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Damena D, Barry A, Morrison R, Gaoussou S, Mahamar A, Attaher O, Issiaka D, Dicko Y, Dicko A, Duffy P, Fried M. A novel locus in CSMD1 gene is associated with increased susceptibility to severe malaria in Malian children. Front Genet 2024; 15:1390786. [PMID: 38854427 PMCID: PMC11157005 DOI: 10.3389/fgene.2024.1390786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/02/2024] [Indexed: 06/11/2024] Open
Abstract
Background Plasmodium falciparum malaria is still a leading cause of child mortality in sub-Saharan Africa. The clinical manifestations of malaria range from asymptomatic infection to severe disease. The variation in clinical presentation is partly attributed to host genetic factors with estimated narrow-sense heritability of 23%. Here, we investigate the associations between candidate gene polymorphisms and the likelihood of severe malaria (SM) in a cohort of Malian children. Methods Based on our previous genome-wide association studies (GWAS) analysis, candidate genes were selected for in-depth analysis using several criteria including gene-level GWAS scores, functional overlap with malaria pathogenesis, and evidence of association with protection or susceptibility to other infectious or inflammatory diseases. Single Nucleotide Polymorphisms (SNPs) residing within these genes were selected mainly based on p-values from previous severe malaria susceptibility GWAS studies and minor allele frequency (MAF) in West African populations. Results Of 182 candidate genes reported in our previous study, 11 genes and 22 SNPs residing in these genes were selected. The selected SNPs were genotyped using KASP technology in 477 DNA samples (87 SM and 390 controls). Logistic regression analysis revealed that a common intron variant, rs13340578 in CUB and Sushi Multi Domain (CSMD1) gene, is associated with increased odds of SM in recessive mode of inheritance (MAF = 0.42, OR = 1.8, 95% CI = [1.78, 1.84], p = 0.029). The SNP is in linkage disequilibrium (LD) with multiple variants with regulatory features. Conclusion Taken together, the current study showed that an intron variant rs13340578, residing in CSMD1 gene, is associated with increased susceptibility to malaria. This finding suggests that modified regulation of complement may contribute to malaria disease severity. Further studies are needed to identify the causal variants and the underlying molecular mechanisms.
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Affiliation(s)
- Delesa Damena
- Molecular Pathogenesis and Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Amadou Barry
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Robert Morrison
- Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Santara Gaoussou
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Almahamoudou Mahamar
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Oumar Attaher
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Djibrilla Issiaka
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Yahia Dicko
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Alassane Dicko
- Malaria Research and Training Center, University of Sciences Techniques and Technologies of Bamako, Bamako, Mali
| | - Patrick Duffy
- Pathogenesis and Immunity Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Michal Fried
- Molecular Pathogenesis and Biomarkers Section, Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Yimthin T, Phunpang R, Wright SW, Thiansukhon E, Chaisuksant S, Chetchotisakd P, Tanwisaid K, Chuananont S, Morakot C, Sangsa N, Silakun W, Chayangsu S, Buasi N, Lertmemongkolchai G, Chantratita N, West TE. Lack of Association of TLR1 and TLR5 Coding Variants with Mortality in a Large Multicenter Cohort of Melioidosis Patients. Am J Trop Med Hyg 2024; 110:994-998. [PMID: 38507807 PMCID: PMC11066355 DOI: 10.4269/ajtmh.23-0381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/20/2023] [Indexed: 03/22/2024] Open
Abstract
Melioidosis, infection caused by Burkholderia pseudomallei, is characterized by robust innate immune responses. We have previously reported associations of TLR1 single nucleotide missense variant rs76600635 with mortality and of TLR5 nonsense variant rs5744168 with both bacteremia and mortality in single-center studies of patients with melioidosis in northeastern Thailand. The objective of this study was to externally validate the associations of rs76600635 and rs5744168 with bacteremia and mortality in a large multicenter cohort of melioidosis patients. We genotyped rs76600635 and rs5744168 in 1,338 melioidosis patients enrolled in a prospective parent cohort study conducted at nine hospitals in northeastern Thailand. The genotype frequencies of rs76600635 did not differ by bacteremia status (P = 0.27) or 28-day mortality (P = 0.84). The genotype frequencies of rs5744168 did not differ by either bacteremia status (P = 0.46) or 28-day mortality (P = 0.10). Assuming a dominant genetic model, there was no association of the rs76600635 variant with bacteremia (adjusted odds ratio [OR], 0.75; 95% CI, 0.54-1.04, P = 0.08) or 28-day mortality (adjusted OR, 0.96; 95% CI, 0.71-1.28, P = 0.77). There was no association of the rs5744168 variant with bacteremia (adjusted OR, 1.24; 95% CI, 0.76-2.03, P = 0.39) or 28-day mortality (adjusted OR, 1.22; 95% CI, 0.83-1.79, P = 0.21). There was also no association of either variant with 1-year mortality. We conclude that in a large multicenter cohort of patients hospitalized with melioidosis in northeastern Thailand, neither TLR1 missense variant rs76600635 nor TLR5 nonsense variant rs5744168 is associated with bacteremia or mortality.
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Affiliation(s)
- Thatcha Yimthin
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Institute of Veterinary Bacteriology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Bern, Switzerland
| | - Rungnapa Phunpang
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Shelton W. Wright
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - Seksan Chaisuksant
- Department of Medicine, Khon Kaen Regional Hospital, Khon Kaen, Thailand
| | | | | | | | - Chumpol Morakot
- Department of Medicine, Mukdahan Hospital, Mukdahan, Thailand
| | | | | | | | - Noppol Buasi
- Department of Medicine, Sisaket Hospital, Sisaket, Thailand
| | - Ganjana Lertmemongkolchai
- Department of Medical Technology, Faculty of Associated Medical Science, Chiang Mai University, Chiang Mai, Thailand
- The Centre for Research and Development of Medical Diagnostic Laboratories, Khon Kaen University, Khon Kaen, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - T. Eoin West
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Medicine, University of Washington, Seattle, Washington
- Department Global Health, University of Washington, Seattle, Washington
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Deb B, Das A, Vilvadrinath R, Jangra A, Shukla MS, Akhouri RR, Goel S. Glycophorin B-PfEMP1 interaction mediates robust rosetting in Plasmodium falciparum. Int J Biol Macromol 2024; 262:129868. [PMID: 38309398 DOI: 10.1016/j.ijbiomac.2024.129868] [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: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
P. falciparumerythrocyte membrane protein 1 (PfEMP1) is the major parasite protein responsible for rosetting by binding to host receptors such as heparan sulfate, CR1 on RBC surface. Usually monomeric protein-carbohydrate interactions are weak [1], therefore PfEMP1 binds to plasma proteins like IgM or α2-macroglobulin that facilitate its clustering on parasitized RBC surface and augment rosetting [2,3]. We show that 3D7A expresses PfEMP1, PF3D7_0412900, and employs its CIDRγ2 domain to interact with glycophorin B on uninfected RBC to form large rosettes but more importantly even in the absence of plasma proteins. Overall, we established the role of PF3D7_0412900 in rosetting as antibodies against CIDRγ2 domain reduced rosetting and also identified its receptor, glycophorin B which could provide clue why glycophorin B null phenotype, S-s-U- RBCs prevalent in malaria endemic areas is protective against severe malaria.
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Affiliation(s)
- Bijayeeta Deb
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | - Adrita Das
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | - Ramya Vilvadrinath
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | - Arvind Jangra
- Indian Institute of Science Education and Research (IISER) Tirupati, India
| | | | | | - Suchi Goel
- Indian Institute of Science Education and Research (IISER) Tirupati, India.
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Chaumier T, Yang F, Manirakiza E, Ait-Mohamed O, Wu Y, Chandola U, Jesus B, Piganeau G, Groisillier A, Tirichine L. Genome-wide assessment of genetic diversity and transcript variations in 17 accessions of the model diatom Phaeodactylum tricornutum. ISME COMMUNICATIONS 2024; 4:ycad008. [PMID: 38304080 PMCID: PMC10833087 DOI: 10.1093/ismeco/ycad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/01/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
Diatoms, a prominent group of phytoplankton, have a significant impact on both the oceanic food chain and carbon sequestration, thereby playing a crucial role in regulating the climate. These highly diverse organisms show a wide geographic distribution across various latitudes. In addition to their ecological significance, diatoms represent a vital source of bioactive compounds that are widely used in biotechnology applications. In the present study, we investigated the genetic and transcriptomic diversity of 17 accessions of the model diatom Phaeodactylum tricornutum including those sampled a century ago as well as more recently collected accessions. The analysis of the data reveals a higher genetic diversity and the emergence of novel clades, indicating an increasing diversity within the P. tricornutum population structure, compared to the previous study and a persistent long-term balancing selection of genes in old and newly sampled accessions. However, the study did not establish a clear link between the year of sampling and genetic diversity, thereby, rejecting the hypothesis of loss of heterozygoty in cultured strains. Transcript analysis identified novel transcript including noncoding RNA and other categories of small RNA such as PiwiRNAs. Additionally, transcripts analysis using differential expression as well as Weighted Gene Correlation Network Analysis has provided evidence that the suppression or downregulation of genes cannot be solely attributed to loss-of-function mutations. This implies that other contributing factors, such as epigenetic modifications, may play a crucial role in regulating gene expression. Our study provides novel genetic resources, which are now accessible through the platform PhaeoEpiview (https://PhaeoEpiView.univ-nantes.fr), that offer both ease of use and advanced tools to further investigate microalgae biology and ecology, consequently enriching our current understanding of these organisms.
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Affiliation(s)
| | - Feng Yang
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Eric Manirakiza
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Ouardia Ait-Mohamed
- Immunity and Cancer Department, Institut Curie, PSL Research University, INSERM U932, Paris 75005, France
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Udita Chandola
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
| | - Bruno Jesus
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes F-44000, France
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes, LBBM, F-66650 Banyuls-sur-Mer, France
| | | | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, Nantes F-44000, France
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Osborne A, Phelan JE, Vanheer LN, Manjurano A, Gitaka J, Drakeley CJ, Kaneko A, Kita K, Campino S, Clark TG. High throughput human genotyping for variants associated with malarial disease outcomes using custom targeted amplicon sequencing. Sci Rep 2023; 13:12062. [PMID: 37495620 PMCID: PMC10371994 DOI: 10.1038/s41598-023-39233-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023] Open
Abstract
Malaria has exhibited the strongest known selective pressure on the human genome in recent history and is the evolutionary driving force behind genetic conditions, such as sickle-cell disease, glucose-6-phosphatase deficiency, and some other erythrocyte defects. Genomic studies (e.g., The 1000 Genomes project) have provided an invaluable baseline for human genetics, but with an estimated two thousand ethno-linguistic groups thought to exist across the African continent, our understanding of the genetic differences between indigenous populations and their implications on disease is still limited. Low-cost sequencing-based approaches make it possible to target specific molecular markers and genes of interest, leading to potential insights into genetic diversity. Here we demonstrate the versatility of custom dual-indexing technology and Illumina next generation sequencing to generate a genetic profile of human polymorphisms associated with malaria pathology. For 100 individuals diagnosed with severe malaria in Northeast Tanzania, variants were successfully characterised on the haemoglobin subunit beta (HBB), glucose-6-phosphate dehydrogenase (G6PD), atypical chemokine receptor 1 (ACKR1) genes, and the intergenic Dantu genetic blood variant, then validated using pre-existing genotyping data. High sequencing coverage was observed across all amplicon targets in HBB, G6PD, ACKR1, and the Dantu blood group, with variants identified at frequencies previously observed within this region of Tanzania. Sequencing data exhibited high concordance rates to pre-existing genotyping data (> 99.5%). Our work demonstrates the potential utility of amplicon sequencing for applications in human genetics, including to personalise medicine and understand the genetic diversity of loci linked to important host phenotypes, such as malaria susceptibility.
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Affiliation(s)
- Ashley Osborne
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Leen N Vanheer
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Alphaxard Manjurano
- Mwanza Medical Research Centre, National Institute for Medical Research, Mwanza, Tanzania
- Joint Malaria Program, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Jesse Gitaka
- Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
- Centre for Malaria Elimination, Mount Kenya University, Thika, Kenya
| | - Christopher J Drakeley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Akira Kaneko
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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Mok C, Xiao MA, Wan YC, Zhao W, Ahmed SM, Luallen RJ, Reinke AW. High-throughput phenotyping of infection by diverse microsporidia species reveals a wild C. elegans strain with opposing resistance and susceptibility traits. PLoS Pathog 2023; 19:e1011225. [PMID: 36893187 PMCID: PMC10030041 DOI: 10.1371/journal.ppat.1011225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/21/2023] [Accepted: 02/20/2023] [Indexed: 03/10/2023] Open
Abstract
Animals are under constant selective pressure from a myriad of diverse pathogens. Microsporidia are ubiquitous animal parasites, but the influence they exert on shaping animal genomes is mostly unknown. Using multiplexed competition assays, we measured the impact of four different species of microsporidia on 22 wild isolates of Caenorhabditis elegans. This resulted in the identification and confirmation of 13 strains with significantly altered population fitness profiles under infection conditions. One of these identified strains, JU1400, is sensitive to an epidermal-infecting species by lacking tolerance to infection. JU1400 is also resistant to an intestinal-infecting species and can specifically recognize and destroy this pathogen. Genetic mapping of JU1400 demonstrates that these two opposing phenotypes are caused by separate loci. Transcriptional analysis reveals the JU1400 sensitivity to epidermal microsporidia infection results in a response pattern that shares similarity to toxin-induced responses. In contrast, we do not observe JU1400 intestinal resistance being regulated at the transcriptional level. The transcriptional response to these four microsporidia species is conserved, with C. elegans strain-specific differences in potential immune genes. Together, our results show that phenotypic differences to microsporidia infection amongst C. elegans are common and that animals can evolve species-specific genetic interactions.
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Affiliation(s)
- Calvin Mok
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Meng A Xiao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yin C Wan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Winnie Zhao
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shanzeh M Ahmed
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Robert J Luallen
- Department of Biology, San Diego State University, San Diego, California, United States of America
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Thiam A, Nisar S, Adjemout M, Gallardo F, Ka O, Mbengue B, Diop G, Dieye A, Marquet S, Rihet P. ATP2B4 regulatory genetic variants are associated with mild malaria. Malar J 2023; 22:68. [PMID: 36849945 PMCID: PMC9972758 DOI: 10.1186/s12936-023-04503-8] [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: 06/21/2022] [Accepted: 02/18/2023] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND Genome-wide association studies have identified ATP2B4 as a severe malaria resistance gene. Recently, 8 potential causal regulatory variants have been shown to be associated with severe malaria. METHODS Genotyping of rs10900585, rs11240734, rs1541252, rs1541253, rs1541254, rs1541255, rs10751450, rs10751451 and rs10751452 was performed in 154 unrelated individuals (79 controls and 75 mild malaria patients). rs10751450, rs10751451 and rs10751452 were genotyped by Taqman assays, whereas the fragment of the ATP2B4 gene containing the remaining SNPs was sequenced. Logistic regression analysis was used to assess the association between the SNPs and mild malaria. RESULTS The results showed that mild malaria was associated with rs10900585, rs11240734, rs1541252, rs1541253, rs1541254, rs1541255, rs10751450, rs10751451 and rs10751452. The homozygous genotypes for the major alleles were associated with an increased risk of mild malaria. Furthermore, the haplotype containing the major alleles and that containing the minor alleles were the most frequent haplotypes. Individuals with the major haplotypes had a significantly higher risk of mild malaria compared to the carriers of the minor allele haplotype. CONCLUSIONS ATP2B4 polymorphisms that have been associated with severe malaria are also associated with mild malaria.
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Affiliation(s)
- Alassane Thiam
- grid.418508.00000 0001 1956 9596Unité d’Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samia Nisar
- grid.5399.60000 0001 2176 4817Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France ,grid.444997.30000 0004 1761 3137Sardar Bahadur Khan Women’s University, Quetta, 1800 Balochistan Pakistan
| | - Mathieu Adjemout
- grid.5399.60000 0001 2176 4817Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France
| | - Frederic Gallardo
- grid.5399.60000 0001 2176 4817Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France
| | - Oumar Ka
- grid.8191.10000 0001 2186 9619Service d’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Babacar Mbengue
- grid.8191.10000 0001 2186 9619Service d’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Gora Diop
- grid.418508.00000 0001 1956 9596Unité d’Immunogénétique, Institut Pasteur de Dakar, Dakar, Senegal
| | - Alioune Dieye
- grid.8191.10000 0001 2186 9619Service d’Immunologie, Université Cheikh Anta Diop de Dakar, Dakar, Senegal
| | - Sandrine Marquet
- Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France.
| | - Pascal Rihet
- Aix Marseille Univ, INSERM, TAGC, MarMaRa Institute, Marseille, France.
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Yu Z, Abdel-Azim S, Duggal P, Vergara C. Identity by descent mapping of HCV spontaneous clearance in populations of diverse ancestry. RESEARCH SQUARE 2023:rs.3.rs-2433454. [PMID: 36712049 PMCID: PMC9882640 DOI: 10.21203/rs.3.rs-2433454/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Acute infection with hepatitis C virus (HCV) affects millions of individuals worldwide. Host genetics plays a role in spontaneous clearance of the acute infection which occurs in approximately 30% of the individuals. Common variants in GPR158, genes in the interferon lambda (IFNL) cluster, and the MHC region have been associated with HCV clearance in populations of diverse ancestry. Fine mapping of those regions has identified some key variants and amino acids as potential causal variants but the role of rare variants in those regions and in the genome, in general, has not been explored. We aimed to detect haplotypes containing rare variants related to HCV clearance using identity-by-descent (IBD) haplotype sharing between unrelated cases/case pairs and case/controls pairs in 3,608 individuals with European and African ancestry. Results We detected 1,711,832 and 5,678,043 and individual pairs of IBD segments in the European and African ancestry individuals, respectively. As expected, individuals of African descent had more, and shorter segments compared to Europeans. We did not detect any significant IBD signals in the known associated gene regions. Conclusions IBD is based on sharing of haplotypes and is most powerful in populations with a shared founder or recent common ancestor. For the complex trait of HCV clearance, we used two outbred, global populations that limited our power to detect IBD associations. Overall, in this population-based sample we failed to detect rare variations associated with HCV clearance in individuals of European and African ancestry.
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Affiliation(s)
- Zixuan Yu
- Johns Hopkins University, Bloomberg School of Public Health
| | | | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health
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9
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Joof F, Hartmann E, Jarvis A, Colley A, Cross JH, Avril M, Prentice AM, Cerami C. Genetic variations in human ATP2B4 gene alter Plasmodium falciparum in vitro growth in RBCs from Gambian adults. Malar J 2023; 22:5. [PMID: 36604655 PMCID: PMC9817369 DOI: 10.1186/s12936-022-04359-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Polymorphisms in ATP2B4 coding for PMCA4b, the primary regulator of erythrocyte calcium concentration, have been shown by GWAS and cross-sectional studies to protect against severe malaria but the mechanism remains unknown. METHODS Using a recall-by-genotype design, we investigated the impact of a common haplotype variant in ATP2B4 using in vitro assays that model erythrocyte stage malaria pathogenesis. Ninety-six donors representing homozygote (carriers of the minor allele, C/C), heterozygote (T/C) and wildtype (T/T) carriers of the tagging SNP rs1541252 were selected from a cohort of over 12,000 participants in the Keneba Biobank. RESULTS Red blood cells (RBCs) from homozygotes showed reduced PMCA4b protein expression (mean fluorescence intensities (MFI = 2428 ± 124, 3544 ± 159 and 4261 ± 283], for homozygotes, heterozygotes and wildtypes respectively, p < 0.0001) and slower rates of calcium expulsion (calcium t½ ± SD = 4.7 ± 0.5, 1.8 ± 0.3 and 1.9 ± 0.4 min, p < 0.0001). Growth of a Plasmodium falciparum laboratory strain (FCR3) and two Gambian field isolates was decreased in RBCs from homozygotes compared to heterozygotes and wildtypes (p < 0.01). Genotype group did not affect parasite adhesion in vitro or var-gene expression in malaria-infected RBCs. Parasite growth was inhibited by a known inhibitor of PMCA4b, aurintricarboxylic acid (IC50 = 122uM CI: 110-134) confirming its sensitivity to calcium channel blockade. CONCLUSION The data support the hypothesis that this ATP2B4 genotype, common in The Gambia and other malaria-endemic areas, protects against severe malaria through the suppression of parasitaemia during an infection. Reduction in parasite density plays a pivotal role in disease outcome by minimizing all aspects of malaria pathogenesis. Follow up studies are needed to further elucidate the mechanism of protection and to determine if this ATP2B4 genotype carries a fitness cost or increases susceptibility to other human disease.
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Affiliation(s)
- Fatou Joof
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | | | - Alhassan Colley
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - James H Cross
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Andrew M Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Carla Cerami
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
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Nortey LN, Anning AS, Nakotey GK, Ussif AM, Opoku YK, Osei SA, Aboagye B, Ghartey-Kwansah G. Genetics of cerebral malaria: pathogenesis, biomarkers and emerging therapeutic interventions. Cell Biosci 2022; 12:91. [PMID: 35715862 PMCID: PMC9204375 DOI: 10.1186/s13578-022-00830-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Cerebral malaria (CM) is a preeminent cause of severe disease and premature deaths in Sub-Saharan Africa, where an estimated 90% of cases occur. The key features of CM are a deep, unarousable coma that persists for longer than 1 h in patients with peripheral Plasmodium falciparum and no other explanation for encephalopathy. Significant research efforts on CM in the last few decades have focused on unravelling the molecular underpinnings of the disease pathogenesis and the identification of potential targets for therapeutic or pharmacologic intervention. These efforts have been greatly aided by the generation and study of mouse models of CM, which have provided great insights into key events of CM pathogenesis, revealed an interesting interplay of host versus parasite factors that determine the progression of malaria to severe disease and exposed possible targets for therapeutic intervention in severe disease.
Main Body
This paper reviews our current understanding of the pathogenic and immunologic factors involved in CM. We present the current view of the roles of certain gene products e.g., the var gene, ABCA-1, ICAM-1, TNF-alpha, CD-36, PfEMP-1 and G6PD, in CM pathogenesis. We also present alterations in the blood–brain barrier as a consequence of disease proliferation as well as complicated host and parasite interactions, including the T-cell immune reaction, reduced deformation of erythrocytes and cytoadherence. We further looked at recent advances in cerebral malaria treatment interventions by emphasizing on biomarkers, new diagnostic tools and emerging therapeutic options.
Conclusion
Finally, we discuss how the current understanding of some of these pathogenic and immunologic factors could inform the development of novel therapeutic interventions to fight CM.
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11
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Erythrocyte-Plasmodium interactions: genetic manipulation of the erythroid lineage. Curr Opin Microbiol 2022; 70:102221. [PMID: 36242898 DOI: 10.1016/j.mib.2022.102221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 09/12/2022] [Indexed: 01/25/2023]
Abstract
Targeting critical host factors is an emerging concept in the treatment of infectious diseases. As obligate pathogens of erythrocytes, the Plasmodium spp. parasites that cause malaria must exploit erythroid host factors for their survival. However, our understanding of this important aspect of the malaria lifecycle is limited, in part because erythrocytes are enucleated cells that lack a nucleus and DNA, rendering them genetically intractable. Recent advances in genetic analysis of the erythroid lineage using small-hairpin RNAs and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) in red-blood cells derived from stem cells have generated new insights into the functions of several candidate host factors for Plasmodium parasites. Along with efforts in other hematopoietic cells, these advances have also laid a strong foundation for genetic screens to identify novel erythrocyte host factors for malaria.
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12
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Su XZ, Wu J, Xu F, Pattaradilokrat S. Genetic mapping of determinants in drug resistance, virulence, disease susceptibility, and interaction of host-rodent malaria parasites. Parasitol Int 2022; 91:102637. [PMID: 35926693 PMCID: PMC9452477 DOI: 10.1016/j.parint.2022.102637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 12/31/2022]
Abstract
Genetic mapping has been widely employed to search for genes linked to phenotypes/traits of interest. Because of the ease of maintaining rodent malaria parasites in laboratory mice, many genetic crosses of rodent malaria parasites have been performed to map the parasite genes contributing to malaria parasite development, drug resistance, host immune response, and disease pathogenesis. Drs. Richard Carter, David Walliker, and colleagues at the University of Edinburgh, UK, were the pioneers in developing the systems for genetic mapping of malaria parasite traits, including characterization of genetic markers to follow the inheritance and recombination of parasite chromosomes and performing the first genetic cross using rodent malaria parasites. Additionally, many genetic crosses of inbred mice have been performed to link mouse chromosomal loci to the susceptibility to malaria parasite infections. In this chapter, we review and discuss past and recent advances in genetic marker development, performing genetic crosses, and genetic mapping of both parasite and host genes. Genetic mappings using models of rodent malaria parasites and inbred mice have contributed greatly to our understanding of malaria, including parasite development within their hosts, mechanism of drug resistance, and host-parasite interaction.
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Affiliation(s)
- Xin-Zhuan Su
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Jian Wu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Fangzheng Xu
- Malaria Functional Genomics Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
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13
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Abstract
Since the identification of sickle cell trait as a heritable form of resistance to malaria, candidate gene studies, linkage analysis paired with sequencing, and genome-wide association (GWA) studies have revealed many examples of genetic resistance and susceptibility to infectious diseases. GWA studies enabled the identification of many common variants associated with small shifts in susceptibility to infectious diseases. This is exemplified by multiple loci associated with leprosy, malaria, HIV, tuberculosis, and coronavirus disease 2019 (COVID-19), which illuminate genetic architecture and implicate pathways underlying pathophysiology. Despite these successes, most of the heritability of infectious diseases remains to be explained. As the field advances, current limitations may be overcome by applying methodological innovations such as cellular GWA studies and phenome-wide association (PheWA) studies as well as by improving methodological rigor with more precise case definitions, deeper phenotyping, increased cohort diversity, and functional validation of candidate loci in the laboratory or human challenge studies.
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Affiliation(s)
- Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA;
| | - Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA; .,Duke University Program in Genetics and Genomics, Duke University, Durham, North Carolina, USA.,Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, North Carolina, USA
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14
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Zhu W, Yang C, Yong B, Wang Y, Li B, Gu Y, Wei S, An Z, Sun W, Qiu L, He C. An enhancing effect attributed to a nonsynonymous mutation in SOYBEAN SEED SIZE 1, a SPINDLY-like gene, is exploited in soybean domestication and improvement. THE NEW PHYTOLOGIST 2022; 236:1375-1392. [PMID: 36068955 DOI: 10.1111/nph.18461] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/12/2022] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. One-hundred-seed weight is one of the most important domesticated traits determining soybean yield; however, its underlying genetic basis remains elusive. We characterized a soybean seed size 1 (sss1) mutant featuring large seeds compared to its wild-type background. Positional cloning revealed that the candidate gene GmSSS1 encoded a SPINDLY homolog and was co-located in a well-identified quantitative trait locus (QTL)-rich region on chromosome 19. Knocking out GmSSS1 resulted in small seeds, while overexpressing GmSSS1/Gmsss1 induced large seeds. Modulating GmSSS1/Gmsss1 in transgenic plants can positively influence cell expansion and cell division. Relative to GmSSS1, one mutation leading to an E to Q substitution at the 182nd residue in Gmsss1 conferred an enhancing effect on seed weight. GmSSS1 underwent diversification in wild-type and cultivated soybean, and the alleles encoding the Gmsss1-type substitution of 182nd -Q, which originated along the central and downstream parts of the Yellow River, were selected and expanded during soybean domestication and improvement. We cloned the causative gene for the sss1 mutant, which is linked with a seed weight QTL, identified an elite allele of this gene for increasing seed weight, and provided new insights into soybean domestication and breeding.
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Affiliation(s)
- Weiwei Zhu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Ce Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Bin Yong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
| | - Bingbing Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Yongzhe Gu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Siming Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Zhenghong An
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Wenkai Sun
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Lijuan Qiu
- National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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15
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Chen H, Lin R, Lu Y, Zhang R, Gao Y, He Y, Xu S. Tracing Bai-Yue Ancestry in Aboriginal Li People on Hainan Island. Mol Biol Evol 2022; 39:6731089. [PMID: 36173765 PMCID: PMC9585476 DOI: 10.1093/molbev/msac210] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
As the most prevalent aboriginal group on Hainan Island located between South China and the mainland of Southeast Asia, the Li people are believed to preserve some unique genetic information due to their isolated circumstances, although this has been largely uninvestigated. We performed the first whole-genome sequencing of 55 Hainan Li (HNL) individuals with high coverage (∼30-50×) to gain insight into their genetic history and potential adaptations. We identified the ancestry enriched in HNL (∼85%) is well preserved in present-day Tai-Kadai speakers residing in South China and North Vietnam, that is, Bai-Yue populations. A lack of admixture signature due to the geographical restriction exacerbated the bottleneck in the present-day HNL. The genetic divergence among Bai-Yue populations began ∼4,000-3,000 years ago when the proto-HNL underwent migration and the settling of Hainan Island. Finally, we identified signatures of positive selection in the HNL, some outstanding examples included FADS1 and FADS2 related to a diet rich in polyunsaturated fatty acids. In addition, we observed that malaria-driven selection had occurred in the HNL, with population-specific variants of malaria-related genes (e.g., CR1) present. Interestingly, HNL harbors a high prevalence of malaria leveraged gene variants related to hematopoietic function (e.g., CD3G) that may explain the high incidence of blood disorders such as B-cell lymphomas in the present-day HNL. The results have advanced our understanding of the genetic history of the Bai-Yue populations and have provided new insights into the adaptive scenarios of the Li people.
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Affiliation(s)
| | | | - Yan Lu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200438, China,Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
| | - Rui Zhang
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yang Gao
- Human Phenome Institute, Zhangjiang Fudan International Innovation Center, and Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 201203, China
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16
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Olatunde AC, Cornwall DH, Roedel M, Lamb TJ. Mouse Models for Unravelling Immunology of Blood Stage Malaria. Vaccines (Basel) 2022; 10:1525. [PMID: 36146602 PMCID: PMC9501382 DOI: 10.3390/vaccines10091525] [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: 07/10/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Malaria comprises a spectrum of disease syndromes and the immune system is a major participant in malarial disease. This is particularly true in relation to the immune responses elicited against blood stages of Plasmodium-parasites that are responsible for the pathogenesis of infection. Mouse models of malaria are commonly used to dissect the immune mechanisms underlying disease. While no single mouse model of Plasmodium infection completely recapitulates all the features of malaria in humans, collectively the existing models are invaluable for defining the events that lead to the immunopathogenesis of malaria. Here we review the different mouse models of Plasmodium infection that are available, and highlight some of the main contributions these models have made with regards to identifying immune mechanisms of parasite control and the immunopathogenesis of malaria.
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Affiliation(s)
| | | | | | - Tracey J. Lamb
- Department of Pathology, University of Utah, Emma Eccles Jones Medical Research Building, 15 N Medical Drive E, Room 1420A, Salt Lake City, UT 84112, USA
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17
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Gilchrist JJ, Auckland K, Parks T, Mentzer AJ, Goldblatt L, Naranbhai V, Band G, Rockett KA, Toure OB, Konate S, Sissoko S, Djimdé AA, Thera MA, Doumbo OK, Sow S, Floyd S, Pönnighaus JM, Warndorff DK, Crampin AC, Fine PEM, Fairfax BP, Hill AVS. Genome-wide association study of leprosy in Malawi and Mali. PLoS Pathog 2022; 18:e1010312. [PMID: 36121873 PMCID: PMC9624411 DOI: 10.1371/journal.ppat.1010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 11/01/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
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Affiliation(s)
- James J. Gilchrist
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ousmane B. Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibiri Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Samba Sow
- Center for Vaccine Development, Bamako, Mali
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jörg M. Pönnighaus
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - David K. Warndorff
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Amelia C. Crampin
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Paul E. M. Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Benjamin P. Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
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18
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Risk score prediction model based on single nucleotide polymorphism for predicting malaria: a machine learning approach. BMC Bioinformatics 2022; 23:325. [PMID: 35934714 PMCID: PMC9358850 DOI: 10.1186/s12859-022-04870-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/01/2022] [Indexed: 11/25/2022] Open
Abstract
Background The malaria risk prediction is currently limited to using advanced statistical methods, such as time series and cluster analysis on epidemiological data. Nevertheless, machine learning models have been explored to study the complexity of malaria through blood smear images and environmental data. However, to the best of our knowledge, no study analyses the contribution of Single Nucleotide Polymorphisms (SNPs) to malaria using a machine learning model. More specifically, this study aims to quantify an individual's susceptibility to the development of malaria by using risk scores obtained from the cumulative effects of SNPs, known as weighted genetic risk scores (wGRS).
Results We proposed an SNP-based feature extraction algorithm that incorporates the susceptibility information of an individual to malaria to generate the feature set. However, it can become computationally expensive for a machine learning model to learn from many SNPs. Therefore, we reduced the feature set by employing the Logistic Regression and Recursive Feature Elimination (LR-RFE) method to select SNPs that improve the efficacy of our model. Next, we calculated the wGRS of the selected feature set, which is used as the model's target variables. Moreover, to compare the performance of the wGRS-only model, we calculated and evaluated the combination of wGRS with genotype frequency (wGRS + GF). Finally, Light Gradient Boosting Machine (LightGBM), eXtreme Gradient Boosting (XGBoost), and Ridge regression algorithms are utilized to establish the machine learning models for malaria risk prediction. Conclusions Our proposed approach identified SNP rs334 as the most contributing feature with an importance score of 6.224 compared to the baseline, with an importance score of 1.1314. This is an important result as prior studies have proven that rs334 is a major genetic risk factor for malaria. The analysis and comparison of the three machine learning models demonstrated that LightGBM achieves the highest model performance with a Mean Absolute Error (MAE) score of 0.0373. Furthermore, based on wGRS + GF, all models performed significantly better than wGRS alone, in which LightGBM obtained the best performance (0.0033 MAE score). Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04870-0.
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19
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Henry B, Volle G, Akpovi H, Gineau L, Roussel C, Ndour PA, Tossou F, Suarez F, Palstra F, Fricot A, Chambrion C, Solinc J, Nguyen J, Garé M, Aussenac F, Cottart CH, Keyser C, Adamou R, Tichit M, Hardy D, Fievet N, Clain J, Garcia A, Courtin D, Hermine O, Sabbagh A, Buffet P. Splenic clearance of rigid erythrocytes as an inherited mechanism for splenomegaly and natural resistance to malaria. EBioMedicine 2022; 82:104167. [PMID: 35843175 PMCID: PMC9297103 DOI: 10.1016/j.ebiom.2022.104167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Benoît Henry
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France; Service des maladies infectieuses et tropicales, APHP, Hôpital Necker Enfants Malades, Centre d'Infectiologie Necker-Pasteur, Institut Imagine, Paris, France; Service des maladies infectieuses et tropicales, APHP. Université Paris Saclay, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Geoffroy Volle
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Hilaire Akpovi
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin
| | - Laure Gineau
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Camille Roussel
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Papa Alioune Ndour
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Félicien Tossou
- Centre Interfacultaire de Formation et de Recherche en Environnement pour le Développement Durable (CIFRED), Université d'Abomey-Calavi, Cotonou, Bénin; Ministère de la Santé, Cotonou, Bénin
| | - Felipe Suarez
- Laboratoire d'Excellence Gr-Ex, Paris, France; Service d'hématologie adultes, APHP, Hôpital Necker Enfants Malades, Paris, France; Université Paris Cité, INSERM U1163, CNRS ERL 8654, Paris, France
| | - Friso Palstra
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Aurélie Fricot
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Charlotte Chambrion
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Julien Solinc
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France
| | - Julie Nguyen
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Mathilde Garé
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Florentin Aussenac
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Charles-Henry Cottart
- Service de biochimie générale, APHP, Hôpital Necker Enfants Malades, Faculté de pharmacie, Paris, France
| | | | - Rafiou Adamou
- CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin
| | - Magali Tichit
- Institut Pasteur, Experimental Neuropathology Unit, Paris, France
| | - David Hardy
- Institut Pasteur, Experimental Neuropathology Unit, Paris, France
| | - Nadine Fievet
- Laboratoire d'Excellence Gr-Ex, Paris, France; CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Jérôme Clain
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - André Garcia
- Laboratoire d'Excellence Gr-Ex, Paris, France; CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - David Courtin
- Laboratoire d'Excellence Gr-Ex, Paris, France; CERPAGE (Centre d'Etude et de Recherche sur les Pathologies Associées à la Grossesse et à l'Enfance), Cotonou, Bénin; Université Paris Cité, IRD, MERIT, Paris, France
| | - Olivier Hermine
- Laboratoire d'Excellence Gr-Ex, Paris, France; Service d'hématologie adultes, APHP, Hôpital Necker Enfants Malades, Paris, France; Université Paris Cité, INSERM U1163, CNRS ERL 8654, Paris, France
| | - Audrey Sabbagh
- Laboratoire d'Excellence Gr-Ex, Paris, France; Université Paris Cité, IRD, MERIT, Paris, France
| | - Pierre Buffet
- Université Paris Cité, Biologie Intégrée du Globule Rouge, UMR_S1134, BIGR, INSERM, Paris, France; Laboratoire d'Excellence Gr-Ex, Paris, France; Institut National de la Transfusion Sanguine, Paris, France; Institut Pasteur, Paris, France.
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20
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Introini V, Govendir MA, Rayner JC, Cicuta P, Bernabeu M. Biophysical Tools and Concepts Enable Understanding of Asexual Blood Stage Malaria. Front Cell Infect Microbiol 2022; 12:908241. [PMID: 35711656 PMCID: PMC9192966 DOI: 10.3389/fcimb.2022.908241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 12/02/2022] Open
Abstract
Forces and mechanical properties of cells and tissues set constraints on biological functions, and are key determinants of human physiology. Changes in cell mechanics may arise from disease, or directly contribute to pathogenesis. Malaria gives many striking examples. Plasmodium parasites, the causative agents of malaria, are single-celled organisms that cannot survive outside their hosts; thus, thost-pathogen interactions are fundamental for parasite’s biological success and to the host response to infection. These interactions are often combinations of biochemical and mechanical factors, but most research focuses on the molecular side. However, Plasmodium infection of human red blood cells leads to changes in their mechanical properties, which has a crucial impact on disease pathogenesis because of the interaction of infected red blood cells with other human tissues through various adhesion mechanisms, which can be probed and modelled with biophysical techniques. Recently, natural polymorphisms affecting red blood cell biomechanics have also been shown to protect human populations, highlighting the potential of understanding biomechanical factors to inform future vaccines and drug development. Here we review biophysical techniques that have revealed new aspects of Plasmodium falciparum invasion of red blood cells and cytoadhesion of infected cells to the host vasculature. These mechanisms occur differently across Plasmodium species and are linked to malaria pathogenesis. We highlight promising techniques from the fields of bioengineering, immunomechanics, and soft matter physics that could be beneficial for studying malaria. Some approaches might also be applied to other phases of the malaria lifecycle and to apicomplexan infections with complex host-pathogen interactions.
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Affiliation(s)
- Viola Introini
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Viola Introini,
| | - Matt A. Govendir
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
| | - Maria Bernabeu
- European Molecular Biology Laboratory (EMBL) Barcelona, Barcelona, Spain
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21
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Awoyemi T, Adenipekun A, Chima-Kalu R, Adedayo O, Obarombi J, Bello O, Bello O, Adamu D. COVID-19 in Africa: An Explorative Cross-Sectional Analysis of Twenty-One African Countries From January to June 2020. Cureus 2022; 14:e24767. [PMID: 35686270 PMCID: PMC9170426 DOI: 10.7759/cureus.24767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction: Africa has surprisingly recorded better gains in containing the coronavirus spread than countries with the better health indices, such as the USA and UK. The low rate of coronavirus disease 2019 (COVID-19) cases and death in Africa represents a puzzle with different biological and social theories such as low COVID-19 testing capacity, substantial young population, few old people, favourable climate, genetic admixture, infectious disease antibodies, and sound community health care systems proposed. We aimed to understand the COVID-19 preventive measures in a group of twenty-one systematically selected African countries that may explain the low burden of COVID-19 in Africa. Methods: Data (COVID-19, health, socioeconomic, and demographics indices) of twenty-one systemically selected African countries were retrieved from the various official country and multilateral organization sources such as Worldbank, and the United nations development Programme (UNDP). The extracted data were analyzed in three large groups: international travel restrictions, physical and social distancing, and movement restrictions (lockdown measures; curfews, partial or/and national lockdowns). Data cleaning, analysis (including Pearson correlation), and visualization were done with Microsoft Excel and Graph Pad Prism version 9 (https://www.graphpad.com/). Result: Southern Africa had the greatest number of cases and deaths within the period studied compared to East Africa, which was the least COVID-19 affected sub-region (in terms of COVID-19 cases and deaths). We observed that coronary artery disease death rate was highly correlated with COVID-19 death density (number of COVID-19 deaths/total population) and similarly observed a correlation between the number of cases and deaths and number of in-country arrivals, pandemic preparedness (health security index), COVID-19 containment, and health index (not correlated with deaths). Finally, we noted that the most effective preventive strategy was the 'use of a face mask'. Conclusion: Africa had fewer COVID-19 cases and COVID-19 related deaths. Our data shows that the rapidity and stringency of COVID-19 preventive measures and government policies, and the low level of tourism in Africa compared to other countries (i.e., low COVID-19 seeding rate) may have been contributory to these favorable statistics. We hope these findings impact how the preparedness for pandemics can be enhanced to decrease the burden of preventable deaths and morbidity.
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22
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Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria. Int J Mol Sci 2022; 23:ijms23094849. [PMID: 35563239 PMCID: PMC9101746 DOI: 10.3390/ijms23094849] [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: 03/14/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/04/2022] Open
Abstract
Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.
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23
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Albrecht-Schgoer K, Lackner P, Schmutzhard E, Baier G. Cerebral Malaria: Current Clinical and Immunological Aspects. Front Immunol 2022; 13:863568. [PMID: 35514965 PMCID: PMC9067128 DOI: 10.3389/fimmu.2022.863568] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 03/21/2022] [Indexed: 11/23/2022] Open
Abstract
This review focuses on current clinical and immunological aspects of cerebral malaria induced by Plasmodium falciparum infection. Albeit many issues concerning the inflammatory responses remain unresolved and need further investigations, current knowledge of the underlying molecular mechanisms is highlighted. Furthermore, and in the light of significant limitations in preventative diagnosis and treatment of cerebral malaria, this review mainly discusses our understanding of immune mechanisms in the light of the most recent research findings. Remarkably, the newly proposed CD8+ T cell-driven pathophysiological aspects within the central nervous system are summarized, giving first rational insights into encouraging studies with immune-modulating adjunctive therapies that protect from symptomatic cerebral participation of Plasmodium falciparum infection.
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Affiliation(s)
- Karin Albrecht-Schgoer
- Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Lackner
- Department of Neurology, Klinik Floridsdorf, Wien, Austria
| | - Erich Schmutzhard
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gottfried Baier
- Division of Translational Cell Genetics, Medical University of Innsbruck, Innsbruck, Austria
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24
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Groomes PV, Kanjee U, Duraisingh MT. RBC membrane biomechanics and Plasmodium falciparum invasion: probing beyond ligand-receptor interactions. Trends Parasitol 2022; 38:302-315. [PMID: 34991983 PMCID: PMC8917059 DOI: 10.1016/j.pt.2021.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 10/19/2022]
Abstract
A critical step in malaria blood-stage infections is the invasion of red blood cells (RBCs) by merozoite forms of the Plasmodium parasite. Much progress has been made in defining the parasite ligands and host receptors that mediate this critical step. However, less well understood are the RBC biophysical determinants that influence parasite invasion. In this review we explore how Plasmodium falciparum merozoites interact with the RBC membrane during invasion to modulate RBC deformability and facilitate invasion. We further highlight RBC biomechanics-related polymorphisms that might have been selected for in human populations due to their ability to reduce parasite invasion. Such an understanding will reveal the translational potential of targeting host pathways affecting RBC biomechanical properties for the treatment of malaria.
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Affiliation(s)
- Patrice V Groomes
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Usheer Kanjee
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Manoj T Duraisingh
- Department of Immunology & Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.
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25
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Tai KY, Dhaliwal J, Balasubramaniam V. Leveraging Mann-Whitney U test on large-scale genetic variation data for analysing malaria genetic markers. Malar J 2022; 21:79. [PMID: 35264165 PMCID: PMC8905822 DOI: 10.1186/s12936-022-04104-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background The malaria risk analysis of multiple populations is crucial and of great importance whilst compressing limitations. However, the exponential growth in diversity and accumulation of genetic variation data obtained from malaria-infected patients through Genome-Wide Association Studies opens up unprecedented opportunities to explore the significant differences between genetic markers (risk factors), particularly in the resistance or susceptibility of populations to malaria risk. Thus, this study proposes using statistical tests to analyse large-scale genetic variation data, comprising 20,854 samples from 11 populations within three continents: Africa, Oceania, and Asia. Methods Even though statistical tests have been utilized to conduct case–control studies since the 1950s to link risk factors to a particular disease, several challenges faced, including the choice of data (ordinal vs. non-ordinal) and test (parametric vs. non-parametric). This study overcomes these challenges by adopting the Mann–Whitney U test to analyse large-scale genetic variation data; to explore the statistical significance of markers between populations; and to further identify the highly differentiated markers. Results The findings of this study revealed a significant difference in the genetic markers between populations (p < 0.01) in all the case groups and most control groups. However, for the highly differentiated genetic markers, a significant difference (p < 0.01) was present for most genetic markers with varying p-values between the populations in the case and control groups. Moreover, several genetic markers were observed to have very significant differences (p < 0.001) across all populations, while others exist between certain specific populations. Also, several genetic markers have no significant differences between populations. Conclusions These findings further support that the genetic markers contribute differently between populations towards malaria resistance or susceptibility, thus showing differences in the likelihood of malaria infection. In addition, this study demonstrated the robustness of the Mann–Whitney U test in analysing genetic markers in large-scale genetic variation data, thereby indicating an alternative method to explore genetic markers in other complex diseases. The findings hold great promise for genetic markers analysis, and the pipeline emphasized in this study can fully be reproduced to analyse new data. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04104-x.
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Affiliation(s)
- Kah Yee Tai
- School of Information Technology, Monash University Malaysia, Subang Jaya, Selangor, Malaysia
| | - Jasbir Dhaliwal
- School of Information Technology, Monash University Malaysia, Subang Jaya, Selangor, Malaysia.
| | - Vinod Balasubramaniam
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Subang Jaya, Selangor, Malaysia
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26
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Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE. Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
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Affiliation(s)
- Myo T. Naung
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Elijah Martin
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Jacob Munro
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Somya Mehra
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Andrew J. Guy
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - G. L. Abby Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Livingstone Tavul
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Manuel Hetzel
- Swiss Tropical Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dominic Kwiatkowski
- Sanger Institute, Hinxton, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Division of Parasites and Insect Vectors, Pasteur Institute, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
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27
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Gilchrist JJ, Kariuki SN, Watson JA, Band G, Uyoga S, Ndila CM, Mturi N, Mwarumba S, Mohammed S, Mosobo M, Alasoo K, Rockett KA, Mentzer AJ, Kwiatkowski DP, Hill AVS, Maitland K, Scott JAG, Williams TN. BIRC6 modifies risk of invasive bacterial infection in Kenyan children. eLife 2022; 11:77461. [PMID: 35866869 PMCID: PMC9391038 DOI: 10.7554/elife.77461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
Abstract
Invasive bacterial disease is a major cause of morbidity and mortality in African children. Despite being caused by diverse pathogens, children with sepsis are clinically indistinguishable from one another. In spite of this, most genetic susceptibility loci for invasive infection that have been discovered to date are pathogen specific and are not therefore suggestive of a shared genetic architecture of bacterial sepsis. Here, we utilise probabilistic diagnostic models to identify children with a high probability of invasive bacterial disease among critically unwell Kenyan children with Plasmodium falciparum parasitaemia. We construct a joint dataset including 1445 bacteraemia cases and 1143 severe malaria cases, and population controls, among critically unwell Kenyan children that have previously been genotyped for human genetic variation. Using these data, we perform a cross-trait genome-wide association study of invasive bacterial infection, weighting cases according to their probability of bacterial disease. In doing so, we identify and validate a novel risk locus for invasive infection secondary to multiple bacterial pathogens, that has no apparent effect on malaria risk. The locus identified modifies splicing of BIRC6 in stimulated monocytes, implicating regulation of apoptosis and autophagy in the pathogenesis of sepsis in Kenyan children.
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Affiliation(s)
- James J Gilchrist
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom,MRC–Weatherall Institute of Molecular Medicine, University of OxfordOxfordUnited Kingdom,Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Silvia N Kariuki
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - James A Watson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom,Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Shebe Mohammed
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Moses Mosobo
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya
| | - Kaur Alasoo
- Institute of Computer Science, University of TartuTartuEstonia
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom,Wellcome Sanger InstituteCambridgeUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom,The Jenner Institute, University of OxfordOxfordUnited Kingdom
| | - Kathryn Maitland
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Division of Medicine, Imperial CollegeLondonUnited Kingdom
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-CoastKilifiKenya,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial CollegeLondonUnited Kingdom
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28
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Band G, Leffler EM, Jallow M, Sisay-Joof F, Ndila CM, Macharia AW, Hubbart C, Jeffreys AE, Rowlands K, Nguyen T, Gonçalves S, Ariani CV, Stalker J, Pearson RD, Amato R, Drury E, Sirugo G, d'Alessandro U, Bojang KA, Marsh K, Peshu N, Saelens JW, Diakité M, Taylor SM, Conway DJ, Williams TN, Rockett KA, Kwiatkowski DP. Malaria protection due to sickle haemoglobin depends on parasite genotype. Nature 2021; 602:106-111. [PMID: 34883497 PMCID: PMC8810385 DOI: 10.1038/s41586-021-04288-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/29/2021] [Indexed: 11/30/2022]
Abstract
Host genetic factors can confer resistance against malaria1, raising the question of whether this has led to evolutionary adaptation of parasite populations. Here we searched for association between candidate host and parasite genetic variants in 3,346 Gambian and Kenyan children with severe malaria caused by Plasmodium falciparum. We identified a strong association between sickle haemoglobin (HbS) in the host and three regions of the parasite genome, which is not explained by population structure or other covariates, and which is replicated in additional samples. The HbS-associated alleles include nonsynonymous variants in the gene for the acyl-CoA synthetase family member2–4PfACS8 on chromosome 2, in a second region of chromosome 2, and in a region containing structural variation on chromosome 11. The alleles are in strong linkage disequilibrium and have frequencies that covary with the frequency of HbS across populations, in particular being much more common in Africa than other parts of the world. The estimated protective effect of HbS against severe malaria, as determined by comparison of cases with population controls, varies greatly according to the parasite genotype at these three loci. These findings open up a new avenue of enquiry into the biological and epidemiological significance of the HbS-associated polymorphisms in the parasite genome and the evolutionary forces that have led to their high frequency and strong linkage disequilibrium in African P. falciparum populations. A strong association has been found between three regions of the Plasmodium falciparum genome and sickle haemoglobin in children with severe malaria, suggesting parasites have adapted to overcome natural host immunity.
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Affiliation(s)
- Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Edward Francis Small Teaching Hospital (formerly Royal Victoria Teaching Hospital), Independence Drive, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Carolyne M Ndila
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | | | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Thuy Nguyen
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | - Jim Stalker
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Richard D Pearson
- Wellcome Sanger Institute, Hinxton, Cambridge, UK.,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA
| | | | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Division of Translational Medicine and Human Genetics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Umberto d'Alessandro
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kalifa A Bojang
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford, UK
| | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya
| | - Joseph W Saelens
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Techniques, and Technologies of Bamako, Bamako, Mali
| | - Steve M Taylor
- Division of Infectious Diseases, Duke University School of Medicine, Durham, NC, USA.,Duke Global Health Institute, Duke University, Durham, NC, USA
| | - David J Conway
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, The Gambia.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, PO Box 230, Kilifi, Kenya.,Institute for Global Health Innovation, Department of Surgery and Cancer, Imperial College, London, London, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Sanger Institute, Hinxton, Cambridge, UK. .,Big Data Institute, Li Ka Shing Centre for Health and Information Discovery, Old Road Campus, Oxford, USA.
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29
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Damena D, Agamah FE, Kimathi PO, Kabongo NE, Girma H, Choga WT, Golassa L, Chimusa ER. Insilico Functional Analysis of Genome-Wide Dataset From 17,000 Individuals Identifies Candidate Malaria Resistance Genes Enriched in Malaria Pathogenic Pathways. Front Genet 2021; 12:676960. [PMID: 34868193 PMCID: PMC8639191 DOI: 10.3389/fgene.2021.676960] [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: 03/10/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
Recent genome-wide association studies (GWASs) of severe malaria have identified several association variants. However, much about the underlying biological functions are yet to be discovered. Here, we systematically predicted plausible candidate genes and pathways from functional analysis of severe malaria resistance GWAS summary statistics (N = 17,000) meta-analysed across 11 populations in malaria endemic regions. We applied positional mapping, expression quantitative trait locus (eQTL), chromatin interaction mapping, and gene-based association analyses to identify candidate severe malaria resistance genes. We further applied rare variant analysis to raw GWAS datasets (N = 11,000) of three malaria endemic populations including Kenya, Malawi, and Gambia and performed various population genetic structures of the identified genes in the three populations and global populations. We performed network and pathway analyses to investigate their shared biological functions. Our functional mapping analysis identified 57 genes located in the known malaria genomic loci, while our gene-based GWAS analysis identified additional 125 genes across the genome. The identified genes were significantly enriched in malaria pathogenic pathways including multiple overlapping pathways in erythrocyte-related functions, blood coagulations, ion channels, adhesion molecules, membrane signalling elements, and neuronal systems. Our population genetic analysis revealed that the minor allele frequencies (MAF) of the single nucleotide polymorphisms (SNPs) residing in the identified genes are generally higher in the three malaria endemic populations compared to global populations. Overall, our results suggest that severe malaria resistance trait is attributed to multiple genes, highlighting the possibility of harnessing new malaria therapeutics that can simultaneously target multiple malaria protective host molecular pathways.
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Affiliation(s)
- Delesa Damena
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Francis E Agamah
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Peter O Kimathi
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ntumba E Kabongo
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Hundaol Girma
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wonderful T Choga
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Lemu Golassa
- Aklilu Lema Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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30
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Tonen-Wolyec S, Batina-Agasa S. High susceptibility to severe malaria among patients with A blood group versus those with O blood group: A cross-sectional study in the Democratic Republic of the Congo. Trop Parasitol 2021; 11:97-101. [PMID: 34765530 PMCID: PMC8579772 DOI: 10.4103/tp.tp_87_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/23/2020] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
This study aimed to assess the association of severe malaria infection with the ABO blood groups among acute febrile patients at the General Hospital of Rungu, in the Democratic Republic of the Congo. This cross-sectional study was conducted between August and October 2018. Plasmodium falciparum-infected individuals were categorized as severe malaria and uncomplicated malaria. A total of 400 febrile patients were enrolled. The majority (n = 251; 62.8%) was positive P. falciparum in microscopy test, of whom 180 (71.7%) had uncomplicated malaria and 71 (28.3%) severe malaria; 32.3%, 18.3%, 2.8%, and 46.6% were found to be blood group of A, B, AB, and O, respectively. In the multivariate analysis using the logistic regression models, severe malaria was high among patients with A blood group compared to those with O blood group (45.8% vs. 13.7%; adjusted odds ratio: 5.3 [95% confidence interval: 2.7–10.5]; P < 0.001). This survey demonstrates that patients with A blood group had a high susceptibility to severe malaria compared to those with O blood group.
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Affiliation(s)
- Serge Tonen-Wolyec
- Department of Internal Medicine, Faculty of Medicine and Pharmacy, University of Kisangani, Kisangani.,Department of Internal Medicine, Faculty of Medicine, University of Bunia, Bunia, The Democratic Republic of the Congo
| | - Salomon Batina-Agasa
- Department of Internal Medicine, Faculty of Medicine and Pharmacy, University of Kisangani, Kisangani
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31
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Ndila CM, Nyirongo V, Macharia AW, Jeffreys AE, Rowlands K, Hubbart C, Busby GBJ, Band G, Harding RM, Rockett KA, Williams TN. Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α 3.7I form of α-thalassaemia using genome-wide microarray data. Wellcome Open Res 2021; 5:287. [PMID: 34632085 PMCID: PMC8474104 DOI: 10.12688/wellcomeopenres.16320.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 12/26/2022] Open
Abstract
Background: The -α
3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any confounding effects of α-thalassaemia to rule out spurious associations. Methods: In this study, we have used direct α-thalassaemia genotyping to understand why GWAS data from a large malaria association study in Kilifi Kenya did not identify the α-thalassaemia signal. We then explored the potential use of a number of new approaches to using GWAS data for imputing α-thalassaemia as an alternative to direct genotyping by PCR. Results: We found very low linkage-disequilibrium of the directly typed data with the GWAS SNP markers around α-thalassaemia and across the haemoglobin-alpha (
HBA) gene region, which along with a complex haplotype structure, could explain the lack of an association signal from the GWAS SNP data. Some indirect typing methods gave results that were in broad agreement with those derived from direct genotyping and could identify an association signal, but none were sufficiently accurate to allow correct interpretation compared with direct typing, leading to confusing or erroneous results. Conclusions: We conclude that going forwards, direct typing methods such as PCR will still be required to account for α-thalassaemia in GWAS studies.
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Affiliation(s)
- Carolyne M Ndila
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya
| | - Vysaul Nyirongo
- United Nation Statistics Division, United Nations, New York, New York, 10017, USA
| | - Alexander W Macharia
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK
| | - George B J Busby
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.,Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, Oxfordshire, OX3 7LF, UK
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.,Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Rosalind M Harding
- Departments of Zoology and Statistics, University of Oxford, Oxford, Oxfordshire, OX1 3SZ, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, Oxfordshire, OX3 7BN, UK.,Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Thomas N Williams
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, PO BOX 230-80108, Kenya.,Department of Infectious Diseases, Imperial College Faculty of Medicine, London, W2 1NY, UK
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32
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Zhou C, Zhang Q, Chen Y, Huang J, Guo Q, Li Y, Wang W, Qiu Y, Guan W, Zhang J, Guo J, Shi S, Wu D, Zheng X, Nie L, Tan J, Huang C, Ma Y, Yang F, Fu X, Du B, Zhu L, Chen R, Li Z, Yuan L, He G. Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1695-1711. [PMID: 34302720 DOI: 10.1111/jipb.13157] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Interactions and co-evolution between plants and herbivorous insects are critically important in agriculture. Brown planthopper (BPH) is the most severe insect of rice, and the biotypes adapt to feed on different rice genotypes. Here, we present genomics analyses on 1,520 global rice germplasms for resistance to three BPH biotypes. Genome-wide association studies identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with BPH resistance in rice. We cloned a previously unidentified gene Bph37 that confers resistance to BPH. The associated loci showed high nucleotide diversity. Genome-wide scans for trans-species polymorphisms revealed ancient balancing selection at the loci. The secondarily evolved insect biotypes II and III exhibited significantly higher virulence and overcame more rice varieties than the primary biotype I. In response, more SNPs and loci evolved in rice for resistance to biotypes II and III. Notably, three exceptional large regions with high SNP density and resistance-associated loci on chromosomes 4 and 6 appear distinct between the resistant and susceptible rice varieties. Surprisingly, these regions in resistant rice might have been retained from wild species Oryza nivara. Our findings expand the understanding of long-term interactions between rice and BPH and provide resistance genes and germplasm resources for breeding durable BPH-resistant rice varieties.
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Affiliation(s)
- Cong Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qian Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yu Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jin Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Qin Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Yongfu Qiu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Agricultural College, Guangxi University, Nanning, 530004, China
| | - Wei Guan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jianping Guo
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shaojie Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Di Wu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaohong Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lingyun Nie
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiaoyan Tan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chaomei Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yinhua Ma
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fang Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiqin Fu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Bo Du
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lili Zhu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Rongzhi Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Agronomy, Anhui Agricultural University, Hefei, 230036, China
| | - Longping Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Guangcun He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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33
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Ebel ER, Kuypers FA, Lin C, Petrov DA, Egan ES. Common host variation drives malaria parasite fitness in healthy human red cells. eLife 2021; 10:e69808. [PMID: 34553687 PMCID: PMC8497061 DOI: 10.7554/elife.69808] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 09/22/2021] [Indexed: 12/11/2022] Open
Abstract
The replication of Plasmodium falciparum parasites within red blood cells (RBCs) causes severe disease in humans, especially in Africa. Deleterious alleles like hemoglobin S are well-known to confer strong resistance to malaria, but the effects of common RBC variation are largely undetermined. Here, we collected fresh blood samples from 121 healthy donors, most with African ancestry, and performed exome sequencing, detailed RBC phenotyping, and parasite fitness assays. Over one-third of healthy donors unknowingly carried alleles for G6PD deficiency or hemoglobinopathies, which were associated with characteristic RBC phenotypes. Among non-carriers alone, variation in RBC hydration, membrane deformability, and volume was strongly associated with P. falciparum growth rate. Common genetic variants in PIEZO1, SPTA1/SPTB, and several P. falciparum invasion receptors were also associated with parasite growth rate. Interestingly, we observed little or negative evidence for divergent selection on non-pathogenic RBC variation between Africans and Europeans. These findings suggest a model in which globally widespread variation in a moderate number of genes and phenotypes modulates P. falciparum fitness in RBCs.
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Affiliation(s)
- Emily R Ebel
- Department of Biology, Stanford UniversityStanfordUnited States
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Frans A Kuypers
- Children's Hospital Oakland Research InstituteOaklandUnited States
| | - Carrie Lin
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
| | - Dmitri A Petrov
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Elizabeth S Egan
- Department of Pediatrics, Stanford University School of MedicineStanfordUnited States
- Department of Microbiology & Immunology, Stanford University School of MedicineStanfordUnited States
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34
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Buggiotti L, Yurchenko AA, Yudin NS, Vander Jagt CJ, Vorobieva NV, Kusliy MA, Vasiliev SK, Rodionov AN, Boronetskaya OI, Zinovieva NA, Graphodatsky AS, Daetwyler HD, Larkin DM. Demographic History, Adaptation, and NRAP Convergent Evolution at Amino Acid Residue 100 in the World Northernmost Cattle from Siberia. Mol Biol Evol 2021; 38:3093-3110. [PMID: 33784744 PMCID: PMC8321547 DOI: 10.1093/molbev/msab078] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Native cattle breeds represent an important cultural heritage. They are a reservoir of genetic variation useful for properly responding to agriculture needs in the light of ongoing climate changes. Evolutionary processes that occur in response to extreme environmental conditions could also be better understood using adapted local populations. Herein, different evolutionary histories of the world northernmost native cattle breeds from Russia were investigated. They highlighted Kholmogory as a typical taurine cattle, whereas Yakut cattle separated from European taurines approximately 5,000 years ago and contain numerous ancestral and some novel genetic variants allowing their adaptation to harsh conditions of living above the Polar Circle. Scans for selection signatures pointed to several common gene pathways related to adaptation to harsh climates in both breeds. But genes affected by selection from these pathways were mostly different. A Yakut cattle breed-specific missense mutation in a highly conserved NRAP gene represents a unique example of a young amino acid residue convergent change shared with at least 16 species of hibernating/cold-adapted mammals from six distinct phylogenetic orders. This suggests a convergent evolution event along the mammalian phylogenetic tree and fast fixation in a single isolated cattle population exposed to a harsh climate.
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Affiliation(s)
- Laura Buggiotti
- Royal Veterinary College, University of London, London, United Kingdom
| | - Andrey A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | - Nikolay S Yudin
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
| | | | - Nadezhda V Vorobieva
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Mariya A Kusliy
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Sergei K Vasiliev
- Paleometal Archeology Department, Institute of Archaeology and Ethnography SB RAS, Novosibirsk, Russia
| | - Andrey N Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Podolsk, Russia
| | - Oksana I Boronetskaya
- Moscow Agrarian Academy, Timiryazev Russian State Agrarian University, Moscow, Russia
| | | | - Alexander S Graphodatsky
- Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Denis M Larkin
- Royal Veterinary College, University of London, London, United Kingdom
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Science, Novosibirsk, Russia
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35
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Wang L, Balmat TJ, Antonia AL, Constantine FJ, Henao R, Burke TW, Ingham A, McClain MT, Tsalik EL, Ko ER, Ginsburg GS, DeLong MR, Shen X, Woods CW, Hauser ER, Ko DC. An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility. Genome Med 2021; 13:83. [PMID: 34001247 PMCID: PMC8127495 DOI: 10.1186/s13073-021-00904-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysiology remains an important challenge. Methods are needed to systematically bridge this crucial gap to facilitate experimental testing of hypotheses and translation to clinical utility. RESULTS Here, we leveraged cross-phenotype associations to identify traits with shared genetic architecture, using linkage disequilibrium (LD) information to accurately capture shared SNPs by proxy, and calculate significance of enrichment. This shared genetic architecture was examined across differing biological scales through incorporating data from catalogs of clinical, cellular, and molecular GWAS. We have created an interactive web database (interactive Cross-Phenotype Analysis of GWAS database (iCPAGdb)) to facilitate exploration and allow rapid analysis of user-uploaded GWAS summary statistics. This database revealed well-known relationships among phenotypes, as well as the generation of novel hypotheses to explain the pathophysiology of common diseases. Application of iCPAGdb to a recent GWAS of severe COVID-19 demonstrated unexpected overlap of GWAS signals between COVID-19 and human diseases, including with idiopathic pulmonary fibrosis driven by the DPP9 locus. Transcriptomics from peripheral blood of COVID-19 patients demonstrated that DPP9 was induced in SARS-CoV-2 compared to healthy controls or those with bacterial infection. Further investigation of cross-phenotype SNPs associated with both severe COVID-19 and other human traits demonstrated colocalization of the GWAS signal at the ABO locus with plasma protein levels of a reported receptor of SARS-CoV-2, CD209 (DC-SIGN). This finding points to a possible mechanism whereby glycosylation of CD209 by ABO may regulate COVID-19 disease severity. CONCLUSIONS Thus, connecting genetically related traits across phenotypic scales links human diseases to molecular and cellular measurements that can reveal mechanisms and lead to novel biomarkers and therapeutic approaches. The iCPAGdb web portal is accessible at http://cpag.oit.duke.edu and the software code at https://github.com/tbalmat/iCPAGdb .
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Thomas J Balmat
- Duke Research Computing, Duke University, Durham, NC, 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
| | - Florica J Constantine
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Andy Ingham
- Duke Research Computing, Duke University, Durham, NC, 27710, USA
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Ephraim L Tsalik
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Department of Hospital Medicine, Duke Regional Hospital, Durham, NC, 27705, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
| | - Mark R DeLong
- Duke Research Computing, Duke University, Durham, NC, 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Woo Center for Big Data and Precision Health, Duke University, Durham, NC, 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC, 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC, 27705, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
| | - Elizabeth R Hauser
- Duke Molecular Physiology Institute and Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, 27710, USA
- Cooperative Studies Program Epidemiology Center-Durham, Durham VA Health Care System, Durham, NC, 27705, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0049 CARL Building Box 3053, 213 Research Drive, Durham, NC, 27710, USA.
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
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36
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African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet 2021; 22:284-306. [PMID: 33432191 DOI: 10.1038/s41576-020-00306-8] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/29/2023]
Abstract
The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.
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37
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Rusmini M, Uva P, Amoroso A, Tolomeo M, Cavalli A. How Genetics Might Explain the Unusual Link Between Malaria and COVID-19. Front Med (Lausanne) 2021; 8:650231. [PMID: 33981715 PMCID: PMC8107224 DOI: 10.3389/fmed.2021.650231] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) pandemic has been the subject of a large number of studies in recent times. Here, starting from the evidence that in Italy, the areas with the lowest number of COVID-19 cases were those with the highest incidence of malaria in the early 1900's, we explore possible inverse relationships between malaria and COVID-19. Indeed, some genetic variants, which have been demonstrated to give an advantage against malaria, can also play a role in the incidence and severity of SARS-CoV-2 infections (e.g., the ACE2 receptor). To verify this scientific hypothesis, we here use public data from whole-genome sequencing (WGS) experiments to extrapolate the genetic information of 46 world populations with matched COVID-19 data. In particular, we focus on 47 genes, including ACE2 and genes which have previously been reported to play a role in malaria. Only common variants (>5%) in at least 30% of the selected populations were considered, and, for this subset, we correlate the intra-population allele frequency with the COVID-19 data (cases/million inhabitants), eventually pinpointing meaningful variants in 6 genes. This study allows us to distinguish between positive and negative correlations, i.e., variants whose frequency significantly increases with increasing or decreasing COVID-19 cases. Finally, we discuss the possible molecular mechanisms associated with these variants and advance potential therapeutic options, which may help fight and/or prevent COVID-19.
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Affiliation(s)
- Marta Rusmini
- Computational and Chemical Biology, Italian Institute of Technology, Genova, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) G. Gaslini, Genova, Italy
| | - Paolo Uva
- Computational and Chemical Biology, Italian Institute of Technology, Genova, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) G. Gaslini, Genova, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manlio Tolomeo
- Department of Health Promotion Sciences, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, Palermo, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Italian Institute of Technology, Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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38
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Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
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39
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Kerner G, Laval G, Patin E, Boisson-Dupuis S, Abel L, Casanova JL, Quintana-Murci L. Human ancient DNA analyses reveal the high burden of tuberculosis in Europeans over the last 2,000 years. Am J Hum Genet 2021; 108:517-524. [PMID: 33667394 PMCID: PMC8008489 DOI: 10.1016/j.ajhg.2021.02.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB), usually caused by Mycobacterium tuberculosis bacteria, is the first cause of death from an infectious disease at the worldwide scale, yet the mode and tempo of TB pressure on humans remain unknown. The recent discovery that homozygotes for the P1104A polymorphism of TYK2 are at higher risk to develop clinical forms of TB provided the first evidence of a common, monogenic predisposition to TB, offering a unique opportunity to inform on human co-evolution with a deadly pathogen. Here, we investigate the history of human exposure to TB by determining the evolutionary trajectory of the TYK2 P1104A variant in Europe, where TB is considered to be the deadliest documented infectious disease. Leveraging a large dataset of 1,013 ancient human genomes and using an approximate Bayesian computation approach, we find that the P1104A variant originated in the common ancestors of West Eurasians ∼30,000 years ago. Furthermore, we show that, following large-scale population movements of Anatolian Neolithic farmers and Eurasian steppe herders into Europe, P1104A has markedly fluctuated in frequency over the last 10,000 years of European history, with a dramatic decrease in frequency after the Bronze Age. Our analyses indicate that such a frequency drop is attributable to strong negative selection starting ∼2,000 years ago, with a relative fitness reduction on homozygotes of 20%, among the highest in the human genome. Together, our results provide genetic evidence that TB has imposed a heavy burden on European health over the last two millennia.
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40
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Altable M, de la Serna JM. Protection against COVID-19 in African population: Immunology, genetics, and malaria clues for therapeutic targets. Virus Res 2021; 299:198347. [PMID: 33631219 PMCID: PMC7898966 DOI: 10.1016/j.virusres.2021.198347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 02/14/2021] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND There is a marked discrepancy between SARS-CoV-2 seroprevalence and COVID-19 cases and deaths in Africa. MAIN: SARS-CoV-2 stimulates humoral and cellular immunity systems, as well as mitogen-activated protein kinase (MAPK) and nuclear NF-kB signalling pathways, which regulate inflammatory gene expression and immune cell differentiation. The result is pro-inflammatory cytokines release, hyperinflammatory condition, and cytokine storm, which provoke severe lung alterations that can lead to multi-organ failure in COVID-19. Multiple genetic and immunologic factors may contribute to the severity of COVID-19 in African individuals when compared to the rest of the global population. In this article, the role of malaria, NF-kB and MAPK pathways, caspase-12 expression, high level of LAIR-1-containing antibodies, and differential glycophorins (GYPA/B) expression in COVID-19 are discussed. CONCLUSION Understanding pathophysiological mechanisms can help identify target points for drugs and vaccines development against COVID-19. To our knowledge, this is the first study that explores this link and proposes a biological and molecular answer to the epidemiologic discrepancy in COVID-19 in Africa.
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Affiliation(s)
- Marcos Altable
- Private Practice of Neurology, Neuroceuta. (Virgen de África Clinic), Ceuta, Spain.
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41
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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42
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Esoh KK, Apinjoh TO, Nyanjom SG, Wonkam A, Chimusa ER, Amenga-Etego L, Amambua-Ngwa A, Achidi EA. Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection. Sci Rep 2021; 11:1039. [PMID: 33441574 PMCID: PMC7807043 DOI: 10.1038/s41598-020-79124-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/28/2020] [Indexed: 01/29/2023] Open
Abstract
Inferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.
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Affiliation(s)
- Kevin K Esoh
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, City Square, Kenya
| | - Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon.
| | - Steven G Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, Nairobi, City Square, Kenya
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Health Sciences Campus, Anzio Rd, Observatory, 7925, South Africa
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Accra, Ghana
| | | | - Eric A Achidi
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, South West Region, Cameroon
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43
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Abstract
Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV infection, has progressed from early candidate gene studies to recent multi-omic efforts, benefiting from spectacular advances in sequencing technology and data science. In addition to invading cells and co-opting the host machinery for replication, HIV also stably integrates into our own genome. The study of the complex interactions between the human and retroviral genomes has improved our understanding of pathogenic mechanisms and suggested novel preventive and therapeutic approaches against HIV infection.
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Affiliation(s)
- Paul J. McLaren
- grid.415368.d0000 0001 0805 4386National HIV and Retrovirology Laboratory at the JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB Canada ,grid.21613.370000 0004 1936 9609Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
| | - Jacques Fellay
- grid.5333.60000000121839049School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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44
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Wang L, Balmat TJ, Antonia AL, Constantine FJ, Henao R, Burke TW, Ingham A, McClain MT, Tsalik EL, Ko ER, Ginsburg GS, DeLong MR, Shen X, Woods CW, Hauser ER, Ko DC. An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.12.20.20248572. [PMID: 33398303 PMCID: PMC7781346 DOI: 10.1101/2020.12.20.20248572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
While genome-wide associations studies (GWAS) have successfully elucidated the genetic architecture of complex human traits and diseases, understanding mechanisms that lead from genetic variation to pathophysiology remains an important challenge. Methods are needed to systematically bridge this crucial gap to facilitate experimental testing of hypotheses and translation to clinical utility. Here, we leveraged cross-phenotype associations to identify traits with shared genetic architecture, using linkage disequilibrium (LD) information to accurately capture shared SNPs by proxy, and calculate significance of enrichment. This shared genetic architecture was examined across differing biological scales through incorporating data from catalogs of clinical, cellular, and molecular GWAS. We have created an interactive web database (interactive Cross-Phenotype Analysis of GWAS database (iCPAGdb); http://cpag.oit.duke.edu) to facilitate exploration and allow rapid analysis of user-uploaded GWAS summary statistics. This database revealed well-known relationships among phenotypes, as well as the generation of novel hypotheses to explain the pathophysiology of common diseases. Application of iCPAGdb to a recent GWAS of severe COVID-19 demonstrated unexpected overlap of GWAS signals between COVID-19 and human diseases, including with idiopathic pulmonary fibrosis driven by the DPP9 locus. Transcriptomics from peripheral blood of COVID-19 patients demonstrated that DPP9 was induced in SARS-CoV-2 compared to healthy controls or those with bacterial infection. Further investigation of cross-phenotype SNPs with severe COVID-19 demonstrated colocalization of the GWAS signal of the ABO locus with plasma protein levels of a reported receptor of SARS-CoV-2, CD209 (DC-SIGN), pointing to a possible mechanism whereby glycosylation of CD209 by ABO may regulate COVID-19 disease severity. Thus, connecting genetically related traits across phenotypic scales links human diseases to molecular and cellular measurements that can reveal mechanisms and lead to novel biomarkers and therapeutic approaches.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Alejandro L. Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Florica J. Constantine
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Andy Ingham
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Ephraim L. Tsalik
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Department of Hospital Medicine, Duke Regional Hospital, Durham, NC, 27705, USA
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mark R. DeLong
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Woo Center for Big Data and Precision Health, Duke University, Durham, NC 27710, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Elizabeth R. Hauser
- Duke Molecular Physiology Institute and Department of Biostatistics and Bioinformatics, Duke University Medical Center Durham, NC 27710, USA
- Cooperative Studies Program Epidemiology Center-Durham, Durham VA Health Care System, Durham, NC 27705, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Lead contact
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45
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Amuzu DS, Rockett KA, Leffler EM, Ansah F, Amoako N, Morang'a CM, Hubbart C, Rowlands K, Jeffreys AE, Amenga-Etego LN, Kwiatkowski DP, Awandare GA. High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies. Exp Biol Med (Maywood) 2020; 246:916-928. [PMID: 33325748 PMCID: PMC8022085 DOI: 10.1177/1535370220968545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Glycophorins are the most abundant sialoglycoproteins on the surface of human erythrocyte membranes. Genetic variation in glycophorin region of human chromosome 4 (containing GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as receptors for pathogens of major public health interest, including Plasmodiumsp., Babesiasp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in East African populations, has been linked with a 40% reduction in risk for severe malaria. Apart from Dantu, other large structural variants exist, with the most common being deletion of the whole GYPB gene and its surrounding region, resulting in multiple different deletion forms. In West Africa particularly, these deletions are estimated to account for between 5 and 15% of the variation in different populations, mostly attributed to the forms known as DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from three study sites in Ghana as well as samples from HapMap and 1000 G projects for validation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and other diseases.
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Affiliation(s)
- Dominic Sy Amuzu
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana.,Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kirk A Rockett
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Ellen M Leffler
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112-5330, USA
| | - Felix Ansah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Nicholas Amoako
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Collins M Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Anna E Jeffreys
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Lucas N Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
| | - Dominic P Kwiatkowski
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK.,Wellcome Sanger Institute, Hinxton CB10 1SA, UK.,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, GH 0233, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, GH 0233, Ghana
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46
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Siewert KM, Voight BF. BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data. Genome Biol Evol 2020; 12:3873-3877. [PMID: 32011695 PMCID: PMC7058154 DOI: 10.1093/gbe/evaa013] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2020] [Indexed: 12/24/2022] Open
Abstract
Long-term balancing selection results in a build-up of alleles at similar frequencies and a deficit of substitutions when compared with an outgroup at a locus. The previously published β(1) statistics detect balancing selection using only polymorphism data. We now propose the β(2) statistic which detects balancing selection using both polymorphism and substitution data. In addition, we derive the variance of all β statistics, allowing for their standardization and thereby reducing the influence of parameters which can confound other selection tests. The standardized β statistics outperform existing summary statistics in simulations, indicating β is a well-powered and widely applicable approach for detecting balancing selection. We apply the β(2) statistic to 1000 Genomes data and report two missense mutations with high β scores in the ACSBG2 gene. An implementation of all β statistics and their standardization are available in the BetaScan2 software package at https://github.com/ksiewert/BetaScan.
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Affiliation(s)
- Katherine M Siewert
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania
| | - Benjamin F Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania
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47
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Ndila CM, Nyirongo V, Macharia AW, Jeffreys AE, Rowlands K, Hubbart C, Busby GBJ, Band G, Harding RM, Rockett KA, Williams TN. Haplotype heterogeneity and low linkage disequilibrium reduce reliable prediction of genotypes for the ‑α3.7I form of α-thalassaemia using genome-wide microarray data. Wellcome Open Res 2020; 5:287. [DOI: 10.12688/wellcomeopenres.16320.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2020] [Indexed: 11/20/2022] Open
Abstract
Background: The -α3.7I-thalassaemia deletion is very common throughout Africa because it protects against malaria. When undertaking studies to investigate human genetic adaptations to malaria or other diseases, it is important to account for any confounding effects of α-thalassaemia to rule out spurious associations. Methods: In this study we have used direct α-thalassaemia genotyping to understand why GWAS data from a large malaria association study in Kilifi Kenya did not identify the α-thalassaemia signal. We then explored the potential use of a number of new approaches to using GWAS data for imputing α-thalassaemia as an alternative to direct genotyping by PCR. Results: We found very low linkage-disequilibrium of the directly typed data with the GWAS SNP markers around α-thalassaemia and across the haemoglobin-alpha (HBA) gene region, which along with a complex haplotype structure, could explain the lack of an association signal from the GWAS SNP data. Some indirect typing methods gave results that were in broad agreement with those derived from direct genotyping and could identify an association signal, but none were sufficiently accurate to allow correct interpretation compared with direct typing, leading to confusing or erroneous results. Conclusions: We conclude that going forwards, direct typing methods such as PCR will still be required to account for α-thalassaemia in GWAS studies.
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48
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Host genetics and infectious disease: new tools, insights and translational opportunities. Nat Rev Genet 2020; 22:137-153. [PMID: 33277640 PMCID: PMC7716795 DOI: 10.1038/s41576-020-00297-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Understanding how human genetics influence infectious disease susceptibility offers the opportunity for new insights into pathogenesis, potential drug targets, risk stratification, response to therapy and vaccination. As new infectious diseases continue to emerge, together with growing levels of antimicrobial resistance and an increasing awareness of substantial differences between populations in genetic associations, the need for such work is expanding. In this Review, we illustrate how our understanding of the host–pathogen relationship is advancing through holistic approaches, describing current strategies to investigate the role of host genetic variation in established and emerging infections, including COVID-19, the need for wider application to diverse global populations mirroring the burden of disease, the impact of pathogen and vector genetic diversity and a broad array of immune and inflammation phenotypes that can be mapped as traits in health and disease. Insights from study of inborn errors of immunity and multi-omics profiling together with developments in analytical methods are further advancing our knowledge of this important area. Infectious diseases are an ever-present global threat. In this Review, Kwok, Mentzer and Knight discuss our latest understanding of how human genetics influence susceptibility to disease. Furthermore, they discuss emerging progress in the interplay between host and pathogen genetics, molecular responses to infection and vaccination, and opportunities to bring these aspects together for rapid responses to emerging diseases such as COVID-19.
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49
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Dieng MM, Diawara A, Manikandan V, Tamim El Jarkass H, Sermé SS, Sombié S, Barry A, Coulibaly SA, Diarra A, Drou N, Arnoux M, Yousif A, Tiono AB, Sirima SB, Soulama I, Idaghdour Y. Integrative genomic analysis reveals mechanisms of immune evasion in P. falciparum malaria. Nat Commun 2020; 11:5093. [PMID: 33037226 PMCID: PMC7547729 DOI: 10.1038/s41467-020-18915-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 09/16/2020] [Indexed: 02/04/2023] Open
Abstract
The mechanisms behind the ability of Plasmodium falciparum to evade host immune system are poorly understood and are a major roadblock in achieving malaria elimination. Here, we use integrative genomic profiling and a longitudinal pediatric cohort in Burkina Faso to demonstrate the role of post-transcriptional regulation in host immune response in malaria. We report a strong signature of miRNA expression differentiation associated with P. falciparum infection (127 out of 320 miRNAs, B-H FDR 5%) and parasitemia (72 miRNAs, B-H FDR 5%). Integrative miRNA-mRNA analysis implicates several infection-responsive miRNAs (e.g., miR-16-5p, miR-15a-5p and miR-181c-5p) promoting lymphocyte cell death. miRNA cis-eQTL analysis using whole-genome sequencing data identified 1,376 genetic variants associated with the expression of 34 miRNAs (B-H FDR 5%). We report a protective effect of rs114136945 minor allele on parasitemia mediated through miR-598-3p expression. These results highlight the impact of post-transcriptional regulation, immune cell death processes and host genetic regulatory control in malaria.
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Affiliation(s)
- Mame Massar Dieng
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Aïssatou Diawara
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Vinu Manikandan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Hala Tamim El Jarkass
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Samuel Sindié Sermé
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Salif Sombié
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Aïssata Barry
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | | | - Amidou Diarra
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Nizar Drou
- Bioinformatics Core, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Marc Arnoux
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ayman Yousif
- Bioinformatics Core, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Alfred B Tiono
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
- Groupe de Recherche Action en Santé, Ouagadougou, Burkina Faso
| | - Issiaka Soulama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi, Abu Dhabi, UAE.
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Xu G, van Bruggen R, Gualtieri CO, Moradin N, Fois A, Vallerand D, De Sa Tavares Russo M, Bassenden A, Lu W, Tam M, Lesage S, Girouard H, Avizonis DZ, Deblois G, Prchal JT, Stevenson M, Berghuis A, Muir T, Rabinowitz J, Vidal SM, Fodil N, Gros P. Bisphosphoglycerate Mutase Deficiency Protects against Cerebral Malaria and Severe Malaria-Induced Anemia. Cell Rep 2020; 32:108170. [PMID: 32966787 DOI: 10.1016/j.celrep.2020.108170] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 07/07/2020] [Accepted: 08/27/2020] [Indexed: 11/30/2022] Open
Abstract
The replication cycle and pathogenesis of the Plasmodium malarial parasite involves rapid expansion in red blood cells (RBCs), and variants of certain RBC-specific proteins protect against malaria in humans. In RBCs, bisphosphoglycerate mutase (BPGM) acts as a key allosteric regulator of hemoglobin/oxyhemoglobin. We demonstrate here that a loss-of-function mutation in the murine Bpgm (BpgmL166P) gene confers protection against both Plasmodium-induced cerebral malaria and blood-stage malaria. The malaria protection seen in BpgmL166P mutant mice is associated with reduced blood parasitemia levels, milder clinical symptoms, and increased survival. The protective effect of BpgmL166P involves a dual mechanism that enhances the host's stress erythroid response to Plasmodium-driven RBC loss and simultaneously alters the intracellular milieu of the RBCs, including increased oxyhemoglobin and reduced energy metabolism, reducing Plasmodium maturation, and replication. Overall, our study highlights the importance of BPGM as a regulator of hemoglobin/oxyhemoglobin in malaria pathogenesis and suggests a new potential malaria therapeutic target.
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Affiliation(s)
- Guoyue Xu
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Rebekah van Bruggen
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Christian O Gualtieri
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Neda Moradin
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Adrien Fois
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Diane Vallerand
- Université de Montréal, Département de Pharmacologie et Physiologie, Pav Roger-Gaudry, 2900 Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | | | - Angelia Bassenden
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Mifong Tam
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Sylvie Lesage
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montréal, QC H1T 2M4, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Hélène Girouard
- Université de Montréal, Département de Pharmacologie et Physiologie, Pav Roger-Gaudry, 2900 Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Daina Zofija Avizonis
- Rosalind and Morris Goodman Cancer Research Centre, 1160 Pin Avenue West, Montréal, QC H3A 1A3, Canada
| | - Geneviève Deblois
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3T 1J4, Canada; Faculté de Pharmacie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Josef T Prchal
- Division of Hematology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA
| | - Mary Stevenson
- Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Albert Berghuis
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
| | - Tom Muir
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Joshua Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC H3A 2B4, Canada
| | - Nassima Fodil
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Centre CERMO-FC Pavillon des Sciences Biologiques, 141 Avenue du Président Kennedy, Montréal, QC H2X 3Y7, Canada.
| | - Philippe Gros
- Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada; McGill University Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada.
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