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Stankovic S, Shekari S, Huang QQ, Gardner EJ, Ivarsdottir EV, Owens NDL, Mavaddat N, Azad A, Hawkes G, Kentistou KA, Beaumont RN, Day FR, Zhao Y, Jonsson H, Rafnar T, Tragante V, Sveinbjornsson G, Oddsson A, Styrkarsdottir U, Gudmundsson J, Stacey SN, Gudbjartsson DF, Kennedy K, Wood AR, Weedon MN, Ong KK, Wright CF, Hoffmann ER, Sulem P, Hurles ME, Ruth KS, Martin HC, Stefansson K, Perry JRB, Murray A. Genetic links between ovarian ageing, cancer risk and de novo mutation rates. Nature 2024; 633:608-614. [PMID: 39261734 PMCID: PMC11410666 DOI: 10.1038/s41586-024-07931-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/08/2024] [Indexed: 09/13/2024]
Abstract
Human genetic studies of common variants have provided substantial insight into the biological mechanisms that govern ovarian ageing1. Here we report analyses of rare protein-coding variants in 106,973 women from the UK Biobank study, implicating genes with effects around five times larger than previously found for common variants (ETAA1, ZNF518A, PNPLA8, PALB2 and SAMHD1). The SAMHD1 association reinforces the link between ovarian ageing and cancer susceptibility1, with damaging germline variants being associated with extended reproductive lifespan and increased all-cause cancer risk in both men and women. Protein-truncating variants in ZNF518A are associated with shorter reproductive lifespan-that is, earlier age at menopause (by 5.61 years) and later age at menarche (by 0.56 years). Finally, using 8,089 sequenced trios from the 100,000 Genomes Project (100kGP), we observe that common genetic variants associated with earlier ovarian ageing associate with an increased rate of maternally derived de novo mutations. Although we were unable to replicate the finding in independent samples from the deCODE study, it is consistent with the expected role of DNA damage response genes in maintaining the genetic integrity of germ cells. This study provides evidence of genetic links between age of menopause and cancer risk.
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Affiliation(s)
- Stasa Stankovic
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Saleh Shekari
- University of Exeter Medical School, University of Exeter, Exeter, UK
- School of Public Health, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Qin Qin Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Eugene J Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Nick D L Owens
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Nasim Mavaddat
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ajuna Azad
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gareth Hawkes
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Robin N Beaumont
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Felix R Day
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | - Kitale Kennedy
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Andrew R Wood
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Michael N Weedon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ken K Ong
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Caroline F Wright
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Katherine S Ruth
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - John R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
| | - Anna Murray
- University of Exeter Medical School, University of Exeter, Exeter, UK.
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2
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Zhou PY, Zhu DX, Chen YJ, Feng QY, Mao YH, Zhuang AB, Xu JM. High patatin like phospholipase domain containing 8 expression as a biomarker for poor prognosis of colorectal cancer. World J Gastrointest Oncol 2024; 16:787-797. [PMID: 38577466 PMCID: PMC10989391 DOI: 10.4251/wjgo.v16.i3.787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/19/2023] [Accepted: 01/22/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Patatin like phospholipase domain containing 8 (PNPLA8) has been shown to play a significant role in various cancer entities. Previous studies have focused on its roles as an antioxidant and in lipid peroxidation. However, the role of PNPLA8 in colorectal cancer (CRC) progression is unclear. AIM To explore the prognostic effects of PNPLA8 expression in CRC. METHODS A retrospective cohort containing 751 consecutive CRC patients was enrolled. PNPLA8 expression in tumor samples was evaluated by immunohistochemistry staining and semi-quantitated with immunoreactive scores. CRC patients were divided into high and low PNPLA8 expression groups based on the cut-off values, which were calculated by X-tile software. The prognostic value of PNPLA8 was identified using univariate and multivariate Cox regression analysis. The overall survival (OS) rates of CRC patients in the study cohort were compared with Kaplan-Meier analysis and Log-rank test. RESULTS PNPLA8 expression was significantly associated with distant metastases in our cohort (P = 0.048). CRC patients with high PNPLA8 expression indicated poor OS (median OS = 35.3, P = 0.005). CRC patients with a higher PNPLA8 expression at either stage I and II or stage III and IV had statistically significant shorter OS. For patients with left-sided colon and rectal cancer, the survival curves of two PNPLA8-expression groups showed statistically significant differences. Multivariate analysis also confirmed that high PNPLA8 expression was an independent prognostic factor for overall survival (hazard ratio HR = 1.328, 95%CI: 1.016-1.734, P = 0.038). CONCLUSION PNPLA8 is a novel independent prognostic factor for CRC. These findings suggest that PNPLA8 is a potential target in clinical CRC management.
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Affiliation(s)
- Peng-Yang Zhou
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - De-Xiang Zhu
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Yi-Jiao Chen
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Qing-Yang Feng
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Yi-Hao Mao
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Ao-Bo Zhuang
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Jian-Min Xu
- Department of General Surgery, Zhongshan Hospital Fudan University, Shanghai 200032, China
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Abdel-Hamid MS, Abdel-Salam GMH, Abdel-Ghafar SF, Zaki MS. Delineating the phenotype of PNPLA8-related mitochondriopathies. Clin Genet 2024; 105:92-98. [PMID: 37671596 DOI: 10.1111/cge.14421] [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: 07/13/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/07/2023]
Abstract
Pathogenic variants in PNPLA8 have been described either with congenital onset displaying congenital microcephaly, early onset epileptic encephalopathy and early lethality or childhood neurodegeneration with progressive microcephaly. Moreover, a phenotype comprising adulthood onset cerebellar ataxia and peripheral neuropathy was also reported. To our knowledge, only six patients with biallelic variants in PNPLA8 have been reported so far. Here, we report the clinical and molecular characterizations of three additional patients in whom exome sequencing identified a loss of function variant (c.1231C>T, p.Arg411Ter) in Family I and a missense variant (c.1559T>A, p.Val520Asp) in Family II in PNPLA8. Patient 1 presented with the congenital form of the disease while Patients 2 and 3 showed progressive microcephaly, infantile onset seizures, progressive cortical atrophy, white matter loss, bilateral degeneration of basal ganglia, and cystic encephalomalacia. Therefore, our results add the infantile onset as a new distinct phenotype of the disease and suggest that the site of the variant rather than its type is strongly correlated with the disease onset. In addition, these conditions demonstrate some overlapping features representing a spectrum with clinical features always aligning with different age of onset.
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Affiliation(s)
- Mohamed S Abdel-Hamid
- Medical Molecular Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Sherif F Abdel-Ghafar
- Medical Molecular Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
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Grigalionienė K, Burnytė B, Ambrozaitytė L, Utkus A. Wide diagnostic and genotypic spectrum in patients with suspected mitochondrial disease. Orphanet J Rare Dis 2023; 18:307. [PMID: 37784170 PMCID: PMC10544509 DOI: 10.1186/s13023-023-02921-0] [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: 04/25/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Mitochondrial Diseases (MDs) are a diverse group of neurometabolic disorders characterized by impaired mitochondrial oxidative phosphorylation and caused by pathogenic variants in more than 400 genes. The implementation of next-generation sequencing (NGS) technologies helps to increase the understanding of molecular basis and diagnostic yield of these conditions. The purpose of the study was to investigate diagnostic and genotypic spectrum in patients with suspected MD. The comprehensive analysis of mtDNA variants using Sanger sequencing was performed in the group of 83 unrelated individuals with clinically suspected mitochondrial disease. Additionally, targeted next generation sequencing or whole exome sequencing (WES) was performed for 30 patients of the study group. RESULTS The overall diagnostic rate was 21.7% for the patients with suspected MD, increasing to 36.7% in the group of patients where NGS methods were applied. Mitochondrial disease was confirmed in 11 patients (13.3%), including few classical mitochondrial syndromes (MELAS, MERRF, Leigh and Kearns-Sayre syndrome) caused by pathogenic mtDNA variants (8.4%) and MDs caused by pathogenic variants in five nDNA genes. Other neuromuscular diseases caused by pathogenic variants in seven nDNA genes, were confirmed in seven patients (23.3%). CONCLUSION The wide spectrum of identified rare mitochondrial or neurodevelopmental diseases proves that MD suspected patients would mostly benefit from an extensive genetic profiling allowing rapid diagnostics and improving the care of these patients.
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Affiliation(s)
- Kristina Grigalionienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania.
| | - Birutė Burnytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| | - Laima Ambrozaitytė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Santariškių Str. 2, Vilnius, LT-08661, Lithuania
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Moon SH, Dilthey BG, Guan S, Sims HF, Pittman SK, Keith AL, Jenkins CM, Weihl CC, Gross RW. Genetic deletion of skeletal muscle iPLA 2γ results in mitochondrial dysfunction, muscle atrophy and alterations in whole-body energy metabolism. iScience 2023; 26:106895. [PMID: 37275531 PMCID: PMC10239068 DOI: 10.1016/j.isci.2023.106895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 02/28/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023] Open
Abstract
Skeletal muscle is the major site of glucose utilization in mammals integrating serum glucose clearance with mitochondrial respiration. To mechanistically elucidate the roles of iPLA2γ in skeletal muscle mitochondria, we generated a skeletal muscle-specific calcium-independent phospholipase A2γ knockout (SKMiPLA2γKO) mouse. Genetic ablation of skeletal muscle iPLA2γ resulted in pronounced muscle weakness, muscle atrophy, and increased blood lactate resulting from defects in mitochondrial function impairing metabolic processing of pyruvate and resultant bioenergetic inefficiency. Mitochondria from SKMiPLA2γKO mice were dysmorphic displaying marked changes in size, shape, and interfibrillar juxtaposition. Mitochondrial respirometry demonstrated a marked impairment in respiratory efficiency with decreases in the mass and function of oxidative phosphorylation complexes and cytochrome c. Further, a pronounced decrease in mitochondrial membrane potential and remodeling of cardiolipin molecular species were prominent. Collectively, these alterations prevented body weight gain during high-fat feeding through enhanced glucose disposal without efficient capture of chemical energy thereby altering whole-body bioenergetics.
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Affiliation(s)
- Sung Ho Moon
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Beverly Gibson Dilthey
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shaoping Guan
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Harold F. Sims
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Sara K. Pittman
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Amy L. Keith
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Christopher M. Jenkins
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Conrad C. Weihl
- Department of Neurology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Richard W. Gross
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Center for Cardiovascular Research, Washington University School of Medicine, Saint Louis, MO 63110, USA
- Department of Chemistry, Washington University, Saint Louis, MO 63130, USA
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Lulić AM, Katalinić M. The PNPLA family of enzymes: characterisation and biological role. Arh Hig Rada Toksikol 2023; 74:75-89. [PMID: 37357879 PMCID: PMC10291501 DOI: 10.2478/aiht-2023-74-3723] [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: 02/01/2023] [Revised: 02/01/2023] [Accepted: 05/01/2023] [Indexed: 06/27/2023] Open
Abstract
This paper brings a brief review of the human patatin-like phospholipase domain-containing protein (PNPLA) family. Even though it consists of only nine members, their physiological roles and mechanisms of their catalytic activity are not fully understood. However, the results of a number of knock-out and gain- or loss-of-function research models suggest that these enzymes have an important role in maintaining the homeostasis and integrity of organelle membranes, in cell growth, signalling, cell death, and the metabolism of lipids such as triacylglycerol, phospholipids, ceramides, and retinyl esters. Research has also revealed a connection between PNPLA family member mutations or irregular catalytic activity and the development of various diseases. Here we summarise important findings published so far and discuss their structure, localisation in the cell, distribution in the tissues, specificity for substrates, and their potential physiological role, especially in view of their potential as drug targets.
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Affiliation(s)
- Ana-Marija Lulić
- Institute for Medical Research and Occupational Health, Biochemistry and Organic Analytical Chemistry Unit, Zagreb, Croatia
| | - Maja Katalinić
- Institute for Medical Research and Occupational Health, Biochemistry and Organic Analytical Chemistry Unit, Zagreb, Croatia
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Burnyte B, Vilimiene R, Grigalioniene K, Adomaitiene I, Utkus A. Cerebellar Ataxia and Peripheral Neuropathy in a Family With PNPLA8-Associated Disease. Neurol Genet 2023; 9:e200068. [PMID: 37057294 PMCID: PMC10088641 DOI: 10.1212/nxg.0000000000200068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/13/2023] [Indexed: 04/15/2023]
Abstract
Objectives To describe clinical and genetic findings in 2 siblings with slowly progressive ataxia. Methods We studied 2 adult siblings through detailed physical and instrumental examinations. Whole-exome sequencing was used to identify an underlying genetic cause. Results Both siblings presented with adolescence-onset ataxia, progressive sensorimotor polyneuropathy, and preserved cognition over time. The onset of symptoms was between 10 and 14 years of age. A brain MRI demonstrated mild cerebellar atrophy in the older brother at age 45 years. Exome sequencing revealed compound heterozygous loss-of-function variants c.2269del (p.(Thr757GlnfsTer10)) and c.2275_2276del (p.(Leu759AlafsTer4)) in PNPLA8. The novel variant c.2269del results in frameshift with a premature stop codon p.(Thr757GlnfsTer10) and loss of normal enzyme function. Discussion Our findings support the theory that biallelic loss-of-function PNPLA8 variants are involved in neurodegenerative mitochondrial disease. Compared with patients previously described, these patients' phenotype may be interpreted as a milder phenotype associated with a slight progression of ataxia throughout adulthood.
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Affiliation(s)
- Birute Burnyte
- Institute of Biomedical Sciences (B.B., K.G., A.U.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; Institute of Clinical Medicine (R.V.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; and Vilnius University Hospital Santaros Klinikos (I.A.), Vilnius, Lithuania
| | - Ramune Vilimiene
- Institute of Biomedical Sciences (B.B., K.G., A.U.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; Institute of Clinical Medicine (R.V.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; and Vilnius University Hospital Santaros Klinikos (I.A.), Vilnius, Lithuania
| | - Kristina Grigalioniene
- Institute of Biomedical Sciences (B.B., K.G., A.U.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; Institute of Clinical Medicine (R.V.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; and Vilnius University Hospital Santaros Klinikos (I.A.), Vilnius, Lithuania
| | - Irina Adomaitiene
- Institute of Biomedical Sciences (B.B., K.G., A.U.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; Institute of Clinical Medicine (R.V.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; and Vilnius University Hospital Santaros Klinikos (I.A.), Vilnius, Lithuania
| | - Algirdas Utkus
- Institute of Biomedical Sciences (B.B., K.G., A.U.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; Institute of Clinical Medicine (R.V.), Faculty of Medicine, Vilnius University, Vilnius, Lithuania; and Vilnius University Hospital Santaros Klinikos (I.A.), Vilnius, Lithuania
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8
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The phospholipase A 2 superfamily as a central hub of bioactive lipids and beyond. Pharmacol Ther 2023; 244:108382. [PMID: 36918102 DOI: 10.1016/j.pharmthera.2023.108382] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
In essence, "phospholipase A2" (PLA2) means a group of enzymes that release fatty acids and lysophospholipids by hydrolyzing the sn-2 position of glycerophospholipids. To date, more than 50 enzymes possessing PLA2 or related lipid-metabolizing activities have been identified in mammals, and these are subdivided into several families in terms of their structures, catalytic mechanisms, tissue/cellular localizations, and evolutionary relationships. From a general viewpoint, the PLA2 superfamily has mainly been implicated in signal transduction, driving the production of a wide variety of bioactive lipid mediators. However, a growing body of evidence indicates that PLA2s also contribute to phospholipid remodeling or recycling for membrane homeostasis, fatty acid β-oxidation for energy production, and barrier lipid formation on the body surface. Accordingly, PLA2 enzymes are considered one of the key regulators of a broad range of lipid metabolism, and perturbation of specific PLA2-driven lipid pathways often disrupts tissue and cellular homeostasis and may be associated with a variety of diseases. This review covers current understanding of the physiological functions of the PLA2 superfamily, focusing particularly on the two major intracellular PLA2 families (Ca2+-dependent cytosolic PLA2s and Ca2+-independent patatin-like PLA2s) as well as other PLA2 families, based on studies using gene-manipulated mice and human diseases in combination with comprehensive lipidomics.
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Hirabayashi T, Kawaguchi M, Harada S, Mouri M, Takamiya R, Miki Y, Sato H, Taketomi Y, Yokoyama K, Kobayashi T, Tokuoka SM, Kita Y, Yoda E, Hara S, Mikami K, Nishito Y, Kikuchi N, Nakata R, Kaneko M, Kiyonari H, Kasahara K, Aiba T, Ikeda K, Soga T, Kurano M, Yatomi Y, Murakami M. Hepatic phosphatidylcholine catabolism driven by PNPLA7 and PNPLA8 supplies endogenous choline to replenish the methionine cycle with methyl groups. Cell Rep 2023; 42:111940. [PMID: 36719796 DOI: 10.1016/j.celrep.2022.111940] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Choline supplies methyl groups for regeneration of methionine and the methyl donor S-adenosylmethionine in the liver. Here, we report that the catabolism of membrane phosphatidylcholine (PC) into water-soluble glycerophosphocholine (GPC) by the phospholipase/lysophospholipase PNPLA8-PNPLA7 axis enables endogenous choline stored in hepatic PC to be utilized in methyl metabolism. PNPLA7-deficient mice show marked decreases in hepatic GPC, choline, and several metabolites related to the methionine cycle, accompanied by various signs of methionine insufficiency, including growth retardation, hypoglycemia, hypolipidemia, increased energy consumption, reduced adiposity, increased fibroblast growth factor 21 (FGF21), and an altered histone/DNA methylation landscape. Moreover, PNPLA8-deficient mice recapitulate most of these phenotypes. In contrast to wild-type mice fed a methionine/choline-deficient diet, both knockout strains display decreased hepatic triglyceride, likely via reductions of lipogenesis and GPC-derived glycerol flux. Collectively, our findings highlight the biological importance of phospholipid catabolism driven by PNPLA8/PNPLA7 in methyl group flux and triglyceride synthesis in the liver.
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Affiliation(s)
- Tetsuya Hirabayashi
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan.
| | - Mai Kawaguchi
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Sayaka Harada
- Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Misa Mouri
- Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Department of Biology, Faculty of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Rina Takamiya
- Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yoshimi Miki
- Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Hiroyasu Sato
- Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yoshitaka Taketomi
- Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Kohei Yokoyama
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Tetsuyuki Kobayashi
- Department of Biology, Faculty of Science, Ochanomizu University, Tokyo 112-8610, Japan
| | - Suzumi M Tokuoka
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshihiro Kita
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan; Life Sciences Core Facility, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Emiko Yoda
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Shuntaro Hara
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Kyohei Mikami
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yasumasa Nishito
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Norihito Kikuchi
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Rieko Nakata
- Department of Food Science and Nutrition, Nara Women's University, Nara, 630-8506, Japan
| | - Mari Kaneko
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Kiyonari
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Kohji Kasahara
- Laboratory of Biomembrane, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Toshiki Aiba
- Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Chiba 263-8555, Japan
| | - Kazutaka Ikeda
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Makoto Kurano
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Makoto Murakami
- Lipid Metabolism Project, Department of Advanced Science for Biomolecules, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; Laboratory of Microenvironmental Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Tokyo 100-0004, Japan.
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10
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Abitbol M, Jagannathan V, Laurent N, Noblet E, Dutil GF, Troupel T, de Dufaure de Citres C, Gache V, Blot S, Escriou C, Leeb T. A PNPLA8 frameshift variant in Australian shepherd dogs with hereditary ataxia. Anim Genet 2022; 53:709-712. [PMID: 35864734 PMCID: PMC9545373 DOI: 10.1111/age.13245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/28/2022] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
Abstract
Hereditary ataxias are common among canine breeds with various molecular etiology. We identified a hereditary ataxia in young‐adult Australian Shepherd dogs characterized by uncoordinated movements and spasticity, worsening progressively and leading to inability to walk. Pedigree analysis suggested an autosomal recessive transmission. By whole genome sequencing and variant filtering of an affected dog we identified a PNPLA8:c.1169_1170dupTT variant. This variant, located in PNPLA8 (Patatin Like Phospholipase Domain Containing 8), was predicted to induce a PNPLA8:p.(His391PhefsTer394) frameshift, leading to a premature stop codon in the protein. The truncated protein was predicted to lack the functional patatin catalytic domain of PNPLA8, a calcium‐independent phospholipase. PNPLA8 is known to be essential for maintaining mitochondrial energy production through tailoring mitochondrial membrane lipid metabolism and composition. The Australian Shepherd ataxia shares molecular and clinical features with Weaver syndrome in cattle and the mitochondrial‐related neurodegeneration associated with PNPLA8 loss‐of‐function variants in humans. By genotyping a cohort of 85 control Australian Shepherd dogs sampled in France, we found a 4.7% carrier frequency. The PNPLA8:c.[1169_1170dupTT] allele is easily detectable with a genetic test to avoid at‐risk matings.
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Affiliation(s)
- Marie Abitbol
- Univ Lyon, VetAgro Sup, Marcy-l'Etoile, France.,Institut NeuroMyoGène INMG-PNMG, CNRS UMR5261, INSERM U1315, Faculté de Médecine, Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | | | - Guillaume F Dutil
- Division of Clinical Neurology and Neurosurgery, CHV Atlantia, Nantes, France
| | - Thibaut Troupel
- Ecole Nationale Vétérinaire d'Alfort, Univ Paris Est Créteil, INSERM, IMRB, Maisons-Alfort, France
| | | | - Vincent Gache
- Institut NeuroMyoGène INMG-PNMG, CNRS UMR5261, INSERM U1315, Faculté de Médecine, Rockefeller, Université Claude Bernard Lyon 1, Lyon, France
| | - Stéphane Blot
- Ecole Nationale Vétérinaire d'Alfort, Univ Paris Est Créteil, INSERM, IMRB, Maisons-Alfort, France
| | | | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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11
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Current Knowledge on Mammalian Phospholipase A1, Brief History, Structures, Biochemical and Pathophysiological Roles. Molecules 2022; 27:molecules27082487. [PMID: 35458682 PMCID: PMC9031518 DOI: 10.3390/molecules27082487] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 12/29/2022] Open
Abstract
Phospholipase A1 (PLA1) is an enzyme that cleaves an ester bond at the sn-1 position of glycerophospholipids, producing a free fatty acid and a lysophospholipid. PLA1 activities have been detected both extracellularly and intracellularly, which are well conserved in higher eukaryotes, including fish and mammals. All extracellular PLA1s belong to the lipase family. In addition to PLA1 activity, most mammalian extracellular PLA1s exhibit lipase activity to hydrolyze triacylglycerol, cleaving the fatty acid and contributing to its absorption into the intestinal tract and tissues. Some extracellular PLA1s exhibit PLA1 activities specific to phosphatidic acid (PA) or phosphatidylserine (PS) and serve to produce lysophospholipid mediators such as lysophosphatidic acid (LPA) and lysophosphatidylserine (LysoPS). A high level of PLA1 activity has been detected in the cytosol fractions, where PA-PLA1/DDHD1/iPLA1 was responsible for the activity. Many homologs of PA-PLA1 and PLA2 have been shown to exhibit PLA1 activity. Although much has been learned about the pathophysiological roles of PLA1 molecules through studies of knockout mice and human genetic diseases, many questions regarding their biochemical properties, including their genuine in vivo substrate, remain elusive.
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12
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Vogel P, Read RW, Hansen GM, Powell DR. Histopathology is required to identify and characterize myopathies in high-throughput phenotype screening of genetically engineered mice. Vet Pathol 2021; 58:1158-1171. [PMID: 34269122 DOI: 10.1177/03009858211030541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The development of mouse models that replicate the genetic and pathological features of human disease is important in preclinical research because these types of models enable the completion of meaningful pharmacokinetic, safety, and efficacy studies. Numerous relevant mouse models of human disease have been discovered in high-throughput screening programs, but there are important specific phenotypes revealed by histopathology that are not reliably detected by any other physiological or behavioral screening tests. As part of comprehensive phenotypic analyses of over 4000 knockout (KO) mice, histopathology identified 12 lines of KO mice with lesions indicative of an autosomal recessive myopathy. This report includes a brief summary of histological and other findings in these 12 lines. Notably, the inverted screen test detected muscle weakness in only 4 of these 12 lines (Scyl1, Plpp7, Chkb, and Asnsd1), all 4 of which have been previously recognized and published. In contrast, 6 of 8 KO lines showing negative or inconclusive findings on the inverted screen test (Plppr2, Pnpla7, Tenm1, Srpk3, Sidt2, Yif1b, Mrs2, and Pnpla2) had not been previously identified as having myopathies. These findings support the need to include histopathology in phenotype screening protocols in order to identify novel genetic myopathies that are not clinically evident or not detected by the inverted screen test.
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Affiliation(s)
- Peter Vogel
- 5417St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert W Read
- 57636Lexicon Pharmaceuticals Inc, The Woodlands, TX, USA
| | | | - David R Powell
- 57636Lexicon Pharmaceuticals Inc, The Woodlands, TX, USA
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13
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Xiao C, Rossignol F, Vaz FM, Ferreira CR. Inherited disorders of complex lipid metabolism: A clinical review. J Inherit Metab Dis 2021; 44:809-825. [PMID: 33594685 DOI: 10.1002/jimd.12369] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023]
Abstract
Over 80 human diseases have been attributed to defects in complex lipid metabolism. A majority of them have been reported recently in the setting of rapid advances in genomic technology and their increased use in clinical settings. Lipids are ubiquitous in human biology and play roles in many cellular and intercellular processes. While inborn errors in lipid metabolism can affect every organ system with many examples of genetic heterogeneity and pleiotropy, the clinical manifestations of many of these disorders can be explained based on the disruption of the metabolic pathway involved. In this review, we will discuss the physiological function of major pathways in complex lipid metabolism, including nonlysosomal sphingolipid metabolism, acylceramide metabolism, de novo phospholipid synthesis, phospholipid remodeling, phosphatidylinositol metabolism, mitochondrial cardiolipin synthesis and remodeling, and ether lipid metabolism as well as common clinical phenotypes associated with each.
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Affiliation(s)
- Changrui Xiao
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Francis Rossignol
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
- Core Facility Metabolomics, Amsterdam UMC, Amsterdam, The Netherlands
| | - Carlos R Ferreira
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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14
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Masih S, Moirangthem A, Phadke SR. Homozygous Missense Variation in PNPLA8 Causes Prenatal-Onset Severe Neurodegeneration. Mol Syndromol 2021; 12:174-178. [PMID: 34177434 DOI: 10.1159/000513524] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
The patatin-like protein family plays an important role in various biological functions including lipid homeostasis, cellular growth, and signaling. Conserved across species, the patatin domain is shared by all 9 members of the PNPLA family without redundancy in the coding sequences. The defective function of PNPLA2, PNPLA6, and PNPLA9 are known to cause mitochondrial-related neurodegeneration. Recently, PNPLA8 has been associated with mitochondrial myopathy and poor weight gain with lactic acidosis in 3 unrelated families. Using whole-exome sequencing, we identified a homozygous novel missense variation c.1874A>G in the patatin domain of PNPLA8. The patient had prenatal-onset severe and progressive neurodegeneration with mortality in infancy.
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Affiliation(s)
- Suzena Masih
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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15
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Murakami M, Sato H, Taketomi Y. Updating Phospholipase A 2 Biology. Biomolecules 2020; 10:E1457. [PMID: 33086624 PMCID: PMC7603386 DOI: 10.3390/biom10101457] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/30/2022] Open
Abstract
The phospholipase A2 (PLA2) superfamily contains more than 50 enzymes in mammals that are subdivided into several distinct families on a structural and biochemical basis. In principle, PLA2 has the capacity to hydrolyze the sn-2 position of glycerophospholipids to release fatty acids and lysophospholipids, yet several enzymes in this superfamily catalyze other reactions rather than or in addition to the PLA2 reaction. PLA2 enzymes play crucial roles in not only the production of lipid mediators, but also membrane remodeling, bioenergetics, and body surface barrier, thereby participating in a number of biological events. Accordingly, disturbance of PLA2-regulated lipid metabolism is often associated with various diseases. This review updates the current state of understanding of the classification, enzymatic properties, and biological functions of various enzymes belonging to the PLA2 superfamily, focusing particularly on the novel roles of PLA2s in vivo.
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Affiliation(s)
- Makoto Murakami
- Laboratory of Microenvironmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan; (H.S.); (Y.T.)
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16
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Kasahara T, Kubota-Sakashita M, Nagatsuka Y, Hirabayashi Y, Hanasaka T, Tohyama K, Kato T. Cardiolipin is essential for early embryonic viability and mitochondrial integrity of neurons in mammals. FASEB J 2019; 34:1465-1480. [PMID: 31914590 DOI: 10.1096/fj.201901598r] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/08/2019] [Accepted: 10/23/2019] [Indexed: 11/11/2022]
Abstract
Cardiolipin (CL) is a hallmark phospholipid of mitochondria and plays a significant role in maintaining the mitochondrial structure and functions. Despite the physiological importance of CL, mutant organisms, yeast, Arabidopsis, C elegans, and Drosophila, which lack CL synthase (Crls1) gene and consequently are deprived of CL, are viable. Here we report conditional Crls1-deficient mice using targeted insertion of loxP sequences flanking the functional domain of CRLS1 enzyme. Homozygous null mutant mice exhibited early embryonic lethality at the peri-implantation stage. We generated neuron-specific Crls1 knockout (cKO) mice by crossing with Camk2α-Cre mice. Neuronal loss and gliosis were gradually manifested in the forebrains, where CL levels were significantly decreased. In the surviving neurons, malformed mitochondria with bubble-like or onion-like inner membrane structures were observed. We showed decreased supercomplex assembly and reduced enzymatic activities of electron transport chain complexes in the forebrain of cKO mice, resulting in affected mitochondrial calcium dynamics, a slower rate of Ca2+ uptake and a smaller calcium retention capacity. These observations clearly demonstrate indispensable roles of CL as well as of Crls1 gene in mammals.
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Affiliation(s)
- Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako-shi, Japan
| | - Mie Kubota-Sakashita
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako-shi, Japan
| | - Yasuko Nagatsuka
- Division of Hematology and Rheumatology, Department of Medicine, Nihon University School of Medicine, Itabashi-ku, Japan
| | - Yoshio Hirabayashi
- Cellular Informatics Laboratory, RIKEN Cluster for Pioneering Research, Wako-shi, Japan.,Institute for Environmental and Gender Specific Medicine, Juntendo University, Graduate School of Medicine, Urayasu-shi, Japan
| | - Tomohito Hanasaka
- Department of Physiology School of Dentistry, The Center for Electron Microscopy and Bio-Imaging Research, Iwate Medical University, Yahaba-cho, Japan
| | - Koujiro Tohyama
- Department of Physiology School of Dentistry, The Center for Electron Microscopy and Bio-Imaging Research, Iwate Medical University, Yahaba-cho, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako-shi, Japan
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17
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Elimam H, Papillon J, Guillemette J, Navarro-Betancourt JR, Cybulsky AV. Genetic Ablation of Calcium-independent Phospholipase A 2γ Exacerbates Glomerular Injury in Adriamycin Nephrosis in Mice. Sci Rep 2019; 9:16229. [PMID: 31700134 PMCID: PMC6838178 DOI: 10.1038/s41598-019-52834-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
Genetic ablation of calcium-independent phospholipase A2γ (iPLA2γ) in mice results in marked damage of mitochondria and enhanced autophagy in glomerular visceral epithelial cells (GECs) or podocytes. The present study addresses the role of iPLA2γ in glomerular injury. In adriamycin nephrosis, deletion of iPLA2γ exacerbated albuminuria and reduced podocyte number. Glomerular LC3-II increased and p62 decreased in adriamycin-treated iPLA2γ knockout (KO) mice, compared with treated control, in keeping with increased autophagy in KO. iPLA2γ KO GECs in culture also demonstrated increased autophagy, compared with control GECs. iPLA2γ KO GECs showed a reduced oxygen consumption rate and increased phosphorylation of AMP kinase (pAMPK), consistent with mitochondrial dysfunction. Adriamycin further stimulated pAMPK and autophagy. After co-transfection of GECs with mito-YFP (to label mitochondria) and RFP-LC3 (to label autophagosomes), or RFP-LAMP1 (to label lysosomes), there was greater colocalization of mito-YFP with RFP-LC3-II and with RFP-LAMP1 in iPLA2γ KO GECs, compared with WT, indicating enhanced mitophagy in KO. Adriamycin increased mitophagy in WT cells. Thus, iPLA2γ has a cytoprotective function in the normal glomerulus and in glomerulopathy, as deletion of iPLA2γ leads to mitochondrial damage and impaired energy homeostasis, as well as autophagy and mitophagy.
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Affiliation(s)
- Hanan Elimam
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Monufia, Egypt
| | - Joan Papillon
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - Julie Guillemette
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - José R Navarro-Betancourt
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada
| | - Andrey V Cybulsky
- Department of Medicine, McGill University Health Centre Research Institute, McGill University, Montreal, Quebec, Canada.
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18
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Shukla A, Saneto RP, Hebbar M, Mirzaa G, Girisha KM. A neurodegenerative mitochondrial disease phenotype due to biallelic loss-of-function variants in PNPLA8 encoding calcium-independent phospholipase A2γ. Am J Med Genet A 2019; 176:1232-1237. [PMID: 29681094 DOI: 10.1002/ajmg.a.38687] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 12/19/2022]
Abstract
Animal studies have demonstrated the critical roles of the patatin-like protein family plays in cellular growth, lipid homeostasis, and second messenger signaling the nervous system. Of the nine known calcium-independent phospholipase A2γ, only PNPLA2, PNLPA6, PNPLA9 and most recently a single patient with PNPLA8 are associated with mitochondrial-related neurodegeneration. Using whole exome sequencing, we report two unrelated individuals with variable but similar clinical features of microcephaly, severe global developmental delay, spasticity, lactic acidosis, and progressive cerebellar atrophy with biallelic loss-of-function variants in PNPLA8.
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Affiliation(s)
- Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Russell P Saneto
- Center for Integrative Brain Research, Neuroscience Institute, Seattle Children's Research Institute, Seattle, Washington, USA.,Division of Pediatric Neurology, Department of Neurology, Neuroscience Institute, Seattle Children's Hospital, Seattle, Washington, USA
| | - Malavika Hebbar
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
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19
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Hara S, Yoda E, Sasaki Y, Nakatani Y, Kuwata H. Calcium-independent phospholipase A 2γ (iPLA 2γ) and its roles in cellular functions and diseases. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:861-868. [PMID: 30391710 DOI: 10.1016/j.bbalip.2018.10.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022]
Abstract
Calcium-independent phospholipase A2γ (iPLA2γ)/patatin-like phospholipase domain-containing lipase 8 (PNPLA8) is one of the iPLA2 enzymes, which do not require Ca2+ ion for their activity. iPLA2γ is a membrane-bound enzyme with unique features, including the utilization of four distinct translation initiation sites and the presence of mitochondrial and peroxisomal localization signals. This enzyme is preferentially distributed in the mitochondria and peroxisomes and is thought to be responsible for the maintenance of lipid homeostasis in these organelles. Thus, both the overexpression and the deletion of iPLA2γ in vivo caused mitochondrial abnormalities and dysfunction. Roles of iPLA2γ in lipid mediator production and cytoprotection against oxidative stress have also been suggested by in vitro and in vivo studies. The dysregulation of iPLA2γ can therefore be a critical factor in the development of many diseases, including metabolic diseases and cancer. In this review, we provide an overview of the biochemical properties of iPLA2γ and then summarize the current understanding of the in vivo roles of iPLA2γ revealed by knockout mouse studies.
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Affiliation(s)
- Shuntaro Hara
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan.
| | - Emiko Yoda
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Yuka Sasaki
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Yoshihito Nakatani
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Hiroshi Kuwata
- Division of Health Chemistry, Department of Healthcare and Regulatory Sciences, School of Pharmacy, Showa University, Tokyo 142-8555, Japan
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20
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Lowered iPLA2γ activity causes increased mitochondrial lipid peroxidation and mitochondrial dysfunction in a rotenone-induced model of Parkinson's disease. Exp Neurol 2018; 300:74-86. [DOI: 10.1016/j.expneurol.2017.10.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 12/25/2022]
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21
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Abstract
Phospholipases are lipolytic enzymes that hydrolyze phospholipid substrates at specific ester bonds. Phospholipases are widespread in nature and play very diverse roles from aggression in snake venom to signal transduction, lipid mediator production, and metabolite digestion in humans. Phospholipases vary considerably in structure, function, regulation, and mode of action. Tremendous advances in understanding the structure and function of phospholipases have occurred in the last decades. This introductory chapter is aimed at providing a general framework of the current understanding of phospholipases and a discussion of their mechanisms of action and emerging biological functions.
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22
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MURAKAMI M. Lipoquality control by phospholipase A 2 enzymes. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:677-702. [PMID: 29129849 PMCID: PMC5743847 DOI: 10.2183/pjab.93.043] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The phospholipase A2 (PLA2) family comprises a group of lipolytic enzymes that typically hydrolyze the sn-2 position of glycerophospholipids to give rise to fatty acids and lysophospholipids. The mammalian genome encodes more than 50 PLA2s or related enzymes, which are classified into several subfamilies on the basis of their structures and functions. From a general viewpoint, the PLA2 family has mainly been implicated in signal transduction, producing bioactive lipid mediators derived from fatty acids and lysophospholipids. Recent evidence indicates that PLA2s also contribute to phospholipid remodeling for membrane homeostasis or energy production for fatty acid β-oxidation. Accordingly, PLA2 enzymes can be regarded as one of the key regulators of the quality of lipids, which I herein refer to as lipoquality. Disturbance of PLA2-regulated lipoquality hampers tissue and cellular homeostasis and can be linked to various diseases. Here I overview the current state of understanding of the classification, enzymatic properties, and physiological functions of the PLA2 family.
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Affiliation(s)
- Makoto MURAKAMI
- Laboratory of Environmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Lipid Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
- Correspondence should be addressed: M. Murakami, Laboratory of Environmental and Metabolic Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan (e-mail: )
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23
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Flex E, Niceta M, Cecchetti S, Thiffault I, Au MG, Capuano A, Piermarini E, Ivanova AA, Francis JW, Chillemi G, Chandramouli B, Carpentieri G, Haaxma CA, Ciolfi A, Pizzi S, Douglas GV, Levine K, Sferra A, Dentici ML, Pfundt RR, Le Pichon JB, Farrow E, Baas F, Piemonte F, Dallapiccola B, Graham JM, Saunders CJ, Bertini E, Kahn RA, Koolen DA, Tartaglia M. Biallelic Mutations in TBCD, Encoding the Tubulin Folding Cofactor D, Perturb Microtubule Dynamics and Cause Early-Onset Encephalopathy. Am J Hum Genet 2016; 99:962-973. [PMID: 27666370 DOI: 10.1016/j.ajhg.2016.08.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/09/2016] [Indexed: 12/13/2022] Open
Abstract
Microtubules are dynamic cytoskeletal elements coordinating and supporting a variety of neuronal processes, including cell division, migration, polarity, intracellular trafficking, and signal transduction. Mutations in genes encoding tubulins and microtubule-associated proteins are known to cause neurodevelopmental and neurodegenerative disorders. Growing evidence suggests that altered microtubule dynamics may also underlie or contribute to neurodevelopmental disorders and neurodegeneration. We report that biallelic mutations in TBCD, encoding one of the five co-chaperones required for assembly and disassembly of the αβ-tubulin heterodimer, the structural unit of microtubules, cause a disease with neurodevelopmental and neurodegenerative features characterized by early-onset cortical atrophy, secondary hypomyelination, microcephaly, thin corpus callosum, developmental delay, intellectual disability, seizures, optic atrophy, and spastic quadriplegia. Molecular dynamics simulations predicted long-range and/or local structural perturbations associated with the disease-causing mutations. Biochemical analyses documented variably reduced levels of TBCD, indicating relative instability of mutant proteins, and defective β-tubulin binding in a subset of the tested mutants. Reduced or defective TBCD function resulted in decreased soluble α/β-tubulin levels and accelerated microtubule polymerization in fibroblasts from affected subjects, demonstrating an overall shift toward a more rapidly growing and stable microtubule population. These cells displayed an aberrant mitotic spindle with disorganized, tangle-shaped microtubules and reduced aster formation, which however did not alter appreciably the rate of cell proliferation. Our findings establish that defective TBCD function underlies a recognizable encephalopathy and drives accelerated microtubule polymerization and enhanced microtubule stability, underscoring an additional cause of altered microtubule dynamics with impact on neuronal function and survival in the developing brain.
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24
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Thiffault I, Farrow E, Smith L, Lowry J, Zellmer L, Black B, Abdelmoity A, Miller N, Soden S, Saunders C. PCDH19-related epileptic encephalopathy in a male mosaic for a truncating variant. Am J Med Genet A 2016; 170:1585-9. [PMID: 27016041 DOI: 10.1002/ajmg.a.37617] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/29/2016] [Indexed: 12/12/2022]
Abstract
Variants in the X-linked gene PCDH19 are associated with early infantile epileptic encephalopathy-9. This unusual condition spares hemizygous males except for psychiatric and behavioral abnormalities, and for this reason is also known as female limited epilepsy. Some cases are due to de novo PCDH19 variants, but may also be paternally inherited. Our patient is a 6-year-old male with epileptic encephalopathy. Exome sequencing revealed apparent heterozygosity in PCDH19 for a novel nonsense variant, c.605C>A (p.Ser202*), inconsistent with expectations for a male. Testing of other tissues revealed a mixture of mutant and normal alleles. These results are consistent with somatic mosaicism for p.Ser202*. This is the second male with somatic mosaicism for PCDH19 deficiency, providing further support for cellular interference as the pathogenic mechanism for this condition, which leads to this unusual mode of inheritance in which females are more severely affected than males. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Emily Farrow
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
| | - Laurie Smith
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jennifer Lowry
- University of Missouri-Kansas City School of Medicine, Kansas City, Missouri.,Individualized Pediatric Therapeutic Medicine Clinic, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Lee Zellmer
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Benjamin Black
- Individualized Pediatric Therapeutic Medicine Clinic, Children's Mercy Hospital, Kansas City, Missouri
| | - Ahmed Abdelmoity
- Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Neil Miller
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri
| | - Sarah Soden
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri.,Individualized Pediatric Therapeutic Medicine Clinic, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pediatrics, Children's Mercy Hospital, Kansas City, Missouri
| | - Carol Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, Missouri.,Department of Pathology and Laboratory Medicine, Children's Mercy Hospitals, Kansas City, Missouri.,University of Missouri-Kansas City School of Medicine, Kansas City, Missouri
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25
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Kunz E, Rothammer S, Pausch H, Schwarzenbacher H, Seefried FR, Matiasek K, Seichter D, Russ I, Fries R, Medugorac I. Confirmation of a non-synonymous SNP in PNPLA8 as a candidate causal mutation for Weaver syndrome in Brown Swiss cattle. Genet Sel Evol 2016; 48:21. [PMID: 26992691 PMCID: PMC4797220 DOI: 10.1186/s12711-016-0201-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/09/2016] [Indexed: 11/10/2022] Open
Abstract
Background Bovine progressive degenerative myeloencephalopathy (Weaver syndrome) is a neurodegenerative disorder in Brown Swiss cattle that is characterized by progressive hind leg weakness and ataxia, while sensorium and spinal reflexes remain unaffected. Although the causal mutation has not been identified yet, an indirect genetic test based on six microsatellite markers and consequent exclusion of Weaver carriers from breeding have led to the complete absence of new cases for over two decades. Evaluation of disease status by imputation of 41 diagnostic single nucleotide polymorphisms (SNPs) and a common haplotype published in 2013 identified several suspected carriers in the current breeding population, which suggests a higher frequency of the Weaver allele than anticipated. In order to prevent the reemergence of the disease, this study aimed at mapping the gene that underlies Weaver syndrome and thus at providing the basis for direct genetic testing and monitoring of today’s Braunvieh/Brown Swiss herds. Results Combined linkage/linkage disequilibrium mapping on Bos taurus chromosome (BTA) 4 based on Illumina Bovine SNP50 genotypes of 43 Weaver-affected, 31 Weaver carrier and 86 Weaver-free animals resulted in a maximum likelihood ratio test statistic value at position 49,812,384 bp. The confidence interval (0.853 Mb) determined by the 2-LOD drop-off method was contained within a 1.72-Mb segment of extended homozygosity. Exploitation of whole-genome sequence data from two official Weaver carriers and 1145 other bulls that were sequenced in Run4 of the 1000 bull genomes project showed that only a non-synonymous SNP (rs800397662) within the PNPLA8 gene at position 49,878,773 bp was concordant with the Weaver carrier status. Targeted SNP genotyping confirmed this SNP as a candidate causal mutation for Weaver syndrome. Genotyping for the candidate causal mutation in a random sample of 2334 current Braunvieh animals suggested a frequency of the Weaver allele of 0.26 %. Conclusions Through combined use of exhaustive sequencing data and SNP genotyping results, we were able to provide evidence that supports the non-synonymous mutation at position 49,878,773 bp as the most likely causal mutation for Weaver syndrome. Further studies are needed to uncover the exact mechanisms that underlie this syndrome. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0201-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisabeth Kunz
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universitaet Muenchen, Veterinaerstr. 13, 80539, Munich, Germany.,Tierzuchtforschung e.V. Muenchen, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Sophie Rothammer
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universitaet Muenchen, Veterinaerstr. 13, 80539, Munich, Germany
| | - Hubert Pausch
- Chair of Animal Breeding, Technische Universitaet Muenchen, Liesel-Beckmann-Straße (Hochfeldweg) 1, 85354, Freising-Weihenstephan, Germany
| | | | | | - Kaspar Matiasek
- Institute of Veterinary Pathology, Ludwig-Maximilians-Universitaet Muenchen, Veterinaerstr. 13, 80539, Munich, Germany
| | - Doris Seichter
- Tierzuchtforschung e.V. Muenchen, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ingolf Russ
- Tierzuchtforschung e.V. Muenchen, Senator-Gerauer-Str. 23, 85586, Poing, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universitaet Muenchen, Liesel-Beckmann-Straße (Hochfeldweg) 1, 85354, Freising-Weihenstephan, Germany
| | - Ivica Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universitaet Muenchen, Veterinaerstr. 13, 80539, Munich, Germany.
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26
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Kohda M, Tokuzawa Y, Kishita Y, Nyuzuki H, Moriyama Y, Mizuno Y, Hirata T, Yatsuka Y, Yamashita-Sugahara Y, Nakachi Y, Kato H, Okuda A, Tamaru S, Borna NN, Banshoya K, Aigaki T, Sato-Miyata Y, Ohnuma K, Suzuki T, Nagao A, Maehata H, Matsuda F, Higasa K, Nagasaki M, Yasuda J, Yamamoto M, Fushimi T, Shimura M, Kaiho-Ichimoto K, Harashima H, Yamazaki T, Mori M, Murayama K, Ohtake A, Okazaki Y. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies. PLoS Genet 2016; 12:e1005679. [PMID: 26741492 PMCID: PMC4704781 DOI: 10.1371/journal.pgen.1005679] [Citation(s) in RCA: 214] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/27/2015] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. Mitochondria play a crucial role in ATP biosynthesis and comprise proteins encoded in both the nuclear and mitochondrial genomes. Although more than 250 mitochondrial disease-causing genes have been reported, the exact genetic causes in patients remain largely unknown. Here, we aimed to provide further insights into the pathogenic mechanisms of mitochondrial disorders. We investigated the genes encoded in the nuclear and mitochondrial genomes using comprehensive genomic analysis in 142 patients with mitochondrial respiratory chain complex deficiencies. We identified 3 novel disease-causing mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as well as other disease-causing genes and novel pathogenic mutations in known mitochondrial disease-causing genes. All pathogenic mutations in this study are validated by genetic and/or functional evidence. Our findings, including the achievement of firm genetic diagnoses for 49 of 142 patients (34.5%), were higher than the general diagnosis rate of approximately 25% and demonstrated the value of comprehensive genomic analysis. Accordingly, we have shed light on the genetic heterogeneity underlying mitochondrial disorders.
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Affiliation(s)
- Masakazu Kohda
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yoshimi Tokuzawa
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yoshihito Kishita
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Hiromi Nyuzuki
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yohsuke Moriyama
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yosuke Mizuno
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Tomoko Hirata
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yukiko Yatsuka
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yzumi Yamashita-Sugahara
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Yutaka Nakachi
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Hidemasa Kato
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Akihiko Okuda
- Division of Developmental Biology, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Shunsuke Tamaru
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Nurun Nahar Borna
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
| | - Kengo Banshoya
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
- Chemicals Assessment and Research Center, Chemicals Evaluation and Research Institute, Japan (CERI), Sugito-machi, Kitakatsushika-gun, Saitama, Japan
| | - Toshiro Aigaki
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Yukiko Sato-Miyata
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Kohei Ohnuma
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Asuteka Nagao
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hazuki Maehata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
- Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, Japan
| | | | - Hiroko Harashima
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama, Japan
| | - Taro Yamazaki
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama, Japan
| | - Masato Mori
- Department of Pediatrics, Matsudo City Hospital, Matsudo-shi, Chiba, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Midori, Chiba, Japan
| | - Akira Ohtake
- Department of Pediatrics, Saitama Medical University, Moroyama-machi, Iruma-gun, Saitama, Japan
- * E-mail: (AOh); (YO)
| | - Yasushi Okazaki
- Division of Translational Research, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
- Division of Functional Genomics & Systems Medicine, Research Center for Genomic Medicine, Saitama Medical University, Hidaka-shi, Saitama, Japan
- * E-mail: (AOh); (YO)
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27
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Lin R, Du X, Peng S, Yang L, Ma Y, Gong Y, Li S. Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos). Evol Bioinform Online 2015; 11:67-76. [PMID: 26819540 PMCID: PMC4721680 DOI: 10.4137/ebo.s21545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 12/21/2022] Open
Abstract
The duck is one of the most economically important waterfowl as a source of meat, eggs, and feathers. Characterizing the genetic variation in duck species is an important step toward linking genes or genomic regions with phenotypes. Human-driven selection during duck domestication and subsequent breed formation has likely left detectable signatures in duck genome. In this study, we employed a panel of >1.4 million single-nucleotide polymorphisms (SNPs) identified from the RNA sequencing (RNA-seq) data of 15 duck individuals. The density of the resulting SNPs is significantly positively correlated with the density of genes across the duck genome, which demonstrates that the usage of the RNA-seq data allowed us to enrich variant functional categories, such as coding exons, untranslated regions (UTRs), introns, and downstream/upstream. We performed a complete scan of selection signatures in the ducks using the composite likelihood ratio (CLR) and found 76 candidate regions of selection, many of which harbor genes related to phenotypes relevant to the function of the digestive system and fat metabolism, including TCF7L2, EIF2AK3, ELOVL2, and fatty acid-binding protein family. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to increase the known genetic information about this economically important animal.
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Affiliation(s)
- Ruiyi Lin
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaoyong Du
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.; College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Sixue Peng
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Liubin Yang
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yunlong Ma
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanzhang Gong
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shijun Li
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
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28
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Bello SM, Smith CL, Eppig JT. Allele, phenotype and disease data at Mouse Genome Informatics: improving access and analysis. Mamm Genome 2015; 26:285-94. [PMID: 26162703 PMCID: PMC4534497 DOI: 10.1007/s00335-015-9582-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 11/16/2022]
Abstract
A core part of the Mouse Genome Informatics (MGI) resource is the collection of mouse mutations and the annotation phenotypes and diseases displayed by mice carrying these mutations. These data are integrated with the rest of data in MGI and exported to numerous other resources. The use of mouse phenotype data to drive translational research into human disease has expanded rapidly with the improvements in sequencing technology. MGI has implemented many improvements in allele and phenotype data annotation, search, and display to facilitate access to these data through multiple avenues. For example, the description of alleles has been modified to include more detailed categories of allele attributes. This allows improved discrimination between mutation types. Further, connections have been created between mutations involving multiple genes and each of the genes overlapping the mutation. This allows users to readily find all mutations affecting a gene and see all genes affected by a mutation. In a similar manner, the genes expressed by transgenic or knock-in alleles are now connected to these alleles. The advanced search forms and public reports have been updated to take advantage of these improvements. These search forms and reports are used by an expanding number of researchers to identify novel human disease genes and mouse models of human disease.
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Affiliation(s)
- Susan M Bello
- Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, 04609, USA,
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29
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Ramanadham S, Ali T, Ashley JW, Bone RN, Hancock WD, Lei X. Calcium-independent phospholipases A2 and their roles in biological processes and diseases. J Lipid Res 2015; 56:1643-68. [PMID: 26023050 DOI: 10.1194/jlr.r058701] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 12/24/2022] Open
Abstract
Among the family of phospholipases A2 (PLA2s) are the Ca(2+)-independent PLA2s (iPLA2s) and they are designated group VI iPLA2s. In relation to secretory and cytosolic PLA2s, the iPLA2s are more recently described and details of their expression and roles in biological functions are rapidly emerging. The iPLA2s or patatin-like phospholipases (PNPLAs) are intracellular enzymes that do not require Ca(2+) for activity, and contain lipase (GXSXG) and nucleotide-binding (GXGXXG) consensus sequences. Though nine PNPLAs have been recognized, PNPLA8 (membrane-associated iPLA2γ) and PNPLA9 (cytosol-associated iPLA2β) are the most widely studied and understood. The iPLA2s manifest a variety of activities in addition to phospholipase, are ubiquitously expressed, and participate in a multitude of biological processes, including fat catabolism, cell differentiation, maintenance of mitochondrial integrity, phospholipid remodeling, cell proliferation, signal transduction, and cell death. As might be expected, increased or decreased expression of iPLA2s can have profound effects on the metabolic state, CNS function, cardiovascular performance, and cell survival; therefore, dysregulation of iPLA2s can be a critical factor in the development of many diseases. This review is aimed at providing a general framework of the current understanding of the iPLA2s and discussion of the potential mechanisms of action of the iPLA2s and related involved lipid mediators.
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Affiliation(s)
- Sasanka Ramanadham
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294 Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Tomader Ali
- Undergraduate Research Office, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Jason W Ashley
- Department of Orthopaedic Surgery, University of Pennsylvania, Philadelphia, PA 19104
| | - Robert N Bone
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294 Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294
| | - William D Hancock
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294 Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294
| | - Xiaoyong Lei
- Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294 Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294
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