Mapping of the Co-Transcriptomes of UPEC-Infected Macrophages Reveals New Insights into the Molecular Basis of Host-Pathogen Interactions in Human and Mouse

Handle URI:
http://hdl.handle.net/10754/336484
Title:
Mapping of the Co-Transcriptomes of UPEC-Infected Macrophages Reveals New Insights into the Molecular Basis of Host-Pathogen Interactions in Human and Mouse
Authors:
Mavromatis, Charalampos Harris ( 0000-0002-7327-231X )
Abstract:
Urinary tract infections (UTI) are among the most common infections in humans. Uropathogenic Escherichia coli (UPEC), the main causative agent of UTIs, can invade and replicate within bladder epithelial cells, and recent evidence demonstrated that some UPEC strains also survive within macrophages. To understand the mechanisms of host subversion that enable UPEC to survive within macrophages, and the contribution of macrophages to UPEC-mediated pathology, I performed host􀀔pathogen co-transcriptome analyses using RNA sequencing. I developed an effective computational framework that simultaneously separated, annotated, and quantified the mammalian and bacterial transcriptomes. First, mouse bone morrow-derived macrophages (BMM) were challenged over a 24 h time course with UPEC reference strains, UTI89 (cystitis strain), 83972 and VR50 (asymptomatic bacteriuria strains) that possess contrasting intramacrophage phenotypes. My results showed that BMM responded to the three different UPEC strains with broadly similar gene expression programs. In contrast to the conserved pattern of BMM responses, the transcriptional responses of the different UPEC strains diverged markedly from each other. Hypothesizing that genes upregulated at 24 h post-infection may contribute to intramacrophage survival, I identified UTI89 genes upregulated at this time point, and showed that deletion of one of these genes (pspA) compromised intramacrophage survival of UPEC strain UTI89. Second, human monocyte-derived macrophages (HMDM) and BMM were challenged over a 24 h course with the UPEC strain EC958, a globally disseminated, multi-drug resistant strain. My analysis identified extensive divergence in UPEC-regulated orthologous gene expression between HMDM and BMM, and I validated both known and novel genes in the context of differential regulation. On the contrary, the transcriptional response of EC958 showed a broad conservation across both mammalian intramacrophage environments. My study thus provides both a unique co-culture approach to study infection in vitro and a technological framework for simultaneously capturing global changes in host􀀔pathogen interactions at the transcriptional level in co-cultures. In conclusion, this work has generated new insights into the mechanisms that UPEC strains exploit to persist within the mouse intramacrophage environment, as well as differences in the transcriptional repertoire of HMDM and BMM challenged with the same UPEC strain.
Advisors:
Ravasi, Timothy ( 0000-0002-9950-465X )
Committee Member:
Merzaban, Jasmeen ( 0000-0002-7276-2907 ) ; Kalnis, Panos ( 0000-0002-5060-1360 ) ; Sweet, Matthew
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Program:
Bioscience
Issue Date:
2014
Type:
Dissertation
Appears in Collections:
Bioscience Program; Dissertations; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorRavasi, Timothyen
dc.contributor.authorMavromatis, Charalampos Harrisen
dc.date.accessioned2014-12-02T13:55:12Z-
dc.date.available2014-12-02T13:55:12Z-
dc.date.issued2014en
dc.identifier.urihttp://hdl.handle.net/10754/336484en
dc.description.abstractUrinary tract infections (UTI) are among the most common infections in humans. Uropathogenic Escherichia coli (UPEC), the main causative agent of UTIs, can invade and replicate within bladder epithelial cells, and recent evidence demonstrated that some UPEC strains also survive within macrophages. To understand the mechanisms of host subversion that enable UPEC to survive within macrophages, and the contribution of macrophages to UPEC-mediated pathology, I performed host􀀔pathogen co-transcriptome analyses using RNA sequencing. I developed an effective computational framework that simultaneously separated, annotated, and quantified the mammalian and bacterial transcriptomes. First, mouse bone morrow-derived macrophages (BMM) were challenged over a 24 h time course with UPEC reference strains, UTI89 (cystitis strain), 83972 and VR50 (asymptomatic bacteriuria strains) that possess contrasting intramacrophage phenotypes. My results showed that BMM responded to the three different UPEC strains with broadly similar gene expression programs. In contrast to the conserved pattern of BMM responses, the transcriptional responses of the different UPEC strains diverged markedly from each other. Hypothesizing that genes upregulated at 24 h post-infection may contribute to intramacrophage survival, I identified UTI89 genes upregulated at this time point, and showed that deletion of one of these genes (pspA) compromised intramacrophage survival of UPEC strain UTI89. Second, human monocyte-derived macrophages (HMDM) and BMM were challenged over a 24 h course with the UPEC strain EC958, a globally disseminated, multi-drug resistant strain. My analysis identified extensive divergence in UPEC-regulated orthologous gene expression between HMDM and BMM, and I validated both known and novel genes in the context of differential regulation. On the contrary, the transcriptional response of EC958 showed a broad conservation across both mammalian intramacrophage environments. My study thus provides both a unique co-culture approach to study infection in vitro and a technological framework for simultaneously capturing global changes in host􀀔pathogen interactions at the transcriptional level in co-cultures. In conclusion, this work has generated new insights into the mechanisms that UPEC strains exploit to persist within the mouse intramacrophage environment, as well as differences in the transcriptional repertoire of HMDM and BMM challenged with the same UPEC strain.en
dc.language.isoenen
dc.subjectCo-transcriptomeen
dc.subjectInnate Immunityen
dc.subjectUropthogenic E. Colien
dc.subjectRNA-Seqen
dc.subjectUrinary Tract Infectionen
dc.subjectHost-pathogenen
dc.titleMapping of the Co-Transcriptomes of UPEC-Infected Macrophages Reveals New Insights into the Molecular Basis of Host-Pathogen Interactions in Human and Mouseen
dc.typeDissertationen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberMerzaban, Jasmeenen
dc.contributor.committeememberKalnis, Panosen
dc.contributor.committeememberSweet, Matthewen
thesis.degree.disciplineBioscienceen
thesis.degree.nameDoctor of Philosophyen
dc.person.id101967en
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