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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 2024:10.1038/s41589-024-01704-3. [PMID: 39103634 DOI: 10.1038/s41589-024-01704-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [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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2
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Rivedal M, Mikkelsen H, Marti HP, Liu L, Kiryluk K, Knoop T, Bjørneklett R, Haaskjold YL, Furriol J, Leh S, Paunas F, Bábíčková J, Scherer A, Serre C, Eikrem O, Strauss P. Glomerular transcriptomics predicts long term outcome and identifies therapeutic strategies for patients with assumed benign IgA nephropathy. Kidney Int 2024; 105:717-730. [PMID: 38154557 DOI: 10.1016/j.kint.2023.12.010] [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: 10/21/2022] [Revised: 11/17/2023] [Accepted: 12/08/2023] [Indexed: 12/30/2023]
Abstract
Some patients diagnosed with benign IgA nephropathy (IgAN) develop a progressive clinical course, not predictable by known clinical or histopathological parameters. To assess if gene expression can differentiate between progressors and non-progressors with assumed benign IgAN, we tested microdissected glomeruli from archival kidney biopsy sections from adult patients with stable clinical remission (21 non-progressors) or from 15 patients that had undergone clinical progression within a 25-year time frame. Based on 1 240 differentially expressed genes from patients with suitable sequencing results, we identified eight IgAN progressor and nine non-progressor genes using a two-component classifier. These genes, including APOL5 and ZXDC, predicted disease progression with 88% accuracy, 75% sensitivity and 100% specificity on average 21.6 years before progressive disease was clinically documented. APOL lipoproteins are associated with inflammation, autophagy and kidney disease while ZXDC is a zinc-finger transcription factor modulating adaptive immunity. Ten genes from our transcriptomics data overlapped with an external genome wide association study dataset, although the gene set enrichment test was not statistically significant. We also identified 45 drug targets in the DrugBank database, including angiotensinogen, a target of sparsentan (dual antagonist of the endothelin type A receptor and the angiotensin II type 1 receptor) currently investigated for IgAN treatment. Two validation cohorts were used for substantiating key results, one by immunohistochemistry and the other by nCounter technology. Thus, glomerular mRNA sequencing from diagnostic kidney biopsies from patients with assumed benign IgAN can differentiate between future progressors and non-progressors at the time of diagnosis.
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Affiliation(s)
- Mariell Rivedal
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Håvard Mikkelsen
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Lili Liu
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA
| | - Krzysztof Kiryluk
- Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York, New York, USA; Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Thomas Knoop
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Rune Bjørneklett
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Emergency Care Clinic, Haukeland University Hospital, Bergen, Norway
| | - Yngvar Lunde Haaskjold
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Jessica Furriol
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sabine Leh
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Flavia Paunas
- Department of Medicine, Haugesund Hospital, Haugesund, Norway
| | - Janka Bábíčková
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Andreas Scherer
- Spheromics, Kontiolahti, Finland; Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Camille Serre
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Oystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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Qu H, Mao M, Wang K, Mu Z, Hu B. Knockdown of ADAM8 inhibits the proliferation, migration, invasion, and tumorigenesis of renal clear cell carcinoma cells to enhance the immunotherapy efficacy. Transl Res 2024; 266:32-48. [PMID: 37992987 DOI: 10.1016/j.trsl.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/13/2023] [Indexed: 11/24/2023]
Abstract
The current study performed bioinformatics and in vitro and in vivo experiments to explore the effects of ADAM8 on the malignant behaviors and immunotherapeutic efficacy of renal clear cell carcinoma (ccRCC) Cells. The modular genes most associated with immune cells were screened. Then, prognostic risk models were constructed by univariate COX analysis, LASSO regression analysis and multivariate COX analysis, and their diagnostic value was determined. The correlation between tumor mutation load (TMB) scores and the prognosis of ccRCC patients was clarified. Finally, six key genes (ABI3, ADAM8, APOL3, MX2, CCDC69, and STAC3) were analyzed for immunotherapy efficacy. Human and mouse ccRCC cell lines and human proximal tubular epithelial cell lines were used for in vitro cell experiments. The effect of ADAM8 overexpression or knockdown on tumor formation and survival in ccRCC cells was examined by constructing subcutaneous transplanted tumor model. Totally, 636 Black module genes were screened as being most associated with immune cell infiltration. Six genes were subsequently confirmed for the construction of prognostic risk models, of which ABI3, APOL3 and CCDC69 were low-risk factors, while ADAM8, MX2 and STAC3 were high-risk factors. The constructed risk model based on the identified six genes could accurately predict the prognosis of ccRCC patients. Besides, TMB was significantly associated with the prognosis of ccRCC patients. Furthermore, ABI3, ADAM8, APOL3, MX2, CCDC69 and STAC3 might play important roles in treatment concerning CTLA4 inhibitors or PD-1 inhibitors or combined inhibitors. Finally, we confirmed that ADAM8 could promote the proliferation, migration and invasion of ccRCC cells through in vitro experiments, and further found that in in vivo experiments, ADAM8 knockdown could inhibit tumor formation in ccRCC cells, improve the therapeutic effect of anti-PD1, and prolong the survival of mice. Our study highlighted the alleviative role of silencing ADAM8 in ccRCC patients.
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Affiliation(s)
- Hongchen Qu
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China
| | - Minghuan Mao
- Department of Urological Surgery, Fourth affiliated Hospital of China Medical University, Shenyang 110000, PR China
| | - Kai Wang
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China
| | - Zhongyi Mu
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China
| | - Bin Hu
- Department of Urological Surgery, Liaoning Cancer Hospital & Institute, Cancer Hospital of China Medical University, No.44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province 110042, PR China.
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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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5
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Lecordier L, Heo P, Graversen JH, Hennig D, Skytthe MK, Cornet d'Elzius A, Pincet F, Pérez-Morga D, Pays E. Apolipoproteins L1 and L3 control mitochondrial membrane dynamics. Cell Rep 2023; 42:113528. [PMID: 38041817 PMCID: PMC10765320 DOI: 10.1016/j.celrep.2023.113528] [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: 07/12/2023] [Revised: 11/08/2023] [Accepted: 11/17/2023] [Indexed: 12/04/2023] Open
Abstract
Apolipoproteins L1 and L3 (APOLs) are associated at the Golgi with the membrane fission factors phosphatidylinositol 4-kinase-IIIB (PI4KB) and non-muscular myosin 2A. Either APOL1 C-terminal truncation (APOL1Δ) or APOL3 deletion (APOL3-KO [knockout]) reduces PI4KB activity and triggers actomyosin reorganization. We report that APOL3, but not APOL1, controls PI4KB activity through interaction with PI4KB and neuronal calcium sensor-1 or calneuron-1. Both APOLs are present in Golgi-derived autophagy-related protein 9A vesicles, which are involved in PI4KB trafficking. Like APOL3-KO, APOL1Δ induces PI4KB dissociation from APOL3, linked to reduction of mitophagy flux and production of mitochondrial reactive oxygen species. APOL1 and APOL3, respectively, can interact with the mitophagy receptor prohibitin-2 and the mitophagosome membrane fusion factor vesicle-associated membrane protein-8 (VAMP8). While APOL1 conditions PI4KB and APOL3 involvement in mitochondrion fission and mitophagy, APOL3-VAMP8 interaction promotes fusion between mitophagosomal and endolysosomal membranes. We propose that APOL3 controls mitochondrial membrane dynamics through interactions with the fission factor PI4KB and the fusion factor VAMP8.
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Affiliation(s)
- Laurence Lecordier
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Paul Heo
- Laboratoire de Physique de l'Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris-Cité, 75005 Paris, France; Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, 75014 Paris, France
| | - Jonas H Graversen
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Dorle Hennig
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Maria Kløjgaard Skytthe
- Department of Molecular Medicine, Cancer and Inflammation Research, University of Southern Denmark, 5000 Odense C, Denmark
| | | | - Frédéric Pincet
- Laboratoire de Physique de l'Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris-Cité, 75005 Paris, France
| | - David Pérez-Morga
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium; Center for Microscopy and Molecular Imaging (CMMI), Université Libre de Bruxelles, 6041 Gosselies, Belgium
| | - Etienne Pays
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium.
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Fan Z, Ardicoglu R, Batavia AA, Rust R, von Ziegler L, Waag R, Zhang J, Desgeorges T, Sturman O, Dang H, Weber R, Roszkowski M, Moor AE, Schwab ME, Germain PL, Bohacek J, De Bock K. The vascular gene Apold1 is dispensable for normal development but controls angiogenesis under pathological conditions. Angiogenesis 2023; 26:385-407. [PMID: 36933174 PMCID: PMC10328887 DOI: 10.1007/s10456-023-09870-z] [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: 12/09/2022] [Accepted: 02/06/2023] [Indexed: 03/19/2023]
Abstract
The molecular mechanisms of angiogenesis have been intensely studied, but many genes that control endothelial behavior and fate still need to be described. Here, we characterize the role of Apold1 (Apolipoprotein L domain containing 1) in angiogenesis in vivo and in vitro. Single-cell analyses reveal that - across tissues - the expression of Apold1 is restricted to the vasculature and that Apold1 expression in endothelial cells (ECs) is highly sensitive to environmental factors. Using Apold1-/- mice, we find that Apold1 is dispensable for development and does not affect postnatal retinal angiogenesis nor alters the vascular network in adult brain and muscle. However, when exposed to ischemic conditions following photothrombotic stroke as well as femoral artery ligation, Apold1-/- mice display dramatic impairments in recovery and revascularization. We also find that human tumor endothelial cells express strikingly higher levels of Apold1 and that Apold1 deletion in mice stunts the growth of subcutaneous B16 melanoma tumors, which have smaller and poorly perfused vessels. Mechanistically, Apold1 is activated in ECs upon growth factor stimulation as well as in hypoxia, and Apold1 intrinsically controls EC proliferation but not migration. Our data demonstrate that Apold1 is a key regulator of angiogenesis in pathological settings, whereas it does not affect developmental angiogenesis, thus making it a promising candidate for clinical investigation.
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Affiliation(s)
- Zheng Fan
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- Institute of Anatomy, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Raphaela Ardicoglu
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Aashil A Batavia
- Department of Pathology and Molecular Pathology, University and University Hospital Zürich, Zurich, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ruslan Rust
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Lukas von Ziegler
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Rebecca Waag
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Jing Zhang
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
| | - Thibaut Desgeorges
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
| | - Oliver Sturman
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Hairuo Dang
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland
- DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Rebecca Weber
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Martin Roszkowski
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Martin E Schwab
- Department of Health Sciences and Technology, Institute for Regenerative Medicine, University of Zürich, ETH Zürich, Zurich, Switzerland
| | - Pierre-Luc Germain
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland
- Department of Health Sciences and Technology, Computational Neurogenomics, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland
- Department for Molecular Life Sciences, Laboratory of Statistical Bioinformatics, University of Zürich, Zurich, Switzerland
| | - Johannes Bohacek
- Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, ETH Zürich, Zurich, Switzerland.
- Neuroscience Center Zurich, ETH Zürich, University of Zürich, Zurich, Switzerland.
| | - Katrien De Bock
- Department of Health Sciences and Technology, Laboratory of Exercise and Health, ETH Zürich, Zurich, Switzerland.
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Abstract
African trypanosomes are bloodstream protozoan parasites that infect mammals including humans, where they cause sleeping sickness. Long-lasting infection is required to favor parasite transmission between hosts. Therefore, trypanosomes have developed strategies to continuously escape innate and adaptive responses of the immune system, while also preventing premature death of the host. The pathology linked to infection mainly results from inflammation and includes anemia and brain dysfunction in addition to loss of specificity and memory of the antibody response. The serum of humans contains an efficient trypanolytic factor, the membrane pore-forming protein apolipoprotein L1 (APOL1). In the two human-infective trypanosomes, specific parasite resistance factors inhibit APOL1 activity. In turn, many African individuals express APOL1 variants that counteract these resistance factors, enabling them to avoid sleeping sickness. However, these variants are associated with chronic kidney disease, particularly in the context of virus-induced inflammation such as coronavirus disease 2019. Vaccination perspectives are discussed.
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Affiliation(s)
- Etienne Pays
- Laboratory of Molecular Parasitology, Université Libre de Bruxelles, Gosselies, Belgium;
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium;
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium; .,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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Ge Y, Xia J, He C, Liu S. Identification of circRNA-lncRNA-miRNA-mRNA competitive endogenous RNA networks as prognostic bio-markers in head and neck squamous cell carcinoma. Technol Health Care 2023; 31:2193-2212. [PMID: 37522233 DOI: 10.3233/thc-230083] [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: 08/01/2023]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent neoplasms of malignancy. The pathogenesis of HNSCC is involved in the change of gene expression and the abnormal interaction between genes. OBJECTIVE The purpose of our research is to find genes that affect the survival time of patients and construct circRNA-lncRNA-miRNA-mRNA network. This paper aims to reveal the development mechanism of HNSCC and provide new ideas for clinical prognosis prediction. METHODS Transcriptome data were obtained from TCGA and GEO databases. A total of 556 samples were included. We screened the differentially expressed lncRNAs, circRNAs and mRNAs to predict interactions between lncRNA-miRNA, circRNA-miRNA and miRNA-mRNA. Then, we selected the hub mRNAs to predict the prognosis of patients. RESULTS We identified 8 hub prognostic mRNAs (FAM111A, IFIT2, CAV1, KLF9, OCIAD2, SLCO3A1, S100A16 and APOL3) by a series of bioinformatics analyses and established the prognostic ceRNA network of 8 mRNAs, 3 miRNAs, 2 circRNAs and 1 lncRNAs according to the targeting relationship by using databases. CONCLUSION We established the circRNA-lncRNA-miRNA-mRNA gene interaction network in HNSCC. We illuminated the molecular mechanism underlying the gene regulation associated with the pathogenesis of HNSCC and predicted the biomarkers related to prognosis.
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Mayanja R, Kintu C, Diabate O, Soremekun O, Oluwagbemi OO, Wele M, Kalyesubula R, Jjingo D, Chikowore T, Fatumo S. Molecular Dynamic Simulation Reveals Structure Differences in APOL1 Variants and Implication in Pathogenesis of Chronic Kidney Disease. Genes (Basel) 2022; 13:1460. [PMID: 36011371 PMCID: PMC9408642 DOI: 10.3390/genes13081460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/28/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND According to observational studies, two polymorphisms in the apolipoprotein L1 (APOL1) gene have been linked to an increased risk of chronic kidney disease (CKD) in Africans. One polymorphism involves the substitution of two amino-acid residues (S342G and I384M; known as G1), while the other involves the deletion of two amino-acid residues in a row (N388 and Y389; termed G2). Despite the strong link between APOL1 polymorphisms and kidney disease, the molecular mechanisms via which these APOL1 mutations influence the onset and progression of CKD remain unknown. METHODS To predict the active site and allosteric site on the APOL1 protein, we used the Computed Atlas of Surface Topography of Proteins (CASTp) and the Protein Allosteric Sites Server (PASSer). Using an extended molecular dynamics simulation, we investigated the characteristic structural perturbations in the 3D structures of APOL1 variants. RESULTS According to CASTp's active site characterization, the topmost predicted site had a surface area of 964.892 Å2 and a pocket volume of 900.792 Å3. For the top three allosteric pockets, the allostery probability was 52.44%, 46.30%, and 38.50%, respectively. The systems reached equilibrium in about 125 ns. From 0-100 ns, there was also significant structural instability. When compared to G1 and G2, the wildtype protein (G0) had overall high stability throughout the simulation. The root-mean-square fluctuation (RMSF) of wildtype and variant protein backbone Cα fluctuations revealed that the Cα of the variants had a large structural fluctuation when compared to the wildtype. CONCLUSION Using a combination of different computational techniques, we identified binding sites within the APOL1 protein that could be an attractive site for potential inhibitors of APOL1. Furthermore, the G1 and G2 mutations reduced the structural stability of APOL1.
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Affiliation(s)
- Richard Mayanja
- The African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe 31405, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala 10101, Uganda
| | - Christopher Kintu
- The African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe 31405, Uganda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala 10101, Uganda
| | - Oudou Diabate
- The African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe 31405, Uganda
- African Center of Excellence in Bioinformatics (ACE-B), University of Science, Technique and Technologies of Bamako (USTTB), Bamako 3206, Mali
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe 31405, Uganda
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | | | - Mamadou Wele
- African Center of Excellence in Bioinformatics (ACE-B), University of Science, Technique and Technologies of Bamako (USTTB), Bamako 3206, Mali
| | - Robert Kalyesubula
- Department of Internal Medicine and Department of Physiology, Makerere University, Kampala 10101, Uganda
| | - Daudi Jjingo
- African Center of Excellence in Bioinformatics (ACE-B), Makerere University, Kampala 10101, Uganda
| | - Tinashe Chikowore
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2050, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe 31405, Uganda
- Department of Non-Communicable Disease Epidemiology (NCDE), London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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10
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Identification of Ten-Gene Related to Lipid Metabolism for Predicting Overall Survival of Breast Invasive Carcinoma. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:8348780. [PMID: 35919504 PMCID: PMC9293542 DOI: 10.1155/2022/8348780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 12/11/2022]
Abstract
Background. Predicting the risk of poor prognosis of breast cancer is crucial to treating breast cancer. This study investigated the prognostic assessment of 10 lipid metabolism-related genes constructed as breast cancer models based on this study. Methods. The TCGA database was used to obtain clinical information and expression data of breast cancer patients, and GSEA analysis and univariate and multivariate Cox proportional risk regression models were performed to identify lipid metabolism genes closely associated with overall survival (OS) of breast cancer patients and to construct a prognostic risk score model based on lipid metabolism gene markers. The Kaplan–Meier method was used to analyze the survival status of patients with high and low-risk scores, and ROC curves assessed the accuracy of this risk score. Finally, the relationship between this risk score and clinicopathological characteristics of BRCA was analyzed in a stratified manner, and the validity of this risk score as an independent prognostic factor was determined using univariate and multivariate Cox regression analyses. Results. One hundred and forty-four differentially expressed lipid metabolism-related genes were identified in cancer and paracancerous tissues in BRCA, 21 of which were associated with overall survival (OS) in BRCA
. Univariate and multivariate Cox analyses revealed that age, grade, and risk score were independent prognostic factors for BRCA. Multivariate Cox regression analysis further identified APOL4, NR1H3, SLC25A5, APOL3, OSBPL1A, DYNLT1, IMMT, MAP2K6, ZDHHC8, and RAB2A lipid metabolism-related genes as independent prognostic markers for BRCA. A prognostic risk score model was developed by labeling lipid metabolism genes with these 10 genes, and patients with BRCA with high-risk scores in the model sample had significantly worse OS than those with low-risk
. The ROC curve area (AUC) of this risk score model was 0.712. Conclusion. By mining the TCGA database, we identified 10 lipid metabolism-related genes APOL4, NR1H3, SLC25A5, APOL3, OSBPL1A, DYNLT1, IMMT, MAP2K6, ZDHHC8, and RAB2A, which are closely related to the prognosis of BRCA patients, and constructed a prognostic risk scoring system based on 10 lipid metabolism genes tags.
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11
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Hubacek JA, Hruba P, Adamkova V, Pokorna E, Viklicky O. Apolipoprotein L1 variability is associated with increased risk of renal failure in the Czech population. Gene X 2022; 818:146248. [PMID: 35085711 DOI: 10.1016/j.gene.2022.146248] [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: 04/29/2021] [Revised: 12/23/2021] [Accepted: 01/21/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND With stage 5 chronic kidney disease (CKD5) more prevalent in the Czech Republic than in most European countries, genetic susceptibility is potentially implicated. METHODS In a group of 1489 CKD5 kidney transplantation patients (93% with complete clinical characteristics; mean age 52.0 years, 37% females) and 2559 healthy controls (mean age 49.0 years, 51% females), we examined the prevalence of six APOL1 SNPs (rs73885319, rs71785313, rs13056427, rs136147, rs10854688 and rs9610473) and one newly detected 55-nucleotide insertion/deletion polymorphism. RESULTS The rs73885319 and rs71785313 variants were monomorphic in the Czech Caucasian population. Genotype frequencies of the three SNPs examined (rs13056427, rs136147 and rs9610473) were almost identical in patients and controls (all P values were between 0.39 and 0.91). Minor homozygotes of rs10854688 were more common between the patients (13.2%) than in controls (10.7%) (OR [95% CI]; 1.32 [1.08-1.64]; P < 0.01). Prevalence of the newly detected 55-bp APOL1 deletion was significantly higher in CKD5 patients (3.0% vs. 1.7%; OR [95% CI]; 1.80 [1.16-2.80]; P < 0.01) compared to controls. Frequencies of some individual APOL1 haplotypes were borderline different between patients and controls. CONCLUSION We found an association between rs10854688 SNP within the APOL1 gene and end-stage renal disease in the Czech Caucasian population. Further independent studies are required before a conclusive association between the newly detected APOL1 insertion/deletion polymorphism and CKD5 can be confirmed.
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Affiliation(s)
- Jaroslav A Hubacek
- Experimental Medicine Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic.
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Vera Adamkova
- Department of Preventive Cardiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Eva Pokorna
- Transplantation Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czech Republic; Department of Nephrology, Transplantation Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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12
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Mu T, Hu H, Feng X, Ma Y, Wang Y, Liu J, Yu B, Wen W, Zhang J, Gu Y. Screening and Conjoint Analysis of Key lncRNAs for Milk Fat Metabolism in Dairy Cows. Front Genet 2022; 13:772115. [PMID: 35186023 PMCID: PMC8850724 DOI: 10.3389/fgene.2022.772115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play an important regulatory role in various biological processes as a key regulatory factor. However, the complete expression profile of lncRNAs in dairy cows and its function in milk fat synthesis are unknown. In this study, RNA sequencing (RNA-seq) was used to research the whole genome expression of lncRNAs and mRNA transcripts in high and low milk fat percentage (MFP) bovine mammary epithelial cells (BMECs), and joint analysis was carried out. We identified a total of 47 differentially expressed genes (DEGs) and 38 differentially expressed lncRNAs (DELs, Padj <0.05), enrichment analysis screened out 11 candidate DEGs that may regulate milk fat metabolism. Downregulated differential gene ENPP2 (The expression level in BMECs of high milk fat dairy cows was lower than that of low milk fat cows) and upregulated differential gene BCAT1 are more likely to participate in the milk fat metabolism, and its function needs further experiments verification. The enrichment analysis of target genes predicted by DELs identified 7 cis (co-localization) and 10 trans (co-expression) candidate target genes related to milk lipid metabolism, corresponding to a total of 18 DELs. Among them, the targeting relationship between long intervening/intergenic noncoding RNA (lincRNA) TCONS_00082721 and FABP4 is worthy of attention. One hundred and fifty-six competing endogenous RNAs (ceRNAs) interaction regulation networks related to milk fat metabolism were constructed based on the expression information of DELs, differential microRNAs (miRNAs), and lipid metabolism-related target genes. The regulatory network centered on miR-145 will be the focus of subsequent experimental research. The ceRNAs regulatory network related to TCONS_00082721 and TCONS_00172817 are more likely to be involved in milk fat synthesis. These results will provide new ways to understand the complex biology of dairy cow milk fat synthesis and provide valuable information for breed improvement of Chinese Holstein cow.
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Affiliation(s)
- Tong Mu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Honghong Hu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Xiaofang Feng
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yanfen Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, Ningxia Hui Autonomous Region, Ningxia University, Yinchuan, China
| | - Ying Wang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Jiamin Liu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Baojun Yu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Wan Wen
- Animal Husbandry Extension Station, Yinchuan, China
| | - Juan Zhang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yaling Gu
- School of Agriculture, Ningxia University, Yinchuan, China
- *Correspondence: Yaling Gu,
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13
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Min Y, Feng Y, Luo H, Hu D, Wei X, He D, Yin G, Fan S. Identifying and Validating of an Autophagy-Related Gene Signature for the Prediction of Early Relapse in Breast Cancer. Front Endocrinol (Lausanne) 2022; 13:824362. [PMID: 35250881 PMCID: PMC8888901 DOI: 10.3389/fendo.2022.824362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/26/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Compelling evidence has demonstrated the pivotal role of autophagy in the prognosis of breast cancer. Breast cancer (BC) patients with early relapse consistently exhibited worse survival. METHODS The autophagy-related genes were derived from the Human Autophagy Database (HADb) and high-sequencing data were obtained from The Cancer Genome Atlas (TCGA). Discrepantly expressed autophagy genes (DEAGs) between early relapse and long-term survival groups were performed using the Linear Models for Microarray data (LIMMA) method. Lasso Cox regression analysis was conducted for the selection of the 4-gene autophagy-related gene signature. GSE42568 and GSE21653 databases were enrolled in this study for the external validation of the signature. Then patients were divided into high and low-risk groups based on the specific score formula. GSEA was used to discover the related signaling pathway. The Kaplan-Meier curves and the receiver operating characteristic (ROC) curves were used to evaluate the discrimination and accuracy of the 4-gene signature. RESULTS A signature composed of four autophagy-related mRNA including APOL1, HSPA8, SIRT1, and TP73, was identified as significantly associated with the early relapse in BC patients. Time-dependent receiver-operating characteristic at 1 year suggested remarkable accuracy of the signature [area under the curve (AUC = 0.748)]. The risk score model based on the autophagy-related signature showed favorable predicting value in 1-, 2-, and 3-year relapse-free survival (RFS) in training and two validating cohorts. The GSEA displayed gene sets were remarkably enriched in carcinogenic activation pathways and autophagy-related pathways. The nomogram involving three variables (progesterone receptor status, T stage, and 4-gene signature) exhibited relatively good discrimination with a C-index of 0.766. CONCLUSIONS Our study establishes an autophagy-related 4-gene signature that can effectively stratify the high-risk and low-risk BC patients for early relapse. Combined with the clinicopathological variables, the signature could significantly help oncologists tailor more efficient treatment strategies for BC patients.
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Affiliation(s)
- Yu Min
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yang Feng
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Haojun Luo
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Daixing Hu
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaoyuan Wei
- Department of Cardiology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Danshuang He
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guobing Yin
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shenghao Fan
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Shenghao Fan, ; orcid.org/0000-0002-0929-2199
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14
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Ning B, Guo C, Kong A, Li K, Xie Y, Shi H, Gu J. Calcium Signaling Mediates Cell Death and Crosstalk with Autophagy in Kidney Disease. Cells 2021; 10:cells10113204. [PMID: 34831428 PMCID: PMC8622220 DOI: 10.3390/cells10113204] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/13/2021] [Indexed: 12/15/2022] Open
Abstract
The kidney is an important organ for the maintenance of Ca2+ homeostasis in the body. However, disruption of Ca2+ homeostasis will cause a series of kidney diseases, such as acute kidney injury (AKI), chronic kidney disease (CKD), renal ischemia/reperfusion (I/R) injury, autosomal dominant polycystic kidney disease (ADPKD), podocytopathy, and diabetic nephropathy. During the progression of kidney disease, Ca2+ signaling plays key roles in various cell activities such as necrosis, apoptosis, eryptosis and autophagy. Importantly, there are complex Ca2+ flux networks between the endoplasmic reticulum (ER), mitochondria and lysosomes which regulate intracellular Ca2+ signaling in renal cells and contribute to kidney disease. In addition, Ca2+ signaling also links the crosstalk between various cell deaths and autophagy under the stress of heavy metals or high glucose. In this regard, we present a review of Ca2+ signaling in cell death and crosstalk with autophagy and its potential as a therapeutic target for the development of new and efficient drugs against kidney diseases.
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Affiliation(s)
- Bo Ning
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (B.N.); (C.G.); (A.K.); (K.L.); (H.S.)
| | - Chuanzhi Guo
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (B.N.); (C.G.); (A.K.); (K.L.); (H.S.)
| | - Anqi Kong
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (B.N.); (C.G.); (A.K.); (K.L.); (H.S.)
| | - Kongdong Li
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (B.N.); (C.G.); (A.K.); (K.L.); (H.S.)
| | - Yimin Xie
- Affiliated Hospital of Jiangsu University—Yixing Hospital, Yixing 214200, China;
| | - Haifeng Shi
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (B.N.); (C.G.); (A.K.); (K.L.); (H.S.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jie Gu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (B.N.); (C.G.); (A.K.); (K.L.); (H.S.)
- Correspondence: ; Tel.: +86-0511-88791923
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15
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Ultsch M, Holliday MJ, Gerhardy S, Moran P, Scales SJ, Gupta N, Oltrabella F, Chiu C, Fairbrother W, Eigenbrot C, Kirchhofer D. Structures of the ApoL1 and ApoL2 N-terminal domains reveal a non-classical four-helix bundle motif. Commun Biol 2021; 4:916. [PMID: 34316015 PMCID: PMC8316464 DOI: 10.1038/s42003-021-02387-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Apolipoprotein L1 (ApoL1) is a circulating innate immunity protein protecting against trypanosome infection. However, two ApoL1 coding variants are associated with a highly increased risk of chronic kidney disease. Here we present X-ray and NMR structures of the N-terminal domain (NTD) of ApoL1 and of its closest relative ApoL2. In both proteins, four of the five NTD helices form a four-helix core structure which is different from the classical four-helix bundle and from the pore-forming domain of colicin A. The reactivity with a conformation-specific antibody and structural models predict that this four-helix motif is also present in the NTDs of ApoL3 and ApoL4, suggesting related functions within the small ApoL family. The long helix 5 of ApoL1 is conformationally flexible and contains the BH3-like region. This BH3-like α-helix resembles true BH3 domains only in sequence and structure but not in function, since it does not bind to the pro-survival members of the Bcl-2 family, suggesting a Bcl-2-independent role in cytotoxicity. These findings should expedite a more comprehensive structural and functional understanding of the ApoL immune protein family.
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Affiliation(s)
- Mark Ultsch
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Michael J Holliday
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Stefan Gerhardy
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Paul Moran
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Suzie J Scales
- Department of Immunology, Genentech Inc., South San Francisco, CA, USA
| | - Nidhi Gupta
- Department of Immunology, Genentech Inc., South San Francisco, CA, USA
| | | | - Cecilia Chiu
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, USA
| | - Wayne Fairbrother
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA
| | - Charles Eigenbrot
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Daniel Kirchhofer
- Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA, USA.
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16
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Pays E, Nolan DP. Genetic and immunological basis of human African trypanosomiasis. Curr Opin Immunol 2021; 72:13-20. [PMID: 33721725 PMCID: PMC8589022 DOI: 10.1016/j.coi.2021.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 12/11/2022]
Abstract
Human African trypanosomiasis, or sleeping sickness, results from infection by two subspecies of the protozoan flagellate parasite Trypanosoma brucei, termed Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, prevalent in western and eastern Africa respectively. These subspecies escape the trypanolytic potential of human serum, which efficiently acts against the prototype species Trypanosoma brucei brucei, responsible for the Nagana disease in cattle. We review the various strategies and components used by trypanosomes to counteract the immune defences of their host, highlighting the adaptive genomic evolution that occurred in both parasite and host to take the lead in this battle. The main parasite surface antigen, named Variant Surface Glycoprotein or VSG, appears to play a key role in different processes involved in the dialogue with the host.
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Affiliation(s)
- Etienne Pays
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, 6041 Gosselies, Belgium.
| | - Derek P Nolan
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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17
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Affiliation(s)
- Etienne Pays
- Laboratory of Molecular Parasitology, IBMM, Université Libre de Bruxelles, Gosselies, Belgium
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18
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APOL1 variant-associated kidney disease: from trypanosomes to podocyte cytoskeleton. Kidney Int 2020; 98:1373-1377. [PMID: 32835731 DOI: 10.1016/j.kint.2020.07.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/15/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022]
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