Expanding lipidome coverage using MS/MS-aided untargeted data-independent RP-UPLC-TOF-MSE acquisition

Lipid function and importance in disease are being rediscovered due to modern advancements in chemical analysis. RP–UPLC–TOF–MSE is now the lipidomics tool of choice and can provide the demanded specificity for detecting the great diversity of the lipidome. It can offer simplicity, rapidity, robustness and high throughputness, without the need for further optimization in current sample preparation protocols. This method can cover the major lipid categories with the ability to detect several corresponding subclasses. It can deliver adequate information for deciphering fatty chain length, unsaturation and regioisomerism. It has enabled the detection of a vast number of lipids, of which more than 250 are reported here. These lipids were detected from applications in a variety of biological matrices and species

Metabolic profiling and pathway mapping of cardiovascular disease

In this thesis, metabolic profiling (MP) platforms were utilised to interrogate the manifestation of cardiovascular disease and provide candidate biomarkers. A number of LC-MS and NMR methodologies were employed. Data processing was followed by assessment using multivariate (MVDA) and univariate (UV) statistics. MP is applied under three cardiovascular disease themes: 1) plaque rupture, 2) plaque formation, and 3) arterial ectopic calcification. Statistically significant features were structurally assigned. Identified metabolites were mapped to their corresponding biochemical pathways. For MP of ruptured plaque, tissue from symptomatic and asymptomatic patients for stroke was used. After detection of statistically significant features and structural assignment, two biochemical pathways showed dysregulations: the arachidonic acid pathway, indicating increased levels of inflammation, and the β-oxidation pathway with increased levels of three acyl-carnitines. Tissue extracts were used to investigate plaque formation. Arterial intima tissue, incorporating plaque lesions (carotid and femoral), was compared to intimal thickening tissue. Intima thickening demonstrated distinct MP compared to plaques. Plaques from different anatomical locations also demonstrated altered MP. After metabolite assignment, pathway mapping revealed dysregulations common to both anatomical locations. These were cholesterol, ceramide, purine, pyrimidine and β-oxidation pathways. These pathways are related to inflammation and apoptosis. A metabolite previously unassociated to atherogenesis was detected with strong statistical significance (t-test; p≥9.8x10-12), namely phosphatidylethanolamine-ceramide. It also demonstrated high correlations to cholesterol, a well-established risk-factor of atherosclerosis. The third theme of the project explores ectopic cardiovascular calcification. Experiments were conducted on blood serum. Patients with coronary artery and aortic valve calcification were compared with non-calcified controls. Phosphatidylcholine moieties and sphingomyelins were the major discriminating metabolites between cases and controls. These are involved in inflammation and apoptosis. The two diseases manifested different profiles with only three commonly dysregulated metabolites. A number of experiments using additional samples and bottom-up approaches will follow to provide validation of results.Open Acces

Discovery of Infection Associated Metabolic Markers in Human African Trypanosomiasis

Peer reviewedPublisher PD

Tuberculosis Drug Resistance and Outcomes among Tuberculosis Inpatients in Lilongwe, Malawi

Setting/Objective: We evaluated clinical characteristics, yield of solid vs. liquid culture, polymerase chain reaction (PCR)-based drug-resistance profiles, and clinical outcomes of tuberculosis (TB) inpatients in Lilongwe, Malawi.Design: We enrolled adult patients admitted to the Bwaila TB Ward from Jan-Aug/2010. Evaluations included questionnaires, clinical exam, chest radiograph, HIV status, CD4 lymphocyte count, plasma HIVRNA and sputum analysis including Auramine-O stain, Lowenstein-Jensen (LJ) and Mycobacterial Growth Indicator Tube (MGIT) culture, and susceptibility testing using the HAIN GenoType® MTBDRplus.Results: Eighty-eight patients were enrolled (88% re-treatment, 42% smear positive, 93% pulmonary TB, 74% HIV co-infected). At baseline, 44/88 (50%) MGIT and 28 (32%) LJ cultures were positive with a mean time to positivity of 12.1 (Range 1-42) and 21.5 (Range 7-58) days, respectively. Four percent (3/77) of retreatment patients or 8% of the 38 MGIT+ PCR-confirmed retreatment cases had multi-drug resistant tuberculosis (MDR TB). One MDR TB patient was smear negative and only one MDR patient was identified with LJ. Lower mean hemoglobin at admission was associated with mortality (10.5 vs. 7.5; p<0.01; CI 101 9.8-11.0).Conclusions: The MDR TB burden among the retreatment population in Lilongwe, Malawi is similar to regional estimates by the WHO (7.7% 95% CI 0-18.1). MDR TB patients are not routinely identified with sputum smear or LJ, suggesting more efficient technology should be adopted

Efficient 5-OP-RU-induced enrichment of mucosa-associated invariant t cells in the murine lung does not enhance control of aerosol mycobacterium tuberculosis infection

Mucosa-associated invariant T (MAIT) cells are an innate-like T cell subset in mammals that recognize microbial vitamin B metabolites presented by the evolutionarily conserved major histocompatibility complex class I (MHC I)-related molecule, MR1. Emerging data suggest that MAIT cells may be an attractive target for vaccine-induced protection against bacterial infections because of their rapid cytotoxic responses at mucosal services to a widely conserved bacterial ligand. In this study, we tested whether a MAIT cell priming strategy could protect against aerosol Mycobacterium tuberculosis infection in mice. Intranasal costimulation with the lipopeptide Toll-like receptor (TLR)2/6 agonist, Pam2Cys (P2C), and the synthetic MR1 ligand, 5-OP-RU, resulted in robust expansion of MAIT cells in the lung. Although MAIT cell priming significantly enhanced MAIT cell activation and expansion early after M. tuberculosis challenge, these MAIT cells did not restrict M. tuberculosis bacterial load. MAIT cells were depleted by the onset of the adaptive immune response, with decreased detection of granzyme B+ and gamma interferon (IFN-γ)+ MAIT cells relative to that in uninfected P2C/5-OP-RU-treated mice. Decreasing the infectious inoculum, varying the time between priming and aerosol infection, and testing MAIT cell priming in nitric oxide synthase 2 (NOS2)-deficient mice all failed to reveal an effect of P2C/5-OP-RU-induced MAIT cells on M. tuberculosis control. We conclude that intranasal MAIT cell priming in mice induces early MAIT cell activation and expansion after M. tuberculosis exposure, without attenuating M. tuberculosis growth, suggesting that MAIT cell enrichment in the lung is not sufficient to control M. tuberculosis infection

Altered mental status is an indicator of mortality and associated with both infectious and non-communicable disease in Lilongwe, Malawi

Little is known about diseases associated with Altered Mental Status in resource-poor settings. We studied adult medicine patients presenting with AMS in Lilongwe, Malawi and found that AMS and HIV infection were each significantly associated with mortality. It is therefore critical that evaluation and management in this patient population is improved

Single-Cell Transcriptional Profiling Reveals Signatures of Helper, Effector, and Regulatory MAIT Cells during Homeostasis and Activation

Mucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that recognize microbial vitamin B metabolites and have emerging roles in infectious disease, autoimmunity, and cancer. Although MAIT cells are identified by a semi-invariant TCR, their phenotypic and functional heterogeneity is not well understood. Here we present an integrated single cell transcriptomic analysis of over 76,000 human MAIT cells during early and prolonged Ag-specific activation with the MR1 ligand 5-OP-RU and nonspecific TCR stimulation. We show that MAIT cells span a broad range of homeostatic, effector, helper, tissue-infiltrating, regulatory, and exhausted phenotypes, with distinct gene expression programs associated with CD4+ or CD8+ coexpression. During early activation, MAIT cells rapidly adopt a cytotoxic phenotype characterized by high expression of GZMB, IFNG and TNF In contrast, prolonged stimulation induces heterogeneous states defined by proliferation, cytotoxicity, immune modulation, and exhaustion. We further demonstrate a FOXP3 expressing MAIT cell subset that phenotypically resembles conventional regulatory T cells. Moreover, scRNAseq-defined MAIT cell subpopulations were also detected in individuals recently exposed to Mycobacterium tuberculosis, confirming their presence during human infection. To our knowledge, our study provides the first comprehensive atlas of human MAIT cells in activation conditions and defines substantial functional heterogeneity, suggesting complex roles in health and disease

Untargeted UPLC-MS Profiling Pipeline to Expand Tissue Metabolome Coverage: Application to Cardiovascular Disease.

Metabolic profiling studies aim to achieve broad metabolome coverage in specific biological samples. However, wide metabolome coverage has proven difficult to achieve, mostly because of the diverse physicochemical properties of small molecules, obligating analysts to seek multiplatform and multimethod approaches. Challenges are even greater when it comes to applications to tissue samples, where tissue lysis and metabolite extraction can induce significant systematic variation in composition. We have developed a pipeline for obtaining the aqueous and organic compounds from diseased arterial tissue using two consecutive extractions, followed by a different untargeted UPLC-MS analysis method for each extract. Methods were rationally chosen and optimized to address the different physicochemical properties of each extract: hydrophilic interaction liquid chromatography (HILIC) for the aqueous extract and reversed-phase chromatography for the organic. This pipeline can be generic for tissue analysis as demonstrated by applications to different tissue types. The experimental setup and fast turnaround time of the two methods contributed toward obtaining highly reproducible features with exceptional chromatographic performance (CV % < 0.5%), making this pipeline suitable for metabolic profiling applications. We structurally assigned 226 metabolites from a range of chemical classes (e.g., carnitines, α-amino acids, purines, pyrimidines, phospholipids, sphingolipids, free fatty acids, and glycerolipids) which were mapped to their corresponding pathways, biological functions and known disease mechanisms. The combination of the two untargeted UPLC-MS methods showed high metabolite complementarity. We demonstrate the application of this pipeline to cardiovascular disease, where we show that the analyzed diseased groups (<i>n </i>= 120) of arterial tissue could be distinguished based on their metabolic profiles

Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis

The composition of the gastrointestinal microbiota influences systemic immune responses, but how this affects infectious disease pathogenesis and antibiotic therapy outcome is poorly understood. This question is rarely examined in humans due to the difficulty in dissociating the immunologic effects of antibiotic-induced pathogen clearance and microbiome alteration. Here, we analyze data from two longitudinal studies of tuberculosis (TB) therapy (35 and 20 individuals) and a cross sectional study from 55 healthy controls, in which we collected fecal samples (for microbiome analysis), sputum (for determination of Mycobacterium tuberculosis (Mtb) bacterial load), and peripheral blood (for transcriptomic analysis). We decouple microbiome effects from pathogen sterilization by comparing standard TB therapy with an experimental TB treatment that did not reduce Mtb bacterial load. Random forest regression to the microbiome-transcriptome-sputum data from the two longitudinal datasets reveals that renormalization of the TB inflammatory state is associated with Mtb pathogen clearance, increased abundance of Clusters IV and XIVa Clostridia, and decreased abundance of Bacilli and Proteobacteria. We find similar associations when applying machine learning to peripheral gene expression and microbiota profiling in the independent cohort of healthy individuals. Our findings indicate that antibiotic-induced reduction in pathogen burden and changes in the microbiome are independently associated with treatment-induced changes of the inflammatory response of active TB, and the response to antibiotic therapy may be a combined effect of pathogen killing and microbiome driven immunomodulation

The Child and Adolescent Psychiatry: Study of Training in Europe (CAP-STATE)

There is great cultural diversity across Europe. This is reflected in the organisation of child and adolescent mental health (CAMH) services and the training of the respective professionals in different countries in Europe. Patients and their parents will want a high quality, knowledgeable, and skillful service from child and adolescent psychiatrists (CAPs) wherever they see them in Europe. A European comparison of training programs allows all stakeholders in different European countries to assess the diversity and to initiate discussions as to the introduction of improvements within national training programs. Major issues to be addressed in comparing child and adolescent psychiatric training programs across Europe include: (1) formal organisation and content of training programs and the relationship to adult psychiatry and paediatrics; (2) flexibility of training, given different trainee interests and that many trainees will have young families; (3) quality of governance of training systems; (4) access to research; and (5) networking. The Child and Adolescent Psychiatry-Study of Training in Europe (CAP-State) is a survey of training for child and adolescent psychiatrists (CAPs) across European countries. It aims to revisit and extend the survey carried out in 2006 by Karabekiroglu and colleagues. The current article is embedded in a special issue of European Child + Adolescent Psychiatry attempting to for the first time address training in CAP at the European and global levels. Structured information was sought from each of 38 European and neighboring countries (subsequently loosely referred to as Europe) and obtained from 31. The information was provided by a senior trainee or recently qualified specialist and their information was checked and supplemented by information from a senior child and adolescent psychiatry trainer. Results showed that there is a very wide range of provision of training in child and adolescent psychiatry in different countries in Europe. There remains very substantial diversity in training across Europe and in the degree to which it is subject to national oversight and governance. Some possible reasons for this variation are discussed and some recommendations made.info:eu-repo/semantics/publishedVersio