1
|
Lackner K, Sailer S, van Klinken JB, Wever E, Pras-Raves ML, Dane AD, Honsho M, Abe Y, Keller MA, Golderer G, Werner-Felmayer G, Fujiki Y, Vaz FM, Werner ER, Watschinger K. Alterations in ether lipid metabolism and the consequences for the mouse lipidome. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159285. [PMID: 36690320 DOI: 10.1016/j.bbalip.2023.159285] [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: 09/13/2022] [Revised: 12/18/2022] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Alkylglycerol monooxygenase (AGMO) and plasmanylethanolamine desaturase (PEDS1) are enzymes involved in ether lipid metabolism. While AGMO degrades plasmanyl lipids by oxidative cleavage of the ether bond, PEDS1 exclusively synthesizes a specific subclass of ether lipids, the plasmalogens, by introducing a vinyl ether double bond into plasmanylethanolamine phospholipids. Ether lipids are characterized by an ether linkage at the sn-1 position of the glycerol backbone and they are found in membranes of different cell types. Decreased plasmalogen levels have been associated with neurological diseases like Alzheimer's disease. Agmo-deficient mice do not present an obvious phenotype under unchallenged conditions. In contrast, Peds1 knockout mice display a growth phenotype. To investigate the molecular consequences of Agmo and Peds1 deficiency on the mouse lipidome, five tissues from each mouse model were isolated and subjected to high resolution mass spectrometry allowing the characterization of up to 2013 lipid species from 42 lipid subclasses. Agmo knockout mice moderately accumulated plasmanyl and plasmenyl lipid species. Peds1-deficient mice manifested striking changes characterized by a strong reduction of plasmenyl lipids and a concomitant massive accumulation of plasmanyl lipids resulting in increased total ether lipid levels in the analyzed tissues except for the class of phosphatidylethanolamines where total levels remained remarkably constant also in Peds1 knockout mice. The rate-limiting enzyme in ether lipid metabolism, FAR1, was not upregulated in Peds1-deficient mice, indicating that the selective loss of plasmalogens is not sufficient to activate the feedback mechanism observed in total ether lipid deficiency.
Collapse
Affiliation(s)
- Katharina Lackner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Sabrina Sailer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria; Institute of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Strasse 1, 6020 Innsbruck, Austria.
| | - Jan-Bert van Klinken
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Department of Human Genetics, Leiden University Medical Center (LUMC), Einthovenweg 20, Leiden, 2333, ZC, the Netherlands.
| | - Eric Wever
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands.
| | - Mia L Pras-Raves
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands.
| | - Adrie D Dane
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Bioinformatics Laboratory, Department of Epidemiology & Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands.
| | - Masanori Honsho
- Department of Neuroinflammation and Brain Fatigue Science, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan.
| | - Yuichi Abe
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan.
| | - Markus A Keller
- Institute of Human Genetics, Medical University of Innsbruck, Peter-Mayr-Strasse 1, 6020 Innsbruck, Austria.
| | - Georg Golderer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Gabriele Werner-Felmayer
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Yukio Fujiki
- Institute of Rheological Functions of Food, Kyushu University Collaboration Program, Kyushu University, 3-1-1 Maidashi, Fukuoka 812-8582, Japan; Graduate School of Science, University of Hyogo, Hyogo, Japan.
| | - Frédéric M Vaz
- Amsterdam UMC location University of Amsterdam, Department of Clinical Chemistry and Pediatrics, Laboratory Genetic Metabolic Diseases, Emma Children's Hospital, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Core Facility Metabolomics, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam, 1105, AZ, the Netherlands; Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of Metabolism, Amsterdam UMC location University of Amsterdam, Meibergdreef 9, Amsterdam 1105, AZ, The Netherlands.
| | - Ernst R Werner
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| | - Katrin Watschinger
- Institute of Biological Chemistry, Biocenter, Medical University of Innsbruck, Innrain 80, 6020 Innsbruck, Austria.
| |
Collapse
|
2
|
Xu NY, Liu ZY, Yang QM, Bian PP, Li M, Zhao X. Genomic Analyses for Selective Signatures and Genes Involved in Hot Adaptation Among Indigenous Chickens From Different Tropical Climate Regions. Front Genet 2022; 13:906447. [PMID: 35979430 PMCID: PMC9377314 DOI: 10.3389/fgene.2022.906447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change, especially weather extremes like extreme cold or extreme hot, is a major challenge for global livestock. One of the animal breeding goals for sustainable livestock production should be to breed animals with excellent climate adaptability. Indigenous livestock and poultry are well adapted to the local climate, and they are good resources to study the genetic footprints and mechanism of the resilience to weather extremes. In order to identify selection signatures and genes that might be involved in hot adaptation in indigenous chickens from different tropical climates, we conducted a genomic analysis of 65 indigenous chickens that inhabit different climates. Several important unique positively selected genes (PSGs) were identified for each local chicken group by the cross-population extended haplotype homozygosity (XP-EHH). These PSGs, verified by composite likelihood ratio, genetic differentiation index, nucleotide diversity, Tajima’s D, and decorrelated composite of multiple signals, are related to nerve regulation, vascular function, immune function, lipid metabolism, kidney development, and function, which are involved in thermoregulation and hot adaptation. However, one common PSG was detected for all three tropical groups of chickens via XP-EHH but was not confirmed by other five types of selective sweep analyses. These results suggest that the hot adaptability of indigenous chickens from different tropical climate regions has evolved in parallel by taking different pathways with different sets of genes. The results from our study have provided reasonable explanations and insights for the rapid adaptation of chickens to diverse tropical climates and provide practical values for poultry breeding.
Collapse
Affiliation(s)
- Nai-Yi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhen-Yu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi-Meng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Pei-Pei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, QC, Canada
- *Correspondence: Xin Zhao,
| |
Collapse
|
3
|
Taylor JP, Malhotra A, Burns NJ, Clause AR, Brown CM, Burns BT, Chandrasekhar A, Schlachetzki Z, Bennett M, Thorpe E, Taft RJ, Perry DL, Coffey AJ. A clinical laboratory's experience using GeneMatcher - building stronger gene-disease relationships. Hum Mutat 2022; 43:765-771. [PMID: 35181961 DOI: 10.1002/humu.24356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/08/2022]
Abstract
The use of whole-genome sequencing (WGS) has accelerated the pace of gene discovery and highlighted the need for open and collaborative data sharing in the search for novel disease genes and variants. GeneMatcher (GM) is designed to facilitate connections between researchers, clinicians, health-care providers and others to help in the identification of additional patients with variants in the same candidate disease genes. The Illumina Clinical Services Laboratory offers a WGS test for patients with suspected rare and undiagnosed genetic disease and regularly submits potential candidate genes to GM to strengthen gene-disease relationships. We describe our experience with GM, including criteria for evaluation of candidate genes, and our workflow for the submission and review process. We have made 69 submissions, 36 of which are currently active. Ten per cent of submissions have resulted in publications, with an additional 14 submissions part of ongoing collaborations and expected to result in a publication. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Julie P Taylor
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Alka Malhotra
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Nicole J Burns
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Amanda R Clause
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Carolyn M Brown
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Brendan T Burns
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Anjana Chandrasekhar
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Zina Schlachetzki
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Maren Bennett
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Erin Thorpe
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Ryan J Taft
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Denise L Perry
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Alison J Coffey
- Medical Genomics Research, Illumina Inc., 5200 Illumina Way, San Diego, CA, 92122, USA
| |
Collapse
|
4
|
Rostamzadeh Mahdabi E, Esmailizadeh A, Ayatollahi Mehrgardi A, Asadi Fozi M. A genome-wide scan to identify signatures of selection in two Iranian indigenous chicken ecotypes. Genet Sel Evol 2021; 53:72. [PMID: 34503452 PMCID: PMC8428137 DOI: 10.1186/s12711-021-00664-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several statistics have been developed to detect genomic regions that are under selection. In this study, we applied approaches based on differences in allele or haplotype frequencies (FST and hapFLK, respectively) between populations, differences in long stretches of consecutive homozygous sequences (ROH), and differences in allele frequencies within populations (composite likelihood ratio (CLR)) to identify inter- and intra-populations traces of selection in two Iranian indigenous chicken ecotypes, the Lari fighting chicken and the Khazak or creeper (short-leg) chicken. Results Using whole-genome resequencing data of 32 individuals from the two chicken ecotypes, approximately 11.9 million single nucleotide polymorphisms (SNPs) were detected and used in genomic analyses after quality processing. Examination of the distribution of ROH in the two populations indicated short to long ROH, ranging from 0.3 to 5.4 Mb. We found 90 genes that were detected by at least two of the four applied methods. Gene annotation of the detected putative regions under selection revealed candidate genes associated with growth (DCN, MEOX2 and CACNB1), reproduction (ESR1 and CALCR), disease resistance (S1PR1, ALPK1 and MHC-B), behavior pattern (AGMO, GNAO1 and PSEN1), and morphological traits (IHH and NHEJ1). Conclusions Our findings show that these two phenotypically different indigenous chicken populations have been under selection for reproduction, immune, behavioral, and morphology traits. The results illustrate that selection can play an important role in shaping signatures of differentiation across the genomic landscape of two chicken populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00664-9.
Collapse
Affiliation(s)
- Elaheh Rostamzadeh Mahdabi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, 22 Bahman Blvd, Kerman, Iran.
| |
Collapse
|
5
|
Sailer S, Keller MA, Werner ER, Watschinger K. The Emerging Physiological Role of AGMO 10 Years after Its Gene Identification. Life (Basel) 2021; 11:life11020088. [PMID: 33530536 PMCID: PMC7911779 DOI: 10.3390/life11020088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/21/2021] [Accepted: 01/21/2021] [Indexed: 02/07/2023] Open
Abstract
The gene encoding alkylglycerol monooxygenase (AGMO) was assigned 10 years ago. So far, AGMO is the only known enzyme capable of catalysing the breakdown of alkylglycerols and lyso-alkylglycerophospholipids. With the knowledge of the genetic information, it was possible to relate a potential contribution for mutations in the AGMO locus to human diseases by genome-wide association studies. A possible role for AGMO was implicated by genetic analyses in a variety of human pathologies such as type 2 diabetes, neurodevelopmental disorders, cancer, and immune defence. Deficient catabolism of stored lipids carrying an alkyl bond by an absence of AGMO was shown to impact on the overall lipid composition also outside the ether lipid pool. This review focuses on the current evidence of AGMO in human diseases and summarises experimental evidence for its role in immunity, energy homeostasis, and development in humans and several model organisms. With the progress in lipidomics platform and genetic identification of enzymes involved in ether lipid metabolism such as AGMO, it is now possible to study the consequence of gene ablation on the global lipid pool and further on certain signalling cascades in a variety of model organisms in more detail.
Collapse
Affiliation(s)
- Sabrina Sailer
- Biocenter, Institute of Biological Chemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria; (S.S.); (E.R.W.)
| | - Markus A. Keller
- Institute of Human Genetics, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Ernst R. Werner
- Biocenter, Institute of Biological Chemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria; (S.S.); (E.R.W.)
| | - Katrin Watschinger
- Biocenter, Institute of Biological Chemistry, Medical University of Innsbruck, 6020 Innsbruck, Austria; (S.S.); (E.R.W.)
- Correspondence: ; Tel.: +43-512-9003-70344
| |
Collapse
|
6
|
Dorninger F, Forss-Petter S, Wimmer I, Berger J. Plasmalogens, platelet-activating factor and beyond - Ether lipids in signaling and neurodegeneration. Neurobiol Dis 2020; 145:105061. [PMID: 32861763 PMCID: PMC7116601 DOI: 10.1016/j.nbd.2020.105061] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022] Open
Abstract
Glycerol-based ether lipids including ether phospholipids form a specialized branch of lipids that in mammals require peroxisomes for their biosynthesis. They are major components of biological membranes and one particular subgroup, the plasmalogens, is widely regarded as a cellular antioxidant. Their vast potential to influence signal transduction pathways is less well known. Here, we summarize the literature showing associations with essential signaling cascades for a wide variety of ether lipids, including platelet-activating factor, alkylglycerols, ether-linked lysophosphatidic acid and plasmalogen-derived polyunsaturated fatty acids. The available experimental evidence demonstrates links to several common players like protein kinase C, peroxisome proliferator-activated receptors or mitogen-activated protein kinases. Furthermore, ether lipid levels have repeatedly been connected to some of the most abundant neurological diseases, particularly Alzheimer's disease and more recently also neurodevelopmental disorders like autism. Thus, we critically discuss the potential role of these compounds in the etiology and pathophysiology of these diseases with an emphasis on signaling processes. Finally, we review the emerging interest in plasmalogens as treatment target in neurological diseases, assessing available data and highlighting future perspectives. Although many aspects of ether lipid involvement in cellular signaling identified in vitro still have to be confirmed in vivo, the compiled data show many intriguing properties and contributions of these lipids to health and disease that will trigger further research.
Collapse
Affiliation(s)
- Fabian Dorninger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, Vienna 1090, Austria.
| | - Sonja Forss-Petter
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, Vienna 1090, Austria
| | - Isabella Wimmer
- Department of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, Vienna 1090, Austria
| | - Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, Vienna 1090, Austria.
| |
Collapse
|
7
|
Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken. Sci Rep 2020; 10:14532. [PMID: 32883984 PMCID: PMC7471287 DOI: 10.1038/s41598-020-71421-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/03/2020] [Indexed: 02/07/2023] Open
Abstract
Gamecock chickens are one of the earliest recorded birds in China, and have accumulated some unique morphological and behavioral signatures such as large body size, muscularity and aggressive behavior, whereby being excellent breeding materials and a good model for studying bird muscular development and behavior. In this study, we sequenced 126 chicken genomes from 19 populations, including four commercial chicken breeds that are commonly farmed in China, 13 nationwide Chinese typical indigenous chicken breeds (including two Chinese gamecock breeds), one red jungle fowl from Guangxi Province of China and three gamecock chickens from Laos. Combined with 31 published chicken genomes from three populations, a comparative genomics analysis was performed across 157 chickens. We found a severe confounding effect on potential cold adaptation exerted by introgression from commercial chickens into Chinese indigenous chickens, and argued that the genetic introgression from commercial chickens into indigenous chickens should be seriously considered for identifying selection footprint in indigenous chickens. LX gamecock chickens might have played a core role in recent breeding and conservation of other Chinese gamecock chickens. Importantly, AGMO (Alkylglycerol monooxygenase) and CPZ (Carboxypeptidase Z) might be crucial for determining the behavioral pattern of gamecock chickens, while ISPD (Isoprenoid synthase domain containing) might be essential for the muscularity of gamecock chickens. Our results can further the understanding of the evolution of Chinese gamecock chickens, especially the genetic basis of gamecock chickens revealed here was valuable for us to better understand the mechanisms underlying the behavioral pattern and the muscular development in chicken.
Collapse
|