Biology subjects

MacLeod, A.

Publications and source records attributed to MacLeod, A..

15 recordsLinked to original sources

bioRxiv2024

GENETIC DIVERSITY OF T. B. RHODESIENSE SERUM RESISTANCE ASSOCIATED GENE IN MALAWIAN ISOLATES

BackgroundHuman African Trypanosomiasis (HAT) is a health burden in most remote areas of Sub-Saharan Africa. Only 2 species of the Trypanosome parasites, namely, T. b. rhodesiense and T. b. gambiense can establish infection in humans whereas other trypanosome parasites are lysed by human serum APOL-1 protein. The mechanism of T. b. gambiense resistance to APOL-1 activity is complex and involves several parasite factors. On the other hand, T. b. rhodesiense evades the lytic activity of APOL-1 by intracellular expression of a Serum Resistance Associated (SRA) gene that binds to APOL-1 when uptaken by the parasite thereby disabling APOL-1 from causing cellular membrane rupture. APOL-1 has 2 variants, namely, APOL-1 G1 and APOL-1 G2 with the later having mutations on the SRA binding sites which restores APOL-1 lytic activity in parasite lysis assays. This phenomenon remains elusive in clinical setting as limited data is available. In the present study we investigated the genetic diversity of T. b. rhodesiense SRA gene and APOL-1 genotypes in Malawian r-HAT clinical phenotypes. MethodsT. b. rhodesiense SRA gene from Malawi endemic HAT samples (n= 77) as well as from Zambia and Uganda (n= 13) was amplified by PCR and PCR products were commercially sequenced. APOL-1 variants were identified by restriction fragment length polymorphism (RFLP) after a PCR amplification (n= 61). Results and conclusionSequencing data revealed a heterozygosity of the SRA gene within Malawi T. b. rhodesiense isolates. Malawian SRA gene was genetically different from some isolates in Uganda and Zambia. Contrary to the current understanding that APOL-1 G2 variants are immune to T. b. rhodesiense infection, severe cases of r-HAT in G2 individuals were identified. This study has brought new insight in understanding the determinants of r-HAT severity.

genomics↗

bioRxiv2024

Murine trypanosomiasis recapitulates transcriptomic features of acute kidney injury

The African trypanosome, Trypanosoma brucei, disseminates systemically in tissues of the infected host resulting in complex immunopathology. The kidneys which are important in the response to the anaemia characteristic of African trypanosomiasis, are prone to acute kidney injury (AKI) from multiple noxious stimuli. Little is known about the transcriptional responses of the kidney to trypanosome infection. To assess the tissue-specific response to infection with Trypanosoma brucei, we profiled the clinicopathologic and transcriptional responses of the kidney in BALB/C (susceptible) and C57BL/6 (tolerant) murine models, at early (7 dpi) and late (21 dpi) time points of infection. Trypanosomes in the renal interstitium, tubular necrosis and inflammation characterised early infection in both mouse strains. By late infection, we observed extensive tubular necrosis in the susceptible BALB/C but reparative tubular regeneration in the tolerant C57BL/6 mice. T.b. brucei infection resulted in significant increases in serum creatinine in both strains. Consistent with the clinicopathologic findings, RNA-seq detected both mouse strain- and time-dependent transcriptional responses in the kidney. These included perturbations in genes associated with solute/ion transport, upregulation of markers of tubular injury, hypoxia, glycolysis, and a profound inflammatory and immune response, mirroring the responses observed in other models of AKI. Differential tissue pathology at late time point is preceded by expansion of CD8+ T cells, profound expression of transcription factors and upregulation of anti-inflammatory pathways in C57BL/6 mice. Our findings demonstrate that experimental T. brucei infection-induced kidney injury (TIKI) is a model of AKI and may have clinical implications for Human African Trypanosomiasis cases, who currently are not routinely screened for markers of kidney function.

microbiology↗

bioRxiv2024

Iguanas from above: Citizen scientists provide reliable counts of endangered Galapagos marine iguanas from drone imagery

Population surveys are vital for wildlife management, yet traditional methods often demand excessive time and resources, leading to data gaps for many species. Modern technologies such as drones can facilitate field surveys but may also increase data analysis challenges. Citizen Science (CS) can address this issue by engaging non-specialists for data collection and analysis. We evaluated CS for population monitoring using the endangered Galapagos marine iguana as a case study, assessing online volunteers ability to detect and count animals in aerial images. Comparing against a Gold Standard dataset of expert counts in 4345 images, we explored optimal aggregation methods from CS inputs, considering image quality and filtering data from infrequent and anonymous participants. During three phases of our project -- hosted on the Zooniverse platform -- over 13,000 volunteers made 1,375,201 classifications from 57,838 aerial images; each being independently classified 20 (phases 1 & 2) or 30 (phase 3) times. Volunteers achieved 68% to 94% accuracy in detecting iguanas, with more false negatives than false positives. Image quality strongly influenced accuracy; by excluding data from suboptimal pilot-phase images, volunteers counted with 90% to 92% of accuracy. For detecting presence or absence of iguanas, the commonly used majority vote aggregation approach (where the answer selected is that given by the majority of individual inputs) produced less accurate results than when a minimum threshold of five (from the 20/30 independent classifications) was used. For counting iguanas, HDBSCAN clustering yielded the best results. Excluding inputs from anonymous and inexperienced volunteers decreased accuracy. We conclude that online volunteers can accurately identify and count marine iguanas from drone images, though a tendency to underestimate warrants further consideration. CS-based data analysis is faster than manual counting but still resource-intensive, underscoring the need to develop a Machine Learning approach.

zoology↗

bioRxiv2023

Transcriptome profiles of T.b. rhodesiense parasites in Malawi reveal focus specific gene expression Profiles associated with pathology

BackgroundSleeping sickness caused by T.b. rhodesiense is a fatal disease and endemic in Southern and Eastern Africa. There is an urgent need to develop novel diagnostic and control tools in order to achieve elimination of rhodesiense sleeping sickness which might be achieved through a better understanding of trypanosome gene expression and genetics using endemic isolates. Here, we describe transcriptome profiles and population structure of endemic T. b. rhodesiense isolates in human blood in Malawi. MethodologyBlood samples of r-HAT cases from Nkhotakota and Rumphi foci were collected in PaxGene tubes for RNA extraction before initiation of r-HAT treatment. 100 million reads were obtained per sample, reads were initially mapped to the human genome reference GRCh38 using HiSat2 and then the unmapped reads were mapped against Trypanosoma brucei reference transcriptome (TriTrypDB54_TbruceiTREU927) using HiSat2. Differential gene expression analysis was done using the DeSeq2 package in R. SNPs calling from reads that were mapped to the T. brucei genome was done using GATK in order to identify T.b. rhodesiense population structure. Results24 samples were collected from r-HAT cases of which 8 were from Rumphi and 16 from Nkhotakota foci. The isolates from Nkhotakota were enriched with transcripts for cell cycle arrest and stumpy form markers, whereas isolates in Rumphi focus were enriched with transcripts for folate biosynthesis and antigenic variation pathways. These parasite focus-specific transcriptome profiles are consistent with the more virulent disease observed in Rumphi and a more silent disease in Nkhotakota associated with the non-dividing stumpy form. Interestingly, the Malawi T.b. rhodesiense isolates expressed genes enriched for reduced cell proliferation compared to the Uganda T.b. rhodesiense isolates. PCA analysis using SNPs called from the RNAseq data showed that T. b. rhodesiense parasites from Nkhotakota are genetically distinct from those collected in Rumphi. ConclusionOur results have added new insights on how clinical phenotypes of r-HAT in Malawi might be associated with differences in gene expression profiles and population structure of T. b. rhodesiense from its two major endemic foci of Rumphi and Nkhotakota. Author SummaryA better understanding of T. b. rhodesiense gene expression profiles and population structure using endemic isolate may fast track the current search for novel diagnostic and control tools for rhodesiense sleeping sickness. Here, we analysed T. b. rhodesiense transcriptome profiles from endemic isolated from peripheral blood in Nkhotakota and Rumphi foci in Malawi. In Nkhotakota focus, T. b. rhodesiense transcripts were enriched for cell cycle arrest and stumpy marker whereas in Rumphi focus, the isolates were enriched for antigenic variation and folate biosynthesis biological pathways. Furthermore, we also found that T. b. rhodesiense population structure in Nkhotakota focus is different from Rumphi focus. The differences in trypanosome gene expression profiles and population structure are consistent with a less severe and acute sleeping sickness clinical profiles in Nkhotakota and Rumphi foci respectively.

genomics↗

bioRxiv2023

FISHtoFigure: An easy-to-use tool for rapid, multi-target partitioning and analysis of sub-cellular mRNA transcripts in smFISH data

Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of bioinformatic expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for bioinformatics expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation of T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis.

bioinformatics↗

bioRxiv2023

The murine meninges acquire lymphoid tissue properties and harbour autoreactive B cells during chronic Trypanosoma brucei infection

The meningeal space is a critical brain structure providing immunosurveillance for the central nervous system, but the impact of infections on the meningeal immune landscape is far from being fully understood. The extracellular protozoan parasite Trypanosoma brucei, which causes Human African Trypanosomiasis (HAT) or sleeping sickness, accumulates in the meningeal spaces, ultimately inducing severe meningitis and resulting in death if left untreated. Thus, sleeping sickness represents an attractive model to study immunological dynamics in the meninges during infection. Here, by combining single cell transcriptomics and mass cytometry by time of flight (CyTOF) with in vivo interventions, we found that chronic T. brucei infection triggers the development of ectopic lymphoid aggregates (ELAs) in the murine meninges. These infection-induced ELAs were defined by the presence of ER-TR7+ fibroblastic reticular cells, CD21/35+ follicular dendritic cells, CXCR5+ PD1+ T follicular helper-like phenotype, GL7+ CD95+ GC-like B cells, and plasmablasts/plasma cells. Furthermore, the B cells found in the infected meninges produced high-affinity autoantibodies able to recognise mouse brain antigens, in a process dependent on LT{beta} signalling. A mid-throughput screening identified several host factors recognised by these autoantibodies, including myelin basic protein (MBP), coinciding with cortical demyelination and brain pathology. In humans, we identified the presence of autoreactive IgG antibodies in the cerebrospinal fluid of second stage HAT patients that recognised human brain lysates and MBP, consistent with our findings in experimental infections. Lastly, we found that the pathological B cell responses we observed in the meninges required the presence of T. brucei in the CNS, as suramin treatment before the onset of the CNS stage prevented the accumulation of GL7+ CD95+ GC-like B cells and brain-specific autoantibody deposition. Taken together, our data provide evidence that the meningeal immune response during chronic T. brucei infection results in the acquisition of lymphoid tissue-like properties, broadening our understanding of meningeal immunity in the context of chronic infections. These findings have wider implications for understanding the mechanisms underlying the formation ELAs during chronic inflammation resulting in autoimmunity in mice and humans, as observed in other autoimmune neurodegenerative disorders, including neuropsychiatric lupus and multiple sclerosis.

immunology↗

bioRxiv2023

Spatially-resolved single cell transcriptomics reveal a critical role for γδ T cells in the control of skin inflammation and subcutaneous adipose wasting during chronic Trypanosoma brucei infection

African trypanosome parasites colonise the skin in a process important for parasite transmission. However, how the skin responses to trypanosome infection remain unresolved. Here, using a combination of spatial and single cell transcriptomics, coupled with in vivo genetic models, we investigated the local immune response of the skin in a murine model of infection. First, we detected a significant expansion of IL-17A-producing {gamma}{delta} T cells (primarily V{gamma}6+) in the infected murine skin compared to naive controls that occur mainly in the subcutaneous adipose tissue. Second, interstitial preadipocytes located in the subcutaneous adipose tissue upregulate several genes involved in inflammation and antigen presentation, including T cell activation and survival. In silico cell-cell communication suggests that adipocytes trigger {gamma}{delta} T cell activation locally via Cd40, Il6, Il10, and Tnfsf18 signalling, amongst others. Third, mice deficient in IL-17A-producing {gamma}{delta} T cells show extensive inflammation, increased frequency of skin-resident IFN{gamma}-producing CD8+ T cells and limited subcutaneous adipose tissue wasting compared to wild-type infected controls, independent of TH1 CD4+ T cells and parasite burden. Based on these observations, we proposed a model whereby adipocytes as well as V{gamma}6+ cells act concertedly in the subcutaneous adipose tissue to limit skin inflammation and tissue wasting. These studies shed light onto the mechanisms of {gamma}{delta} T cell-mediated immunity in the skin in the context of African trypanosome infection, as well as a potential role of immature and mature adipocytes as homeostatic regulators in the skin during chronic infection.

immunology↗

bioRxiv2023

FLAgellum Member 8 modulates extravasation and extravascular distribution of African trypanosomes.

In the mammalian host, the biology of tissue-dwelling Trypanosoma brucei parasites is not completely understood, especially the mechanisms involved in their extravascular colonization. The trypanosome flagellum is an essential organelle in multiple aspects of the parasites development. The flagellar protein termed FLAgellar Member 8 (FLAM8) acts as a docking platform for a pool of Cyclic AMP response protein 3 (CARP3) that is involved in signaling. FLAM8 exhibits a stage-specific distribution suggesting specific functions in the mammalian and vector stages of the parasite. Analyses of knockdown and knockout trypanosomes in their mammalian forms demonstrated that FLAM8 is not essential in vitro for survival, growth, motility and stumpy differentiation. Functional investigations in experimental infections showed that FLAM8-deprived trypanosomes can establish and maintain an infection in the blood circulation and differentiate into insect transmissible forms. However, quantitative bioluminescence imaging and gene expression analysis revealed that FLAM8-null parasites exhibit a significantly impaired dissemination in the extravascular compartment, that is restored by the addition of a single rescue copy of FLAM8. In vitro trans-endothelial migration assays revealed significant defects in trypanosomes lacking FLAM8. FLAM8 is the first flagellar component shown to modulate T. brucei distribution in the host tissues, possibly through sensing functions, contributing to the maintenance of extravascular parasite populations in mammalian anatomical niches, especially in the skin. Author SummaryTrypanosoma brucei parasites cause neglected tropical diseases termed human and animal African trypanosomiases. Transmitted by the bite of an infected tsetse fly, upon deposition in the skin of a mammalian host, these parasites occupy both the vasculature and extravascular tissues. Currently, the biology of tissue-resident parasites is not well understood, and the parasite factors that mediate extravascular colonization are not known. Using quantitative in vivo bioluminescence imaging and ex vivo gene expression quantification in host infected tissues and blood, we reveal that the flagellar parasite protein FLAM8 modulates the extravascular dissemination of trypanosomes in the mammalian host. FLAM8 is known to act as a docking platform for signaling complexes in the flagellum, but we observe that it does not influence parasite differentiation into transmissible stages. However, we show that the absence of FLAM8 results in the loss of a key component of the flagellar adenylate cyclase signaling complexes, and reduces parasite migration through endothelial cell monolayers, suggesting that FLAM8 is important for parasite exchanges between the intravascular and the extravascular compartments. This work identifies a key trypanosome flagellar component involved in host-parasite interactions, including the modulation of parasite tropism and extravascular dissemination.

microbiology↗

bioRxiv2022

Distinct Differences in Gene Expression Profiles in Early and Late Stage Rhodesiense HAT Individuals in Malawi

T. b. rhodesiense is the causative agent of rhodesian Human African trypanosomiasis (r-HAT) in Malawi. Clinical presentation of r-HAT in Malawi varies between the different foci and differs from East African HAT clinical phenotypes. The purpose of this study was to gain more insights into the transcriptomic profiles of patients with early stage 1 and late stage 2 HAT disease in Malawi. Whole blood from individuals infected with T. b. rhodesiense was used for RNA-Seq. Control samples were from healthy trypanosome negative individuals matched on sex, age range, and disease focus. Illumina sequence FASTQ reads were aligned to the GRCh38 release 84 human genome sequence using HiSat2 and differential analysis was done in R using the DESeq2 package. XGR, ExpressAnalyst and InnateDB algorithms were used for functional annotation and gene enrichment analysis of significant differentially expressed genes. RNA-seq was done on 25 healthy controls and 23 r-HAT case samples of which 3 case samples were excluded for downstream analysis as outliers. 4519 genes were significantly differentially expressed (p adjusted <0.05) in individuals with early stage 1 r-HAT disease (n = 12) and 1824 genes in individuals with late stage 2 r-HAT disease (n = 8). Enrichment of innate immune response genes through neutrophil activation was identified in individuals with both early and late stages of the disease. Additionally, lipid metabolism genes were enriched in late stage 2 disease. We further identified uniquely upregulated genes (log2 Fold Change 1.4 - 2.0) in stage 1 (ZNF354C) and stage 2 (TCN1 and MAGI3) blood. Our data brings new insight into the human transcriptome landscape during T. b. rhodesiense infection. We have further identified key biological pathways and transcripts during stage 1 and stage 2 r-HAT. Lastly, we have identified potential diagnostic biomarkers that may be used for staging of r-HAT disease.

genetics↗

bioRxiv2022

Interleukin-17 drives sex-dependent weight loss and changes in feeding behaviour during Trypanosoma brucei infection

In the skin, Trypanosoma brucei colonises the subcutaneous white adipose tissue (scWAT) and harbours a pool of parasites that are proposed to be competent for forward transmission. The interaction between parasites, adipose tissue, and the local immune system is likely to drive the adipose tissue wasting and weight loss observed in cattle and humans infected with T. brucei. However, mechanistically, the events leading to scWAT wasting are not fully understood. Here, using several complementary approaches, including mass cytometry by time of flight, bulk and single cell transcriptomics, and in vivo genetic models, we found that T. brucei infection drives local expansion of several IL-17A-producing cells in the murine WAT, including TH17 and V{gamma}6+ T cells. We also found that global IL-17 deficiency, or mice lacking IL-17 receptor expression exclusively in adipocytes, were protected from infection-induced WAT wasting and weight loss. Unexpectedly, we found that abrogation of IL-17 signalling in adipocytes results in a significant accumulation of Dpp4+ Pi16+ interstitial preadipocytes and a higher burden of extravascular parasites in the WAT, highlighting a critical role for IL-17 signalling in controlling preadipocyte fate, scWAT tissue dynamics, and local parasite burden. Taken together, our study highlights the central role of adipocyte IL-17 signalling in controlling WAT responses to infection, suggesting that adipocytes are a critical coordinator of the tissue dynamics and immune responses to T. brucei infection.

immunology↗

bioRxiv2022

Integrative single cell and spatial transcriptomic analysis reveal reciprocal microglia - plasma cell crosstalk in the mouse brain during chronic Trypanosoma brucei infection

Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identified that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic Cx3cr1+ microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.

pathology↗

bioRxiv2017

Genomic evidence for population specific selection in Nilo-Saharan and Niger-Congo linguistic groups in Africa

BackgroundThere are over 2000 genetically diverse ethno-linguistic groups in Africa that could help decipher human evolutionary history and the genetic basis of phenotypic variation. We have sequenced 300 genomes from Niger-Congo populations from six sub-Saharan African countries (Uganda, Democratic Republic of Congo, Cameroon, Zambia, Ivory Coast, Guinea) and a Nilo-Saharan population from Uganda. Of these, we analysed 289 samples for population structure, genetic admixture, population history and signatures of selection. These samples were collected as part of the TrypanoGEN consortium project [1].\n\nResultsThe population genetic structure of the 289 individuals revealed four clusters, which correlated with ethno-linguistic group and geographical latitude. These were the West African Niger-Congo A, Central African Niger-Congo B, East African Niger-Congo B and the Nilo-Saharan. We observed a spatial distribution of positive natural selection signatures in genes previously associated with AIDS, Tuberculosis, Malaria and Human African Trypanosomiasis among the TrypanoGEN samples. Having observed a marked difference between the Nilo-Saharan Lugbara and Niger-Congo populations, we identified four genes (APOBEC3G, TOP2B, CAPN9, LANCL2), which are highly differentiated between the two ethnic groups and under positive selection in the Lugbara population (_iHS -log p > 3.0, Rsb -log p > 3.0, Fst > 0.1 bonferroni p > 1.8x10e4).\n\nConclusionThe signatures that differentiate ethnically distinct populations could provide information on the specific ecological adaptations with respect to disease history and susceptibility/resistance. For instance in this study we identified APOBEC3G which is believed to be involved in the susceptibility of the Nilo-Saharan Lugbara population to Hepatitis B virus infection.

genomics↗

bioRxiv2017

Candidate genes-based investigation of susceptibility to Human African Trypanosomiasis in Côte d’Ivoire

Human African Trypanosomiasis (HAT) or sleeping sickness is a Neglected Tropical Disease. Long regarded as an invariably fatal disease, there is increasing evidence that infection by T. b. gambiense can result in a wide range of clinical outcomes, including latent infections, which are long lasting infections with no parasites detectable by microscopy. The determinants of this clinical diversity are not well understood but could be due in part to parasite or host genetic diversity in multiple genes, or their interactions. A candidate gene association study was conducted in Cote dIvoire using a case-control design which included a total of 233 subjects (100 active HAT cases, 100 controls and 33 latent infections). All three possible pairwise comparisons between the three phenotypes were tested using 96 SNPs in16 candidate genes (IL1, IL4, IL4R, IL6, IL8, IL10, IL12, IL12R, TNFA, INFG, MIF, APOL1, HPR, CFH, HLA-A and HLA-G). Data from 77 SNPs passed quality control. There were suggestive associations at three loci in IL6 and TNFA in the comparison between active cases and controls, one SNP in each of APOL1, MIF and IL6 in the comparison between latent infections and active cases and seven SNP in IL4, HLA-G and TNFA between latent infections and controls. No associations remained significant after Bonferroni correction, but the Benjamini Hochberg false discovery rate test indicated that there were strong probabilities that at least some of the associations were genuine.\n\nThe excess of associations with latent infections despite the small number of samples available suggests that these subjects form a distinct genetic cluster different from active HAT cases and controls, although no clustering by phenotype was observed by principle component analysis. This underlines the complexity of the interactions existing between host genetic polymorphisms and parasite diversity.\n\nAuthor summarySince it was first identified, human African trypanosomiasis (HAT) or sleeping sickness has been described as invariably fatal. Recent data however suggest that infection by T. b. gambiense can result in a wide range of clinical outcomes in its human host including long lasting infections, that can be detected by the presence of antibodies, but in which parasites cannot be seen by microscopy; these cases are known as latent infections. While the factors determining this varied response have not been clearly characterized, the effectors of the immune responses have been partially implicated as key players. We collected samples from people with active HAT, latent infections and controls in endemic foci in the Cote dIvoire. We tested the role of single nucleotide polymorphisms (SNPs) in 16 genes on susceptibility/resistance to HAT by means of a candidate gene association study. There was some evidence that variants of the genes for IL4, IL6, APOL1, HLAG, MIF and TNFA modified the risk of developing HAT. These proteins regulate the inflammatory response to many infections or are directly involved in killing the parasites. In this study, the results were statistically weak and would be inconclusive on their own, however other studies have also found associations in these genes, increasing the chance that the variants that we have identified play a genuine role in the response to trypanosome infection in Cote DIvoire.

genetics↗

bioRxiv2017

T cell activation and the HLA locus associate with latent infections of human African trypanosomiasis

Infections by many pathogens can result in a wide range of phenotypes, from severe to mild, or even asymptomatic. Understanding the genetic basis of these phenotypes can lead to better tools to treat patients or detect reservoirs. To identify human genetic factors that contribute to symptoms diversity, we examined the range of disease severities caused by the parasite T. b. gambiense, the primary cause of human African trypanosomiasis (HAT). We analyzed the transcriptomes of immune cells from both symptomatic HAT cases and individuals with latent infections. Our analysis identified several genes and pathways that associated with the latent phenotype, primarily suggesting increased T and B cell activation in HAT patients relative to latent infections. We also used these transcriptome data to conduct an exome-wide single nucleotide polymorphism (SNP) association study. This suggested that SNPs in the human major histocompatibility locus (HLA) associate with severity, supporting the transcription data and suggesting that T cell activation is a determining factor in outcome. Finally, to establish if T cell activation controls disease severity, we blocked co-stimulatory dependent T cell activation in an animal model for HAT. This showed that reducing T cell activation during trypanosome infection improves symptoms and reduces parasitemia. Our data has used a combination of transcriptome-wide analysis and an in vivo model to reveal that T cell activation and the HLA locus associate with the development of symptoms during HAT. This may open new avenues for the development of new therapeutics and prognostics.

genetics↗

bioRxiv2017

No evidence for association with APOL1 kidney disease risk alleles and Human African Trypanosomiasis in two Ugandan populations

BackgroundHuman African trypanosomiasis (HAT) manifests as an acute form caused by Trypanosoma brucei rhodesiense (Tbr) and a chronic form caused by Trypanosoma brucei gambiense (Tbg). Previous studies have suggested a host genetic role in infection outcomes, particularly for APOL1. We have undertaken a candidate gene association studies (CGAS) in a Ugandan Tbr and a Tbg HAT endemic area, to determine whether polymorphisms in IL10, IL8, IL4, HLAG, TNFA, TNX4LB, IL6, IFNG, MIF, APOL1, HLAA, IL1B, IL4R, IL12B, IL12R, HP, HPR, and CFH have a role in HAT.\n\nMethodology and resultsWe included 238 and 202 participants from the Busoga Tbr and Northwest Uganda Tbg endemic areas respectively. Single Nucleotide Polymorphism (SNP) genotype data were analysed in the CGAS. The study was powered to find odds ratios > 2 but association testing of the SNPs with HAT yielded no positive associations i.e. none significant after correction for multiple testing. However there was strong evidence for no association with Tbr HAT and APOL1 G2 of the size previously reported in the Kabermaido district.\n\nConclusions/significanceA recent study in the Soroti and Kaberamaido focus in Central Uganda found that the APOL1 G2 allele was strongly associated with protection against Tbr HAT (odds ratio = 0.2). However, in our study no effect of G2 on Tbr HAT was found, despite being well powered to find a similar sized effect. It is possible that the G2 allele is protective from Tbr in the Soroti/Kabermaido focus but not in the Iganga district of Busoga, which differ in ethnicity and infection history. Mechanisms underlying HAT infection outcome and virulence are complex and might differ between populations, and likely involve several host, parasite or even environmental factors.\n\nAuthor SummaryHuman African Trypanosomiasis (HAT) occurs in two distinct disease forms; the acute form and the chronic form which are caused by microscopically indistinguishable hemo-parasites, Trypanosoma brucei rhodesiense and Trypanosoma brucei gambiense respectively. Uganda is the only country where both forms of the disease are found, though in geographically distinct areas. Recent studies have shown that host genetic factors play a role in HAT resistance and/or susceptibility, particularly by genes involved in the immune response. In this study, we identified single nucleotide polymorphisms in selected genes involved in immune responses and carried out a case-control candidate gene association study in Ugandan participants from the two endemic areas. We were unable to detect any polymorphisms that were robustly associated with either Tbr or Tbg HAT. However, our findings differ from recent studies carried out in the Tbr HAT another endemic area of Uganda that showed the APOL1 (Apolipoprotein 1) G2 allele to be protective against the disease which merits further investigation. Larger studies such as genome wide association studies (GWAS) by the TrypanoGEN network that has >3000 cases and controls covering seven countries (Cameroon, Cote dIvoire, DRC, Malawi, Uganda, Zambia) using the H3Africa customized chip reflective of African genetic diversity will present novel association targets.

genetics↗