1
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Zhang X, Scadden AW, Marthi A, Buchanan VL, Qu Y, Ferrier KR, Chen BD, Graff M, Avila J, Boerwinkle E, Buyske S, Clish CB, Cruz D, Fornage M, Gerzsten RE, Gignoux CR, Glover L, Hou L, Justice AE, Kooperberg C, Kramer H, Lange L, Loos RJF, Matise T, Mychaleckyj JC, Olabisi OA, Peters U, Raffield LM, Reiner AP, Rich SS, Rotter JI, Taylor KD, Yu B, Zheng Y, North KE, Mottl AK, Highland HM, Stanislawski MA. Alterations in DNA Methylation, Proteomic, and Metabolomic Profiles in African Ancestry Populations with APOL1 Risk Alleles. J Am Soc Nephrol 2025:00001751-990000000-00616. [PMID: 40193202 DOI: 10.1681/asn.0000000688] [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: 09/26/2024] [Accepted: 04/01/2025] [Indexed: 05/17/2025] Open
Abstract
Key Points
We aimed to elucidate potential methylation, proteomic, and metabolomic mechanisms by which APOL1 variants may be linked to kidney disease.We report distinct methylation profiling between APOL1 risk allele carriers and noncarriers, many near APOL gene family.We report higher APOL1 protein and lower C18:1 cholesteryl ester in two risk allele carriers.
Background
The APOL1 high-risk haplotype has been associated with CKD and the deterioration of kidney function, particularly in populations with West African ancestry. However, the mechanisms by which APOL1 risk variants increase the risk for kidney disease and its progression have not been fully elucidated.
Methods
We compared methylation (N=3191; 715 [22%] carriers), proteomic (N=1240; 169 [14%] carriers), and metabolomic (N=6309; 674 [11%] carriers) profiles in African and Hispanic/Latino carriers of two APOL1 high-risk alleles (G1/G1, G2/G2, G1/G2) and noncarriers (G0/G0), excluding heterozygotes (G0/G1, G0/G2), from the Population Architecture using Genomics and Epidemiology Consortium and UK Biobank. In each study, the associations between the APOL1 high-risk haplotype and up to 722,719 cytosine-phosphate-guanine (CpG) sites, 2923 proteins, or 836 metabolites were estimated using covariate-adjusted linear regression models, followed by fixed-effects sample size–weighted meta-analyses.
Results
Significant associations were observed between APOL1 high-risk haplotype and methylation at 52 CpG sites, with 48 located on chromosome 22 and 18 in the vicinity of APOL1–4 and MYH9. All significant CpG sites near APOL2 were hypomethylated, whereas those near APOL3 and APOL4 were hypermethylated. APOL1-associated CpG sites were also identified in genes involved in ion transport and mitochondrial stress pathways. Sensitivity analyses indicated consistent yet attenuated effects among heterozygotes, supporting an additive effect of APOL1 risk alleles. Further analyses of the 52 CpG sites identified two near APOL4 exhibiting G1-specific effects, eight associated with CKD but none with eGFR, and three showing heterogeneity by CKD status. In addition, carrying two APOL1 risk alleles was associated with higher plasma APOL1 protein (β=1.12, P
FDR
= 2.26e-70) and lower C18:1 cholesteryl ester metabolite (Z=−4.50, P
FDR = 4.83e-3).
Conclusions
Our results demonstrate differential methylation, proteomic, and metabolomic profiles associated with APOL1 high-risk haplotypes.
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Affiliation(s)
- Xinruo Zhang
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashley W Scadden
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Amarnath Marthi
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Victoria L Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Yishu Qu
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kendra R Ferrier
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Brian D Chen
- Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Julian Avila
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Steven Buyske
- Department of Statistics, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey
| | - Clary B Clish
- Metabolomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Dan Cruz
- Internal Medicine, Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Robert E Gerzsten
- Division of Cardiovascular Medicine, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Christopher R Gignoux
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - LaShaunta Glover
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- Department of Population Health Sciences, School of Medicine, Duke University, Durham, North Carolina
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Anne E Justice
- Department of Population Health Sciences, Geisinger, Danville, Pennsylvania
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Holly Kramer
- Departments of Public Health Sciences and Medicine, Loyola University Chicago, Maywood, Illinois
| | - Leslie Lange
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
- Department of Epidemiology, School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tara Matise
- Department of Genetics, School of Arts and Sciences, Rutgers University, Piscataway, New Jersey
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia
| | - Opeyemi A Olabisi
- Department of Medicine, Nephrology, Duke University, Durham, North Carolina
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Laura M Raffield
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Stephen S Rich
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia
- Department of Genome Sciences, University of Virginia, Charlottesville, Virginia
| | - Jerome I Rotter
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Kent D Taylor
- Department of Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, California
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Amy K Mottl
- UNC Kidney Center, UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Maggie A Stanislawski
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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2
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Gan L, Jiang Q, Huang D, Wu X, Zhu X, Wang L, Xie W, Huang J, Fan R, Jing Y, Tang G, Li XD, Guo J, Yin S. A natural small molecule alleviates liver fibrosis by targeting apolipoprotein L2. Nat Chem Biol 2025; 21:80-90. [PMID: 39103634 DOI: 10.1038/s41589-024-01704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 07/16/2024] [Indexed: 08/07/2024]
Abstract
Liver fibrosis is an urgent clinical problem without effective therapies. Here we conducted a high-content screening on a natural Euphorbiaceae diterpenoid library to identify a potent anti-liver fibrosis lead, 12-deoxyphorbol 13-palmitate (DP). Leveraging a photo-affinity labeling approach, apolipoprotein L2 (APOL2), an endoplasmic reticulum (ER)-rich protein, was identified as the direct target of DP. Mechanistically, APOL2 is induced in activated hepatic stellate cells upon transforming growth factor-β1 (TGF-β1) stimulation, which then binds to sarcoplasmic/ER calcium ATPase 2 (SERCA2) to trigger ER stress and elevate its downstream protein kinase R-like ER kinase (PERK)-hairy and enhancer of split 1 (HES1) axis, ultimately promoting liver fibrosis. As a result, targeting APOL2 by DP or ablation of APOL2 significantly impairs APOL2-SERCA2-PERK-HES1 signaling and mitigates fibrosis progression. Our findings not only define APOL2 as a novel therapeutic target for liver fibrosis but also highlight DP as a promising lead for treatment of this symptom.
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Affiliation(s)
- Lu Gan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiwei Jiang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dong Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xueji Wu
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinying Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Lei Wang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei Xie
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jialuo Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Runzhu Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yihang Jing
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
| | - Guihua Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiang David Li
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory (SZBL), Shenzhen, China
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Jianping Guo
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Sheng Yin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China.
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3
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Gonzales GA, Huang S, Wilkinson L, Nguyen JA, Sikdar S, Piot C, Naumenko V, Rajwani J, Wood CM, Dinh I, Moore M, Cedeño E, McKenna N, Polyak MJ, Amidian S, Ebacher V, Rosin NL, Carneiro MB, Surewaard B, Peters NC, Mody CH, Biernaskie J, Yates RM, Mahoney DJ, Canton J. The pore-forming apolipoprotein APOL7C drives phagosomal rupture and antigen cross-presentation by dendritic cells. Sci Immunol 2024; 9:eadn2168. [PMID: 39485861 DOI: 10.1126/sciimmunol.adn2168] [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: 11/28/2023] [Revised: 07/23/2024] [Accepted: 10/07/2024] [Indexed: 11/03/2024]
Abstract
Conventional dendritic cells (cDCs) generate protective cytotoxic T lymphocyte (CTL) responses against extracellular pathogens and tumors. This is achieved through a process known as cross-presentation (XP), and, despite its biological importance, the mechanism(s) driving XP remains unclear. Here, we show that a cDC-specific pore-forming protein called apolipoprotein L 7C (APOL7C) is up-regulated in response to innate immune stimuli and is recruited to phagosomes. Association of APOL7C with phagosomes led to phagosomal rupture and escape of engulfed antigens to the cytosol, where they could be processed via the endogenous MHC class I antigen processing pathway. Accordingly, mice deficient in APOL7C did not efficiently prime CD8+ T cells in response to immunization with bead-bound and cell-associated antigens. Together, our data indicate the presence of dedicated apolipoproteins that mediate the delivery of phagocytosed proteins to the cytosol of activated cDCs to facilitate XP.
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Affiliation(s)
- Gerone A Gonzales
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Song Huang
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Liam Wilkinson
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jenny A Nguyen
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Saif Sikdar
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Research Institute, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Calgary, Alberta, Canada
| | - Cécile Piot
- Immunobiology Laboratory, Francis Crick Institute, London, UK
| | - Victor Naumenko
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Calgary, Alberta, Canada
- Riddell Centre for Cancer Immunotherapy, Calgary, Alberta, Canada
| | - Jahanara Rajwani
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Research Institute, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Calgary, Alberta, Canada
| | - Cassandra M Wood
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Irene Dinh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Melanie Moore
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Eymi Cedeño
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Neil McKenna
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Maria J Polyak
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
| | - Sara Amidian
- Cell Imaging Core, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | | | - Nicole L Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Matheus B Carneiro
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
| | - Bas Surewaard
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
| | - Nathan C Peters
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
| | - Christopher H Mody
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Robin M Yates
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
| | - Douglas J Mahoney
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
- Alberta Children's Research Institute, Calgary, Alberta, Canada
- Arnie Charbonneau Cancer Research Institute, Calgary, Alberta, Canada
- Riddell Centre for Cancer Immunotherapy, Calgary, Alberta, Canada
| | - Johnathan Canton
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Riddell Centre for Cancer Immunotherapy, Calgary, Alberta, Canada
- Calvin, Joan and Phoebe Snyder Institute for Chronic Disease, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, Calgary, Alberta, Canada
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4
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Wang Y, Nguyen HP, Xue P, Xie Y, Yi D, Lin F, Dinh J, Viscarra JA, Ibe NU, Duncan RE, Sul HS. ApoL6 associates with lipid droplets and disrupts Perilipin1-HSL interaction to inhibit lipolysis. Nat Commun 2024; 15:186. [PMID: 38167864 PMCID: PMC10762002 DOI: 10.1038/s41467-023-44559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
Adipose tissue stores triacylglycerol (TAG) in lipid droplets (LD) and release fatty acids upon lipolysis during energy shortage. We identify ApoL6 as a LD-associated protein mainly found in adipose tissue, specifically in adipocytes. ApoL6 expression is low during fasting but induced upon feeding. ApoL6 knockdown results in smaller LD with lower TAG content in adipocytes, while ApoL6 overexpression causes larger LD with higher TAG content. We show that the ApoL6 affects adipocytes through inhibition of lipolysis. While ApoL6, Perilipin 1 (Plin1), and HSL can form a complex on LD, C-terminal ApoL6 directly interacts with N-terminal Plin1 to prevent Plin1 binding to HSL, to inhibit lipolysis. Thus, ApoL6 ablation decreases white adipose tissue mass, protecting mice from diet-induced obesity, while ApoL6 overexpression in adipose brings obesity and insulin resistance, making ApoL6 a potential future target against obesity and diabetes.
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Affiliation(s)
- Yuhui Wang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Hai P Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Pengya Xue
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ying Xie
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Danielle Yi
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Frances Lin
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jennie Dinh
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Jose A Viscarra
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Nnejiuwa U Ibe
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Robin E Duncan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Kinesiology and Health Sciences, University of Waterloo, Waterloo, ON, N2T 2N4, Canada
| | - Hei S Sul
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, 94720, USA.
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5
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Chailertrit V, Panthum T, Kongkaew L, Chalermwong P, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Peyachoknagul S, Han K, Srikulnath K. Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus). Genomics Inform 2023; 21:e47. [PMID: 38224714 PMCID: PMC10788355 DOI: 10.5808/gi.23075] [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: 09/18/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 01/17/2024] Open
Abstract
Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.
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Affiliation(s)
- Visarut Chailertrit
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani 12120, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Lalida Kongkaew
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Piangjai Chalermwong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Botany, Kasetsart University, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Surin Peyachoknagul
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Korea
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok 10900, Thailand
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6
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APOL4, a Novel Immune-Related Prognostic Biomarker for Glioma. J Clin Med 2022; 11:jcm11195765. [PMID: 36233633 PMCID: PMC9572388 DOI: 10.3390/jcm11195765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Glioma is the common, most aggressive and poorest prognostic tumor type in the brain. More and more biomarkers associated with glioma treatment, prognosis, and immunity are being discovered. Here, we aimed to explore the underlying biological functions and prognostic predictive value of Apolipoprotein L4 (APOL4) in glioma. We downloaded the expression data of APOL4 and clinical information from several databases and used R software for preprocessing. The clinical significance of APOL4 in a glioma outcome was explored by the Cox regression analysis and Kaplan–Meier survival analysis. In addition, immune infiltrates and microenvironmental indicators were assessed by CIBERSORT and TIMER. GO and KEGG analyses were used to analyze the potential functions of APOL4 in gliomas. APOL4 expression was increased in glioma specimens compared to normal tissues and correlated dramatically with the WHO grade. A survival analysis showed a shorter overall survival (OS) in glioma patients with APOL4 overexpression, and a Cox regression analysis showed that APOL4 was an independent prognostic factor for the OS of glioma patients. GSEA, GO, and KEGG enrichment analyses showed remarkable enrichment in immune-related pathways. APOL4 expression was positively correlated with immune infiltration (including DC cells, neutrophils, CD8+ T cells, B cells, macrophages, CD4+ T cells, etc.) and microenvironmental parameters (including immune, stromal, and ESTIMATE scores) in gliomas. Glioma patients with a higher expression of APOL4 may be more sensitive to immune checkpoint inhibitors (ICI). In conclusion, these findings suggest that APOL4 is associated with the tumor grade and immune infiltrates; APOL4 may be a new and potential biomarker for therapeutic and prognostic evaluations that may further suggest the therapeutic efficacy of immunotherapy.
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Gerstner L, Chen M, Kampf LL, Milosavljevic J, Lang K, Schneider R, Hildebrandt F, Helmstädter M, Walz G, Hermle T. Inhibition of endoplasmic reticulum stress signaling rescues cytotoxicity of human apolipoprotein-L1 risk variants in Drosophila. Kidney Int 2022; 101:1216-1231. [PMID: 35120995 PMCID: PMC10061223 DOI: 10.1016/j.kint.2021.12.031] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 01/01/2023]
Abstract
Risk variants of the apolipoprotein-L1 (APOL1) gene are associated with severe kidney disease, putting homozygous carriers at risk. Since APOL1 lacks orthologs in all major model organisms, a wide range of mechanisms frequently in conflict have been described for APOL1-associated nephropathies. The genetic toolkit in Drosophila allows unique in vivo insights into disrupted cellular homeostasis. To perform a mechanistic analysis, we expressed human APOL1 control and gain-of-function kidney risk variants in the podocyte-like garland cells of Drosophila nephrocytes and a wing precursor tissue. Expression of APOL1 risk variants was found to elevate endocytic function of garland cell nephrocytes that simultaneously showed early signs of cell death. Wild-type APOL1 had a significantly milder effect, while a control transgene with deletion of the short BH3 domain showed no overt phenotype. Nephrocyte endo-lysosomal function and slit diaphragm architecture remained unaffected by APOL1 risk variants, but endoplasmic reticulum (ER) swelling, chaperone induction, and expression of the reporter Xbp1-EGFP suggested an ER stress response. Pharmacological inhibition of ER stress diminished APOL1-mediated cell death and direct ER stress induction enhanced nephrocyte endocytic function similar to expression of APOL1 risk variants. We confirmed APOL1-dependent ER stress in the Drosophila wing precursor where silencing the IRE1-dependent branch of ER stress signaling by inhibition with Xbp1-RNAi abrogated cell death, representing the first rescue of APOL1-associated cytotoxicity in vivo. Thus, we uncovered ER stress as an essential consequence of APOL1 risk variant expression in vivo in Drosophila, suggesting a central role of this pathway in the pathogenesis of APOL1-associated nephropathies.
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Affiliation(s)
- Lea Gerstner
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Mengmeng Chen
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Lina L Kampf
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Julian Milosavljevic
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Konrad Lang
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Ronen Schneider
- Renal Division, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Friedhelm Hildebrandt
- Renal Division, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Martin Helmstädter
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany
| | - Gerd Walz
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany; Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Tobias Hermle
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center-University of Freiburg, Freiburg, Germany.
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Pan X. The Roles of Fatty Acids and Apolipoproteins in the Kidneys. Metabolites 2022; 12:metabo12050462. [PMID: 35629966 PMCID: PMC9145954 DOI: 10.3390/metabo12050462] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
The kidneys are organs that require energy from the metabolism of fatty acids and glucose; several studies have shown that the kidneys are metabolically active tissues with an estimated energy requirement similar to that of the heart. The kidneys may regulate the normal and pathological function of circulating lipids in the body, and their glomerular filtration barrier prevents large molecules or large lipoprotein particles from being filtered into pre-urine. Given the permeable nature of the kidneys, renal lipid metabolism plays an important role in affecting the rest of the body and the kidneys. Lipid metabolism in the kidneys is important because of the exchange of free fatty acids and apolipoproteins from the peripheral circulation. Apolipoproteins have important roles in the transport and metabolism of lipids within the glomeruli and renal tubules. Indeed, evidence indicates that apolipoproteins have multiple functions in regulating lipid import, transport, synthesis, storage, oxidation and export, and they are important for normal physiological function. Apolipoproteins are also risk factors for several renal diseases; for example, apolipoprotein L polymorphisms induce kidney diseases. Furthermore, renal apolipoprotein gene expression is substantially regulated under various physiological and disease conditions. This review is aimed at describing recent clinical and basic studies on the major roles and functions of apolipoproteins in the kidneys.
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Affiliation(s)
- Xiaoyue Pan
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, New York, NY 11501, USA;
- Diabetes and Obesity Research Center, NYU Langone Hospital—Long Island, Mineola, New York, NY 11501, USA
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Feng X, Zhao Z, Zhao Y, Song Z, Ma Y, Wang W. Development of Personalized Signature Based on the Immune Landscape to Predict the Prognosis of Osteosarcoma and the Response to Immunotherapy and Targeted Therapy. Front Mol Biosci 2022; 8:783915. [PMID: 35127816 PMCID: PMC8811188 DOI: 10.3389/fmolb.2021.783915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
As a heterogeneous and aggressive disease, osteosarcoma (OS) faces great challenges to prognosis and individualized treatment. Hence, we explore the role of immune-related genes in predicting prognosis and responsiveness to immunotherapy and targeted therapies in patients with OS based on the immunological landscape of osteosarcoma. Based on the database of the Therapeutical Applicable Research to Generate Effective Treatments (TARGET), single-sample gene set enrichment analysis (ssGSEA) was used to obtain the enrichment scores of 29 immune characteristics. A series of bioinformatics methods were performed to construct the immune-related prognostic signature (IRPS). Gene set enrichment analysis and gene set variation analysis were used to explore the biological functions of IRPS. We also analyzed the relationship between IRPS and tumor microenvironment. Lastly, the reactivity of IRPS to immune checkpoint therapy and targeted drugs was explored. The ssGSEA algorithm was used to define two immune subtypes, namely Immunity_High and Immunity_Low. Immunity_High was associated with a good prognosis and was an independent prognostic factor of OS. The IRPS containing 7 genes was constructed by the least absolute shrinkage and selection operator Cox regression. The IRPS can divide patients into low- and high-risk patients. Compared with high-risk patients, low-risk patients had a better prognosis and were positively correlated with immune cell infiltration and immune function. Low-risk patients benefited more from immunotherapy, and the sensitivity of targeted drugs in high- and low-risk groups was determined. IRPS can be used to predict the prognosis of OS patients, and provide therapeutic responsiveness to immunotherapy and targeted therapy.
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Affiliation(s)
- Xiaofei Feng
- Department of Orthopedics, The First Clinical Medical College of Lanzhou University, Gansu, China
| | - Zhenrui Zhao
- Department of Orthopedics, The First Clinical Medical College of Lanzhou University, Gansu, China
| | - Yuhao Zhao
- Department of Orthopedics, The First Clinical Medical College of Lanzhou University, Gansu, China
| | - Zhengdong Song
- Department of Orthopedics, The First Clinical Medical College of Lanzhou University, Gansu, China
| | - Yao Ma
- Clinical Laboratory Center, Gansu Provincial Maternity and Child-Care Hospital, Gansu, China
| | - Wenji Wang
- Department of Orthopedics, Lanzhou University First Affiliated Hospital, Gansu, China
- *Correspondence: Wenji Wang,
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