Joint and unique multiblock analysis of biological data - multiomics malaria study.

Modern profiling technologies enable us to obtain large amounts of data which can be used later for a comprehensive understanding of the studied system. Proper evaluation of such data is challenging, and cannot be carried out by bare analysis of separate data sets. Integrated approaches are necessary, because only data integration allows us to find correlation trends common for all studied data sets and reveal hidden structures not known a priori. This improves the understanding and interpretation of complex systems. Joint and Unique MultiBlock Analysis (JUMBA) is an analysis method based on the OnPLS-algorithm that decomposes a set of matrices into joint parts containing variations shared with other connected matrices and variations that are unique for each single matrix. Mapping unique variations is important from a data integration perspective, since it certainly cannot be expected that all variation co-varies. In this work we used JUMBA for the integrated analysis of lipidomic, metabolomic and oxylipins data sets obtained from profiling of plasma samples from children infected with P. falciparum malaria. P. falciparum is one of the primary contributors to childhood mortality and obstetric complications in the developing world, which makes the development of new diagnostic and prognostic tools, as well as a better understanding of the disease, of utmost importance. In the presented work, JUMBA made it possible to detect already known trends related to the disease progression, but also to discover new structures in the data connected to food intake and personal differences in metabolism. By separating the variation in each data set into joint and unique, JUMBA reduced the complexity of the analysis and facilitated the detection of samples and variables corresponding to specific structures across multiple data sets, and by doing this enabled fast interpretation of the studied system. All of this makes JUMBA a perfect choice for multiblock analysis of systems biology data.

The HIV care continuum among resident and non-resident populations found in venues in East Africa cross-border areas.

INTRODUCTION: HIV care and treatment in cross-border areas in East Africa face challenges perhaps not seen to the same extent in other geographic areas, particularly for mobile and migrant populations. Here, we estimate the proportion of people with HIV found in these cross-border areas in each stage of the HIV care and treatment cascade, including the proportion who knows their status, the proportion on treatment and the proportion virally suppressed. METHODS: Participants (n = 11,410) working or socializing in public places in selected East Africa cross border areas were recruited between June 2016 and February 2017 using the Priorities for Local AIDS Control Efforts method and administered a behavioural survey and rapid HIV test. This approach was designed to recruit a stratified random sample of people found in public spaces or venues in each cross border area. For participants testing positive for HIV, viral load was measured from dried blood spots. The proportion in each step of the cascade was estimated using inverse probability weights to account for the sampling design and informative HIV test refusals. Estimates are reported separately for residents of the cross border areas and non-residents found in those areas. RESULTS: Overall, 43% of participants with HIV found in cross-border areas knew their status, 87% of those participants were on antiretroviral therapy (ART), and 80% of participants on ART were virally suppressed. About 20% of people with HIV found in cross border areas were sampled outside their subdistrict or subcounty of residence. While both resident and non-resident individuals who knew their status were likely to be on ART (85% and 96% respectively), people on ART recruited outside their area of residence were less likely to be suppressed (64% suppressed; 95% CI: 43, 81) compared to residents (84% suppressed; 95% CI: 75, 93). CONCLUSIONS: People living in or travelling through cross-border areas may face barriers in learning their HIV status. Moreover, while non-residents were more likely to be on treatment than residents, they were less likely to be suppressed, suggesting gaps in continuity of care for people in East Africa travelling outside their area of residence despite timely initiation of treatment.

Levels of human proteins in plasma associated with acute paediatric malaria.

BACKGROUND: The intimate interaction between the pathophysiology of the human host and the biology of the Plasmodium falciparum parasite results in a wide spectrum of disease outcomes in malaria. Development of severe disease is associated with a progressively augmented imbalance in pro- and anti-inflammatory responses to high parasite loads and sequestration of parasitized erythrocytes. Although these phenomena collectively constitute common denominators for the wide variety of discrete severe malaria manifestations, the mechanistic rationales behind discrepancies in outcome are poorly understood. Exploration of the human pathophysiological response by variations in protein profiles in plasma presents an excellent opportunity to increase the understanding. This is ultimately required for better prediction, prevention and treatment of malaria, which is essential for ongoing elimination and eradication efforts. RESULTS: An affinity proteomics approach was used to analyse 541 paediatric plasma samples collected from community controls and patients with mild or severe malaria in Rwanda. Protein profiles were generated with an antibody-based suspension bead array containing 255 antibodies targetting 115 human proteins. Here, 57 proteins were identified with significantly altered levels (adjusted p-values < 0.001) in patients with malaria compared to controls. From these, the 27 most significant proteins (adjusted p-values < 10-14) were selected for a stringent analysis approach. Here, 24 proteins showed elevated levels in malaria patients and included proteins involved in acute inflammatory response as well as cell adhesion. The remaining three proteins, also implicated in immune regulation and cellular adhesivity, displayed lower abundance in malaria patients. In addition, 37 proteins (adjusted p-values < 0.05) were identified with increased levels in patients with severe compared to mild malaria. This set includes, proteins involved in tissue remodelling and erythrocyte membrane proteins. Collectively, this approach has been successfully used to identify proteins both with known and unknown association with different stages of malaria. CONCLUSION: In this study, a high-throughput affinity proteomics approach was used to find protein profiles in plasma linked to P. falciparum infection and malaria disease progression. The proteins presented herein are mainly involved in inflammatory response, cellular adhesion and as constituents of erythrocyte membrane. These findings have a great potential to provide increased conceptual understanding of host-parasite interaction and malaria pathogenesis.

CD3ε Expression Defines Functionally Distinct Subsets of Vδ1 T Cells in Patients With Human Immunodeficiency Virus Infection.

Human γδ T cells expressing the Vδ1 T cell receptor (TCR) recognize self and microbial antigens and stress-inducible molecules in a major histocompatibility complex-unrestricted manner and are an important source of innate interleukin (IL)-17. Vδ1 T cells are expanded in the circulation and intestines of patients with human immunodeficiency virus (HIV) infection. In this study, we show that patients with HIV have elevated frequencies, but not absolute numbers, of circulating Vδ1 T cells compared to control subjects. This increase was most striking in the patients with Candida albicans co-infection. Using flow cytometry and confocal microscopy, we identify two populations of Vδ1 T cells, based on low and high expression of the ε chain of the CD3 protein complex responsible for transducing TCR-mediated signals (denoted CD3εlo and CD3εhi Vδ1 T cells). Both Vδ1 T cell populations expressed the CD3 ζ-chain, also used for TCR signaling. Using lines of Vδ1 T cells generated from healthy donors, we show that CD3ε can be transiently downregulated by activation but that its expression is restored over time in culture in the presence of exogenous IL-2. Compared to CD3εhi Vδ1 T cells, CD3εlo Vδ1 T cells more frequently expressed terminally differentiated phenotypes and the negative regulator of T cell activation, programmed death-1 (PD-1), but not lymphocyte-activation gene 3, and upon stimulation in vitro, only the CD3εhi subset of Vδ1 T cells, produced IL-17. Thus, while HIV can infect and kill IL-17-producing CD4+ T cells, Vδ1 T cells are another source of IL-17, but many of them exist in a state of exhaustion, mediated either by the induction of PD-1 or by downregulation of CD3ε expression.

The oxylipin and endocannabidome responses in acute phase Plasmodium falciparum malaria in children.

BACKGROUND: Oxylipins and endocannabinoids are low molecular weight bioactive lipids that are crucial for initiation and resolution of inflammation during microbial infections. Metabolic complications in malaria are recognized contributors to severe and fatal malaria, but the impact of malaria infection on the production of small lipid derived signalling molecules is unknown. Knowledge of immunoregulatory patterns of these molecules in malaria is of great value for better understanding of the disease and improvement of treatment regimes, since the action of these classes of molecules is directly connected to the inflammatory response of the organism. METHODS: Detection of oxylipins and endocannabinoids from plasma samples from forty children with uncomplicated and severe malaria as well as twenty controls was done after solid phase extraction followed by chromatography mass spectrometry analysis. The stable isotope dilution method was used for compound quantification. Data analysis was done with multivariate (principal component analysis (PCA), orthogonal partial least squares discriminant analysis (OPLS-DA®) and univariate approaches (receiver operating characteristic (ROC) curves, t tests, correlation analysis). RESULTS: Forty different oxylipin and thirteen endocannabinoid metabolites were detected in the studied samples, with one oxylipin (thromboxane B2, TXB2) in significantly lower levels and four endocannabinoids (OEA, PEA, DEA and EPEA) at significantly higher levels in infected individuals as compared to controls according to t test analysis with Bonferroni correction. Three oxylipins (13-HODE, 9-HODE and 13-oxo-ODE) were higher in severe compared to uncomplicated malaria cases according to the results from multivariate analysis. Observed changes in oxylipin levels can be connected to activation of cytochrome P450 (CYP) and 5-lipoxygenase (5-LOX) metabolic pathways in malaria infected individuals compared to controls, and related to increased levels of all linoleic acid oxylipins in severe patients compared to uncomplicated ones. The endocannabinoids were extremely responsive to malaria infection with majority of this class of molecules found at higher levels in infected individuals compared to controls. CONCLUSIONS: It was possible to detect oxylipin and endocannabinoid molecules that can be potential biomarkers for differentiation between malaria infected individuals and controls and between different classes of malaria. Metabolic pathways that could be targeted towards an adjunctive therapy in the treatment of malaria were also pinpointed.

Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria.

INTRODUCTION: Several studies have observed serum lipid changes during malaria infection in humans. All of them were focused at analysis of lipoproteins, not specific lipid molecules. The aim of our study was to identify novel patterns of lipid species in malaria infected patients using lipidomics profiling, to enhance diagnosis of malaria and to evaluate biochemical pathways activated during parasite infection. METHODS: Using a multivariate characterization approach, 60 samples were representatively selected, 20 from each category (mild, severe and controls) of the 690 study participants between age of 0.5-6 years. Lipids from patient's plasma were extracted with chloroform/methanol mixture and subjected to lipid profiling with application of the LCMS-QTOF method. RESULTS: We observed a structured plasma lipid response among the malaria-infected patients as compared to healthy controls, demonstrated by higher levels of a majority of plasma lipids with the exception of even-chain length lysophosphatidylcholines and triglycerides with lower mass and higher saturation of the fatty acid chains. An inverse lipid profile relationship was observed when plasma lipids were correlated to parasitaemia. CONCLUSIONS: This study demonstrates how mapping the full physiological lipid response in plasma from malaria-infected individuals can be used to understand biochemical processes during infection. It also gives insights to how the levels of these molecules relate to acute immune responses.

Metabolic Signature Profiling as a Diagnostic and Prognostic Tool in Pediatric Plasmodium falciparum Malaria.

Background. Accuracy in malaria diagnosis and staging is vital to reduce mortality and post infectious sequelae. In this study, we present a metabolomics approach to diagnostic staging of malaria infection, specifically Plasmodium falciparum infection in children. Methods. A group of 421 patients between 6 months and 6 years of age with mild and severe states of malaria with age-matched controls were included in the study, 107, 192, and 122, individuals, respectively. A multivariate design was used as basis for representative selection of 20 patients in each category. Patient plasma was subjected to gas chromatography-mass spectrometry analysis, and a full metabolite profile was produced from each patient. In addition, a proof-of-concept model was tested in a Plasmodium berghei in vivo model where metabolic profiles were discernible over time of infection. Results. A 2-component principal component analysis revealed that the patients could be separated into disease categories according to metabolite profiles, independently of any clinical information. Furthermore, 2 subgroups could be identified in the mild malaria cohort who we believe represent patients with divergent prognoses. Conclusions. Metabolite signature profiling could be used both for decision support in disease staging and prognostication.

Hepatitis B and C seroprevalence among health care workers in a tertiary hospital in Rwanda.

BACKGROUND: Hepatitis B (HBV) and hepatitis C (HCV) are significant global public health challenges with health care workers (HCWs) at especially high risk of exposure in resource-poor settings. We aimed to measure HBV and HCV prevalence, identify exposure risks and evaluate hepatitis-related knowledge amongst Rwandan tertiary hospital HCWs. METHODS: A cross sectional study involving tertiary hospital employees was conducted from October to December 2013. A pre-coded questionnaire was used to collect data on HCWs' socio-demographics, risk factors and knowledge of blood-borne infection prevention. Blood samples were drawn and screened for hepatitis B surface antigen (HBsAg) and anti-HCV antibodies. RESULTS: Among 378 consenting HCWs, the prevalence of HBsAg positivity was 2.9% (11/378; 95% CI: 1.9 to 4.6%) and anti-HCV positivity 1.3% (5/378; 95% CI: 0.7 to 2.7%). Occupational exposure to blood was reported in 57.1% (216/378). Of the 17 participants (4.5%; 17/378) who reported having received the HBV vaccine, only 3 participants (0.8%) had received the three-dose vaccination course. Only 42 HCWs (42/378; 11.1%) were aware that a HBV vaccine was available. Most HCW (95.2%; 360/378) reported having been tested for HIV in the last 6 months. CONCLUSIONS: Despite their high workplace exposure risk, HBV and HCV sero-prevalence rates among HCWs were low. The low HBV vaccination coverage and poor knowledge of preventative measures among HCWs suggest low levels of viral hepatitis awareness despite this high exposure.

Dyspepsia prevalence and impact on quality of life among Rwandan healthcare workers: A cross-sectional survey.

BACKGROUND: Dyspepsia has been demonstrated worldwide to have major personal and societal impacts, but data on the burden of this disease in Africa are lacking. OBJECTIVE: To document the prevalence of dyspepsia and its quality-of-life impact among healthcare workers (HCWs) at Butare University Teaching Hospital (BUTH), Rwanda. METHODS: A cross-sectional survey among consenting HCWs at BUTH was conducted. Multilingual interviewers guided participants through validated questionnaires, including the Short-Form Leeds Dyspepsia Questionnaire (SF-LDQ), to detect the presence and frequency of dyspeptic symptoms, and the Short-Form Nepean Dyspepsia Index (SF-NDI), to examine the impact of dyspepsia on quality of life. RESULTS: The study included 378 enrolled HCWs, all of whom provided responses to the SF-LDQ and 356 of whom responded to the SF-NDI. The prevalence of dyspepsia in the study population was 38.9% (147/378). Of these 147 HCWs, 79 (53.7%) had very mild dyspepsia, 33 (22.4%) had mild dyspepsia, 20 (13.6%) had moderate dyspepsia and 15 (10.2%) had severe dyspepsia. Females were more likely to complain of dyspepsia than males (98/206 v. 49/172; odds ratio (OR) 2.3; 95% confidence interval (CI) 1.5-3.5; p<0.001). Participants with dyspepsia of at least mild severity had SF-NDI scores reflecting reduced quality of life when compared with non-dyspeptic participants (OR 17.0; 95% CI 5.0-57.1; p<0.001), with most marked effects on the 'tension' and 'eating and drinking' subdomains of the SF-NDI. CONCLUSION: The prevalence of dyspepsia among HCWs in Rwanda is high and is associated with lowered quality of life.

The clinical pattern, prevalence, and factors associated with immune reconstitution inflammatory syndrome in Ugandan children.

OBJECTIVE: To determine clinical pattern, prevalence, and factors associated with pediatric immune reconstitution inflammatory syndrome (IRIS) in Uganda. DESIGN: A prospective, multicenter cross-sectional study. METHODS: We enrolled HIV-infected children receiving antiretroviral therapy (ART) between 0.5 and 6 months duration from December 2006 to October 2007 at three pediatric clinics in Uganda. Children were evaluated for IRIS at a one-time study visit by a standardized pediatric case definition. RESULTS: The IRIS prevalence was 38% [95% confidence interval (CI) 31-46] among 162 children (57% female) with a median age of 6 years (interquartile range 2.5-11 years). Of the IRIS events, 77% were unmasking of a new opportunistic infection and 23% were probable paradoxical IRIS events toward prior opportunistic infections. The majority of IRIS events (55%) occurred in the first month of ART. The clinical events were diverse, with tuberculosis-IRIS (29%) being the most frequent presentation. Independent risk factors for IRIS were pre-ART CD4(+) cell percentage below 15% (odds ratio = 3.1, 95% CI 1.2-8.4, P = 0.027), current CD8(+) cell absolute count below 1000 cells/microl (odds ratio = 4.3, 95% CI 1.8-10.4, P = 0.001), male sex (odds ratio = 2.6, 95% CI 1.06-8.4, P = 0.01), and a cough of more than 1 week duration at the current clinic visit (odds ratio = 4.3, 95% CI 1.7-10.7, P = 0.002). A more than 25 CD4(+) T-cells increase at current study visit from the pre-ART baseline was associated with IRIS by univariate (P = 0.005) but not multivariate analysis. CONCLUSION: IRIS events commonly occur early after ART initiation in children with advanced immunosuppression, as commonly seen in resource-limited areas. Both healthcare providers and caregivers of the children need awareness of IRIS to minimize ART nonadherence.