1
|
Zhang W, Zhang Y, Shi X, Wang S, Bao Y. Hemoglobin wonders: a fascinating gas transporter dive into molluscs. Crit Rev Biochem Mol Biol 2023; 58:132-157. [PMID: 38189101 DOI: 10.1080/10409238.2023.2299381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb's potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.
Collapse
Affiliation(s)
- Weifeng Zhang
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Yang Zhang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Key Laboratory of Tropical Marine Bio-resources and Ecology and Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xizhi Shi
- School of Marine Science, Ningbo University, Ningbo, China
| | - Shi Wang
- Sars-Fang Centre & MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China and National Laboratory for Marine Science and Technology (LMBB & LMFSFPP), Qingdao, China
| | - Yongbo Bao
- Key Laboratory of Aquatic Germplasm Resource of Zhejiang, College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, China
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, China
| |
Collapse
|
2
|
Hsu LA, Wu S, Teng MS, Ko YL. Causal links of α-thalassemia indices and cardiometabolic traits and diabetes: MR study. Life Sci Alliance 2023; 6:e202302204. [PMID: 37788909 PMCID: PMC10547910 DOI: 10.26508/lsa.202302204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Our study aimed to investigate if genetic variants around 16p13.3's HBA1 locus, associated with erythrocyte indices and HbA1c levels, predict α-thalassemia-related erythrocyte indices, cardiometabolic traits, and diabetes risk in Taiwanese individuals. We analyzed Taiwan Biobank data, including whole-genome sequencing from 1,493 participants and genotyping arrays from 129,542 individuals. First, we performed regional association analysis using whole-genome sequencing data to identify genetic variants significantly associated with erythrocyte indices, confirming their linkage disequilibrium with the α0 thalassemia --SEA deletion mutation, a common cause of α-thalassemia in Southeast Asian populations. Deletion mutation sequencing further validated these variants' association with α-thalassemia. Subsequently, we analyzed genotyping array data, revealing associations between specific genetic variants and cardiometabolic traits, including lipid profiles, HbA1c levels, bilirubin levels, and diabetes risk. Using Mendelian randomization, we established causal relationships between α-thalassemia-related erythrocyte indices and cardiometabolic traits, elucidating their role in diabetes susceptibility. Our findings highlight genetic variants around the α-globin genes as surrogate markers for common α-thalassemia mutations in Taiwan, emphasizing the causal links between α-thalassemia-related erythrocyte indices, cardiometabolic traits, and heightened diabetes risk.
Collapse
Affiliation(s)
- Lung-An Hsu
- The First Cardiovascular Division, Department of Internal Medicine, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Semon Wu
- Department of Life Science, Chinese Culture University, Taipei, Taiwan
| | - Ming-Sheng Teng
- https://ror.org/00q017g63 Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
| | - Yu-Lin Ko
- https://ror.org/00q017g63 Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
- https://ror.org/00q017g63 The Division of Cardiology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, Taiwan
- School of Medicine, Tzu Chi University, Hualien, Taiwan
| |
Collapse
|
3
|
Preston AE, Frost JN, Badat M, Teh M, Armitage AE, Norfo R, Wideman SK, Hanifi M, White N, Roy N, Ghesquiere B, Babbs C, Kassouf M, Davies J, Hughes JR, Beagrie R, Higgs DR, Drakesmith H. Ancient genomic linkage couples metabolism with erythroid development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558944. [PMID: 37808769 PMCID: PMC10557585 DOI: 10.1101/2023.09.25.558944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Generation of mature cells from progenitors requires tight coupling of differentiation and metabolism. During erythropoiesis, erythroblasts are required to massively upregulate globin synthesis then clear extraneous material and enucleate to produce erythrocytes1-3. Nprl3 has remained in synteny with the α-globin genes for >500 million years4, and harbours the majority of the α-globin enhancers5. Nprl3 is a highly conserved inhibitor of mTORC1, which controls cellular metabolism. However, whether Nprl3 itself serves an erythroid role is unknown. Here, we show that Nprl3 is a key regulator of erythroid metabolism. Using Nprl3-deficient fetal liver and adult competitive bone marrow - fetal liver chimeras, we show that NprI3 is required for sufficient erythropoiesis. Loss of Nprl3 elevates mTORC1 signalling, suppresses autophagy and disrupts erythroblast glycolysis and redox control. Human CD34+ progenitors lacking NPRL3 produce fewer enucleated cells and demonstrate dysregulated mTORC1 signalling in response to nutrient availability and erythropoietin. Finally, we show that the α-globin enhancers upregulate NprI3 expression, and that this activity is necessary for optimal erythropoiesis. Therefore, the anciently conserved linkage of NprI3, α-globin and their associated enhancers has enabled coupling of metabolic and developmental control in erythroid cells. This may enable erythropoiesis to adapt to fluctuating nutritional and environmental conditions.
Collapse
Affiliation(s)
- Alexandra E Preston
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Joe N Frost
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mohsin Badat
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Megan Teh
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew E Armitage
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Ruggiero Norfo
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Sarah K Wideman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Muhammad Hanifi
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Natasha White
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Noémi Roy
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Bart Ghesquiere
- Metabolomics Expertise Center, VIB Center for Cancer Biology, 3000 Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Christian Babbs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Mira Kassouf
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - James Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rob Beagrie
- Chromatin and Disease Group, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Hal Drakesmith
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| |
Collapse
|
4
|
Mao Y, Peng T, Shao F, Zhao Q, Peng Z. Molecular evolution of the hemoglobin gene family across vertebrates. Genetica 2023:10.1007/s10709-023-00187-9. [PMID: 37069365 DOI: 10.1007/s10709-023-00187-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/11/2023] [Indexed: 04/19/2023]
Abstract
Adaptation to various altitudes and oxygen levels is a major aspect of vertebrate evolution. Hemoglobin is an erythrocyte protein belonging to the globin superfamily, and the α-, β-globin genes of jawed vertebrates encode tetrameric ((α2β2) hemoglobin, which contributes to aerobic metabolism by delivering oxygen from the respiratory exchange surfaces into cells. However, there are various gaps in knowledge regarding hemoglobin gene evolution, including patterns in cartilaginous fish and the roles of gene conversion in various taxa. Hence, we evaluated the evolutionary history of the vertebrate hemoglobin gene family by analyses of 97 species representing all classes of vertebrates. By genome-wide analyses, we extracted 879 hemoglobin sequences. Members of the hemoglobin gene family were conserved in birds and reptiles but variable in mammals, amphibians, and teleosts. Gene motifs, structures, and synteny were relatively well-conserved among vertebrates. Our results revealed that purifying selection contributed substantially to the evolution of all vertebrate hemoglobin genes, with mean dN/dS (ω) values ranging from 0.057 in teleosts to 0.359 in reptiles. In general, after the fish-specific genome duplication, the teleost hemoglobin genes showed variation in rates of evolution, and the β-globin genes showed relatively high ω values after a gene transposition event in amniotes. We also observed that the frequency of gene conversion was high in amniotes, with fewer hemoglobin genes and higher rates of evolution. Collectively, our findings provide detail insight into complex evolutionary processes shaping the vertebrate hemoglobin gene family, involving gene duplication, gene loss, purifying selection, and gene conversion.
Collapse
Affiliation(s)
- Yang Mao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
- Clinical Research Center, The Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Taotao Peng
- Department of Anesthesiology, Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
| | - Qingyuan Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China
| | - Zuogang Peng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University School of Life Sciences, Chongqing, 400715, China.
| |
Collapse
|
5
|
Queiroz JPF, Lourenzoni MR, Rocha BAM. Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101055. [PMID: 36566682 DOI: 10.1016/j.cbd.2022.101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.
Collapse
Affiliation(s)
- João Pedro Fernandes Queiroz
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| | - Marcos Roberto Lourenzoni
- Protein Engineering and Health Solutions Group - GEPeSS Fundacao Oswaldo Cruz - Ceara, Eusébio, Ceara, 60175-047, Brazil.
| | - Bruno Anderson Matias Rocha
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| |
Collapse
|
6
|
Jin M, Wang Y, Li J, Wu Z, Liu X, Wang H, Chen Y, Wang Z, Tong Z, Li X, Ren F, Zhu X, Yang Z, Mao G. Anemia is independently associated with mortality in people living with human immunodeficiency virus/acquired immune deficiency syndrome: A propensity score matching-based retrospective cohort study in China. Front Med (Lausanne) 2023; 10:1055115. [PMID: 36873867 PMCID: PMC9975156 DOI: 10.3389/fmed.2023.1055115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
Although previous studies have suggested that hemoglobin is related to the health status of people living with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) (PLWHA), the role of anemia in mortality remains unclear. This study aimed to comprehensively quantify the effect of anemia on the mortality risk of PLWHA. In this retrospective cohort study, we thoroughly estimated the effect of anemia on PLWHA mortality, using data collected from January 2005 to June 2022 in the Huzhou area, in 450 subjects extracted from the database of the China Disease Prevention and Control Information System and matched them using a propensity score matching approach to balance potential confounding bias. The potential exposure-response relationship between anemia, hemoglobin concentration, and the mortality of PLWHA was also carefully estimated. A series of subgroup analyses, including interaction analysis, was further conducted to validate the robustness of the effect of anemia on PLWHA death risk. Anemia was significantly associated with an elevated death risk in PLWHA, with an increase of 74% (adjusted hazard ratio [AHR]: 1.74; 95% confidence interval [CI]: 1.03-2.93; p = 0.038) in those with anemia after adjusting for potential confounders. PLWHA with moderate or severe anemia had a higher risk of death, with an 86% increase (AHR = 1.86; 95% CI: 1.01-3.42; p = 0.045). Meanwhile, the AHR tended to increase by 85% on average (AHR = 1.85, 95% CI: 1.37-2.50; p < 0.001) with a per standard deviation (SD) decrease in plasma hemoglobin. Consistent relationships between plasma hemoglobin and the risk of death were further observed in the results from multiple quantile regression models, restricted cubic spline regression models, and a series of subgroup analyses. Anemia is an independent risk factor for HIV/AIDS-related mortality. Our findings may provide new insights into the relevance of PLWHA administration to public health policy, which demonstrate that this low-cost and routinely measured marker (hemoglobin) can be a marker of poor prognosis even before the start of HAART.
Collapse
Affiliation(s)
- Meihua Jin
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Yanan Wang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China.,Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jing Li
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Zhenqian Wu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Xiaoqi Liu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Hui Wang
- Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuxin Chen
- Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Ziyi Wang
- Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhaowei Tong
- Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Xiaofeng Li
- Department of Infectious Diseases, Huzhou Central Hospital, Huzhou, Zhejiang, China
| | - Feilin Ren
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Xiaojuan Zhu
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Zhongrong Yang
- Huzhou Center for Disease Control and Prevention, Huzhou, Zhejiang, China
| | - Guangyun Mao
- Division of Epidemiology and Health Statistics, Department of Preventive Medicine, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Center on Evidence-Based Medicine & Clinical Epidemiological Research, School of Public Health & Management, Wenzhou Medical University, Wenzhou, Zhejiang, China.,National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang, China
| |
Collapse
|
7
|
Iarovaia OV, Ulianov SV, Ioudinkova ES, Razin SV. Segregation of α- and β-Globin Gene Cluster in Vertebrate Evolution: Chance or Necessity? BIOCHEMISTRY. BIOKHIMIIA 2022; 87:1035-1049. [PMID: 36180994 DOI: 10.1134/s0006297922090140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
The review is devoted to the patterns of evolution of α- and β-globin gene domains. A hypothesis is presented according to which segregation of the ancestral cluster of α/β-globin genes in Amniota occurred due to the performance by α-globins and β-globins of non-canonical functions not related to oxygen transport.
Collapse
Affiliation(s)
- Olga V Iarovaia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Elena S Ioudinkova
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| |
Collapse
|
8
|
Lu Z, Gopalan S, Yuan D, Conti DV, Pasaniuc B, Gusev A, Mancuso N. Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies. Am J Hum Genet 2022; 109:1388-1404. [PMID: 35931050 PMCID: PMC9388396 DOI: 10.1016/j.ajhg.2022.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/30/2022] [Indexed: 02/06/2023] Open
Abstract
Transcriptome-wide association studies (TWASs) are a powerful approach to identify genes whose expression is associated with complex disease risk. However, non-causal genes can exhibit association signals due to confounding by linkage disequilibrium (LD) patterns and eQTL pleiotropy at genomic risk regions, which necessitates fine-mapping of TWAS signals. Here, we present MA-FOCUS, a multi-ancestry framework for the improved identification of genes underlying traits of interest. We demonstrate that by leveraging differences in ancestry-specific patterns of LD and eQTL signals, MA-FOCUS consistently outperforms single-ancestry fine-mapping approaches with equivalent total sample sizes across multiple metrics. We perform TWASs for 15 blood traits using genome-wide summary statistics (average nEA = 511 k, nAA = 13 k) and lymphoblastoid cell line eQTL data from cohorts of primarily European and African continental ancestries. We recapitulate evidence demonstrating shared genetic architectures for eQTL and blood traits between the two ancestry groups and observe that gene-level effects correlate 20% more strongly across ancestries than SNP-level effects. Lastly, we perform fine-mapping using MA-FOCUS and find evidence that genes at TWAS risk regions are more likely to be shared across ancestries than they are to be ancestry specific. Using multiple lines of evidence to validate our findings, we find that gene sets produced by MA-FOCUS are more enriched in hematopoietic categories than alternative approaches (p = 2.36 × 10-15). Our work demonstrates that including and appropriately accounting for genetic diversity can drive more profound insights into the genetic architecture of complex traits.
Collapse
Affiliation(s)
- Zeyun Lu
- Biostatistics Division, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA,Corresponding author
| | - Shyamalika Gopalan
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA,Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Dong Yuan
- Biostatistics Division, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - David V. Conti
- Biostatistics Division, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA,Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, Los Angeles, CA, USA,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA,Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Gusev
- Division of Population Sciences, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA,Division of Genetics, Brigham & Women’s Hospital, Boston, MA, USA,Program in Medical and Population Genetics, The Broad Institute, Cambridge, MA, USA
| | - Nicholas Mancuso
- Biostatistics Division, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA,Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA,Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA,Corresponding author
| |
Collapse
|
9
|
Loissell-Baltazar YA, Dokudovskaya S. SEA and GATOR 10 Years Later. Cells 2021; 10:cells10102689. [PMID: 34685669 PMCID: PMC8534245 DOI: 10.3390/cells10102689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/17/2022] Open
Abstract
The SEA complex was described for the first time in yeast Saccharomyces cerevisiae ten years ago, and its human homologue GATOR complex two years later. During the past decade, many advances on the SEA/GATOR biology in different organisms have been made that allowed its role as an essential upstream regulator of the mTORC1 pathway to be defined. In this review, we describe these advances in relation to the identification of multiple functions of the SEA/GATOR complex in nutrient response and beyond and highlight the consequence of GATOR mutations in cancer and neurodegenerative diseases.
Collapse
|
10
|
A Cambrian origin for globin gene regulation. Blood 2020; 136:261-262. [PMID: 32673391 PMCID: PMC9710423 DOI: 10.1182/blood.2020006649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|