Longitudinal transcriptomic profiling of whole blood during tuberculosis treatment

Date
2020-10-11
Journal Title
Journal ISSN
Volume Title
Publisher
Stellenbosch : Stellenbosch University, 2020
Abstract
ENGLISH ABSTRACT: Pulmonary tuberculosis (PTB) is characterized by lung granulomas, inflammation and tissue destruction. Although the ideal organ for studying PTB pathophysiology is the lung, this is not readily available, but whole blood is. Previous studies have reported changes in blood transcript levels during tuberculosis (TB) treatment. The aim of this study was to correlate the metabolic activity in lungs, as measured by positron emission tomography (PET), with peripheral changes in blood transcript levels during PTB treatment in order to identify biological processes and pathways underlying overall resolution of lung inflammation. We used next-generation RNA sequencing data together with PET-computed tomography (PET-CT) data generated with 18F-labeled fluorodeoxyglucose ([18F]FDG) as metabolic label, that was collected at diagnosis, week 4, and week 24, from 75 successfully cured PTB patients. The metabolic activity measured by [18F]FDG activity is a surrogate for lung inflammation. Linear mixed-effects models, also called multi-level models, were used to constrain changes in transcript levels in peripheral blood to correlate with [18F]FDG measurements in the lungs. We identified 639 genes whose expression profiles correlated with decreasing [18F]FDG uptake levels in the lungs. Gene enrichment over-representation analysis revealed that the biological processes: coagulation, platelet degranulation, response to interferon-gamma, interleukin-1 production and cell adhesion were significantly enriched in the 639 genes. We observed up-regulation in genes known to be associated with B cells, and down-regulation in genes known to be associated with platelet activation. We found 254 transcription factor binding sites to be enriched among the 639 gene promoters. During treatment response, PAX5, EBF1 and SPIB were identified as putative key transcriptional regulators of B cell genes. In addition, the rate of change in expression of the 639 genes stratified TB subjects in two groups with different immune response and regulation of biological processes during TB treatment. Interestingly we observed that the two groups differed in upregulation of genes significantly enriched for “positive regulation of cytokine production” and down-regulation of genes enriched for “negative regulation of cytokine production”, thus suggesting a dysregulation of cytokine production. We demonstrated that of all transcriptomic changes in peripheral blood, only a subset correlated with inflammation in the lungs. This subset of 639 genes provides a description of the biology of resolution of lung inflammation as detectable in peripheral blood. Our results indicate that the resolution of inflammation in the lungs is positively correlated with platelet activation and coagulation, and negatively correlated with B cell activation and B cell receptor signaling. The expression profiles of these 639 genes could serve as a marker for TB treatment response, and as a guide for developing efficient therapeutics for TB.
AFRIKAANS OPSOMMING: Kenmerke van pulmonêre tuberkulose (PTB) sluit in long granulome, ontsteking en weefsel afbraak en vernietiging. Alhoewel die ideale weefsel vir die studie van PTB longweefsel is, is dit nie maklike verkrygbaar nie, waar bloed inteendeel maklik verkrygbaar is. Vorige studies het wel veranderinge in bloed transkripsie gedurende behandeling vir tuberkulose (TB) aangedui. Die doel van hierdie studie was om metaboliese aktiwiteit in die longe, soos dit met positron emissie tomografie (PET) gemeet is, met verandering in bloed transkripsie vlakke te korreleer om sodanig die biologiese prosesse en paaie wat betrokke is by afname en genesing van die ontsteking in die longe, uit te wys. Ons het volgende-generasie RNA volgordebepalingsmetode data saam met PET-computed tomography (CT; rekenaar tomografie) data gebruik. Die PET-CT was met die metaboliese merker 18F-fluorodeoksilglukose ([18F]FDG) uitgevoer, en is by diagnose, week 4 en week 24 van behandeling vergaar van 75 PTB pasiënte wat behandeling suksesvol ondergaan het. Die metaboliese aktiwiteit wat [18F]FDG meet is ‘n indirekte mate van ontsteking. Ons het liniêre gemengde modelle gebruik om die veranderings in bloed transkripsie vlakke te beperk tot die wat met die van die afname in [18F]FDG tydens behandeling gekorreleerd is. Ons het 639 gene waarvan die uitdrukkingsprofiel met afnemende [18F]FDG mate in die longe gekorreleerd was, uitgeken. Oorverteenwoordigingsanalise met die 639 gene het ‘n verryking in die volgende biologiese prossesse aangedui: bloedstolling, degranulasie van bloed plaatjies, reaksie op interferon gamma, produksie van interleukin 1 en selaanhegting. Ons het waargeneem dat gene wat met B selle verwant is, se vlakke toegeneem het, maar die wat met bloed plaatjies verwant is, se vlakke afgeneem het. Ons het ook waargeneem dat daar 254 transkripsie faktore was wat verryk was in die geen promoters van die 639 gene. Die transkripsie faktore, PAX5, EBF1 en SPIB, is uitgeken as waarskynlik belangrike transkripsie faktore in die beheer van B sel gene. Bowedien, het die tempo van verandering van die uitdrukking van die 639 gene, die pasïente in twee groepe verdeel wat verskillende immuunreaksies en beheer van biologiese paaie tydens TB behandeling gehad het. Dit was ook interessant dat oorverteenwoordigingsanalise aangedui het dat die groepe verskil het in die prosesse “positiewe regulering van sitokien produksie” en “negatiewe regulering van sitokien produksie”, wat op ‘n disregulasie van sitokienproduksie dui. Ons het aangedui dat van die totale transkripsie veranderings in bloed, daar net ‘n klein onderafdeling van gene is wat met ontsteking gekorreleerd is. Hierdie onderafdeling van 639 gene bied ‘n beskrywing van opklaring van ontsteking in die longe, soos wat dit meetbaar is in bloed uit die ledemate. Ons resultate dui aan dat opklaring van ontsteking in die longe positef gekorreleerd is met bloed plaatjie aktivering en bloedstolling, en negatief gekorreleerd is met B-sel aktivering en B-sel reseptor seinoordrag. Die uitdrukking van hierdie 639 gene kan dien as a merker vir hoe mense reageer ten opsigte van TB behandeling, asook as gids vir die ontwikkeling van effektiewe TB terapieë.
Description
Thesis (PhD)--Stellenbosch University, 2020
Keywords
Tuberculosis -- Treatment, Pulmonary tuberculosis, Nucleotide sequence, Tomography, Emission, Gene set overrepresentation analysis, Pathway analysis, Bioinformatics, UCTD
Citation