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Stucke EM, Lawton JG, Travassos MA. ApoE: A new piece to the severe malaria puzzle. Pediatr Res 2024; 96:12-14. [PMID: 38388820 DOI: 10.1038/s41390-024-03096-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Affiliation(s)
- Emily M Stucke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Jonathan G Lawton
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mark A Travassos
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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2
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Skitchenko R, Modrusan Z, Loboda A, Kopp JB, Winkler CA, Sergushichev A, Gupta N, Stevens C, Daly MJ, Shaw A, Artomov M. CR1 variants contribute to FSGS susceptibility across multiple populations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.20.23298462. [PMID: 38076851 PMCID: PMC10705641 DOI: 10.1101/2023.11.20.23298462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Focal segmental glomerulosclerosis (FSGS) is a common cause of nephrotic syndrome with an annual incidence in the United States in African-Americans compared to European-Americans of 24 cases and 5 cases per million, respectively. Among glomerular diseases in Europe and Latin-America, FSGS was the second most frequent diagnosis, and in Asia the fifth. We expand previous efforts in understanding genetics of FSGS by performing a case-control study involving ethnically-diverse groups FSGS cases (726) and a pool of controls (13,994), using panel sequencing of approximately 2,500 podocyte-expressed genes. Through rare variant association tests, we replicated known risk genes - KANK1, COL4A4, and APOL1. A novel significant association was observed for the gene encoding complement receptor 1 (CR1). High-risk rare variants in CR1 in the European-American cohort were commonly observed in Latin- and African-Americans. Therefore, a combined rare and common variant analysis was used to replicate the CR1 association in non-European populations. The CR1 risk variant, rs17047661, gives rise to the Sl1/Sl2 (R1601G) allele that was previously associated with protection against cerebral malaria. Pleiotropic effects of rs17047661 may explain the difference in allele frequencies across continental ancestries and suggest a possible role for genetically-driven alterations of adaptive immunity in the pathogenesis of FSGS.
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Affiliation(s)
- Rostislav Skitchenko
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Centre, St. Petersburg, Russia
| | - Zora Modrusan
- Research Biology, Genentech Inc., San Francisco, CA, USA
| | - Alexander Loboda
- ITMO University, St. Petersburg, Russia
- Almazov National Medical Research Centre, St. Petersburg, Russia
- Broad Institute, Cambridge, MA, USA
| | - Jeffrey B. Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Cheryl A. Winkler
- Molecular Genetic Epidemiology Studies Section, National Cancer Institute (NCI), Frederick, Maryland, USA
| | | | | | | | - Mark J. Daly
- Broad Institute, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Andrey Shaw
- Research Biology, Genentech Inc., San Francisco, CA, USA
| | - Mykyta Artomov
- Broad Institute, Cambridge, MA, USA
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
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3
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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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Rashidi S, Mansouri R, Ali-Hassanzadeh M, Muro A, Nguewa P, Manzano-Román R. The Defensive Interactions of Prominent Infectious Protozoan Parasites: The Host's Complement System. Biomolecules 2022; 12:1564. [PMID: 36358913 PMCID: PMC9687244 DOI: 10.3390/biom12111564] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/16/2022] [Accepted: 10/21/2022] [Indexed: 12/30/2023] Open
Abstract
The complement system exerts crucial functions both in innate immune responses and adaptive humoral immunity. This pivotal system plays a major role dealing with pathogen invasions including protozoan parasites. Different pathogens including parasites have developed sophisticated strategies to defend themselves against complement killing. Some of these strategies include the employment, mimicking or inhibition of host's complement regulatory proteins, leading to complement evasion. Therefore, parasites are proven to use the manipulation of the complement system to assist them during infection and persistence. Herein, we attempt to study the interaction´s mechanisms of some prominent infectious protozoan parasites including Plasmodium, Toxoplasma, Trypanosoma, and Leishmania dealing with the complement system. Moreover, several crucial proteins that are expressed, recruited or hijacked by parasites and are involved in the modulation of the host´s complement system are selected and their role for efficient complement killing or lysis evasion is discussed. In addition, parasite's complement regulatory proteins appear as plausible therapeutic and vaccine targets in protozoan parasitic infections. Accordingly, we also suggest some perspectives and insights useful in guiding future investigations.
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Affiliation(s)
- Sajad Rashidi
- Molecular and Medicine Research Center, Khomein University of Medical Sciences, Khomein 38811, Iran
- Department of Medical Laboratory Sciences, Khomein University of Medical Sciences, Khomein 38811, Iran
| | - Reza Mansouri
- Department of Immunology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences and Health Services, Yazd 8915173143, Iran
| | - Mohammad Ali-Hassanzadeh
- Department of Immunology, School of Medicine, Jiroft University of Medical Sciences, Jiroft 7861615765, Iran
| | - Antonio Muro
- Infectious and Tropical Diseases Group (e-INTRO), Institute of Biomedical Research of Salamanca-Research Center for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain
| | - Paul Nguewa
- Department of Microbiology and Parasitology, ISTUN Institute of Tropical Health, IdiSNA (Navarra Institute for Health Research), University of Navarra, C/Irunlarrea 1, 31008 Pamplona, Spain
| | - Raúl Manzano-Román
- Infectious and Tropical Diseases Group (e-INTRO), Institute of Biomedical Research of Salamanca-Research Center for Tropical Diseases at the University of Salamanca (IBSAL-CIETUS), Faculty of Pharmacy, University of Salamanca, 37008 Salamanca, Spain
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5
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The impact of human complement on the clinical outcome of malaria infection. Mol Immunol 2022; 151:19-28. [PMID: 36063583 DOI: 10.1016/j.molimm.2022.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022]
Abstract
The tropical disease malaria remains a major cause of global morbidity. Once transmitted to the human by a blood-feeding mosquito, the unicellular malaria parasite comes into contact with the complement system and continues to interact with human complement during its intraerythrocytic replication cycles. In the course of infection, both the classical and the alternative pathway of complement are activated, leading to parasite opsonization and lysis as well as the induction of complement-binding antibodies. While complement activity can be linked to the severity of malaria, it remains to date unclear, whether human complement is beneficial for protective immunity or if extensive complement reactions may rather enhance pathogenesis. In addition, the parasite has evolved molecular strategies to circumvent attack by human complement and has even developed means to utilize complement factors as mediators of host cell infection. In this review, we highlight current knowledge on the role of human complement for the progression of malaria infection. We discuss the various types of interactions between malaria parasites and complement factors with regard to immunity and infection outcome and set a special emphasis on the dual role of complement in the context of parasite fitness.
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6
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Futagbi G, Otu PS, Abdul-Rahman M, Aidoo EK, Lo AC, Gyan BA, Afrane YA, Amoah LE. Association of TNF-Alpha, MBL2, NOS2, and G6PD with Malaria Outcomes in People in Southern Ghana. Genet Res (Camb) 2022; 2022:6686406. [PMID: 35291755 PMCID: PMC8901335 DOI: 10.1155/2022/6686406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background One major issue that has set back the gains of the numerous malaria control interventions that national malaria control programs have implemented is asymptomatic malaria. Certain host genetic factors are known to influence symptomatic malaria; however, not much is known about how host genetics influences the acquisition of asymptomatic malaria. Methods Genomic DNA was extracted from whole blood collected from 60 symptomatic and 149 nonfebrile (asymptomatic, N = 109, and uninfected, N = 40) volunteers aged between 2 and 69 years from a high (Obom) and a low (Asutsuare) malaria transmission setting in Southern Ghana. Restriction fragment length polymorphism (RFLP) was used to determine polymorphisms at the MBL2 54, TNF-α 308, NOS2 954, and G6PD 202/376 gene loci. Results Polymorphisms at the MBL2 54 and TNF-α 308 loci were significantly different amongst the three categories of volunteers in both Asutsuare (p = 0.006) and Obom (p=0.05). In Asutsuare, a low malaria transmission area, the allele G has significantly higher odds (3.15) of supporting asymptomatic malaria as against symptomatic malaria. There were significantly higher odds of TNF-α genotype GA being associated with symptomatic malaria as against asymptomatic malaria in both sites, Obom (p=0.027) and Asutsuare (p=0.027). The allele B of the G6PD gene was more prevalent in symptomatic rather than asymptomatic parasite-infected individuals in both Obom (p=0.001) and Asutsuare (p=0.003). Conclusion Individuals in Southern Ghana carrying the TNF-α 308 GA genotype are more likely to exhibit symptoms of malaria when infected with the malaria parasite as opposed to harboring an asymptomatic infection. Also, the B allele of the G6PD gene is likely to prevent a P. falciparum-infected person from exhibiting symptoms and thereby promote asymptomatic parasite carriage.
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Affiliation(s)
- Godfred Futagbi
- Department of Animal Biology and Conservation Science, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Paulina S Otu
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Mubarak Abdul-Rahman
- Department of Pathology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Ebenezer K Aidoo
- Department of Medical Laboratory, Accra Technical University, Accra, Ghana
| | - Aminata C Lo
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Medical Parasitology, Faculty of Medicine, University Cheikh Anta Diop, Dakar, Senegal
| | - Ben A Gyan
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Yaw A Afrane
- Department of Medical Microbiology, University of Ghana Medical School, University of Ghana, Accra, Ghana
| | - Linda E Amoah
- Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West Africa Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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7
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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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8
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Lawson A, Pinchbeck G. Study design synopsis: Observational study design in equine research. Equine Vet J 2021; 53:638-644. [PMID: 33719094 DOI: 10.1111/evj.13427] [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: 12/18/2020] [Accepted: 01/10/2021] [Indexed: 11/27/2022]
Abstract
When planning to conduct research, thorough consideration of the study design is essential to enable valid results and purposeful conclusions. A good study design will provide a strong basis for robust conclusions that can contribute to the evidence base. Conversely, a poor study design may unintentionally lead to invalid conclusions with inappropriate claims of the clinical importance. The purpose of this article is to review important aspects of observational study design, with an emphasis on observational clinical research. The value of an observational study can be manifold and the benefit of studying clinical cases can add substantial value to the evidence base and equine health and welfare, however this value will be diminished if study designs are flawed, or are inadequately reported. It is essential that clinicians have the skills to critically appraise observational studies, to determine strengths, limitations and the applicability to their clinical practice.
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Affiliation(s)
- April Lawson
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Neston, Cheshire, UK
| | - Gina Pinchbeck
- Faculty of Health and Life Sciences, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst, Neston, Cheshire, UK
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9
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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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10
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Penman BS, Gandon S. Adaptive immunity selects against malaria infection blocking mutations. PLoS Comput Biol 2020; 16:e1008181. [PMID: 33031369 PMCID: PMC7544067 DOI: 10.1371/journal.pcbi.1008181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 07/22/2020] [Indexed: 11/18/2022] Open
Abstract
The mutation responsible for Duffy negativity, which impedes Plasmodium vivax infection, has reached high frequencies in certain human populations. Conversely, mutations capable of blocking the more lethal P. falciparum have not succeeded in malarious zones. Here we present an evolutionary-epidemiological model of malaria which demonstrates that if adaptive immunity against the most virulent effects of malaria is gained rapidly by the host, mutations which prevent infection per se are unlikely to succeed. Our results (i) explain the rarity of strain-transcending P. falciparum infection blocking adaptations in humans; (ii) make the surprising prediction that mutations which block P. falciparum infection are most likely to be found in populations experiencing low or infrequent malaria transmission, and (iii) predict that immunity against some of the virulent effects of P. vivax malaria may be built up over the course of many infections.
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Affiliation(s)
- Bridget S. Penman
- Zeeman Institute and School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sylvain Gandon
- CEFE, CNRS, University of Montpellier, Paul Valéry University of Montpellier, EPHE, IRD, Montpellier, France
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11
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Abstract
Malaria has been the pre-eminent cause of early mortality in many parts of the world throughout much of the last five thousand years and, as a result, it is the strongest force for selective pressure on the human genome yet described. Around one third of the variability in the risk of severe and complicated malaria is now explained by additive host genetic effects. Many individual variants have been identified that are associated with malaria protection, but the most important all relate to the structure or function of red blood cells. They include the classical polymorphisms that cause sickle cell trait, α-thalassaemia, G6PD deficiency, and the major red cell blood group variants. More recently however, with improving technology and experimental design, others have been identified that include the Dantu blood group variant, polymorphisms in the red cell membrane protein ATP2B4, and several variants related to the immune response. Characterising how these genes confer their effects could eventually inform novel therapeutic approaches to combat malaria. Nevertheless, all together, only a small proportion of the heritable component of malaria resistance can be explained by the variants described so far, underscoring its complex genetic architecture and the need for continued research.
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Affiliation(s)
- Silvia N Kariuki
- Department of Epidemiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Thomas N Williams
- Department of Epidemiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.
- Department of Medicine, Imperial College of Science and Technology, London, UK.
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12
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Bentley AR, Callier SL, Rotimi CN. Evaluating the promise of inclusion of African ancestry populations in genomics. NPJ Genom Med 2020; 5:5. [PMID: 32140257 PMCID: PMC7042246 DOI: 10.1038/s41525-019-0111-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 12/16/2019] [Indexed: 12/24/2022] Open
Abstract
The lack of representation of diverse ancestral backgrounds in genomic research is well-known, and the resultant scientific and ethical limitations are becoming increasingly appreciated. The paucity of data on individuals with African ancestry is especially noteworthy as Africa is the birthplace of modern humans and harbors the greatest genetic diversity. It is expected that greater representation of those with African ancestry in genomic research will bring novel insights into human biology, and lead to improvements in clinical care and improved understanding of health disparities. Now that major efforts have been undertaken to address this failing, is there evidence of these anticipated advances? Here, we evaluate the promise of including diverse individuals in genomic research in the context of recent literature on individuals of African ancestry. In addition, we discuss progress and achievements on related technological challenges and diversity among scientists conducting genomic research.
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Affiliation(s)
- Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Shawneequa L. Callier
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
- Department of Clinical Research and Leadership, The George Washington University School of Medicine and Health Sciences, Washington, DC USA
| | - Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
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13
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Insights into malaria susceptibility using genome-wide data on 17,000 individuals from Africa, Asia and Oceania. Nat Commun 2019; 10:5732. [PMID: 31844061 PMCID: PMC6914791 DOI: 10.1038/s41467-019-13480-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/11/2019] [Indexed: 12/31/2022] Open
Abstract
The human genetic factors that affect resistance to infectious disease are poorly understood. Here we report a genome-wide association study in 17,000 severe malaria cases and population controls from 11 countries, informed by sequencing of family trios and by direct typing of candidate loci in an additional 15,000 samples. We identify five replicable associations with genome-wide levels of evidence including a newly implicated variant on chromosome 6. Jointly, these variants account for around one-tenth of the heritability of severe malaria, which we estimate as ~23% using genome-wide genotypes. We interrogate available functional data and discover an erythroid-specific transcription start site underlying the known association in ATP2B4, but are unable to identify a likely causal mechanism at the chromosome 6 locus. Previously reported HLA associations do not replicate in these samples. This large dataset will provide a foundation for further research on the genetic determinants of malaria resistance in diverse populations. Four genome-wide associated loci are currently known for malaria susceptibility. Here, the authors expand on earlier work by combining data from 11 malaria-endemic countries and additional population sequencing informing an African-enriched imputation reference panel, with findings including a previously unreported association on chromosome 6.
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14
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Rosetting revisited: a critical look at the evidence for host erythrocyte receptors in Plasmodium falciparum rosetting. Parasitology 2019; 147:1-11. [PMID: 31455446 PMCID: PMC7050047 DOI: 10.1017/s0031182019001288] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Malaria remains a major cause of mortality in African children, with no adjunctive treatments currently available to ameliorate the severe clinical forms of the disease. Rosetting, the adhesion of infected erythrocytes (IEs) to uninfected erythrocytes, is a parasite phenotype strongly associated with severe malaria, and hence is a potential therapeutic target. However, the molecular mechanisms of rosetting are complex and involve multiple distinct receptor–ligand interactions, with some similarities to the diverse pathways involved in P. falciparum erythrocyte invasion. This review summarizes the current understanding of the molecular interactions that lead to rosette formation, with a particular focus on host uninfected erythrocyte receptors including the A and B blood group trisaccharides, complement receptor one, heparan sulphate, glycophorin A and glycophorin C. There is strong evidence supporting blood group A trisaccharides as rosetting receptors, but evidence for other molecules is incomplete and requires further study. It is likely that additional host erythrocyte rosetting receptors remain to be discovered. A rosette-disrupting low anti-coagulant heparin derivative is being investigated as an adjunctive therapy for severe malaria, and further research into the receptor–ligand interactions underlying rosetting may reveal additional therapeutic approaches to reduce the unacceptably high mortality rate of severe malaria.
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15
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Damena D, Denis A, Golassa L, Chimusa ER. Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects. BMC Med Genomics 2019; 12:120. [PMID: 31409341 PMCID: PMC6693204 DOI: 10.1186/s12920-019-0564-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 07/29/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND P. falciparum malaria has been recognized as one of the prominent evolutionary selective forces of human genome that led to the emergence of multiple host protective alleles. A comprehensive understanding of the genetic bases of severe malaria susceptibility and resistance can potentially pave ways to the development of new therapeutics and vaccines. Genome-wide association studies (GWASs) have recently been implemented in malaria endemic areas and identified a number of novel association genetic variants. However, there are several open questions around heritability, epistatic interactions, genetic correlations and associated molecular pathways among others. Here, we assess the progress and pitfalls of severe malaria susceptibility GWASs and discuss the biology of the novel variants. RESULTS We obtained all severe malaria susceptibility GWASs published thus far and accessed GWAS dataset of Gambian populations from European Phenome Genome Archive (EGA) through the MalariaGen consortium standard data access protocols. We noticed that, while some of the well-known variants including HbS and ABO blood group were replicated across endemic populations, only few novel variants were convincingly identified and their biological functions remain to be understood. We estimated SNP-heritability of severe malaria at 20.1% in Gambian populations and showed how advanced statistical genetic analytic methods can potentially be implemented in malaria susceptibility studies to provide useful functional insights. CONCLUSIONS The ultimate goal of malaria susceptibility study is to discover a novel causal biological pathway that provide protections against severe malaria; a fundamental step towards translational medicine such as development of vaccine and new therapeutics. Beyond singe locus analysis, the future direction of malaria susceptibility requires a paradigm shift from single -omics to multi-stage and multi-dimensional integrative functional studies that combines multiple data types from the human host, the parasite, the mosquitoes and the environment. The current biotechnological and statistical advances may eventually lead to the feasibility of systems biology studies and revolutionize malaria research.
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Affiliation(s)
- Delesa Damena
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
| | - Awany Denis
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
| | - Lemu Golassa
- Aklilu Lema Institute of Pathobiology, Addis Ababa University, PO box 1176, Addis Ababa, Ethiopia
| | - Emile R. Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7700 South Africa
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Penha-Gonçalves C. Genetics of Malaria Inflammatory Responses: A Pathogenesis Perspective. Front Immunol 2019; 10:1771. [PMID: 31417551 PMCID: PMC6682681 DOI: 10.3389/fimmu.2019.01771] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 07/15/2019] [Indexed: 12/27/2022] Open
Abstract
Despite significant progress in combating malaria in recent years the burden of severe disease and death due to Plasmodium infections remains a global public health concern. Only a fraction of infected people develops severe clinical syndromes motivating a longstanding search for genetic determinants of malaria severity. Strong genetic effects have been repeatedly ascribed to mutations and allelic variants of proteins expressed in red blood cells but the role of inflammatory response genes in disease pathogenesis has been difficult to discern. We revisited genetic evidence provided by inflammatory response genes that have been repeatedly associated to malaria, namely TNF, NOS2, IFNAR1, HMOX1, TLRs, CD36, and CD40LG. This highlighted specific genetic variants having opposing roles in the development of distinct malaria clinical outcomes and unveiled diverse levels of genetic heterogeneity that shaped the complex association landscape of inflammatory response genes with malaria. However, scrutinizing genetic effects of individual variants corroborates a pathogenesis model where pro-inflammatory genetic variants acting in early infection stages contribute to resolve infection but at later stages confer increased vulnerability to severe organ dysfunction driven by tissue inflammation. Human genetics studies are an invaluable tool to find genes and molecular pathways involved in the inflammatory response to malaria but their precise roles in disease pathogenesis are still unexploited. Genome editing in malaria experimental models and novel genotyping-by-sequencing techniques are promising approaches to delineate the relevance of inflammatory response gene variants in the natural history of infection thereby will offer new rational angles on adjuvant therapeutics for prevention and clinical management of severe malaria.
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Lee WC, Russell B, Rénia L. Sticking for a Cause: The Falciparum Malaria Parasites Cytoadherence Paradigm. Front Immunol 2019; 10:1444. [PMID: 31316507 PMCID: PMC6610498 DOI: 10.3389/fimmu.2019.01444] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 06/10/2019] [Indexed: 12/26/2022] Open
Abstract
After a successful invasion, malaria parasite Plasmodium falciparum extensively remodels the infected erythrocyte cellular architecture, conferring cytoadhesive properties to the infected erythrocytes. Cytoadherence plays a central role in the parasite's immune-escape mechanism, at the same time contributing to the pathogenesis of severe falciparum malaria. In this review, we discuss the cytoadhesive interactions between P. falciparum infected erythrocytes and various host cell types, and how these events are linked to malaria pathogenesis. We also highlight the limitations faced by studies attempting to correlate diversity in parasite ligands and host receptors with the development of severe malaria.
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Affiliation(s)
- Wenn-Chyau Lee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Bruce Russell
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Laurent Rénia
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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Drake TM, Knight SR, Harrison EM, Søreide K. Global Inequities in Precision Medicine and Molecular Cancer Research. Front Oncol 2018; 8:346. [PMID: 30234014 PMCID: PMC6131579 DOI: 10.3389/fonc.2018.00346] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022] Open
Abstract
Precision medicine based upon molecular testing is heralded as a revolution in how cancer is prevented, diagnosed, and treated. Large efforts across the world aim to conduct comprehensive molecular profiling of disease to inform preclinical models, translational research studies and clinical trials. However, most studies have only been performed in patients from high-income countries. As the burden on non-communicable diseases increases, cancer will become a pressing burden across the world, disproportionately affecting low-middle income settings. There is emerging evidence that the molecular landscape of disease differs geographically and by genetic ancestry, which cannot be explained by environmental factors alone. There is a lack of good quality evidence that characterises the molecular landscape of cancers found in low-middle income countries. As cancer medicine becomes increasingly driven by molecular alterations in high-income settings, low-income settings may become left behind. Further efforts on an international scale must be made by researchers, funders, and policymakers to ensure cancer research addresses disease across the world, so models are not limited to subtypes of disease found in high-income countries. In this review, we discuss differences found in the molecular profiles of tumours worldwide and the implication this has for the future of global cancer care. Finally, we identify several barriers currently limiting progress in this field and innovative solutions, which may address these shortcomings.
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Affiliation(s)
- Thomas M. Drake
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen R. Knight
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Ewen M. Harrison
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Kjetil Søreide
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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