1
|
Adamson WE, Noyes H, Johnson P, Cooper A, Monckton DG, Ogunsola J, Beckett-Hill G, Sullivan M, Mark P, Parekh RS, MacLeod A. Phenome-wide analysis reveals epistatic associations between APOL1 variants and chronic kidney disease and multiple other disorders. EBioMedicine 2024; 101:105000. [PMID: 38360481 PMCID: PMC10944146 DOI: 10.1016/j.ebiom.2024.105000] [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: 06/26/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND APOL1 variants G1 and G2 are common in populations with recent African ancestry. They are associated with protection from African sleeping sickness, however homozygosity or compound heterozygosity for these variants is associated with chronic kidney disease (CKD) and related conditions. What is not clear is the extent of associations with non-kidney-related disorders, and whether there are clusters of diseases associated with individual APOL1 genotypes. METHODS Using a cohort of 7462 UK Biobank participants with recent African ancestry, we conducted a phenome-wide association study investigating associations between individual APOL1 genotypes and conditions identified by the International Classification of Disease phenotypes. FINDINGS We identified 27 potential associations between individual APOL1 genotypes and a diverse range of conditions. G1/G2 compound heterozygotes were specifically associated with 26 of these conditions (all deleteriously), with an over-representation of infectious diseases (including hospitalisation and death resulting from COVID-19). The analysis also exposed complexities in the relationship between APOL1 and CKD that are not evident when risk variants are grouped together: G1 homozygosity, G2 homozygosity, and G1/G2 compound heterozygosity were each shown to be associated with distinct CKD phenotypes. The multi-locus nature of the G1/G2 genotype means that its associations would go undetected in a standard genome-wide association study. INTERPRETATION Our findings have implications for understanding health risks and better-targeted detection, intervention, and therapeutic strategies, particularly in populations where APOL1 G1 and G2 are common such as in sub-Saharan Africa and its diaspora. FUNDING This study was funded by the Wellcome Trust (209511/Z/17/Z) and H3Africa (H3A/18/004).
Collapse
Affiliation(s)
- Walt E Adamson
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom; TrypanoGEN+ Research Group, Uganda, Member of the H3Africa Consortium, South Africa.
| | - Harry Noyes
- TrypanoGEN+ Research Group, Uganda, Member of the H3Africa Consortium, South Africa; Centre for Genomic Research, University of Liverpool, United Kingdom
| | - Paul Johnson
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Anneli Cooper
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom
| | - Darren G Monckton
- School of Molecular Biosciences, University of Glasgow, United Kingdom
| | - John Ogunsola
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom
| | - Georgia Beckett-Hill
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom
| | - Michael Sullivan
- School of Cardiovascular and Metabolic Health, University of Glasgow, United Kingdom
| | - Patrick Mark
- School of Cardiovascular and Metabolic Health, University of Glasgow, United Kingdom
| | - Rulan S Parekh
- Women's College Hospital, Hospital for Sick Children and University of Toronto, Canada
| | - Annette MacLeod
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, United Kingdom; Wellcome Centre for Integrative Parasitology, University of Glasgow, United Kingdom; TrypanoGEN+ Research Group, Uganda, Member of the H3Africa Consortium, South Africa.
| |
Collapse
|
2
|
Pell J, Nagata S, Menon MC. Nonpodocyte Roles of APOL1 Variants: An Evolving Paradigm. KIDNEY360 2023; 4:e1325-e1331. [PMID: 37461136 PMCID: PMC10550003 DOI: 10.34067/kid.0000000000000216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
Since the seminal discovery of the trypanolytic, exonic variants in apolipoprotein L1 (APOL1) and their association with kidney disease in individuals of recent African ancestry, a wide body of research has emerged offering key insights into the mechanisms of disease. Importantly, the podocyte has become a focal point for our understanding of how risk genotype leads to disease, with activation of putative signaling pathways within the podocyte identified as playing a causal role in podocytopathy, FSGS, and progressive renal failure. However, the complete mechanism of genotype-to-phenotype progression remains incompletely understood in APOL1-risk individuals. An emerging body of evidence reports more than podocyte-intrinsic expression of APOL1 risk variants is needed for disease to manifest. This article reviews the seminal data and reports which placed the podocyte at the center of our understanding of APOL1-FSGS, as well as the evident shortcomings of this podocentric paradigm. We examine existing evidence for environmental and genetic factors that may influence disease, drawing from both clinical data and APOL1's fundamental role as an immune response gene. We also review the current body of data for APOL1's impact on nonpodocyte cells, including endothelial cells, the placenta, and immune cells in both a transplant and native setting. Finally, we discuss the implications of these emerging data and how the paradigm of disease might evolve as a result.
Collapse
Affiliation(s)
- John Pell
- Department of Medicine , Yale University, New Haven , Connecticut
| | | | | |
Collapse
|
3
|
Poudyal NR, Paul KS. Fatty acid uptake in Trypanosoma brucei: Host resources and possible mechanisms. Front Cell Infect Microbiol 2022; 12:949409. [PMID: 36478671 PMCID: PMC9719944 DOI: 10.3389/fcimb.2022.949409] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/24/2022] [Indexed: 11/22/2022] Open
Abstract
Trypanosoma brucei spp. causes African Sleeping Sickness in humans and nagana, a wasting disease, in cattle. As T. brucei goes through its life cycle in its mammalian and insect vector hosts, it is exposed to distinct environments that differ in their nutrient resources. One such nutrient resource is fatty acids, which T. brucei uses to build complex lipids or as a potential carbon source for oxidative metabolism. Of note, fatty acids are the membrane anchoring moiety of the glycosylphosphatidylinositol (GPI)-anchors of the major surface proteins, Variant Surface Glycoprotein (VSG) and the Procyclins, which are implicated in parasite survival in the host. While T. brucei can synthesize fatty acids de novo, it also readily acquires fatty acids from its surroundings. The relative contribution of parasite-derived vs. host-derived fatty acids to T. brucei growth and survival is not known, nor have the molecular mechanisms of fatty acid uptake been defined. To facilitate experimental inquiry into these important aspects of T. brucei biology, we addressed two questions in this review: (1) What is known about the availability of fatty acids in different host tissues where T. brucei can live? (2) What is known about the molecular mechanisms mediating fatty acid uptake in T. brucei? Finally, based on existing biochemical and genomic data, we suggest a model for T. brucei fatty acid uptake that proposes two major routes of fatty acid uptake: diffusion across membranes followed by intracellular trapping, and endocytosis of host lipoproteins.
Collapse
Affiliation(s)
- Nava Raj Poudyal
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States
| | - Kimberly S. Paul
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Eukaryotic Pathogens Innovation Center (EPIC), Clemson University, Clemson, SC, United States
| |
Collapse
|
4
|
Serem EK, Bargul JL, Ngari MM, Abdullahi OA, Mburu DM. Farmers' knowledge, perceptions, and practices on animal trypanosomosis and the tsetse fly vector: A cross-sectional study around Kenya's Arabuko-Sokoke Forest Reserve at the livestock-wildlife interface. OPEN RESEARCH AFRICA 2022; 5:22. [PMID: 37600566 PMCID: PMC10439355 DOI: 10.12688/openresafrica.13397.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/13/2022] [Indexed: 08/22/2023]
Abstract
Background: Animal African trypanosomosis (AAT) is a veterinary disease caused by trypanosomes transmitted cyclically by tsetse flies. AAT causes huge agricultural losses in sub-Saharan Africa. Both tsetse flies and trypanosomosis (T&T) are endemic in the study area inhabited by smallholder livestock farmers at the livestock-wildlife interface around Arabuko-Sokoke Forest Reserve (ASFR) in Kilifi County on the Kenyan coast. We assessed farmers' knowledge, perceptions and control practices towards T&T. Methods: A cross-sectional study was conducted during November and December 2017 to collect data from 404 randomly selected cattle-rearing households using a structured questionnaire. Descriptive statistics were used to determine farmers' knowledge, perceptions, and control practices towards T&T. Demographic factors associated with knowledge of T&T were assessed using a logistic regression model. Results: Participants consisted of 53% female, 77% married, 30% elderly (>55 years), and the majority (81%) had attained primary education or below. Most small-scale farmers (98%) knew the tsetse fly by its local name, and 76% could describe the morphology of the adult tsetse fly by size in comparison to the housefly's ( Musca domestica). Only 16% of the farmers knew tsetse flies as vectors of livestock diseases. Higher chances of adequate knowledge on T&T were associated with the participants' (i) age of 15-24 years (aOR 2.88 (95% CI 1.10-7.52), (ii) level of education including secondary (aOR 2.46 (95% CI 1.43-4.24)) and tertiary (aOR 3.80 (95% CI 1.54-9.37)), and (iii) employment status: self-employed farmers (aOR 6.54 (95% CI 4.36-9.80)). Conclusions: Our findings suggest that small-scale farmers around ASFR have limited knowledge of T&T. It is envisaged that efforts geared towards training of the farmers would bridge this knowledge gap and sharpen the perceptions and disease control tactics to contribute to the prevention and control of T&T.
Collapse
Affiliation(s)
- Erick K Serem
- Department of Public Health, School of Health and Human Sciences, Pwani University, Kilifi, P.O Box 195-80108 Kilifi, Kenya
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, P.O Box 195-80108, Kenya
| | - Joel L Bargul
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi, P.O Box 62000-00200, Kenya
- Animal Health Theme, International Centre of Insect Physiology and Ecology (icipe), Nairobi, P.O Box 30772-00100, Kenya
| | - Moses M Ngari
- Department of Public Health, School of Health and Human Sciences, Pwani University, Kilifi, P.O Box 195-80108 Kilifi, Kenya
- KEMRI/Wellcome Trust Research Programme, Clinical Trials Facility, Kilifi, P.O Box 230-80108, Kenya
| | - Osman A Abdullahi
- Department of Public Health, School of Health and Human Sciences, Pwani University, Kilifi, P.O Box 195-80108 Kilifi, Kenya
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, P.O Box 195-80108, Kenya
| | - David M Mburu
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, P.O Box 195-80108, Kenya
- Department of Biological Sciences, Pwani University, Kilifi, P.O Box 195-80108, Kenya
| |
Collapse
|
5
|
African trypanosome strategies for conquering new hosts and territories: the end of monophyly? Trends Parasitol 2022; 38:724-736. [DOI: 10.1016/j.pt.2022.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/22/2022]
|
6
|
Müller D, Schmitz J, Fischer K, Granado D, Groh AC, Krausel V, Lüttgenau SM, Amelung TM, Pavenstädt H, Weide T. Evolution of Renal-Disease Factor APOL1 Results in Cis and Trans Orientations at the Endoplasmic Reticulum That Both Show Cytotoxic Effects. Mol Biol Evol 2021; 38:4962-4976. [PMID: 34323996 PMCID: PMC8557400 DOI: 10.1093/molbev/msab220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The recent and exclusively in humans and a few other higher primates expressed APOL1 (apolipoprotein L1) gene is linked to African human trypanosomiasis (also known as African sleeping sickness) as well as to different forms of kidney diseases. Whereas APOL1's role as a trypanolytic factor is well established, pathobiological mechanisms explaining its cytotoxicity in renal cells remain unclear. In this study, we compared the APOL family members using a combination of evolutionary studies and cell biological experiments to detect unique features causal for APOL1 nephrotoxic effects. We investigated available primate and mouse genome and transcriptome data to apply comparative phylogenetic and maximum likelihood selection analyses. We suggest that the APOL gene family evolved early in vertebrates and initial splitting occurred in ancestral mammals. Diversification and differentiation of functional domains continued in primates, including developing the two members APOL1 and APOL2. Their close relationship could be diagnosed by sequence similarity and a shared ancestral insertion of an AluY transposable element. Live-cell imaging analyses showed that both expressed proteins show a strong preference to localize at the endoplasmic reticulum (ER). However, glycosylation and secretion assays revealed that-unlike APOL2-APOL1 membrane insertion or association occurs in different orientations at the ER, with the disease-associated mutants facing either the luminal (cis) or cytoplasmic (trans) side of the ER. The various pools of APOL1 at the ER offer a novel perspective in explaining the broad spectrum of its observed toxic effects.
Collapse
Affiliation(s)
- Daria Müller
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Jürgen Schmitz
- Institute of Experimental Pathology, ZMBE, University of Münster, Münster, Germany
| | - Katharina Fischer
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Daniel Granado
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Ann-Christin Groh
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Vanessa Krausel
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Simona Mareike Lüttgenau
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Till Maximilian Amelung
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Hermann Pavenstädt
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| | - Thomas Weide
- Internal Medicine D (MedD), Molecular Nephrology, University Hospital of Münster (UKM), Münster, Germany
| |
Collapse
|
7
|
Magez S, Li Z, Nguyen HTT, Pinto Torres JE, Van Wielendaele P, Radwanska M, Began J, Zoll S, Sterckx YGJ. The History of Anti-Trypanosome Vaccine Development Shows That Highly Immunogenic and Exposed Pathogen-Derived Antigens Are Not Necessarily Good Target Candidates: Enolase and ISG75 as Examples. Pathogens 2021; 10:pathogens10081050. [PMID: 34451514 PMCID: PMC8400590 DOI: 10.3390/pathogens10081050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
Salivarian trypanosomes comprise a group of extracellular anthroponotic and zoonotic parasites. The only sustainable method for global control of these infection is through vaccination of livestock animals. Despite multiple reports describing promising laboratory results, no single field-applicable solution has been successful so far. Conventionally, vaccine research focusses mostly on exposed immunogenic antigens, or the structural molecular knowledge of surface exposed invariant immunogens. Unfortunately, extracellular parasites (or parasites with extracellular life stages) have devised efficient defense systems against host antibody attacks, so they can deal with the mammalian humoral immune response. In the case of trypanosomes, it appears that these mechanisms have been perfected, leading to vaccine failure in natural hosts. Here, we provide two examples of potential vaccine candidates that, despite being immunogenic and accessible to the immune system, failed to induce a functionally protective memory response. First, trypanosomal enolase was tested as a vaccine candidate, as it was recently characterized as a highly conserved enzyme that is readily recognized during infection by the host antibody response. Secondly, we re-addressed a vaccine approach towards the Invariant Surface Glycoprotein ISG75, and showed that despite being highly immunogenic, trypanosomes can avoid anti-ISG75 mediated parasitemia control.
Collapse
Affiliation(s)
- Stefan Magez
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
- Correspondence:
| | - Zeng Li
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| | - Hang Thi Thu Nguyen
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
- Department of Biochemistry and Microbiology, Ghent University, Ledeganckstraat 35, 9000 Ghent, Belgium
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
| | - Joar Esteban Pinto Torres
- Laboratory of Cellular and Molecular Immunology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; (Z.L.); (H.T.T.N.); (J.E.P.T.)
| | - Pieter Van Wielendaele
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Department of Molecular Biotechnology, Environment Technology and Food Technology, Ghent University Global Campus, Songdomunhwa-Ro 119-5, Yeonsu-Gu, Incheon 406-840, Korea;
- Department of Biomedical Molecular Biology, Ghent University, Technologiepark Zwijnaarde 71, 9000 Ghent, Belgium
| | - Jakub Began
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Namesti 2, 16610 Prague 6, Czech Republic; (J.B.); (S.Z.)
| | - Sebastian Zoll
- Laboratory of Structural Parasitology, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo Namesti 2, 16610 Prague 6, Czech Republic; (J.B.); (S.Z.)
| | - Yann G.-J. Sterckx
- Laboratory of Medical Biochemistry (LMB) and the Infla-Med Centre of Excellence, University of Antwerp, Campus Drie Eiken, Universiteitsplein 1, 2610 Wilrijk, Belgium; (P.V.W.); (Y.G.-J.S.)
| |
Collapse
|
8
|
Dean S. Basic Biology of Trypanosoma brucei with Reference to the Development of Chemotherapies. Curr Pharm Des 2021; 27:1650-1670. [PMID: 33463458 DOI: 10.2174/1381612827666210119105008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022]
Abstract
Trypanosoma brucei are protozoan parasites that cause the lethal human disease African sleeping sickness and the economically devastating disease of cattle, Nagana. African sleeping sickness, also known as Human African Trypanosomiasis (HAT), threatens 65 million people and animal trypanosomiasis makes large areas of farmland unusable. There is no vaccine and licensed therapies against the most severe, late-stage disease are toxic, impractical and ineffective. Trypanosomes are transmitted by tsetse flies, and HAT is therefore predominantly confined to the tsetse fly belt in sub-Saharan Africa. They are exclusively extracellular and they differentiate between at least seven developmental forms that are highly adapted to host and vector niches. In the mammalian (human) host they inhabit the blood, cerebrospinal fluid (late-stage disease), skin, and adipose fat. In the tsetse fly vector they travel from the tsetse midgut to the salivary glands via the ectoperitrophic space and proventriculus. Trypanosomes are evolutionarily divergent compared with most branches of eukaryotic life. Perhaps most famous for their extraordinary mechanisms of monoallelic gene expression and antigenic variation, they have also been investigated because much of their biology is either highly unconventional or extreme. Moreover, in addition to their importance as pathogens, many researchers have been attracted to the field because trypanosomes have some of the most advanced molecular genetic tools and database resources of any model system. The following will cover just some aspects of trypanosome biology and how its divergent biochemistry has been leveraged to develop drugs to treat African sleeping sickness. This is by no means intended to be a comprehensive survey of trypanosome features. Rather, I hope to present trypanosomes as one of the most fascinating and tractable systems to do discovery biology.
Collapse
Affiliation(s)
- Samuel Dean
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
| |
Collapse
|
9
|
African Trypanosomosis Obliterates DTPa Vaccine-Induced Functional Memory So That Post-Treatment Bordetella pertussis Challenge Fails to Trigger a Protective Recall Response. Vaccines (Basel) 2021; 9:vaccines9060603. [PMID: 34200074 PMCID: PMC8230080 DOI: 10.3390/vaccines9060603] [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: 04/29/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 11/17/2022] Open
Abstract
Salivarian trypanosomes are extracellular parasites causing anthroponotic and zoonotic infections. Anti-parasite vaccination is considered the only sustainable method for global trypanosomosis control. Unfortunately, no single field applicable vaccine solution has been successful so far. The active destruction of the host’s adaptive immune system by trypanosomes is believed to contribute to this problem. Here, we show that Trypanosome brucei brucei infection results in the lasting obliteration of immunological memory, including vaccine-induced memory against non-related pathogens. Using the well-established DTPa vaccine model in combination with a T. b. brucei infection and a diminazene diaceturate anti-parasite treatment scheme, our results demonstrate that while the latter ensured full recovery from the T. b. brucei infection, it failed to restore an efficacious anti-B. pertussis vaccine recall response. The DTPa vaccine failure coincided with a shift in the IgG1/IgG2a anti-B. pertussis antibody ratio in favor of IgG2a, and a striking impact on all of the spleen immune cell populations. Interestingly, an increased plasma IFNγ level in DTPa-vaccinated trypanosome-infected mice coincided with a temporary antibody-independent improvement in early-stage trypanosomosis control. In conclusion, our results are the first to show that trypanosome-inflicted immune damage is not restored by successful anti-parasite treatment.
Collapse
|
10
|
Salivarian Trypanosomes Have Adopted Intricate Host-Pathogen Interaction Mechanisms That Ensure Survival in Plain Sight of the Adaptive Immune System. Pathogens 2021; 10:pathogens10060679. [PMID: 34072674 PMCID: PMC8229994 DOI: 10.3390/pathogens10060679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 12/21/2022] Open
Abstract
Salivarian trypanosomes are extracellular parasites affecting humans, livestock and game animals. Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense are human infective sub-species of T. brucei causing human African trypanosomiasis (HAT—sleeping sickness). The related T. b. brucei parasite lacks the resistance to survive in human serum, and only inflicts animal infections. Animal trypanosomiasis (AT) is not restricted to Africa, but is present on all continents. T. congolense and T. vivax are the most widespread pathogenic trypanosomes in sub-Saharan Africa. Through mechanical transmission, T. vivax has also been introduced into South America. T. evansi is a unique animal trypanosome that is found in vast territories around the world and can cause atypical human trypanosomiasis (aHT). All salivarian trypanosomes are well adapted to survival inside the host’s immune system. This is not a hostile environment for these parasites, but the place where they thrive. Here we provide an overview of the latest insights into the host-parasite interaction and the unique survival strategies that allow trypanosomes to outsmart the immune system. In addition, we review new developments in treatment and diagnosis as well as the issues that have hampered the development of field-applicable anti-trypanosome vaccines for the implementation of sustainable disease control.
Collapse
|
11
|
de Castro Neto AL, da Silveira JF, Mortara RA. Comparative Analysis of Virulence Mechanisms of Trypanosomatids Pathogenic to Humans. Front Cell Infect Microbiol 2021; 11:669079. [PMID: 33937106 PMCID: PMC8085324 DOI: 10.3389/fcimb.2021.669079] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/30/2021] [Indexed: 11/23/2022] Open
Abstract
Trypanosoma brucei, Leishmania spp., and T. cruzi are flagellate protozoans of the family Trypanosomatidae and the causative agents of human African trypanosomiasis, leishmaniasis, and Chagas disease, respectively. These diseases affect humans worldwide and exert a significant impact on public health. Over the course of evolution, the parasites associated with these pathologies have developed mechanisms to circumvent the immune response system throughout the infection cycle. In cases of human infection, this function is undertaken by a group of proteins and processes that allow the parasites to propagate and survive during host invasion. In T. brucei, antigenic variation is promoted by variant surface glycoproteins and other proteins involved in evasion from the humoral immune response, which helps the parasite sustain itself in the extracellular milieu during infection. Conversely, Leishmania spp. and T. cruzi possess a more complex infection cycle, with specific intracellular stages. In addition to mechanisms for evading humoral immunity, the pathogens have also developed mechanisms for facilitating their adhesion and incorporation into host cells. In this review, the different immune evasion strategies at cellular and molecular levels developed by these human-pathogenic trypanosomatids have been discussed, with a focus on the key molecules responsible for mediating the invasion and evasion mechanisms and the effects of these molecules on virulence.
Collapse
Affiliation(s)
- Artur Leonel de Castro Neto
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - José Franco da Silveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renato Arruda Mortara
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| |
Collapse
|
12
|
Ojo RJ, Enoch GA, Adeh FS, Fompun LC, Bitrus BY, Kugama MA. Comprehensive analysis of oral administration of Vitamin E on the early stage of Trypanosoma brucei brucei infection. J Parasit Dis 2021; 45:512-523. [PMID: 34295050 DOI: 10.1007/s12639-020-01322-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022] Open
Abstract
Reinforcement of the body with exogenous antioxidants have been shown to mitigate the negative effects of African trypanosomiasis on the host and contribute greatly to their survival. This study was therefore conducted to evaluate the effects of oral administration of Vitamin E on the early stage of Trypanosoma brucei brucei infection. To achieve this, parasite free healthy rats were acclimatized for 2 weeks before they were divided into three groups. Two of the groups were infected by intraperitoneal inoculation of 1 × 104 parasites/rat and monitored for the presence of Trypanosoma brucei brucei. Blood samples were collected from the infected rats from the second day post infection to detect the presence of parasites. Vitamin E treatment started day 4 post infection at the onset of parasitaemia. Parasites were monitored till the end of the study. The blood glucose level was determined using a glucometer; the lipid profile, liver and kidney biomarkers, electrolytes and protein were determined by colorimetric method using commercial kits. Haematological parameters were analysed using a sysmex haematology analyser. The results of this study showed that the infection adversely affected the biomarkers examined showing its negative effect on liver, kidney, haematological parameters and host electrolyte balance. Treatments with Vitamin E was however able to mitigate the negative effect of this infection. In conclusion, the treatment was able to ameliorate the anaemia and organ damage caused by Trypanosoma brucei brucei, extend the life span of the treated rats and greatly delay the time taken to get to the second stage of the infection.
Collapse
Affiliation(s)
- Rotimi Johnson Ojo
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nasarawa State Nigeria
| | - Gideon Agyiye Enoch
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nasarawa State Nigeria
| | - Faratu Saleh Adeh
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nasarawa State Nigeria
| | - Luret Carmen Fompun
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nasarawa State Nigeria
| | - Blessing Yohanna Bitrus
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nasarawa State Nigeria
| | - Meshack Anthony Kugama
- Human African Trypanosomiasis Research Department, Nigerian Institute of Trypanosomiasis Research, Kaduna, Kaduna State Nigeria
| |
Collapse
|
13
|
Macleod OJS, Bart JM, MacGregor P, Peacock L, Savill NJ, Hester S, Ravel S, Sunter JD, Trevor C, Rust S, Vaughan TJ, Minter R, Mohammed S, Gibson W, Taylor MC, Higgins MK, Carrington M. A receptor for the complement regulator factor H increases transmission of trypanosomes to tsetse flies. Nat Commun 2020; 11:1326. [PMID: 32165615 PMCID: PMC7067766 DOI: 10.1038/s41467-020-15125-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/15/2020] [Indexed: 11/09/2022] Open
Abstract
Persistent pathogens have evolved to avoid elimination by the mammalian immune system including mechanisms to evade complement. Infections with African trypanosomes can persist for years and cause human and animal disease throughout sub-Saharan Africa. It is not known how trypanosomes limit the action of the alternative complement pathway. Here we identify an African trypanosome receptor for mammalian factor H, a negative regulator of the alternative pathway. Structural studies show how the receptor binds ligand, leaving inhibitory domains of factor H free to inactivate complement C3b deposited on the trypanosome surface. Receptor expression is highest in developmental stages transmitted to the tsetse fly vector and those exposed to blood meals in the tsetse gut. Receptor gene deletion reduced tsetse infection, identifying this receptor as a virulence factor for transmission. This demonstrates how a pathogen evolved a molecular mechanism to increase transmission to an insect vector by exploitation of a mammalian complement regulator.
Collapse
Affiliation(s)
- Olivia J S Macleod
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Jean-Mathieu Bart
- Intertryp, IRD, Cirad, University of Montpellier, Montpellier, France
| | - Paula MacGregor
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Lori Peacock
- School of Biological Sciences, University of Bristol, Bristol, BS8 1UG, UK
| | - Nicholas J Savill
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK
| | - Svenja Hester
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Sophie Ravel
- Intertryp, IRD, Cirad, University of Montpellier, Montpellier, France
| | - Jack D Sunter
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, UK
| | - Camilla Trevor
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
- Department of Antibody Discovery and Protein Engineering, AstraZeneca R&D, Granta Park, Cambridge, CB21 6GH, UK
| | - Steven Rust
- Department of Antibody Discovery and Protein Engineering, AstraZeneca R&D, Granta Park, Cambridge, CB21 6GH, UK
| | - Tristan J Vaughan
- Department of Antibody Discovery and Protein Engineering, AstraZeneca R&D, Granta Park, Cambridge, CB21 6GH, UK
| | - Ralph Minter
- Department of Antibody Discovery and Protein Engineering, AstraZeneca R&D, Granta Park, Cambridge, CB21 6GH, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Wendy Gibson
- School of Biological Sciences, University of Bristol, Bristol, BS8 1UG, UK
| | - Martin C Taylor
- Faculty of Infectious and Tropical diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK.
| |
Collapse
|
14
|
Magez S, Pinto Torres JE, Obishakin E, Radwanska M. Infections With Extracellular Trypanosomes Require Control by Efficient Innate Immune Mechanisms and Can Result in the Destruction of the Mammalian Humoral Immune System. Front Immunol 2020; 11:382. [PMID: 32218784 PMCID: PMC7078162 DOI: 10.3389/fimmu.2020.00382] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Salivarian trypanosomes are extracellular parasites that affect humans, livestock, and game animals around the world. Through co-evolution with the mammalian immune system, trypanosomes have developed defense mechanisms that allow them to thrive in blood, lymphoid vessels, and tissue environments such as the brain, the fat tissue, and testes. Trypanosomes have developed ways to circumvent antibody-mediated killing and block the activation of the lytic arm of the complement pathway. Hence, this makes the innate immune control of the infection a crucial part of the host-parasite interaction, determining infection susceptibility, and parasitemia control. Indeed, trypanosomes use a combination of several independent mechanisms to avoid clearance by the humoral immune system. First, perpetuated antigenic variation of the surface coat allows to escape antibody-mediated elimination. Secondly, when antibodies bind to the coat, they are efficiently transported toward the endocytosis pathway, where they are removed from the coat proteins. Finally, trypanosomes engage in the active destruction of the mammalian humoral immune response. This provides them with a rescue solution in case antigenic variation does not confer total immunological invisibility. Both antigenic variation and B cell destruction pose significant hurdles for the development of anti-trypanosome vaccine strategies. However, developing total immune escape capacity and unlimited growth capabilities within a mammalian host is not beneficial for any parasite, as it will result in the accelerated death of the host itself. Hence, trypanosomes have acquired a system of quorum sensing that results in density-dependent population growth arrest in order to prevent overpopulating the host. The same system could possibly sense the infection-associated host tissue damage resulting from inflammatory innate immune responses, in which case the quorum sensing serves to prevent excessive immunopathology and as such also promotes host survival. In order to put these concepts together, this review summarizes current knowledge on the interaction between trypanosomes and the mammalian innate immune system, the mechanisms involved in population growth regulation, antigenic variation and the immuno-destructive effect of trypanosomes on the humoral immune system. Vaccine trials and a discussion on the role of innate immune modulation in these trials are discussed at the end.
Collapse
Affiliation(s)
- Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Emmanuel Obishakin
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Biotechnology Division, National Veterinary Research Institute, Vom, Nigeria
| | - Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| |
Collapse
|
15
|
Domagalska MA, Dujardin JC. Next-Generation Molecular Surveillance of TriTryp Diseases. Trends Parasitol 2020; 36:356-367. [PMID: 32191850 DOI: 10.1016/j.pt.2020.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 12/20/2022]
Abstract
Elimination programs targeting TriTryp diseases (Leishmaniasis, Chagas' disease, human African trypanosomiasis) significantly reduced the number of cases. Continued surveillance is crucial to sustain this progress, but parasite molecular surveillance by genotyping is currently lacking. We explain here which epidemiological questions of public health and clinical relevance could be answered by means of molecular surveillance. Whole-genome sequencing (WGS) for molecular surveillance will be an important added value, where we advocate that preference should be given to direct sequencing of the parasite's genome in host tissues instead of analysis of cultivated isolates. The main challenges here, and recent technological advances, are discussed. We conclude with a series of recommendations for implementing whole-genome sequencing for molecular surveillance.
Collapse
Affiliation(s)
- Malgorzata Anna Domagalska
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium.
| | - Jean-Claude Dujardin
- Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium
| |
Collapse
|
16
|
Maslov DA. Separating the Wheat from the Chaff: RNA Editing and Selection of Translatable mRNA in Trypanosome Mitochondria. Pathogens 2019; 8:E105. [PMID: 31323762 PMCID: PMC6789859 DOI: 10.3390/pathogens8030105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 11/16/2022] Open
Abstract
In the mitochondria of trypanosomes and related kinetoplastid protists, most mRNAs undergo a long and sophisticated maturation pathway before they can be productively translated by mitochondrial ribosomes. Some of the aspects of this pathway (identity of the promotors, transcription initiation, and termination signals) remain obscure, and some (post-transcriptional modification by U-insertion/deletion, RNA editing, 3'-end maturation) have been illuminated by research during the last decades. The RNA editing creates an open reading frame for a productive translation, but the fully edited mRNA often represents a minor fraction in the pool of pre-edited and partially edited precursors. Therefore, it has been expected that the final stages of the mRNA processing generate molecular hallmarks, which allow for the efficient and selective recognition of translation-competent templates. The general contours and several important details of this process have become known only recently and represent the subject of this review.
Collapse
Affiliation(s)
- Dmitri A Maslov
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA 92521, USA.
| |
Collapse
|
17
|
Kennedy PGE, Rodgers J. Clinical and Neuropathogenetic Aspects of Human African Trypanosomiasis. Front Immunol 2019; 10:39. [PMID: 30740102 PMCID: PMC6355679 DOI: 10.3389/fimmu.2019.00039] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
Abstract
Trypanosomiasis has been recognized as a scourge in sub-Saharan Africa for centuries. The disease, caused by protozoan parasites of the Trypanosoma genus, is a major cause of mortality and morbidity in animals and man. Human African trypanosomiasis (HAT), or sleeping sickness, results from infections with T. brucei (b.) gambiense or T. b. rhodesiense with T. b. gambiense accounting for over 95% of infections. Historically there have been major epidemics of the infection, followed by periods of relative disease control. As a result of concerted disease surveillance and treatment programmes, implemented over the last two decades, there has been a significant reduction in the number of cases of human disease reported. However, the recent identification of asymptomatic disease carriers gives cause for some concern. The parasites evade the host immune system by switching their surface coat, comprised of variable surface glycoprotein (VSG). In addition, they have evolved a variety of strategies, including the production of serum resistance associated protein (SRA) and T. b. gambiense-specific glycoprotein (TgsGP) to counter host defense molecules. Infection with either disease variant results in an early haemolymphatic-stage followed by a late encephalitic-stage when the parasites migrate into the CNS. The clinical features of HAT are diverse and non-specific with early-stage symptoms common to several infections endemic within sub-Saharan Africa which may result in a delayed or mistaken diagnosis. Migration of the parasites into the CNS marks the onset of late-stage disease. Diverse neurological manifestations can develop accompanied by a neuroinflammatory response, comprised of astrocyte activation, and inflammatory cell infiltration. However, the transition between the early and late-stage is insidious and accurate disease staging, although crucial to optimize chemotherapy, remains problematic with neurological symptoms and neuroinflammatory changes recorded in early-stage infections. Further research is required to develop better diagnostic and staging techniques as well as safer more efficacious drug regimens. Clearer information is also required concerning disease pathogenesis, specifically regarding asymptomatic carriers and the mechanisms employed by the trypanosomes to facilitate progression to the CNS and precipitate late-stage disease. Without progress in these areas it may prove difficult to maintain current control over this historically episodic disease.
Collapse
Affiliation(s)
- Peter G. E. Kennedy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Jean Rodgers
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
18
|
Abstract
PURPOSE OF REVIEW Consistent associations between variants of the apolipoprotein L1 (APOL1) gene and nondiabetic nephropathy have been reported in individuals of African descent. Donor APOL1 genotype has also been linked to shorter renal allograft survival. This review summarizes recent advances in understanding the biology of APOL1 and their implications to kidney donors and recipients. RECENT FINDINGS Approximately 12-13% of African Americans have two renal risk APOL1 variants but most do not develop kidney disease. Although the exact mechanisms linking APOL1 genotype to renal injury are not known, evidence from new experimental models suggests APOL1 mutations may accelerate age-related podocyte loss. Recent epidemiological studies indicate potential kidney donors with high-risk APOL1 variants have increased risk of chronic kidney disease (CKD) and donors with high-risk APOL1 variants have lower estimated glomerular filtration rate (eGFR) than those with low-risk variants. The absolute risk of CKD in otherwise healthy individuals carrying high-risk APOL1 mutations is likely low. SUMMARY Recent studies suggest high-risk APOL1 mutations in kidney donors are linked to shorter graft survival and lower postdonation eGFR. APOL1 genotyping may be used as one of many factors that contribute to assessment of the risk of postdonation CKD and informed decision making.
Collapse
|
19
|
Abstract
In this issue of Molecular Cell, Gutierrez et al. (2017) unravel a bacterial survival strategy that they term "density-dependent persistence" or DDP. The authors demonstrate that the majority of isogenic cells in bacterial populations survive lethal antibiotic doses once bacteria consume nutrients and enter stationary growth phase.
Collapse
|
20
|
Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott C, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FC, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM. Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nat Genet 2018; 50:1574-1583. [PMID: 30275530 PMCID: PMC6205630 DOI: 10.1038/s41588-018-0223-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022]
Abstract
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.
Collapse
MESH Headings
- Animals
- Animals, Laboratory
- Chromosome Mapping/veterinary
- Genetic Loci
- Genome
- Haplotypes/genetics
- Mice
- Mice, Inbred BALB C/genetics
- Mice, Inbred C3H/genetics
- Mice, Inbred C57BL/genetics
- Mice, Inbred CBA/genetics
- Mice, Inbred DBA/genetics
- Mice, Inbred NOD/genetics
- Mice, Inbred Strains/classification
- Mice, Inbred Strains/genetics
- Molecular Sequence Annotation
- Phylogeny
- Polymorphism, Single Nucleotide
- Species Specificity
Collapse
Affiliation(s)
- Jingtao Lilue
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Anthony G. Doran
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ian T. Fiddes
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Monica Abrudan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Joel Armstrong
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ruth Bennett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Joanna Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephan Collins
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404 Illkirch, France
- Centre des Sciences du Goût et de l’Alimentation, University of Bourgogne Franche-Comté, 21000 Dijon, France
| | - Anne Czechanski
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Dirk-Dominik Dolle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Matt Dunn
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Richard Durbin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK
| | - Dent Earl
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anne Ferguson-Smith
- Department of Genetics, University of Cambridge, Downing Site, Cambridge CB2 3EH, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jonathan Flint
- Brain Research Institute, University of California, 695 Charles E Young Dr S, Los Angeles, CA 90095, USA
| | - Adam Frankish
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Gerstein
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - James Gilbert
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Leo Goodstadt
- OxFORD Asset Management, OxAM House, 6 George Street, Oxford OX1 2BW
| | - Jennifer Harrow
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | | | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Chris Lelliott
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Darren W. Logan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jane Loveland
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA
| | - Richard Mott
- Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Paul Muir
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Stefanie Nachtweide
- Institute of Mathematics and Computer Science, University of Greifswald, Domstraße 11, 17489 Greifswald, Germany
| | - Fabio C.P. Navarro
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Duncan T. Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, 69120 Heidelberg, Germany
| | - Naomi Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Sarah Pelan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Son K Pham
- BioTuring Inc., San Diego, California, CA92121
| | - Mike Quail
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Laura Reinholdt
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Lars Romoth
- Institute of Mathematics and Computer Science, University of Greifswald, Domstraße 11, 17489 Greifswald, Germany
| | - Lesley Shirley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Cristina Sisu
- Yale Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Bioscience, Brunel University London, Uxbridge UB8 3PH, UK
| | - Marcela Sjoberg-Herrera
- Departamento de Biología Celular y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Mario Stanke
- Institute of Mathematics and Computer Science, University of Greifswald, Domstraße 11, 17489 Greifswald, Germany
| | - Charles Steward
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Mark Thomas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Glen Threadgold
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - David Thybert
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - James Torrance
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Kim Wong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Jonathan Wood
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Binnaz Yalcin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR7104, Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404 Illkirch, France
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - David J. Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Benedict Paten
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- School of Life Sciences, University of Nottingham, Nottingham, UK
| |
Collapse
|
21
|
Radwanska M, Vereecke N, Deleeuw V, Pinto J, Magez S. Salivarian Trypanosomosis: A Review of Parasites Involved, Their Global Distribution and Their Interaction With the Innate and Adaptive Mammalian Host Immune System. Front Immunol 2018; 9:2253. [PMID: 30333827 PMCID: PMC6175991 DOI: 10.3389/fimmu.2018.02253] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/11/2018] [Indexed: 01/27/2023] Open
Abstract
Salivarian trypanosomes are single cell extracellular parasites that cause infections in a wide range of hosts. Most pathogenic infections worldwide are caused by one of four major species of trypanosomes including (i) Trypanosoma brucei and the human infective subspecies T. b. gambiense and T. b. rhodesiense, (ii) Trypanosoma evansi and T. equiperdum, (iii) Trypanosoma congolense and (iv) Trypanosoma vivax. Infections with these parasites are marked by excessive immune dysfunction and immunopathology, both related to prolonged inflammatory host immune responses. Here we review the classification and global distribution of these parasites, highlight the adaptation of human infective trypanosomes that allow them to survive innate defense molecules unique to man, gorilla, and baboon serum and refer to the discovery of sexual reproduction of trypanosomes in the tsetse vector. With respect to the immunology of mammalian host-parasite interactions, the review highlights recent findings with respect to the B cell destruction capacity of trypanosomes and the role of T cells in the governance of infection control. Understanding infection-associated dysfunction and regulation of both these immune compartments is crucial to explain the continued failures of anti-trypanosome vaccine developments as well as the lack of any field-applicable vaccine based anti-trypanosomosis intervention strategy. Finally, the link between infection-associated inflammation and trypanosomosis induced anemia is covered in the context of both livestock and human infections.
Collapse
Affiliation(s)
- Magdalena Radwanska
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
| | - Nick Vereecke
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Violette Deleeuw
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joar Pinto
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea.,Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
22
|
Reidy KJ, Hjorten RC, Simpson CL, Rosenberg AZ, Rosenblum SD, Kovesdy CP, Tylavsky FA, Myrie J, Ruiz BL, Haque S, Mozhui K, Nelson GW, David VA, Yang X, Suzuki M, Jacob J, Reznik SE, Kaskel FJ, Kopp JB, Winkler CA, Davis RL. Fetal-Not Maternal-APOL1 Genotype Associated with Risk for Preeclampsia in Those with African Ancestry. Am J Hum Genet 2018; 103:367-376. [PMID: 30173819 PMCID: PMC6128247 DOI: 10.1016/j.ajhg.2018.08.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 08/01/2018] [Indexed: 12/22/2022] Open
Abstract
Black Americans are at increased risk for preeclampsia. Genetic variants in apolipoprotein L1 (APOL1) account for much of the increased risk for kidney disease in blacks. APOL1 is expressed in human placenta and transgenic mice expressing APOL1 develop preeclampsia. We evaluated the role of APOL1 variants in human preeclampsia. We determined maternal and fetal APOL1 genotypes in black women with preeclampsia in two populations. At Einstein Montefiore Center (EMC) Affiliated Hospitals, we studied 121 pregnancies in black women with preeclampsia. At University of Tennessee Health Science Center (UTHSC), we studied 93 pregnancies in black women with preeclampsia and 793 pregnancies without preeclampsia. We measured serum markers of preeclampsia soluble fms-like tyrosine kinase 1 (sFlt-1), placental growth factor (PlGF), and soluble endoglin (sEng). Fetal APOL1 high-risk (HR) genotype was associated with preeclampsia, with odds ratios at EMC and UTHSC of 1.84 (95% CI 1.11, 2.93) and 1.92 (95% CI 1.05, 3.49), respectively. Maternal APOL1 HR genotype was not associated with preeclampsia. Mothers with the fetal APOL1 HR genotype had more cerebral or visual disturbances (63% versus 37%, p = 0.04). In addition, fetal APOL1 HR genotype was associated with a higher sFLT-1/PlGF ratio at birth (p = 0.04). Fetal APOL1 high-risk genotype increases the risk for preeclampsia, likely by adversely affecting placental function. Further research is needed to assess whether APOL1 genetic testing can predict preeclampsia and improve pregnancy outcomes.
Collapse
Affiliation(s)
- Kimberly J Reidy
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Rebecca C Hjorten
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Pediatrics, Division of Nephrology and Hypertension, Cincinnati Children's Hospital, Cincinnati OH 45229, USA
| | - Claire L Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Avi Z Rosenberg
- Department of Pathology, John's Hopkins University, Baltimore, MD 21218, USA
| | - Stacy D Rosenblum
- Department of Pediatrics, Division of Neonatology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Csaba P Kovesdy
- Department of Medicine, Division of Nephrology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Frances A Tylavsky
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Joseph Myrie
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bianca L Ruiz
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Soulin Haque
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Khyobeni Mozhui
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - George W Nelson
- Advanced Biomedical Computational Science, Biomedical Informatics & Data Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA
| | - Victor A David
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Xiaoping Yang
- Department of Pathology, John's Hopkins University, Baltimore, MD 21218, USA
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jack Jacob
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Sandra E Reznik
- Departments of Pathology and Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Pharmaceutical Sciences, St. John's University, Queens, NY 11439, USA
| | - Frederick J Kaskel
- Department of Pediatrics, Division of Pediatric Nephrology, Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jeffrey B Kopp
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20814, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Molecular Genetic Epidemiology Section, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA.
| | - Robert L Davis
- Center for Biomedical Informatics, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38103, USA.
| |
Collapse
|
23
|
Krafsur ES, Maudlin I. Tsetse fly evolution, genetics and the trypanosomiases - A review. INFECTION GENETICS AND EVOLUTION 2018; 64:185-206. [PMID: 29885477 DOI: 10.1016/j.meegid.2018.05.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 01/27/2023]
Abstract
This reviews work published since 2007. Relative efforts devoted to the agents of African trypanosomiasis and their tsetse fly vectors are given by the numbers of PubMed accessions. In the last 10 years PubMed citations number 3457 for Trypanosoma brucei and 769 for Glossina. The development of simple sequence repeats and single nucleotide polymorphisms afford much higher resolution of Glossina and Trypanosoma population structures than heretofore. Even greater resolution is offered by partial and whole genome sequencing. Reproduction in T. brucei sensu lato is principally clonal although genetic recombination in tsetse salivary glands has been demonstrated in T. b. brucei and T. b. rhodesiense but not in T. b. gambiense. In the past decade most genetic attention was given to the chief human African trypanosomiasis vectors in subgenus Nemorhina e.g., Glossina f. fuscipes, G. p. palpalis, and G. p. gambiense. The chief interest in Nemorhina population genetics seemed to be finding vector populations sufficiently isolated to enable efficient and long-lasting suppression. To this end estimates were made of gene flow, derived from FST and its analogues, and Ne, the size of a hypothetical population equivalent to that under study. Genetic drift was greater, gene flow and Ne typically lesser in savannah inhabiting tsetse (subgenus Glossina) than in riverine forms (Nemorhina). Population stabilities were examined by sequential sampling and genotypic analysis of nuclear and mitochondrial genomes in both groups and found to be stable. Gene frequencies estimated in sequential samplings differed by drift and allowed estimates of effective population numbers that were greater for Nemorhina spp than Glossina spp. Prospects are examined of genetic methods of vector control. The tsetse long generation time (c. 50 d) is a major contraindication to any suggested genetic method of tsetse population manipulation. Ecological and modelling research convincingly show that conventional methods of targeted insecticide applications and traps/targets can achieve cost-effective reduction in tsetse densities.
Collapse
Affiliation(s)
- E S Krafsur
- Department of Entomology, Iowa State University, Ames, IA 50011, USA.
| | - Ian Maudlin
- School of Biomedical Sciences, The University of Edinburgh, Scotland, UK
| |
Collapse
|
24
|
Nikitin D, Penzar D, Garazha A, Sorokin M, Tkachev V, Borisov N, Poltorak A, Prassolov V, Buzdin AA. Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. Front Immunol 2018; 9:30. [PMID: 29441061 PMCID: PMC5797644 DOI: 10.3389/fimmu.2018.00030] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022] Open
Abstract
Endogenous retroviruses and retrotransposons also termed retroelements (REs) are mobile genetic elements that were active until recently in human genome evolution. REs regulate gene expression by actively reshaping chromatin structure or by directly providing transcription factor binding sites (TFBSs). We aimed to identify molecular processes most deeply impacted by the REs in human cells at the level of TFBS regulation. By using ENCODE data, we identified ~2 million TFBS overlapping with putatively regulation-competent human REs located in 5-kb gene promoter neighborhood (~17% of all TFBS in promoter neighborhoods; ~9% of all RE-linked TFBS). Most of REs hosting TFBS were highly diverged repeats, and for the evolutionary young (0–8% diverged) elements we identified only ~7% of all RE-linked TFBS. The gene-specific distributions of RE-linked TFBS generally correlated with the distributions for all TFBS. However, several groups of molecular processes were highly enriched in the RE-linked TFBS regulation. They were strongly connected with the immunity and response to pathogens, with the negative regulation of gene transcription, ubiquitination, and protein degradation, extracellular matrix organization, regulation of STAT signaling, fatty acids metabolism, regulation of GTPase activity, protein targeting to Golgi, regulation of cell division and differentiation, development and functioning of perception organs and reproductive system. By contrast, the processes most weakly affected by the REs were linked with the conservative aspects of embryo development. We also identified differences in the regulation features by the younger and older fractions of the REs. The regulation by the older fraction of the REs was linked mainly with the immunity, cell adhesion, cAMP, IGF1R, Notch, Wnt, and integrin signaling, neuronal development, chondroitin sulfate and heparin metabolism, and endocytosis. The younger REs regulate other aspects of immunity, cell cycle progression and apoptosis, PDGF, TGF beta, EGFR, and p38 signaling, transcriptional repression, structure of nuclear lumen, catabolism of phospholipids, and heterocyclic molecules, insulin and AMPK signaling, retrograde Golgi-ER transport, and estrogen signaling. The immunity-linked pathways were highly represented in both categories, but their functional roles were different and did not overlap. Our results point to the most quickly evolving molecular pathways in the recent and ancient evolution of human genome.
Collapse
Affiliation(s)
- Daniil Nikitin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Penzar
- The Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Andrew Garazha
- D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,OmicsWay Corp., Walnut, CA, United States
| | - Maxim Sorokin
- OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Nicolas Borisov
- OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| | - Alexander Poltorak
- Program in Immunology, Sackler Graduate School, Tufts University, Boston, MA, United States
| | - Vladimir Prassolov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anton A Buzdin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.,D. Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,OmicsWay Corp., Walnut, CA, United States.,National Research Centre Kurchatov Institute, Centre for Convergence of Nano-, Bio-, Information and Cognitive Sciences and Technologies, Moscow, Russia
| |
Collapse
|
25
|
|
26
|
Ponte-Sucre A. An Overview of Trypanosoma brucei Infections: An Intense Host-Parasite Interaction. Front Microbiol 2016; 7:2126. [PMID: 28082973 PMCID: PMC5183608 DOI: 10.3389/fmicb.2016.02126] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/16/2016] [Indexed: 12/14/2022] Open
Abstract
Trypanosoma brucei rhodesiense and T. brucei gambiense, the causative agents of Human African Trypanosomiasis, are transmitted by tsetse flies. Within the vector, the parasite undergoes through transformations that prepares it to infect the human host. Sequentially these developmental stages are the replicative procyclic (in which the parasite surface is covered by procyclins) and trypo-epimastigote forms, as well as the non-replicative, infective, metacyclic form that develops in the vector salivary glands. As a pre-adaptation to their life in humans, metacyclic parasites begin to express and be densely covered by the Variant Surface Glycoprotein (VSG). Once the metacyclic form invades the human host the parasite develops into the bloodstream form. Herein the VSG triggers a humoral immune response. To avoid this humoral response, and essential for survival while in the bloodstream, the parasite changes its cover periodically and sheds into the surroundings the expressed VSG, thus evading the consequences of the immune system activation. Additionally, tools comparable to quorum sensing are used by the parasite for the successful parasite transmission from human to insect. On the other hand, the human host promotes clearance of the parasite triggering innate and adaptive immune responses and stimulating cytokine and chemokine secretion. All in all, the host–parasite interaction is extremely active and leads to responses that need multiple control sites to develop appropriately.
Collapse
Affiliation(s)
- Alicia Ponte-Sucre
- Laboratory of Molecular Physiology, Institute of Experimental Medicine, Luis Razetti School of Medicine, Faculty of Medicine, Universidad Central de Venezuela Caracas, Venezuela
| |
Collapse
|
27
|
Evaluation of Antigens for Development of a Serological Test for Human African Trypanosomiasis. PLoS One 2016; 11:e0168074. [PMID: 27936225 PMCID: PMC5148118 DOI: 10.1371/journal.pone.0168074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/27/2016] [Indexed: 11/19/2022] Open
Abstract
Background Control and elimination of human African trypanosomiasis (HAT) can be accelerated through the use of diagnostic tests that are more accurate and easier to deploy. The goal of this work was to evaluate the immuno-reactivity of antigens and identify candidates to be considered for development of a simple serological test for the detection of Trypanosoma brucei gambiense or T. b. rhodesiense infections, ideally both. Methodology/Principal Findings The reactivity of 35 antigens was independently evaluated by slot blot and ELISA against sera from both T. b. gambiense and T. b. rhodesiense infected patients and controls. The antigens that were most reactive by both tests to T. b. gambiense sera were the membrane proteins VSG LiTat 1.3, VSG LiTat 1.5 and ISG64. Reactivity to T. b. rhodesiense sera was highest with VSG LiTat 1.3, VSG LiTat 1.5 and SRA, although much lower than with T. b. gambiense samples. The reactivity of all possible combinations of antigens was also calculated. When the slot blot results of 2 antigens were paired, a VSG LiTat 1.3- ISG75 combination performed best on T. b. gambiense sera, while a VSG LiTat 1.3-VSG LiTat 1.5 combination was the most reactive using ELISA. A combination of SRA and either VSG LiTat 1.3 or VSG LiTat 1.5 had the highest reactivity on T. b. rhodesiense sera according to slot blot, while in ELISA, pairing SRA with either GM6 or VSG LiTat 1.3 yielded the best results. Conclusions This study identified antigens that were highly reactive to T. b. gambiense sera, which could be considered for developing a serological test for gambiense HAT, either individually or in combination. Antigens with potential for inclusion in a test for T. b. rhodesiense HAT were also identified, but because their reactivity was comparatively lower, a search for additional antigens would be required before developing a test for this form of the disease.
Collapse
|
28
|
Kruzel-Davila E, Shemer R, Ofir A, Bavli-Kertselli I, Darlyuk-Saadon I, Oren-Giladi P, Wasser WG, Magen D, Zaknoun E, Schuldiner M, Salzberg A, Kornitzer D, Marelja Z, Simons M, Skorecki K. APOL1-Mediated Cell Injury Involves Disruption of Conserved Trafficking Processes. J Am Soc Nephrol 2016; 28:1117-1130. [PMID: 27864431 DOI: 10.1681/asn.2016050546] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 10/05/2016] [Indexed: 01/08/2023] Open
Abstract
APOL1 harbors C-terminal sequence variants (G1 and G2), which account for much of the increased risk for kidney disease in sub-Saharan African ancestry populations. Expression of the risk variants has also been shown to cause injury to podocytes and other cell types, but the underlying mechanisms are not understood. We used Drosophila melanogaster and Saccharomyces cerevisiae to help clarify these mechanisms. Ubiquitous expression of the human APOL1 G1 and G2 disease risk alleles caused near-complete lethality in D. melanogaster, with no effect of the G0 nonrisk APOL1 allele, corresponding to the pattern of human disease risk. We also observed a congruent pattern of cellular damage with tissue-specific expression of APOL1. In particular, expression of APOL1 risk variants in D. melanogaster nephrocytes caused cell-autonomous accumulation of the endocytic tracer atrial natriuretic factor-red fluorescent protein at early stages and nephrocyte loss at later stages. We also observed differential toxicity of the APOL1 risk variants compared with the APOL1 nonrisk variants in S. cerevisiae, including impairment of vacuole acidification. Yeast strains defective in endosomal trafficking or organelle acidification but not those defective in autophagy displayed augmented APOL1 toxicity with all isoforms. This pattern of differential injury by the APOL1 risk alleles compared with the nonrisk alleles across evolutionarily divergent species is consistent with an impairment of conserved core intracellular endosomal trafficking processes. This finding should facilitate the identification of cell injury pathways and corresponding therapeutic targets of interest in these amenable experimental platforms.
Collapse
Affiliation(s)
- Etty Kruzel-Davila
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of
| | | | - Ayala Ofir
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of
| | - Ira Bavli-Kertselli
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of
| | | | - Pazit Oren-Giladi
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of
| | - Walter G Wasser
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of.,Department of Nephrology, Mayanei HaYeshua Medical Center, Bnei Brak, Israel
| | - Daniella Magen
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of.,Genetics and Developmental Biology and
| | | | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel; and
| | | | - Daniel Kornitzer
- Microbiology and Inflammation, Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, Israel
| | - Zvonimir Marelja
- Imagine Institute, Paris Descartes University-Sorbonne Paris Cité, Paris, France
| | - Matias Simons
- Imagine Institute, Paris Descartes University-Sorbonne Paris Cité, Paris, France
| | - Karl Skorecki
- Department of Nephrology, Rambam Health Care Campus, Haifa, Israel; Departments of .,Genetics and Developmental Biology and
| |
Collapse
|
29
|
Pharmacogenomic implications of the evolutionary history of infectious diseases in Africa. THE PHARMACOGENOMICS JOURNAL 2016; 17:112-120. [PMID: 27779243 PMCID: PMC5380847 DOI: 10.1038/tpj.2016.78] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 07/06/2016] [Accepted: 07/19/2016] [Indexed: 12/20/2022]
Abstract
As the common birthplace of all human populations, modern humans have lived longer on the African continent than in any other geographical region of the world. This long history, along with the evolutionary need to adapt to environmental challenges such as exposure to infectious agents, has led to greater genetic variation in Africans. The vast genetic variation in Africans also extends to genes involved in the absorption, distribution, metabolism and excretion of pharmaceuticals. Ongoing cataloging of these clinically relevant variants reveals huge allele-frequency differences within and between African populations. Here, we examine Africa's large burden of infectious disease, discuss key examples of known genetic variation modulating disease risk, and provide examples of clinically relevant variants critical for establishing dosing guidelines. We propose that a more systematic characterization of the genetic diversity of African ancestry populations is required if the current benefits of precision medicine are to be extended to these populations.
Collapse
|
30
|
Caljon G, De Muylder G, Durnez L, Jennes W, Vanaerschot M, Dujardin JC. Alice in microbes' land: adaptations and counter-adaptations of vector-borne parasitic protozoa and their hosts. FEMS Microbiol Rev 2016; 40:664-85. [PMID: 27400870 DOI: 10.1093/femsre/fuw018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2016] [Indexed: 12/24/2022] Open
Abstract
In the present review, we aim to provide a general introduction to different facets of the arms race between pathogens and their hosts/environment, emphasizing its evolutionary aspects. We focus on vector-borne parasitic protozoa, which have to adapt to both invertebrate and vertebrate hosts. Using Leishmania, Trypanosoma and Plasmodium as main models, we review successively (i) the adaptations and counter-adaptations of parasites and their invertebrate host, (ii) the adaptations and counter-adaptations of parasites and their vertebrate host and (iii) the impact of human interventions (chemotherapy, vaccination, vector control and environmental changes) on these adaptations. We conclude by discussing the practical impact this knowledge can have on translational research and public health.
Collapse
Affiliation(s)
- Guy Caljon
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium University of Antwerp, Department of Biomedical Sciences, Laboratory of Microbiology, Parasitology and Health, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| | - Géraldine De Muylder
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Lies Durnez
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Wim Jennes
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Manu Vanaerschot
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium Columbia University, College of Physicians and Surgeons, Department of Microbiology and Immunology, Fidock Lab, New York, NY 10032, USA
| | - Jean-Claude Dujardin
- Institute of Tropical Medicine, Department of Biomedical Sciences, Nationalestraat 155, B-2000 Antwerp, Belgium University of Antwerp, Department of Biomedical Sciences, Laboratory of Microbiology, Parasitology and Health, Universiteitsplein 1, B-2610 Wilrijk, Belgium
| |
Collapse
|
31
|
Dummer PD, Limou S, Rosenberg AZ, Heymann J, Nelson G, Winkler CA, Kopp JB. APOL1 Kidney Disease Risk Variants: An Evolving Landscape. Semin Nephrol 2016. [PMID: 26215860 DOI: 10.1016/j.semnephrol.2015.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Apolipoprotein L1 (APOL1) genetic variants account for much of the excess risk of chronic and end-stage kidney disease, which results in a significant global health disparity for persons of African ancestry. We estimate the lifetime risk of kidney disease in APOL1 dual-risk allele individuals to be at least 15%. Experimental evidence suggests a direct role of APOL1 in pore formation, cellular injury, and programmed cell death in renal injury. The APOL1 BH3 motif, often associated with cell death, is unlikely to play a role in APOL1-induced cytotoxicity because it is not conserved within the APOL family and is dispensable for cell death in vitro. We discuss two models for APOL1 trypanolytic activity: one involving lysosome permeabilization and another involving colloid-osmotic swelling of the cell body, as well as their relevance to human pathophysiology. Experimental evidence from human cell culture models suggests that both mechanisms may be operative. A systems biology approach whereby APOL1-associated perturbations in gene and protein expression in affected individuals are correlated with molecular pathways may be productive to elucidate APOL1 function in vivo.
Collapse
Affiliation(s)
- Patrick D Dummer
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Sophie Limou
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Avi Z Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD; Department of Pathology Johns Hopkins University, Baltimore, MD
| | - Jurgen Heymann
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - George Nelson
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Cheryl A Winkler
- Molecular Epidemiology Genetics Section, Center for Cancer Research, National Cancer Institute, Frederick MD
| | - Jeffrey B Kopp
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.
| |
Collapse
|
32
|
Mugnier MR, Papavasiliou FN, Schulz D. Vesicles as Vehicles for Virulence. Trends Parasitol 2016; 32:435-436. [PMID: 27006155 DOI: 10.1016/j.pt.2016.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 12/13/2022]
Abstract
Parasites have long been known to influence host responses to infection through the secretion of virulence factors. Extracellular vesicles are emerging as important mediators of these manipulations, and a new study by Szempruch et al. suggests they could play a crucial role in host responses to African trypanosome infections.
Collapse
Affiliation(s)
- Monica R Mugnier
- Laboratory of Lymphocyte Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; The Rockefeller Graduate Program, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - F Nina Papavasiliou
- Laboratory of Lymphocyte Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Danae Schulz
- Laboratory of Lymphocyte Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Current address: Department of Biology, Harvey Mudd College, 301 Platt Bvd, Claremont, CA 91711, USA.
| |
Collapse
|
33
|
Welburn SC, Molyneux DH, Maudlin I. Beyond Tsetse--Implications for Research and Control of Human African Trypanosomiasis Epidemics. Trends Parasitol 2016; 32:230-241. [PMID: 26826783 DOI: 10.1016/j.pt.2015.11.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/02/2015] [Accepted: 11/13/2015] [Indexed: 01/16/2023]
Abstract
Epidemics of both forms of human African trypanosomiasis (HAT) are confined to spatially stable foci in Sub-Saharan Africa while tsetse distribution is widespread. Infection rates of Trypanosoma brucei gambiense in tsetse are extremely low and cannot account for the catastrophic epidemics of Gambian HAT (gHAT) seen over the past century. Here we examine the origins of gHAT epidemics and evidence implicating human genetics in HAT epidemiology. We discuss the role of stress causing breakdown of heritable tolerance in silent disease carriers generating gHAT outbreaks and see how peculiarities in the epidemiologies of gHAT and Rhodesian HAT (rHAT) impact on strategies for disease control.
Collapse
Affiliation(s)
- Susan C Welburn
- Centre for Infectious Diseases, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK.
| | - David H Molyneux
- Department of Parasitology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Ian Maudlin
- Centre for Infectious Diseases, Edinburgh Medical School, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, UK
| |
Collapse
|
34
|
Krüger T, Engstler M. Flagellar motility in eukaryotic human parasites. Semin Cell Dev Biol 2015; 46:113-27. [DOI: 10.1016/j.semcdb.2015.10.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/26/2015] [Accepted: 10/26/2015] [Indexed: 12/31/2022]
|
35
|
Jackson AP, Goyard S, Xia D, Foth BJ, Sanders M, Wastling JM, Minoprio P, Berriman M. Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax. PLoS Negl Trop Dis 2015; 9:e0003975. [PMID: 26266535 PMCID: PMC4534299 DOI: 10.1371/journal.pntd.0003975] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 07/12/2015] [Indexed: 12/13/2022] Open
Abstract
The parasitic flagellate Trypanosoma vivax is a cause of animal trypanosomiasis across Africa and South America. The parasite has a digenetic life cycle, passing between mammalian hosts and insect vectors, and a series of developmental forms adapted to each life cycle stage. Each point in the life cycle presents radically different challenges to parasite metabolism and physiology and distinct host interactions requiring remodeling of the parasite cell surface. Transcriptomic and proteomic studies of the related parasites T. brucei and T. congolense have shown how gene expression is regulated during their development. New methods for in vitro culture of the T. vivax insect stages have allowed us to describe global gene expression throughout the complete T. vivax life cycle for the first time. We combined transcriptomic and proteomic analysis of each life stage using RNA-seq and mass spectrometry respectively, to identify genes with patterns of preferential transcription or expression. While T. vivax conforms to a pattern of highly conserved gene expression found in other African trypanosomes, (e.g. developmental regulation of energy metabolism, restricted expression of a dominant variant antigen, and expression of ‘Fam50’ proteins in the insect mouthparts), we identified significant differences in gene expression affecting metabolism in the fly and a suite of T. vivax-specific genes with predicted cell-surface expression that are preferentially expressed in the mammal (‘Fam29, 30, 42’) or the vector (‘Fam34, 35, 43’). T. vivax differs significantly from other African trypanosomes in the developmentally-regulated proteins likely to be expressed on its cell surface and thus, in the structure of the host-parasite interface. These unique features may yet explain the species differences in life cycle and could, in the form of bloodstream-stage proteins that do not undergo antigenic variation, provide targets for therapy. Trypanosoma vivax is a single-celled parasite that infects cattle and non-domesticated animals through the bite of the tsetse fly. The parasite causes animal trypanosomiasis, a chronic condition resulting in severe anemia, muscle wastage and ultimately death if untreated. This disease is endemic across sub-Saharan Africa but has also spread to South America and causes considerable losses in animal productivity, impeding economic development in the world’s poorest nations. To develop new ways of preventing and treating animal trypanosomiasis, we need an accurate understanding of how the parasite causes disease. In this study, we present an analysis of gene expression throughout the T. vivax life cycle that compares the abundance of gene transcripts (mRNA) and proteins in the mammalian and insect hosts. We have identified genes that are preferentially expressed in each life stage, including many that are unique to T. vivax and probably expressed on its cell surface. Our findings provide a comprehensive understanding of how gene expression is regulated in T. vivax and further refine a pool of T. vivax-specific genes that could be exploited to prevent and treat animal trypanosomiasis.
Collapse
Affiliation(s)
- Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Sophie Goyard
- Department of Infection and Epidemiology, Institut Pasteur, Paris, France
| | - Dong Xia
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Bernardo J Foth
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mandy Sanders
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jonathan M Wastling
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
| | - Paola Minoprio
- Department of Infection and Epidemiology, Institut Pasteur, Paris, France
| | - Matthew Berriman
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| |
Collapse
|
36
|
Banerji J. Asparaginase treatment side-effects may be due to genes with homopolymeric Asn codons (Review-Hypothesis). Int J Mol Med 2015; 36:607-26. [PMID: 26178806 PMCID: PMC4533780 DOI: 10.3892/ijmm.2015.2285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/15/2015] [Indexed: 12/14/2022] Open
Abstract
The present treatment of childhood T-cell leukemias involves the systemic administration of prokary-otic L-asparaginase (ASNase), which depletes plasma Asparagine (Asn) and inhibits protein synthesis. The mechanism of therapeutic action of ASNase is poorly understood, as are the etiologies of the side-effects incurred by treatment. Protein expression from genes bearing Asn homopolymeric coding regions (N-hCR) may be particularly susceptible to Asn level fluctuation. In mammals, N-hCR are rare, short and conserved. In humans, misfunctions of genes encoding N-hCR are associated with a cluster of disorders that mimic ASNase therapy side-effects which include impaired glycemic control, dislipidemia, pancreatitis, compromised vascular integrity, and neurological dysfunction. This paper proposes that dysregulation of Asn homeostasis, potentially even by ASNase produced by the microbiome, may contribute to several clinically important syndromes by altering expression of N-hCR bearing genes. By altering amino acid abundance and modulating ribosome translocation rates at codon repeats, the microbiomic environment may contribute to genome decoding and to shaping the proteome. We suggest that impaired translation at poly Asn codons elevates diabetes risk and severity.
Collapse
Affiliation(s)
- Julian Banerji
- Center for Computational and Integrative Biology, MGH, Simches Research Center, Boston, MA 02114, USA
| |
Collapse
|