto Gesualdo
- Precision and Regenerative Medicine and Ionian Area, Nephrology, Dialysis and Transplantation Unit, Department of Emergency and Organ Transplantation, University of Bari Aldo Moro, Bari, Italy
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16
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Doshi MD, Li L, Naik AS, Thomas CP. APOL1 Kidney Risk Variants and Long-Term Kidney Function in Healthy Middle-Aged Black Individuals: The Atherosclerosis Risk in Communities (ARIC) Study. Kidney Med 2024; 6:100828. [PMID: 38799783 PMCID: PMC11127222 DOI: 10.1016/j.xkme.2024.100828] [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] [Indexed: 05/29/2024] Open
Abstract
Rationale & Objective The effect of apolipoprotein L1(APOL1) genotype on future risk of kidney disease among middle-aged individuals with good kidney function is not well established. Study Design Longitudinal cohort study. Setting & Participants In total, 5,886 healthy individuals (45-64 years old) enrolled in the Atherosclerosis Risk in Communities study with creatinine-based estimated glomerular filtration rate ≥ 80 mL/min who would be suitable kidney donors. Exposures Race and APOL1 genotype. Outcomes Creatinine- and cystatin C-based estimated glomerular filtration rate (eGFRcr-cys) using the CKD-EPI (Chronic Kidney Disease Epidemiology Collaboration) 2021 equation, urinary albumin-creatinine ratio (UACR), proportion with chronic kidney disease (CKD) 3a or worse, end-stage kidney disease (ESKD), and death. Analytical Approach Participants grouped based on race and APOL1 genotype. Compared eGFRcr-cys and UACR across groups. Multinomial logistic regression models were used compare odds of CKD. Kaplan-Meier survival curves were created to compare rates of ESKD and death at last follow-up. Results There were 5,075 Whites (86%), 701 Blacks carrying the low-risk APOL1 genotype (12%), and 110 Blacks carrying the high-risk APOL1 genotype (2%). The mean age at baseline was 53 ± 6 years. At 10 years, White participants had lower eGFRcr-cys than low-risk and high-risk groups (89 ± 16 vs 91 ± 16 and 92 ± 15 mL/min/1.73 m2, respectively; P < 0.001). At 25 years, White participants continued to have lower eGFRcr-cys than the low-risk group (70 ± 18 vs 72 ± 19 mL/min/1.73 m2; P < 0.001) but not compared with the high-risk APOL1 genotype (67±23 mL/min/1.73 m2). There was no difference in UACR among groups at 10 and 25 years (P = 0.87 and 0.91, respectively). The odds of developing CKD stage 3a or worse were not different between low-risk and high-risk APOL1 group in both unadjusted and adjusted models (P = 0.26 and P = 0.39, respectively). At last follow-up, <5% developed ESKD, and 45% of individuals either died or reached ESKD with no difference in outcomes between the groups. Limitations Low ascertainment because of death and long follow-up. Conclusions Among middle-aged individuals, APOL1 genotype does not appear to be a major driver of future risk of kidney disease.
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Affiliation(s)
- Mona D. Doshi
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Lihua Li
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Abhijit S. Naik
- Division of Nephrology, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Christie P. Thomas
- Department of Medicine and the Iowa Institute of Human Genetics, University of Iowa, Iowa City, IA
- Division of Nephrology, Department of Medicine, Iowa City, IA
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17
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Bonilla M, Efe O, Selvaskandan H, Lerma EV, Wiegley N. A Review of Focal Segmental Glomerulosclerosis Classification With a Focus on Genetic Associations. Kidney Med 2024; 6:100826. [PMID: 38765809 PMCID: PMC11099322 DOI: 10.1016/j.xkme.2024.100826] [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] [Indexed: 05/22/2024] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) defines a distinct histologic pattern observed in kidney tissue that is linked to several distinct underlying causes, all converging on the common factor of podocyte injury. It presents a considerable challenge in terms of classification because of its varied underlying causes and the limited correlation between histopathology and clinical outcomes. Critically, precise nomenclature is key to describe and delineate the pathogenesis, subsequently guiding the selection of suitable and precision therapies. A proposed pathomechanism-based approach has been suggested for FSGS classification. This approach differentiates among primary, secondary, genetic, and undetermined causes, aiming to provide clarity. Genetic FSGS from monogenic mutations can emerge during childhood or adulthood, and it is advisable to conduct genetic testing in cases in which there is a family history of chronic kidney disease, nephrotic syndrome, or resistance to treatment. Genome-wide association studies have identified several genetic risk variants, such as those in apolipoprotein L1 (APOL1), that play a role in the development of FSGS. Currently, no specific treatments have been approved to treat genetic FSGS; however, interventions targeting underlying cofactor deficiencies have shown potential in some cases. Furthermore, encouraging results have emerged from a phase 2 trial investigating inaxaplin, a novel small molecule APOL1 channel inhibitor, in APOL1-associated FSGS.
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Affiliation(s)
- Marco Bonilla
- Section of Nephrology, Department of Medicine, University of Chicago, Chicago, IL
| | - Orhan Efe
- Division of Nephrology, Massachusetts General Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Haresh Selvaskandan
- IgA Mayer Nephropathy Laboratories, Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom
- John Walls Renal Unit, University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
| | - Edgar V. Lerma
- Section of Nephrology, University of Illinois at Chicago/Advocate Christ Medical Center, Oak Lawn, IL
| | - Nasim Wiegley
- University of California Davis School of Medicine, Division of Nephrology, Sacramento, CA
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18
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Zanoni F, Neugut YD, Obayemi JE, Liu L, Zhang JY, Ratner LE, Cohen DJ, Mohan S, Gharavi AG, Keating B, Kiryluk K. Genetic versus self-reported African ancestry of the recipient and neighborhood predictors of kidney transplantation outcomes in 2 multiethnic urban cohorts. Am J Transplant 2024; 24:1003-1015. [PMID: 38331047 PMCID: PMC11144562 DOI: 10.1016/j.ajt.2024.01.033] [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: 09/11/2023] [Revised: 01/25/2024] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
African American (AA) kidney recipients have a higher risk of allograft rejection and failure compared to non-AAs, but to what extent these outcomes are due to genetic versus environmental effects is currently unknown. Herein, we tested the effects of recipient self-reported race versus genetic proportion of African ancestry (pAFR), and neighborhood socioeconomic status (SES) on kidney allograft outcomes in multiethnic kidney transplant recipients from Columbia University (N = 1083) and the University of Pennsylvania (N = 738). All participants were genotyped with SNP arrays to estimate genetic admixture proportions. US census tract variables were used to analyze the effect of neighborhood factors. In both cohorts, self-reported recipient AA race and pAFR were individually associated with increased risk of rejection and failure after adjustment for known clinical risk factors and neighborhood SES factors. Joint analysis confirmed that self-reported recipient AA race and pAFR were both associated with a higher risk of allograft rejection (AA: HR 1.61 (1.31-1.96), P = 4.05E-06; pAFR: HR 1.90 (1.46-2.48), P = 2.40E-06) and allograft failure (AA: HR 1.52 (1.18-1.97), P = .001; pAFR: HR 1.70 (1.22-2.35), P = .002). Further research is needed to disentangle the role of genetics versus environmental, social, and structural factors contributing to poor transplantation outcomes in kidney recipients of African ancestry.
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Affiliation(s)
- Francesca Zanoni
- Department of Nephrology, Dialysis and Kidney Transplantation, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Y Dana Neugut
- Division of Pediatric Gastroenterology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Joy E Obayemi
- Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA
| | - Lili Liu
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Jun Y Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Lloyd E Ratner
- Department of Surgery, Columbia University, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - David J Cohen
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Sumit Mohan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Brendan Keating
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA.
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19
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Charnaya O, Van Arendonk K, Segev D. Strategies for choosing the best living donor: A review of the literature and a proposal of a decision-making paradigm. Pediatr Transplant 2024; 28:e14779. [PMID: 38766997 PMCID: PMC11107570 DOI: 10.1111/petr.14779] [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: 12/19/2023] [Revised: 03/31/2024] [Accepted: 04/24/2024] [Indexed: 05/22/2024]
Abstract
Transplantation remains the gold-standard treatment for pediatric end-stage kidney disease. While living donor transplant is the preferred option for most pediatric patients, it is not the right choice for all. For those who have the option to choose between deceased donor and living donor transplantation, or from among multiple potential living donors, the transplant clinician must weigh multiple dynamic factors to identify the most optimal donor. This review will cover the key considerations when choosing between potential living donors and will propose a decision-making algorithm.
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Affiliation(s)
- Olga Charnaya
- Department of Pediatrics, Johns Hopkins University School of Medicine
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20
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Savige J. Tips for Testing Adults With Suspected Genetic Kidney Disease. Am J Kidney Dis 2024; 83:816-824. [PMID: 38147894 DOI: 10.1053/j.ajkd.2023.10.011] [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: 04/10/2023] [Revised: 10/08/2023] [Accepted: 10/14/2023] [Indexed: 12/28/2023]
Abstract
Genetic kidney disease is common but often unrecognized. It accounts for most cystic kidney diseases and tubulopathies, many forms of congenital abnormalities of the kidney and urinary tract (CAKUT), and some glomerulopathies. Genetic kidney disease is typically suspected where the disease usually has a genetic basis or there is another affected family member, a young age at onset, or extrarenal involvement, but there are also many exceptions to these "rules". Genetic testing requires the patient's written informed consent. When a patient declines testing, another later conversation may be worthwhile. Genetic testing not only indicates the diagnosis but also the inheritance pattern, likely at-risk family members, disease in other organs, clinical course, and possibly effective treatments. Sometimes genetic testing does not identify a pathogenic variant even where other evidence is strong. A variant of uncertain significance (VUS) may be reported but should not be used for clinical decision making. It may be reclassified after more information becomes available without necessarily retesting the patient. Patients should be provided with a copy of their genetic test report, the results explained, and at-risk family members offered "cascade" testing. A referral to a clinical geneticist or genetic counselor helps identify affected family members and in providing advice to assist with reproductive decisions.
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Affiliation(s)
- Judy Savige
- University of Melbourne Department of Medicine (Melbourne Health and Northern health), Royal Melbourne Hospital, Parkville, Australia.
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21
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Hopper T, Olabisi OA. APOL1-Mediated Kidney Disease. JAMA 2024; 331:1668-1669. [PMID: 38662391 DOI: 10.1001/jama.2024.2667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
This JAMA Insights reviews the origin of APOL1 high-risk genetic variants, defines APOL1-mediated kidney disease, and discusses recommendations for screening and management.
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Affiliation(s)
- Timothy Hopper
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Opeyemi A Olabisi
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina
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22
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Labarque V, Okocha EC. Systematic Review of Genetic Modifiers Associated with the Development and/or Progression of Nephropathy in Patients with Sickle Cell Disease. Int J Mol Sci 2024; 25:5427. [PMID: 38791464 PMCID: PMC11121490 DOI: 10.3390/ijms25105427] [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: 04/07/2024] [Revised: 05/05/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Sickle cell nephropathy (SCN) is a common complication of sickle cell disease (SCD) that significantly contributes to morbidity and mortality. In addition to clinical and life-style factors, genetic variants influence this risk. We performed a systematic review, searching five databases. Studies evaluating the effect of genetic modifiers on SCN were eligible. Twenty-eight studies (fair-to-good quality) were included: one genome-wide association study, twenty-six case-control studies, and one article combining both approaches. APOL1 was significantly associated with albuminuria and hyperfiltration in children and with worse glomerular filtration in adults. On the other hand, alpha-thalassemia protected patients against albuminuria and hyperfiltration, while BCL11A variants were protective against albuminuria alone. The HMOX1 long GT-tandem repeat polymorphism led to a lower glomerular filtration rate. No modifiers for the risk of hyposthenuria were identified. A genome-wide association approach identified three new loci for proteinuria (CRYL1, VWF, and ADAMTS7) and nine loci were linked with eGFR (PKD1L2, TOR2A, CUBN, AGGF1, CYP4B1, CD163, LRP1B, linc02288, and FPGT-TNNI3K/TNNI3K). In conclusion, this systematic review supports the role of genetic modifiers in influencing the risk and progression of SCN. Incorporating and expanding this knowledge is crucial to improving the management and clinical outcomes of patients at risk.
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Affiliation(s)
- Veerle Labarque
- Department of Pediatric Hemato-Oncology, University Hospitals Leuven, 3000 Leuven, Belgium
- Center for Molecular and Vascular Biology, KU Leuven, 3000 Leuven, Belgium
| | - Emmanuel Chide Okocha
- Haematology Department, Faculty of Basic Clinical Sciences, College of Health Sciences, Nnamdi Azikiwe University, Nnewi PMB 5025, Anambra State, Nigeria
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23
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Madhavan SM, Schlöndorff JS. Variant upon variant: kidney-disease risk associated with APOL1 G2 genetic variants is abrogated by the APOL1 p.N264K variant. Kidney Int 2024:S0085-2538(24)00325-9. [PMID: 38750901 DOI: 10.1016/j.kint.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/12/2024] [Indexed: 05/25/2024]
Affiliation(s)
- Sethu M Madhavan
- Division of Nephrology, Department of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Johannes S Schlöndorff
- Division of Nephrology, Department of Medicine, The Ohio State University, Columbus, Ohio, USA.
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24
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Finn LS. Nephrotic Syndrome Throughout Childhood: Diagnosing Podocytopathies From the Womb to the Dorm. Pediatr Dev Pathol 2024:10935266241242669. [PMID: 38745407 DOI: 10.1177/10935266241242669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The etiologies of podocyte dysfunction that lead to pediatric nephrotic syndrome (NS) are vast and vary with age at presentation. The discovery of numerous novel genetic podocytopathies and the evolution of diagnostic technologies has transformed the investigation of steroid-resistant NS while simultaneously promoting the replacement of traditional morphology-based disease classifications with a mechanistic approach. Podocytopathies associated with primary and secondary steroid-resistant NS manifest as diffuse mesangial sclerosis, minimal change disease, focal segmental glomerulosclerosis, and collapsing glomerulopathy. Molecular testing, once an ancillary option, has become a vital component of the clinical investigation and when paired with kidney biopsy findings, provides data that can optimize treatment and prognosis. This review focuses on the causes including selected monogenic defects, clinical phenotypes, histopathologic findings, and age-appropriate differential diagnoses of nephrotic syndrome in the pediatric population with an emphasis on podocytopathies.
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Affiliation(s)
- Laura S Finn
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at The University of Pennsylvania, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
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25
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Breeze CE, Lin BM, Winkler CA, Franceschini N. African ancestry-derived APOL1 risk genotypes show proximal epigenetic associations. BMC Genomics 2024; 25:452. [PMID: 38714935 PMCID: PMC11077761 DOI: 10.1186/s12864-024-10226-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/14/2024] [Indexed: 05/12/2024] Open
Abstract
Apolipoprotein L1 (APOL1) coding variants, termed G1 and G2, are established genetic risk factors for a growing spectrum of diseases, including kidney disease, in individuals of African ancestry. Evidence suggests that the risk variants, which show a recessive mode of inheritance, lead to toxic gain-of-function changes of the APOL1 protein. Disease occurrence and presentation vary, likely due to modifiers or second hits. To understand the role of the epigenetic landscape in relation to APOL1 risk variants, we performed methylation quantitative trait locus (meQTL) analysis to identify differentially methylated CpGs influenced by APOL1 risk variants in 611 African American individuals. We identified five CpGs that were significantly associated with APOL1 risk alleles in discovery and replication studies, and one CpG-APOL1 association was independent of other genomic variants. Our study highlights proximal DNA methylation alterations that may help explain the variable disease risk and clinical manifestation of APOL1 variants.
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Affiliation(s)
- Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Cheryl A Winkler
- Cancer Innovation Laboratory, National Cancer Institute, National Institutes of Health, Basic Research Program, Frederick National Laboratory, Frederick, MD, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA.
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26
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Yoshida T, Latt KZ, Santo BA, Shrivastav S, Zhao Y, Fenaroli P, Chung JY, Hewitt SM, Tutino VM, Sarder P, Rosenberg AZ, Winkler CA, Kopp JB. Single-Cell Transcriptional Signatures of Glomerular Disease in Transgenic Mice with APOL1 Variants. J Am Soc Nephrol 2024:00001751-990000000-00309. [PMID: 38709562 DOI: 10.1681/asn.0000000000000370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/26/2024] [Indexed: 05/08/2024] Open
Abstract
Key Points
Apolipoprotein L1 (APOL1)-G1 induced kidney disease in the two APOL1 transgenic mouse models, HIV-associated nephropathy and IFN-γ administration.Glomerular single-nuclear RNA-sequencing identified genes differentially expressed among mice with APOL1-G1 and G0 variants at single-cell resolution.
Background
Apolipoprotein L1 (APOL1) high-risk variants contribute to kidney disease among individuals with African ancestry. We sought to describe cell-specific APOL1 variant–induced pathways using two mouse models.
Methods
We characterized bacterial artificial chromosome/APOL1 transgenic mice crossed with HIV-associated nephropathy (HIVAN) Tg26 mice and bacterial artificial chromosome/APOL1 transgenic mice given IFN-γ.
Results
Both mouse models showed more severe glomerular disease in APOL1-G1 compared with APOL1-G0 mice. Synergistic podocyte-damaging pathways activated by APOL1-G1 and by the HIV transgene were identified by glomerular bulk RNA sequencing (RNA-seq) of HIVAN model. Single-nuclear RNA-seq revealed podocyte-specific patterns of differentially expressed genes as a function of APOL1 alleles. Shared activated pathways, for example, mammalian target of rapamycin, and differentially expressed genes, for example, Ccn2, in podocytes in both models suggest novel markers of APOL1-associated kidney disease. HIVAN mouse-model podocyte single-nuclear RNA-seq data showed similarity to human focal segmental glomerulosclerosis glomerular RNA-seq data. Differential effects of the APOL1-G1 variant on the eukaryotic initiation factor 2 pathway highlighted differences between the two models.
Conclusions
These findings in two mouse models demonstrated both shared and distinct cell type–specific transcriptomic signatures induced by APOL1 variants. These findings suggest novel therapeutic opportunities for APOL1 glomerulopathies.
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Affiliation(s)
- Teruhiko Yoshida
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIH, Bethesda, Maryland
| | - Khun Zaw Latt
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIH, Bethesda, Maryland
| | - Briana A Santo
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Shashi Shrivastav
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIH, Bethesda, Maryland
| | - Yongmei Zhao
- Frederick National Laboratory for Cancer Research, NCI, NIH, Frederick, Maryland
| | - Paride Fenaroli
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- S.C. Nefrologia e Dialisi, AUSL-IRCCS, Reggio Emilia, Italy
| | | | | | - Vincent M Tutino
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Pinaki Sarder
- Department of Pathology and Anatomical Sciences, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, New York
- College of Medicine, University of Florida, Gainesville, Florida
| | - Avi Z Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Cheryl A Winkler
- Frederick National Laboratory for Cancer Research, NCI, NIH, Frederick, Maryland
| | - Jeffrey B Kopp
- Kidney Disease Section, Kidney Diseases Branch, NIDDK, NIH, Bethesda, Maryland
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27
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Shao F, Yao Y, Weng D, Wang R, Liu R, Zhang Y, Li E, Wang M, Tang Y, Ding Y, Xie Y. Causal association of plasma circulating metabolites with nephritis: a Mendelian randomization study. Front Nutr 2024; 11:1364841. [PMID: 38765814 PMCID: PMC11099270 DOI: 10.3389/fnut.2024.1364841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/16/2024] [Indexed: 05/22/2024] Open
Abstract
Background Nephritis is a pivotal catalyst in chronic kidney disease (CKD) progression. Although epidemiological studies have explored the impact of plasma circulating metabolites and drugs on nephritis, few have harnessed genetic methodologies to establish causal relationships. Methods Through Mendelian randomization (MR) in two substantial cohorts, spanning large sample sizes, we evaluated over 100 plasma circulating metabolites and 263 drugs to discern their causal effects on nephritis risk. The primary analytical tool was the inverse variance weighted (IVW) analysis. Our bioinformatic scrutiny of GSE115857 (IgA nephropathy, 86 samples) and GSE72326 (lupus nephritis, 238 samples) unveiled anomalies in lipid metabolism and immunological characteristics in nephritis. Thorough sensitivity analyses (MR-Egger, MR-PRESSO, leave-one-out analysis) were undertaken to verify the instrumental variables' (IVs) assumptions. Results Unique lipoprotein-related molecules established causal links with diverse nephritis subtypes. Notably, docosahexaenoic acid (DHA) emerged as a protective factor for acute tubulointerstitial nephritis (ATIN) (OR1 = 0.84, [95% CI 0.78-0.90], p1 = 0.013; OR2 = 0.89, [95% CI 0.82-0.97], p2 = 0.007). Conversely, multivitamin supplementation minus minerals notably increased the risk of ATIN (OR = 31.25, [95% CI 9.23-105.85], p = 0.004). Reduced α-linolenic acid (ALA) levels due to lipid-lowering drugs were linked to both ATIN (OR = 4.88, [95% CI 3.52-6.77], p < 0.001) and tubulointerstitial nephritis (TIN) (OR = 7.52, [95% CI 2.78-20.30], p = 0.042). While the non-renal drug indivina showed promise for TIN treatment, the use of digoxin, hydroxocobalamin, and liothyronine elevated the risk of chronic tubulointerstitial nephritis (CTIN). Transcriptome analysis affirmed that anomalous lipid metabolism and immune infiltration are characteristic of IgA nephropathy and lupus nephritis. The robustness of these causal links was reinforced by sensitivity analyses and leave-one-out tests, indicating no signs of pleiotropy. Conclusion Dyslipidemia significantly contributes to nephritis development. Strategies aimed at reducing plasma low-density lipoprotein levels or ALA supplementation may enhance the efficacy of existing lipid-lowering drug regimens for nephritis treatment. Renal functional status should also be judiciously considered with regard to the use of nonrenal medications.
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Affiliation(s)
- Fengling Shao
- The Ministry of Education, Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Yingling Yao
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha, China
| | - Dunchu Weng
- The Ministry of Education, Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Runzhi Wang
- The Ministry of Education, Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Ruiling Liu
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha, China
| | - Yongjia Zhang
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha, China
| | - Erhan Li
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha, China
| | - Mengdi Wang
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha, China
| | - Yuewu Tang
- Department of Nephrology, Chongqing Three Gorges Central Hospital, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Yubin Ding
- Department of Obstetrics and Gynecology, Women and Children’s Hospital of Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health, Chongqing Medical University, Chongqing, China
- Department of Pharmacology, Academician Workstation, Changsha Medical University, Changsha, China
| | - Yajun Xie
- The Ministry of Education, Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing, China
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28
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Diana NE, Naicker S. The changing landscape of HIV-associated kidney disease. Nat Rev Nephrol 2024; 20:330-346. [PMID: 38273026 DOI: 10.1038/s41581-023-00801-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2023] [Indexed: 01/27/2024]
Abstract
The HIV epidemic has devastated millions of people globally, with approximately 40 million deaths since its start. The availability of antiretroviral therapy (ART) has transformed the prognosis of millions of individuals infected with HIV such that a diagnosis of HIV infection no longer automatically confers death. However, morbidity and mortality remain substantial among people living with HIV. HIV can directly infect the kidney to cause HIV-associated nephropathy (HIVAN) - a disease characterized by podocyte and tubular damage and associated with an increased risk of kidney failure. The reports of HIVAN occurring primarily in those of African ancestry led to the discovery of its association with APOL1 risk alleles. The advent of ART has led to a substantial decrease in the prevalence of HIVAN; however, reports have emerged of an increase in the prevalence of other kidney pathology, such as focal segmental glomerulosclerosis and pathological conditions associated with co-morbidities of ageing, such as hypertension and diabetes mellitus. Early initiation of ART also results in a longer cumulative exposure to medications, increasing the likelihood of nephrotoxicity. A substantial body of literature supports the use of kidney transplantation in people living with HIV, demonstrating significant survival benefits compared with that of people undergoing chronic dialysis, and similar long-term allograft and patient survival compared with that of HIV-negative kidney transplant recipients.
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Affiliation(s)
- Nina E Diana
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Saraladevi Naicker
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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29
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Duret LC, Hamidouche T, Steers NJ, Pons C, Soubeiran N, Buret D, Gilson E, Gharavi AG, D'Agati VD, Shkreli M. Targeting WIP1 phosphatase promotes partial remission in experimental collapsing glomerulopathy. Kidney Int 2024; 105:980-996. [PMID: 38423182 DOI: 10.1016/j.kint.2024.02.009] [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: 09/08/2023] [Revised: 12/16/2023] [Accepted: 02/02/2024] [Indexed: 03/02/2024]
Abstract
Collapsing focal segmental glomerulosclerosis (FSGS), also known as collapsing glomerulopathy (CG), is the most aggressive variant of FSGS and is characterized by a rapid progression to kidney failure. Understanding CG pathogenesis represents a key step for the development of targeted therapies. Previous work implicated the telomerase protein component TERT in CG pathogenesis, as transgenic TERT expression in adult mice resulted in a CG resembling that seen in human primary CG and HIV-associated nephropathy (HIVAN). Here, we used the telomerase-induced mouse model of CG (i-TERTci mice) to identify mechanisms to inhibit CG pathogenesis. Inactivation of WIP1 phosphatase, a p53 target acting in a negative feedback loop, blocked disease initiation in i-TERTci mice. Repression of disease initiation upon WIP1 deficiency was associated with senescence enhancement and required transforming growth factor-β functions. The efficacy of a pharmacologic treatment to reduce disease severity in both i-TERTci mice and in a mouse model of HIVAN (Tg26 mice) was then assessed. Pharmacologic inhibition of WIP1 enzymatic activity in either the telomerase mice with CG or in the Tg26 mice promoted partial remission of proteinuria and ameliorated kidney histopathologic features. Histological as well as high-throughput sequencing methods further showed that selective inhibition of WIP1 does not promote kidney fibrosis or inflammation. Thus, our findings suggest that targeting WIP1 may be an effective therapeutic strategy for patients with CG.
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Affiliation(s)
- Lou C Duret
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France
| | - Tynhinane Hamidouche
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France
| | - Nicholas J Steers
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Catherine Pons
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France
| | - Nicolas Soubeiran
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France
| | - Delphine Buret
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France
| | - Eric Gilson
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France; International Laboratory in Hematology and Cancer, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/INSERM/Nice University, Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Shanghai Ruijin Hospital, Huangpu, Shanghai, PR China; Department of Genetics, CHU Nice, Nice, France
| | - Ali G Gharavi
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Marina Shkreli
- Université Côte d'Azur (UCA), Centre National de la Recherche Scientifique (CNRS) UMR7284, Institut National de la Santé et de la Recherche Médicale (Inserm) U1081, Institute for Research on Cancer and aging, Nice (IRCAN), Nice, France.
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30
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Lim E, Borden C, Mehta S, Roberts MB, Mazzola S, Zhao F, Wang X. Reclassification of Variants Following Renal Genetics Testing: Uncommon Yet Impactful for Diagnosis and Management. Kidney Int Rep 2024; 9:1441-1450. [PMID: 38707809 PMCID: PMC11068948 DOI: 10.1016/j.ekir.2024.01.055] [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: 11/03/2023] [Revised: 01/08/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Genetic testing is increasingly utilized in nephrology practice, but limited real-world data exist on variant reclassification following renal genetics testing. Methods A cohort of patients at the Cleveland Clinic Renal Genetics Clinic who underwent genetic testing through clinical laboratories was assessed with their clinical and laboratory data analyzed. Results Between January 2019 and June 2023, 425 new patients with variable kidney disorders from 413 pedigrees completed genetic testing through 10 clinical laboratories, including 255 (60%) females with median (25th, 75th percentiles) age of 36 (22-54) years. Multigene panel was the most frequently used modality followed by single-gene testing, exome sequencing (ES), chromosomal microarray (CMA), and genome sequencing (GS). At initial report, 52% of patients had ≥1 variants of uncertain significance (VUS) with or without concurrent pathogenic variant(s). Twenty amendments were issued across 19 pedigrees involving 19 variants in 17 genes. The overall variant reclassification rate was 5%, with 63% being upgrades and 32% downgrades. Of the reclassified variants, 79% were initially reported as VUS. The median time-to-amendments from initial reports was 8.4 (4-27) months. Following the variant reclassifications, 60% of the patients received a new diagnosis or a change in diagnosis. Among these, 67% of patients received significant changes in clinical management. Conclusion Variant reclassification following genetic testing is infrequent but important for diagnosis and management of patients with suspected genetic kidney disease. The majority of variant reclassifications involve VUS and are upgrades in clinically issued amended reports. Further studies are needed to investigate the predictors of such events.
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Affiliation(s)
- Euyn Lim
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Chloe Borden
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Seysha Mehta
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
| | - Mary-Beth Roberts
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Sarah Mazzola
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Fang Zhao
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Xiangling Wang
- Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
- Center for Personalized Genetic Healthcare, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Kidney Medicine, Medical Specialties Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio, USA
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31
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Koehler S, Hengel FE, Dumoulin B, Damashek L, Holzman LB, Susztak K, Huber TB. The 14th International Podocyte Conference 2023: from podocyte biology to glomerular medicine. Kidney Int 2024; 105:935-952. [PMID: 38447880 DOI: 10.1016/j.kint.2024.01.042] [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: 10/30/2023] [Revised: 12/11/2023] [Accepted: 01/02/2024] [Indexed: 03/08/2024]
Abstract
The 14th International Podocyte Conference took place in Philadelphia, Pennsylvania, USA from May 23 to 26, 2023. It commenced with an early-career researchers' meeting on May 23, providing young scientists with a platform to present and discuss their research findings. Throughout the main conference, 29 speakers across 9 sessions shared their insights on podocyte biology, glomerular medicine, novel technologic advancements, and translational approaches. Additionally, the event featured 3 keynote lectures addressing engineered chimeric antigen receptor T cell- and mRNA-based therapies and the use of biobanks for enhanced disease comprehension. Furthermore, 4 brief oral abstract sessions allowed scientists to present their findings to a broad audience. The program also included a panel discussion addressing the challenges of conducting human research within the American Black community. Remarkably, after a 5-year hiatus from in-person conferences, the 14th International Podocyte Conference successfully convened scientists from around the globe, fostering the presentation and discussion of crucial research findings, as summarized in this review. Furthermore, to ensure continuous and sustainable education, research, translation, and trial medicine related to podocyte and glomerular diseases for the benefit of patients, the International Society of Glomerular Disease was officially launched during the conference.
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Affiliation(s)
- Sybille Koehler
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Felicitas E Hengel
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Bernhard Dumoulin
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Laurel Damashek
- International Society of Glomerular Disease, Florence, Massachusetts, USA
| | - Lawrence B Holzman
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA; Institute of Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tobias B Huber
- III. Department of Medicine and Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany; International Society of Glomerular Disease, Florence, Massachusetts, USA.
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Gulati A, Moxey-Mims M. Defining Risk in APOL1-Associated Kidney Disease: The Story is Evolving! Am J Kidney Dis 2024:S0272-6386(24)00742-X. [PMID: 38648881 DOI: 10.1053/j.ajkd.2024.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/16/2024] [Accepted: 03/30/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Ashima Gulati
- Division of Pediatric Nephrology, Children's National Hospital, Washington, DC; Department of Pediatrics, The George Washington University School of Medicine, Washington, DC
| | - Marva Moxey-Mims
- Division of Pediatric Nephrology, Children's National Hospital, Washington, DC; Department of Pediatrics, The George Washington University School of Medicine, Washington, DC.
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Dogan M, Watkins C, Ingram H, Moore N, Rucker GM, Gower EG, Eason JD, Bhalla A, Talwar M, Nezakatgoo N, Eymard C, Helmick R, Vanatta J, Bajwa A, Kuscu C, Kuscu C. Unveiling APOL1 haplotypes in a predominantly African-American cohort of kidney transplant patients: a novel classification using probe-independent quantitative real-time PCR. Front Med (Lausanne) 2024; 11:1325128. [PMID: 38660426 PMCID: PMC11039853 DOI: 10.3389/fmed.2024.1325128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/20/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction Apolipoprotein-L1 (APOL1) is a primate-specific protein component of high-density lipoprotein (HDL). Two variants of APOL1 (G1 and G2), provide resistance to parasitic infections in African Americans but are also implicated in kidney-related diseases and transplant outcomes in recipients. This study aims to identify these risk variants using a novel probe-independent quantitative real-time PCR method in a high African American recipient cohort. Additionally, it aims to develop a new stratification approach based on a haplotype-centric model. Methods Genomic DNA was extracted from recipient PBMCs using SDS lysis buffer and proteinase K. A quantitative PCR assay with modified forward primers and a common reverse primer enabled us to quantitatively identify single nucleotide polymorphisms (SNPs) and the 6-bp deletion. Additionally, we used Sanger sequencing to verify our QPCR findings. Results Our novel probe-independent qPCR effectively distinguished homozygous wild-type, heterozygous SNPs/deletions, and homozygous SNPs/deletions, with at least 4-fold differences. A high prevalence of APOL1 variants was observed (18% two-risk alleles, 34% one-risk allele) in our recipient cohort. Intriguingly, no significant impact of recipient APOL1 variants on transplant outcomes was observed up to 12-month of follow-ups. Ongoing research will encompass more time points and a larger patient cohort, allowing for a comprehensive evaluation of G1/G2 variant subgroups categorized by new haplotype scores, enriching our understanding. Conclusion Our cost-effective and rapid qPCR technique facilitates APOL1 genotyping within hours. Prospective and retrospective studies will enable comparisons with long-term allograft rejection, potentially predicting early/late-stage transplant outcomes based on haplotype evaluation in this diverse group of kidney transplant recipients.
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Affiliation(s)
- Murat Dogan
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Christine Watkins
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Holly Ingram
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Nicholas Moore
- Transplant Research Institute, Memphis, TN, United States
| | - Grace M. Rucker
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | | | | | - Anshul Bhalla
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Methodist Hospital, Memphis, TN, United States
| | - Manish Talwar
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Methodist Hospital, Memphis, TN, United States
| | - Nosratollah Nezakatgoo
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Methodist Hospital, Memphis, TN, United States
| | - Corey Eymard
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Methodist Hospital, Memphis, TN, United States
| | - Ryan Helmick
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Methodist Hospital, Memphis, TN, United States
| | - Jason Vanatta
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
- Methodist Hospital, Memphis, TN, United States
| | - Amandeep Bajwa
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Canan Kuscu
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Cem Kuscu
- Transplant Research Institute, Memphis, TN, United States
- Department of Surgery, College of Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
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Riley R, Mathieson I, Mathieson S. Interpreting generative adversarial networks to infer natural selection from genetic data. Genetics 2024; 226:iyae024. [PMID: 38386895 PMCID: PMC10990424 DOI: 10.1093/genetics/iyae024] [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: 11/10/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/24/2024] Open
Abstract
Understanding natural selection and other forms of non-neutrality is a major focus for the use of machine learning in population genetics. Existing methods rely on computationally intensive simulated training data. Unlike efficient neutral coalescent simulations for demographic inference, realistic simulations of selection typically require slow forward simulations. Because there are many possible modes of selection, a high dimensional parameter space must be explored, with no guarantee that the simulated models are close to the real processes. Finally, it is difficult to interpret trained neural networks, leading to a lack of understanding about what features contribute to classification. Here we develop a new approach to detect selection and other local evolutionary processes that requires relatively few selection simulations during training. We build upon a generative adversarial network trained to simulate realistic neutral data. This consists of a generator (fitted demographic model), and a discriminator (convolutional neural network) that predicts whether a genomic region is real or fake. As the generator can only generate data under neutral demographic processes, regions of real data that the discriminator recognizes as having a high probability of being "real" do not fit the neutral demographic model and are therefore candidates for targets of selection. To incentivize identification of a specific mode of selection, we fine-tune the discriminator with a small number of custom non-neutral simulations. We show that this approach has high power to detect various forms of selection in simulations, and that it finds regions under positive selection identified by state-of-the-art population genetic methods in three human populations. Finally, we show how to interpret the trained networks by clustering hidden units of the discriminator based on their correlation patterns with known summary statistics.
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Affiliation(s)
- Rebecca Riley
- Department of Computer Science, Haverford College, Haverford, PA 19041, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sara Mathieson
- Department of Computer Science, Haverford College, Haverford, PA 19041, USA
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Kovalik ME, Dacanay MA, Crowley SD, Hall G. Swollen Feet: Considering the Paradoxical Roles of Interleukins in Nephrotic Syndrome. Biomedicines 2024; 12:738. [PMID: 38672094 PMCID: PMC11048099 DOI: 10.3390/biomedicines12040738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
Interleukins are a family of 40 bioactive peptides that act through cell surface receptors to induce a variety of intracellular responses. While interleukins are most commonly associated with destructive, pro-inflammatory signaling in cells, some also play a role in promoting cellular resilience and survival. This review will highlight recent evidence of the cytoprotective actions of the interleukin 1 receptor (IL-1R)- and common gamma chain receptor (IL-Rγc)-signaling cytokines in nephrotic syndrome (NS). NS results from the injury or loss of glomerular visceral epithelial cells (i.e., podocytes). Although the causes of podocyte dysfunction vary, it is clear that pro-inflammatory cytokines play a significant role in regulating the propagation, duration and severity of disease. Pro-inflammatory cytokines signaling through IL-1R and IL-Rγc have been shown to exert anti-apoptotic effects in podocytes through the phosphoinositol-3-kinase (PI-3K)/AKT pathway, highlighting the potential utility of IL-1R- and IL-Rγc-signaling interleukins for the treatment of podocytopathy in NS. The paradoxical role of interleukins as drivers and mitigators of podocyte injury is complex and ill-defined. Emerging evidence of the cytoprotective role of some interleukins in NS highlights the urgent need for a nuanced understanding of their pro-survival benefits and reveals their potential as podocyte-sparing therapeutics for NS.
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Affiliation(s)
- Maria E. Kovalik
- Division of Nephrology, Duke University, Durham, NC 27701, USA; (M.E.K.)
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27710, USA
| | - Monique A. Dacanay
- Division of Nephrology, Duke University, Durham, NC 27701, USA; (M.E.K.)
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27710, USA
| | - Steven D. Crowley
- Division of Nephrology, Duke University, Durham, NC 27701, USA; (M.E.K.)
| | - Gentzon Hall
- Division of Nephrology, Duke University, Durham, NC 27701, USA; (M.E.K.)
- Duke Molecular Physiology Institute, Duke University, Durham, NC 27710, USA
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Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS. Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. Front Endocrinol (Lausanne) 2024; 14:1286979. [PMID: 38577257 PMCID: PMC10991756 DOI: 10.3389/fendo.2023.1286979] [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] [Accepted: 12/07/2023] [Indexed: 04/06/2024] Open
Abstract
Both cancer and cardio-metabolic disease disparities exist among specific populations in the US. For example, African Americans experience the highest rates of breast and prostate cancer mortality and the highest incidence of obesity. Native and Hispanic Americans experience the highest rates of liver cancer mortality. At the same time, Pacific Islanders have the highest death rate attributed to type 2 diabetes (T2D), and Asian Americans experience the highest incidence of non-alcoholic fatty liver disease (NAFLD) and cancers induced by infectious agents. Notably, the pathologic progression of both cancer and cardio-metabolic diseases involves innate immunity and mechanisms of inflammation. Innate immunity in individuals is established through genetic inheritance and external stimuli to respond to environmental threats and stresses such as pathogen exposure. Further, individual genomes contain characteristic genetic markers associated with one or more geographic ancestries (ethnic groups), including protective innate immune genetic programming optimized for survival in their corresponding ancestral environment(s). This perspective explores evidence related to our working hypothesis that genetic variations in innate immune genes, particularly those that are commonly found but unevenly distributed between populations, are associated with disparities between populations in both cancer and cardio-metabolic diseases. Identifying conventional and unconventional innate immune genes that fit this profile may provide critical insights into the underlying mechanisms that connect these two families of complex diseases and offer novel targets for precision-based treatment of cancer and/or cardio-metabolic disease.
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Affiliation(s)
- Susan Yeyeodu
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
- Charles River Discovery Services, Morrisville, NC, United States
| | - Donia Hanafi
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - Kenisha Webb
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
| | - Nikia A. Laurie
- Julius L Chambers Biomedical/Biotechnology Institute (JLC-BBRI), North Carolina Central University, Durham, NC, United States
| | - K. Sean Kimbro
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, GA, United States
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Randle RK, Amara VR, Popik W. IFI16 Is Indispensable for Promoting HIF-1α-Mediated APOL1 Expression in Human Podocytes under Hypoxic Conditions. Int J Mol Sci 2024; 25:3324. [PMID: 38542298 PMCID: PMC10970439 DOI: 10.3390/ijms25063324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Genetic variants in the protein-coding regions of APOL1 are associated with an increased risk and progression of chronic kidney disease (CKD) in African Americans. Hypoxia exacerbates CKD progression by stabilizing HIF-1α, which induces APOL1 transcription in kidney podocytes. However, the contribution of additional mediators to regulating APOL1 expression under hypoxia in podocytes is unknown. Here, we report that a transient accumulation of HIF-1α in hypoxia is sufficient to upregulate APOL1 expression in podocytes through a cGAS/STING/IRF3-independent pathway. Notably, IFI16 ablation impedes hypoxia-driven APOL1 expression despite the nuclear accumulation of HIF-1α. Co-immunoprecipitation assays indicate no direct interaction between IFI16 and HIF-1α. Our studies identify hypoxia response elements (HREs) in the APOL1 gene enhancer/promoter region, showing increased HIF-1α binding to HREs located in the APOL1 gene enhancer. Luciferase reporter assays confirm the role of these HREs in transcriptional activation. Chromatin immunoprecipitation (ChIP)-qPCR assays demonstrate that IFI16 is not recruited to HREs, and IFI16 deletion reduces HIF-1α binding to APOL1 HREs. RT-qPCR analysis indicates that IFI16 selectively affects APOL1 expression, with a negligible impact on other hypoxia-responsive genes in podocytes. These findings highlight the unique contribution of IFI16 to hypoxia-driven APOL1 gene expression and suggest alternative IFI16-dependent mechanisms regulating APOL1 gene expression under hypoxic conditions.
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Affiliation(s)
- Richaundra K. Randle
- Department of Biomedical Sciences, School of Graduate Studies, Meharry Medical College, Nashville, TN 37208, USA;
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA;
| | - Venkateswara Rao Amara
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA;
- Department of Regulatory Toxicology, National Institute of Pharmaceutical Education and Research, Hajipur 844102, Bihar, India
| | - Waldemar Popik
- Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA;
- Department of Internal Medicine, School of Medicine, Meharry Medical College, Nashville, TN 37208, USA
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Pays E. The Janus-faced functions of Apolipoproteins L in membrane dynamics. Cell Mol Life Sci 2024; 81:134. [PMID: 38478101 PMCID: PMC10937811 DOI: 10.1007/s00018-024-05180-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/06/2024] [Accepted: 02/18/2024] [Indexed: 03/17/2024]
Abstract
The functions of human Apolipoproteins L (APOLs) are poorly understood, but involve diverse activities like lysis of bloodstream trypanosomes and intracellular bacteria, modulation of viral infection and induction of apoptosis, autophagy, and chronic kidney disease. Based on recent work, I propose that the basic function of APOLs is the control of membrane dynamics, at least in the Golgi and mitochondrion. Together with neuronal calcium sensor-1 (NCS1) and calneuron-1 (CALN1), APOL3 controls the activity of phosphatidylinositol-4-kinase-IIIB (PI4KB), involved in both Golgi and mitochondrion membrane fission. Whereas secreted APOL1 induces African trypanosome lysis through membrane permeabilization of the parasite mitochondrion, intracellular APOL1 conditions non-muscular myosin-2A (NM2A)-mediated transfer of PI4KB and APOL3 from the Golgi to the mitochondrion under conditions interfering with PI4KB-APOL3 interaction, such as APOL1 C-terminal variant expression or virus-induced inflammatory signalling. APOL3 controls mitophagy through complementary interactions with the membrane fission factor PI4KB and the membrane fusion factor vesicle-associated membrane protein-8 (VAMP8). In mice, the basic APOL1 and APOL3 activities could be exerted by mAPOL9 and mAPOL8, respectively. Perspectives regarding the mechanism and treatment of APOL1-related kidney disease are discussed, as well as speculations on additional APOLs functions, such as APOL6 involvement in adipocyte membrane dynamics through interaction with myosin-10 (MYH10).
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Affiliation(s)
- Etienne Pays
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041, Gosselies, Belgium.
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Abstract
Prolonged or excessive exposure to oxidized phospholipids (OxPLs) generates chronic inflammation. OxPLs are present in atherosclerotic lesions and can be detected in plasma on apolipoprotein B (apoB)-containing lipoproteins. When initially conceptualized, OxPL-apoB measurement in plasma was expected to reflect the concentration of minimally oxidized LDL, but, surprisingly, it correlated more strongly with plasma lipoprotein(a) (Lp(a)) levels. Indeed, experimental and clinical studies show that Lp(a) particles carry the largest fraction of OxPLs among apoB-containing lipoproteins. Plasma OxPL-apoB levels provide diagnostic information on the presence and extent of atherosclerosis and improve the prognostication of peripheral artery disease and first and recurrent myocardial infarction and stroke. The addition of OxPL-apoB measurements to traditional cardiovascular risk factors improves risk reclassification, particularly in patients in intermediate risk categories, for whom improving decision-making is most impactful. Moreover, plasma OxPL-apoB levels predict cardiovascular events with similar or greater accuracy than plasma Lp(a) levels, probably because this measurement reflects both the genetics of elevated Lp(a) levels and the generalized or localized oxidation that modifies apoB-containing lipoproteins and leads to inflammation. Plasma OxPL-apoB levels are reduced by Lp(a)-lowering therapy with antisense oligonucleotides and by lipoprotein apheresis, niacin therapy and bariatric surgery. In this Review, we discuss the role of role OxPLs in the pathophysiology of atherosclerosis and Lp(a) atherogenicity, and the use of OxPL-apoB measurement for improving prognosis, risk reclassification and therapeutic interventions.
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Affiliation(s)
- Sotirios Tsimikas
- Division of Cardiovascular Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Joseph L Witztum
- Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, USA
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Adamson WE, Noyes H, Johnson P, Cooper A, Monckton DG, Ogunsola J, Beckett-Hill G, Sullivan M, Mark P, Parekh RS, MacLeod A. Phenome-wide analysis reveals epistatic associations between APOL1 variants and chronic kidney disease and multiple other disorders. EBioMedicine 2024; 101:105000. [PMID: 38360481 PMCID: PMC10944146 DOI: 10.1016/j.ebiom.2024.105000] [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: 06/26/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND APOL1 variants G1 and G2 are common in populations with recent African ancestry. They are associated with protection from African sleeping sickness, however homozygosity or compound heterozygosity for these variants is associated with chronic kidney disease (CKD) and related conditions. What is not clear is the extent of associations with non-kidney-related disorders, and whether there are clusters of diseases associated with individual APOL1 genotypes. METHODS Using a cohort of 7462 UK Biobank participants with recent African ancestry, we conducted a phenome-wide association study investigating associations between individual APOL1 genotypes and conditions identified by the International Classification of Disease phenotypes. FINDINGS We identified 27 potential associations between individual APOL1 genotypes and a diverse range of conditions. G1/G2 compound heterozygotes were specifically associated with 26 of these conditions (all deleteriously), with an over-representation of infectious diseases (including hospitalisation and death resulting from COVID-19). The analysis also exposed complexities in the relationship between APOL1 and CKD that are not evident when risk variants are grouped together: G1 homozygosity, G2 homozygosity, and G1/G2 compound heterozygosity were each shown to be associated with distinct CKD phenotypes. The multi-locus nature of the G1/G2 genotype means that its associations would go undetected in a standard genome-wide association study. INTERPRETATION Our findings have implications for understanding health risks and better-targeted detection, intervention, and therapeutic strategies, particularly in populations where APOL1 G1 and G2 are common such as in sub-Saharan Africa and its diaspora. FUNDING This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004).
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Affiliation(s)
- Walt E Adamson
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom; TrypanoGEN+ Research Group, Uganda, Member of the H3Africa Consortium, South Africa.
| | - Harry Noyes
- TrypanoGEN+ Research Group, Uganda, Member of the H3Africa Consortium, South Africa; Centre for Genomic Research, University of Liverpool, United Kingdom
| | - Paul Johnson
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Anneli Cooper
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom
| | - Darren G Monckton
- School of Molecular Biosciences, University of Glasgow, United Kingdom
| | - John Ogunsola
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom
| | - Georgia Beckett-Hill
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Michael Sullivan
- School of Cardiovascular and Metabolic Health, University of Glasgow, United Kingdom
| | - Patrick Mark
- School of Cardiovascular and Metabolic Health, University of Glasgow, United Kingdom
| | - Rulan S Parekh
- Women's College Hospital, Hospital for Sick Children and University of Toronto, Canada
| | - Annette MacLeod
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom; TrypanoGEN+ Research Group, Uganda, Member of the H3Africa Consortium, South Africa.
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Neves PD, Watanabe A, Watanabe EH, Narcizo AM, Nunes K, Lerario AM, Ferreira FM, Cavalcante LB, Wongboonsin J, Malheiros DM, Jorge LB, Sampson MG, Noronha IL, Onuchic LF. Idiopathic collapsing glomerulopathy is associated with APOL1 high-risk genotypes or Mendelian variants in most affected individuals in a highly admixed population. Kidney Int 2024; 105:593-607. [PMID: 38143038 DOI: 10.1016/j.kint.2023.11.028] [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: 04/19/2023] [Revised: 09/04/2023] [Accepted: 11/16/2023] [Indexed: 12/26/2023]
Abstract
Collapsing glomerulopathy (CG) is most often associated with fast progression to kidney failure with an incidence apparently higher in Brazil than in other countries. However, the reason for this occurrence is unknown. To better understand this, we performed an integrated analysis of clinical, histological, therapeutic, causative genetic and genetic ancestry data in a highly genetically admixed cohort of 70 children and adult patients with idiopathic CG (ICG). The disease onset occurred at 23 (interquartile range: 17-31) years and approximately half of patients progressed to chronic kidney disease requiring kidney replacement therapy (CKD-KRT) 36 months after diagnosis. Causative genetic bases, assessed by targeted-gene panel or whole-exome sequencing, were identified in 58.6% of patients. Among these cases, 80.5% harbored APOL1 high-risk genotypes (HRG) and 19.5% causative Mendelian variants (MV). Self-reported non-White patients more frequently had HRG. MV was an independent risk factor for progression to CKD-KRT by 36 months and the end of follow-up, while remission was an independent protective factor. All patients with HRG manifested CG at 9-44 years of age, whereas in those with APOL1 low-risk genotype, the disease arose throughout life. HRGs were associated with higher proportion of African genetic ancestry. Novel causative MVs were identified in COL4A5, COQ2 and PLCE1 and previously described causative MVs were identified in MYH9, TRPC6, COQ2, COL4A3 and TTC21B. Three patients displayed HRG combined with a variant of uncertain significance (ITGB4, LAMA5 or PTPRO). MVs were associated with worse kidney prognosis. Thus, our data reveal that the genetic status plays a major role in ICG pathogenesis, accounting for more than half of cases in a highly admixed Brazilian population.
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Affiliation(s)
- Precil D Neves
- Division of Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil; Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil; Nephrology and Dialysis Center, Oswaldo Cruz German Hospital, São Paulo, Brazil
| | - Andreia Watanabe
- Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil; Division of Pediatric Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Elieser H Watanabe
- Division of Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil; Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Amanda M Narcizo
- Large-Scale Sequencing Laboratory, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Kelly Nunes
- Human Genome Center, Institute of Biosciences/University of São Paulo, São Paulo, Brazil
| | - Antonio M Lerario
- Division of Endocrinology, University of Michigan, Ann Arbor, Michigan, USA
| | - Frederico M Ferreira
- Department of Pathology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Lívia B Cavalcante
- Department of Pathology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Janewit Wongboonsin
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA; Division of Nephrology, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Denise M Malheiros
- Department of Pathology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Lectícia B Jorge
- Division of Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Matthew G Sampson
- Division of Pediatric Nephrology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Irene L Noronha
- Division of Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil
| | - Luiz F Onuchic
- Division of Nephrology, University of São Paulo School of Medicine, São Paulo, Brazil; Division of Molecular Medicine, University of São Paulo School of Medicine, São Paulo, Brazil.
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Palmer ND, Freedman BI. APOL1-mediated and Mendelian forms of "heretofore" idiopathic collapsing glomerulopathy: lessons from Brazil. Kidney Int 2024; 105:437-439. [PMID: 38388143 DOI: 10.1016/j.kint.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 02/24/2024]
Abstract
APOL1-mediated kidney diseases have forever changed nephrology and kidney transplantation. Neves et al. extend this field with analyses in admixed Brazilians with the most severe type of APOL1-mediated kidney disease, idiopathic collapsing glomerulopathy. Causative gene variants were detected in 58.6% of patients; 80.5% had APOL1 high-risk genotypes, and 19.5% had causative Mendelian variants. Their work identifies the cause of previous idiopathic collapsing glomerulopathy and provides opportunities to identify novel modifiers in severe APOL1-mediated kidney diseases that are relevant beyond Brazil.
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Affiliation(s)
- Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Barry I Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA.
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Arunachalam V, Lea R, Hoy W, Lee S, Mott S, Savige J, Mathews JD, McMorran BJ, Nagaraj SH. Novel genetic markers for chronic kidney disease in a geographically isolated population of Indigenous Australians: Individual and multiple phenotype genome-wide association study. Genome Med 2024; 16:29. [PMID: 38347632 PMCID: PMC10860247 DOI: 10.1186/s13073-024-01299-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 01/30/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is highly prevalent among Indigenous Australians, especially those in remote regions. The Tiwi population has been isolated from mainland Australia for millennia and exhibits unique genetic characteristics that distinguish them from other Indigenous and non-Indigenous populations. Notably, the rate of end-stage renal disease is up to 20 times greater in this population compared to non-Indigenous populations. Despite the identification of numerous genetic loci associated with kidney disease through GWAS, the Indigenous population such as Tiwi remains severely underrepresented and the increased prevalence of CKD in this population may be due to unique disease-causing alleles/genes. METHODS We used albumin-to-creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR) to estimate the prevalence of kidney disease in the Tiwi population (N = 492) in comparison to the UK Biobank (UKBB) (N = 134,724) database. We then performed an exploratory factor analysis to identify correlations among 10 CKD-related phenotypes and identify new multi-phenotype factors. We subsequently conducted a genome-wide association study (GWAS) on all single and multiple phenotype factors using mixed linear regression models, adjusted for age, sex, population stratification, and genetic relatedness between individuals. RESULTS Based on ACR, 20.3% of the population was at severely increased risk of CKD progression and showed elevated levels of ACR compared to the UKBB population independent of HbA1c. A GWAS of ACR revealed novel association loci in the genes MEG3 (chr14:100812018:T:A), RAB36 (rs11704318), and TIAM2 (rs9689640). Additionally, multiple phenotypes GWAS of ACR, eGFR, urine albumin, and serum creatinine identified a novel variant that mapped to the gene MEIS2 (chr15:37218869:A:G). Most of the identified variants were found to be either absent or rare in the UKBB population. CONCLUSIONS Our study highlights the Tiwi population's predisposition towards elevated ACR, and the collection of novel genetic variants associated with kidney function. These associations may prove valuable in the early diagnosis and treatment of renal disease in this underrepresented population. Additionally, further research is needed to comprehensively validate the functions of the identified variants/genes.
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Affiliation(s)
- Vignesh Arunachalam
- Centre for Genomics and Personalised Health and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Rodney Lea
- Centre for Genomics and Personalised Health and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Wendy Hoy
- Centre of chronic disease, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Simon Lee
- Centre for Genomics and Personalised Health and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Susan Mott
- Centre of chronic disease, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Judith Savige
- Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - John D Mathews
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Brendan J McMorran
- National Centre for Indigenous Genomics, The John Curtin of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Shivashankar H Nagaraj
- Centre for Genomics and Personalised Health and School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.
- Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.
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Tuttle KR, Abner CW, Walker PD, Wang K, Rava A, Heo J, Bunke M. Clinical Characteristics and Histopathology in Adults With Focal Segmental Glomerulosclerosis. Kidney Med 2024; 6:100748. [PMID: 38196777 PMCID: PMC10772385 DOI: 10.1016/j.xkme.2023.100748] [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] [Indexed: 01/11/2024] Open
Abstract
Rationale & Objective Few data are available regarding histological features at the time of focal segmental glomerulosclerosis (FSGS) diagnosis among diverse real-world populations. This study describes clinical and histological characteristics and correlates of histological disease severity in adults with FSGS who underwent a clinical kidney biopsy. Study Design Real-world cohort study with data derived from health records. Setting & Participants Adults with FSGS by kidney biopsies from Arkana Laboratories from January 1, 2016 to May 31, 2020. Exposure Race, chronic kidney disease stage, nephrotic proteinuria, age, sex, and hypertension. Outcomes Severe histological disease, defined as global glomerulosclerosis in >50% of glomeruli and >25% interstitial fibrosis and tubular atrophy (IFTA). Analytical Approach Demographic, clinical, and histological characteristics were compared between race groups. Correlates of severe disease were analyzed using multiple logistic regression. Results Among 2,011 patients with FSGS, 40.6% were White, and 23.6% Black. White patients were older (52.8 vs 45.5 years, P < 0.001) with a higher estimated glomerular filtration rate (eGFR) than Black patients (53.5 vs 43.1 mL/min/1.73 m2, P < 0.001). A higher proportion of Black patients had global glomerulosclerosis ≥50% (32.1% vs 14.6%, P < 0.001) or IFTA >50% (34.6% vs 14.7%, P < 0.001). Severe histological disease was more likely in Black patients (OR, 2.46; 95% CI, 1.59-3.79; P < 0.001). A higher proportion of patients with nephrotic than nonnephrotic proteinuria exhibited diffuse foot process effacement. Limitations Unequal representation across United States regions, missing demographic and clinical data, and lack of data on primary versus secondary FSGS, treatments, or outcomes. Conclusions Black patients were more frequently diagnosed at younger age with lower eGFR and more severe histological disease compared with White patients. Timelier identification of FSGS could increase the opportunity for therapeutic intervention, especially for high-risk patients, to mitigate disease progression and complications. Plain-Language Summary Focal segmental glomerulosclerosis (FSGS) accounts for around one-quarter of diagnoses derived from clinical kidney biopsies in the United States. Limited data are available regarding the classes and distribution of histological features at FSGS diagnosis among diverse real-world populations. Analyzing data from US patients who underwent kidney biopsy and were diagnosed with FSGS, we showed that up to half of patients had features of severe histological disease. Of this overall population, Black patients were more frequently diagnosed at a younger age but with more severe histological disease than White patients. The work highlights the need for timelier diagnosis of FSGS to enable intervention at an earlier disease stage.
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Artomov M, Loboda AA, Artyomov MN, Daly MJ. Public platform with 39,472 exome control samples enables association studies without genotype sharing. Nat Genet 2024; 56:327-335. [PMID: 38200129 PMCID: PMC10864173 DOI: 10.1038/s41588-023-01637-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] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 12/01/2023] [Indexed: 01/12/2024]
Abstract
Acquiring a sufficiently powered cohort of control samples matched to a case sample can be time-consuming or, in some cases, impossible. Accordingly, an ability to leverage genetic data from control samples that were already collected elsewhere could dramatically improve power in genetic association studies. Sharing of control samples can pose significant challenges, since most human genetic data are subject to strict sharing regulations. Here, using the properties of singular value decomposition and subsampling algorithm, we developed a method allowing selection of the best-matching controls in an external pool of samples compliant with personal data protection and eliminating the need for genotype sharing. We provide access to a library of 39,472 exome sequencing controls at http://dnascore.net enabling association studies for case cohorts lacking control subjects. Using this approach, control sets can be selected from this online library with a prespecified matching accuracy, ensuring well-calibrated association analysis for both rare and common variants.
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Affiliation(s)
- Mykyta Artomov
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
| | - Alexander A Loboda
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Center, St. Petersburg, Russia
| | - Maxim N Artyomov
- Department of Immunology and Pathology, Washington University in St. Louis, St. Louis, MO, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Cambridge, MA, USA.
- Institute for Molecular Medicine Finland, Helsinki, Finland.
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Xiao H, Qu Y, Li H, Zhang Y, Fei M, Liang C, Yang H, Zhang X. HIF-2α/LINC02609/APOL1-mediated lipid storage promotes endoplasmic reticulum homeostasis and regulates tumor progression in clear-cell renal cell carcinoma. J Exp Clin Cancer Res 2024; 43:29. [PMID: 38263248 PMCID: PMC10804485 DOI: 10.1186/s13046-023-02940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND The VHL-HIF pathway and lipid droplet accumulation are the main characteristics of clear cell renal cell carcinoma (ccRCC). However, the connection between the two features is largely unknown. METHODS We used transcriptional sequencing and TCGA database analysis to identify APOL1 as a novel therapeutic target for ccRCC. The oncogenic functions of APOL1 were investigated by cell proliferation, colony formation, migration and invasion assays in ccRCC cells in vitro and xenografts derived from ccRCC cells in vivo. Oil red O staining and quantification were used to detect lipid droplets. Chromatin immunoprecipitation (ChIP) assays and luciferase reporter assays were carried out to identify HIF-2α bound to the promoter of APOL1 and lncRNA LINC02609. RNA-FISH and luciferase reporter assays were performed to determine that LncRNA LINC02609 functions as a competing endogenous RNA to regulate APOL1 expression by sponging miR-149-5p. FINDINGS RNA-seq data revealed that HIF2α can regulate APOL1 and lncRNA LINC02609 expression. We also found that HIF-2α can bind to the promoter of APOL1 and lncRNA LINC02609 and transcriptionally regulate their expression directly. We further demonstrated that LncRNA LINC02609 functions as a competing endogenous RNA to regulate APOL1 expression by sponging miR-149-5p in ccRCC. Mechanistically, APOL1-dependent lipid storage is required for endoplasmic reticulum (ER) homeostasis and cell viability and metastasis in ccRCC. We also showed that high APOL1 expression correlated with worse clinical outcomes, and knockdown of APOL1 inhibited tumor cell lipid droplet formation, proliferation, metastasis and xenograft tumor formation abilities. Together, our studies identify that HIF2α can regulate the expression of the lipid metabolism related gene APOL1 by direct and indirect means, which are essential for ccRCC tumorigenesis. INTERPRETATION Based on the experimental data, in ccRCC, the HIF-2α/LINC02609/APOL1 axis can regulate the expression of APOL1, thus interfering with lipid storage, promoting endoplasmic reticulum homeostasis and regulating tumor progression in ccRCC. Together, our findings provide potential biomarkers and novel therapeutic targets for future studies in ccRCC.
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Affiliation(s)
- Haibing Xiao
- Department of Urology, Institute of Urology, Anhui Province Key Laboratory of Genitourinary Diseases, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230022, China
- Department of Urology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China
- Department of Pathogenic Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yan Qu
- College of Basic Medicine, Xinxiang Medical University, Xinxiang, Henan, 453000, China
| | - Haolin Li
- Department of Urology, Institute of Urology, Anhui Province Key Laboratory of Genitourinary Diseases, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230022, China
| | - Yi Zhang
- Department of Urology, Institute of Urology, Anhui Province Key Laboratory of Genitourinary Diseases, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230022, China
| | - Mintian Fei
- Department of Urology, Institute of Urology, Anhui Province Key Laboratory of Genitourinary Diseases, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230022, China
| | - Chaozhao Liang
- Department of Urology, Institute of Urology, Anhui Province Key Laboratory of Genitourinary Diseases, The First Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, 230022, China.
| | - Hongmei Yang
- Department of Pathogenic Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Xiaoping Zhang
- Department of Urology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, Hubei Province, 430022, China.
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Datta S, Antonio BM, Zahler NH, Theile JW, Krafte D, Zhang H, Rosenberg PB, Chaves AB, Muoio DM, Zhang G, Silas D, Li G, Soldano K, Nystrom S, Ferreira D, Miller SE, Bain JR, Muehlbauer MJ, Ilkayeva O, Becker TC, Hohmeier HE, Newgard CB, Olabisi OA. APOL1-mediated monovalent cation transport contributes to APOL1-mediated podocytopathy in kidney disease. J Clin Invest 2024; 134:e172262. [PMID: 38227370 PMCID: PMC10904047 DOI: 10.1172/jci172262] [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: 05/15/2023] [Accepted: 01/09/2024] [Indexed: 01/17/2024] Open
Abstract
Two coding variants of apolipoprotein L1 (APOL1), called G1 and G2, explain much of the excess risk of kidney disease in African Americans. While various cytotoxic phenotypes have been reported in experimental models, the proximal mechanism by which G1 and G2 cause kidney disease is poorly understood. Here, we leveraged 3 experimental models and a recently reported small molecule blocker of APOL1 protein, VX-147, to identify the upstream mechanism of G1-induced cytotoxicity. In HEK293 cells, we demonstrated that G1-mediated Na+ import/K+ efflux triggered activation of GPCR/IP3-mediated calcium release from the ER, impaired mitochondrial ATP production, and impaired translation, which were all reversed by VX-147. In human urine-derived podocyte-like epithelial cells (HUPECs), we demonstrated that G1 caused cytotoxicity that was again reversible by VX-147. Finally, in podocytes isolated from APOL1 G1 transgenic mice, we showed that IFN-γ-mediated induction of G1 caused K+ efflux, activation of GPCR/IP3 signaling, and inhibition of translation, podocyte injury, and proteinuria, all reversed by VX-147. Together, these results establish APOL1-mediated Na+/K+ transport as the proximal driver of APOL1-mediated kidney disease.
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Affiliation(s)
- Somenath Datta
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Duke University School of Medicine, Department of Medicine, Division of Nephrology, Durham, North Carolina, USA
| | | | | | | | | | - Hengtao Zhang
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Paul B. Rosenberg
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Cardiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Alec B. Chaves
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Deborah M. Muoio
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Guofang Zhang
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
| | - Daniel Silas
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Duke University School of Medicine, Department of Medicine, Division of Nephrology, Durham, North Carolina, USA
| | - Guojie Li
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Duke University School of Medicine, Department of Medicine, Division of Nephrology, Durham, North Carolina, USA
| | - Karen Soldano
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Duke University School of Medicine, Department of Medicine, Division of Nephrology, Durham, North Carolina, USA
| | - Sarah Nystrom
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Duke University School of Medicine, Department of Medicine, Division of Nephrology, Durham, North Carolina, USA
| | - Davis Ferreira
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - Sara E. Miller
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, USA
| | - James R. Bain
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
| | - Michael J. Muehlbauer
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
| | - Olga Ilkayeva
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
| | - Thomas C. Becker
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
| | - Hans-Ewald Hohmeier
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
| | - Christopher B. Newgard
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Medicine, Division of Endocrinology, Metabolism, and Nutrition, Duke University School of Medicine, Durham, North Carolina, USA
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Opeyemi A. Olabisi
- Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Duke University School of Medicine, Durham, North Carolina, USA
- Duke University School of Medicine, Department of Medicine, Division of Nephrology, Durham, North Carolina, USA
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Hughes O, Bentley AR, Breeze CE, Aguet F, Xu X, Nadkarni G, Sun Q, Lin BM, Gilliland T, Meyer MC, Du J, Raffield LM, Kramer H, Morton RW, Gouveia MH, Atkinson EG, Valladares-Salgado A, Wacher-Rodarte N, Dueker ND, Guo X, Hai Y, Adeyemo A, Best LG, Cai J, Chen G, Chong M, Doumatey A, Eales J, Goodarzi MO, Ipp E, Irvin MR, Jiang M, Jones AC, Kooperberg C, Krieger JE, Lange EM, Lanktree MB, Lash JP, Lotufo PA, Loos RJF, Ha My VT, Peralta-Romero J, Qi L, Raffel LJ, Rich SS, Rodriquez EJ, Tarazona-Santos E, Taylor KD, Umans JG, Wen J, Young BA, Yu Z, Zhang Y, Ida Chen YD, Rundek T, Rotter JI, Cruz M, Fornage M, Lima-Costa MF, Pereira AC, Paré G, Natarajan P, Cole SA, Carson AP, Lange LA, Li Y, Perez-Stable EJ, Do R, Charchar FJ, Tomaszewski M, Mychaleckyj JC, Rotimi C, Morris AP, Franceschini N. Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas. CELL GENOMICS 2024; 4:100468. [PMID: 38190104 PMCID: PMC10794846 DOI: 10.1016/j.xgen.2023.100468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/31/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10-8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.
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Affiliation(s)
- Odessica Hughes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
| | - Amy R Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles E Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department Health and Human Services, Bethesda, MD, USA; UCL Cancer Institute, University College London, London, UK
| | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoguang Xu
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Girish Nadkarni
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Quan Sun
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Gilliland
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mariah C Meyer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jiawen Du
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Holly Kramer
- Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, IL, USA
| | - Robert W Morton
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Mateus H Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth G Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Adan Valladares-Salgado
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Niels Wacher-Rodarte
- Unidad de Investigación Médica en Epidemiologia Clinica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Nicole D Dueker
- John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lyle G Best
- Missouri Breaks Industries Research Inc., Eagle Butte, SD, USA
| | - Jianwen Cai
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Chong
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Ayo Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Eales
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK
| | - Mark O Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Eli Ipp
- Division of Endocrinology and Metabolism, Department of Medicine, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Marguerite Ryan Irvin
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Minzhi Jiang
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alana C Jones
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jose E Krieger
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew B Lanktree
- Division of Nephrology, Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - James P Lash
- Division of Nephrology, Department of Medicine, University of Illinois, Chicago, IL, USA
| | - Paulo A Lotufo
- Center for Clinical and Epidemiological Research, Hospital Universitário, Universidade de São Paulo (USP), São Paulo, Brazil
| | - Ruth J F Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vy Thi Ha My
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jesús Peralta-Romero
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Lihong Qi
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Leslie J Raffel
- Department of Pediatrics, Genetic and Genomic Medicine, University of California, Irvine, Irvine, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Erik J Rodriquez
- Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Jason G Umans
- MedStar Health Research Institute, Hyattsville MD and Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | - Jia Wen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bessie A Young
- University of Washington School of Medicine, Seattle, WA, USA; Office of Healthcare Equity, UW Justice, Equity, Diversity, and Inclusion Center for Transformational Research (UW JEDI-CTR), University of Washington, Seattle, WA, USA; Division of Nephrology, Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Zhi Yu
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA
| | - Ying Zhang
- Center for American Indian Health Research, Department of Biostatistics and Epidemiology, Hudson College of Public Health, The University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Tanja Rundek
- Department of Neurology, Epidemiology and Public Health, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Miguel Cruz
- Unidad de Investigación Médica en Bioquímica, Hospital de Especialidades, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, Houston, TX, USA
| | | | - Alexandre C Pereira
- Laboratório de Genética e Cardiologia Molecular do Instituto do Coração do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil; Aging Division, Brigham Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Guillaume Paré
- Population Health Research Institute, Hamilton, ON, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Shelley A Cole
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Eliseo J Perez-Stable
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD, USA
| | - Ron Do
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fadi J Charchar
- School of Science, Psychology and Sport, Federation University, Ballarat, VIC, Australia; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Department of Physiology, University of Melbourne, Melbourne, VIC, Australia
| | - Maciej Tomaszewski
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, Manchester, UK; Manchester Royal Infirmary, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Josyf C Mychaleckyj
- Department of Public Health Sciences, School of Medicine, University of California Davis, Davis, CA, USA
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK.
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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49
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McClellan JM, Zoghbi AW, Buxbaum JD, Cappi C, Crowley JJ, Flint J, Grice DE, Gulsuner S, Iyegbe C, Jain S, Kuo PH, Lattig MC, Passos-Bueno MR, Purushottam M, Stein DJ, Sunshine AB, Susser ES, Walsh CA, Wootton O, King MC. An evolutionary perspective on complex neuropsychiatric disease. Neuron 2024; 112:7-24. [PMID: 38016473 PMCID: PMC10842497 DOI: 10.1016/j.neuron.2023.10.037] [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: 08/02/2022] [Revised: 08/09/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
The forces of evolution-mutation, selection, migration, and genetic drift-shape the genetic architecture of human traits, including the genetic architecture of complex neuropsychiatric illnesses. Studying these illnesses in populations that are diverse in genetic ancestry, historical demography, and cultural history can reveal how evolutionary forces have guided adaptation over time and place. A fundamental truth of shared human biology is that an allele responsible for a disease in anyone, anywhere, reveals a gene critical to the normal biology underlying that condition in everyone, everywhere. Understanding the genetic causes of neuropsychiatric disease in the widest possible range of human populations thus yields the greatest possible range of insight into genes critical to human brain development. In this perspective, we explore some of the relationships between genes, adaptation, and history that can be illuminated by an evolutionary perspective on studies of complex neuropsychiatric disease in diverse populations.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Anthony W Zoghbi
- Menninger Department of Psychiatry and Behavioral Sciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Crowley
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jonathan Flint
- Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Suleyman Gulsuner
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Conrad Iyegbe
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Po-Hsiu Kuo
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | | | | | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bengaluru 560029, India
| | - Dan J Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Anna B Sunshine
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Ezra S Susser
- Department of Epidemiology, Mailman School of Public Health, and New York State Psychiatric Institute, Columbia University, New York, NY 10032, USA
| | - Christopher A Walsh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Olivia Wootton
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry, University of Cape Town, Cape Town, South Africa
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
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50
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Sedor JR. APOL1 Kidney Disease: Discovery to Targeted Therapy in 10 Years. Clin J Am Soc Nephrol 2024; 19:126-128. [PMID: 37459117 PMCID: PMC10843197 DOI: 10.2215/cjn.0000000000000256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Affiliation(s)
- John R Sedor
- Glickman Urology and Kidney and Lerner Research Institutes , Cleveland Clinic , and Departments of Molecular Medicine and Physiology and Biophysics , Case Western Reserve University, Cleveland , Ohio
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