Identification of host-microbial interaction networks that ... · Identification of host-microbial...
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Identification of host-microbial interaction networks that mediate
intestinal epithelial barrier maturation
David R. Hill, PhD
Basic & Translational GI Research ConferenceNovember 27, 2018
[email protected] hilldr @DRHill_PhD
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Multicellular life did not take over the globe by combat, but by networking
- Dr. Lynn Margulis
Mic
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Inte
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necrotizing enterocolitis
typical development
Birth
Developmental time
● Tissue maturation● Innate defense● Barrier resilience
How is host-microbe mutualism in the gut How is host-microbe mutualism in the gut established and maintained?established and maintained?
David R. Hill, PhD
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Window of opportunity for microbiota modulation from gestation to childhood.
Christian Milani et al. Microbiol. Mol. Biol. Rev. 2017;81:e00036-17
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Development of an intestinal microbial community
Koenig et al. Proc Natl Acad Sci. 2011; 108 Suppl 1:4578-85
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Rook et al 2017 The Lancet
Bacterial succession
Bacterial succession and host sculpting shape the developing intestine and it’s microbiota
Bevins and Salzman 2011 CMLS
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Infant health status and microbiota establishment
Christian Milani et al. Microbiol. Mol. Biol. Rev. 2017;81:e00036-17
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Christian Milani et al. Microbiol. Mol. Biol. Rev. 2017;81:e00036-17
How do differences in microbial colonization produce different health and developmental
outcomes?
Infant health status and microbiota establishment
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Ahmed et al. 2016 Microorganisms
Bacterial interactions with epithelium are central to understanding the mechanistic causes of microbiota-associated diseases
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Comparing intestinal model systems
Young VB. Old and new models for studying host-microbe interactions in health and disease: C. difficile as an example. Am J Physiol Gastrointest Liver Physiol. 2017
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Directed differentiation of pluripotent stem cells into intestinal tissue
Spence, J.R., Mayhew, C.N., Rankin, S.A., Kuhar, M.F., Vallance, J.E., Tolle, K., Hoskins, E.E., Kalinichenko, V. V, Wells, S.I., Zorn, A.M., et al. (2011). Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 470, 105–109.
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Directed differentiation of pluripotent stem cells into intestinal tissue
Spence, J.R., Mayhew, C.N., Rankin, S.A., Kuhar, M.F., Vallance, J.E., Tolle, K., Hoskins, E.E., Kalinichenko, V. V, Wells, S.I., Zorn, A.M., et al. (2011). Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro. Nature 470, 105–109.
In vitro organoid culture
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Stem-cell derived organoids are capable of maturation into adult-like structures upon transplantation
Watson et al. (2014). An in vivo model of human small intestine using pluripotent stem cells. Nat. Med. 20, 1310–1314.
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Stem-cell derived organoids are capable of maturation into adult-like structures upon transplantation
Finkbeiner, S.R., Hill, D.R., Altheim, C.H., Dedhia, P.H., Taylor, M.J., Tsai, Y.H., Chin, A.M., Mahe, M.M., Watson, C.L.,
Freeman, J.J., et al. (2015). Stem Cell Reports 4, 1140–1155.
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Methodology for colonizing HIOs with live bacteria
Hill et al. (2017). eLifeHill et al. (2017). JoVE
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Stable bacterial colonization promotes expression of gene sets critical for epithelial barrier function
Hill et al. eLife 2017
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Measuring epithelial barrier permeability in HIOs
Hill et al. (2017). Journal of Visualized Experiments
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E. coli colonization enhances epithelial barrier resilience
TNFα and IFNγ released during intestinal inflammation increases epithelial barrier permeability
Control HIOs or HIO pre-colonized with E. coli treated with TNFα and IFNγ for 24 hrs
Epithelial barrier integrity is maintained during cytokine challenge in colonized HIOs
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E. coli colonization enhances epithelial barrier resilience
Hill et al. (2017).
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Broad Implications
Hill DR, Huang S, Nagy MS, Yadagiri VK, Fields C, Mukherjee D, Bons B, Dedhia PH, Chin AM, Tsai YH, Thodla S, Schmidt TM, Walk S, Young VB, Spence JR. Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. Elife. 2017 Nov 7;6. pii: e29132. doi:10.7554/eLife.29132.
Immature epithelium and underlying mesenchyme is sufficient to maintain symbiosis with bacteria
–Achieved through enhanced epithelial barrier defense
–No immune cells required
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Is the epithelial response to primary microbial colonization species-specific?
Key questions
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Designing a screen of representative microbial colonists
Novel Alternative Model Systems of Enteric Disease (NAMSED)
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Robust host transcriptional response to bacterial colonization
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Hill et al. Unpublished data
Identification of strain specific host response gene sets
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Hill et al. Unpublished data
The host transcriptional response to bacterial colonization is species-specific
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Hill et al. Unpublished data
The host transcriptional response to bacterial colonization is species-specific
K-means algorithm finds patterns in a large data set without prior knowledge
Each gene is assigned to one of K groups based on expression across all colonization conditions
K is defined a priori as part of the hypothesis (e.g. There are 7 distinct transcriptional responses to the 7 bacterial colonization conditions)
Each cluster is a list of genes that have a shared pattern across conditions
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The host transcriptional response to bacterial colonization is species-specific
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Hill et al. Unpublished data
Evidence of specific transcriptional control over genes in each cluster
Over-abundance test: more genes in a list from a given gene set (TFT) than expected by chance.
Transcription factor target set over-abundance test
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Expression of downstream NF-κB targets varries by bacterial strain
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Network analysis reveals novel correlations between gene expression events
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What are the functional consequences of variation in epithelial transcriptional
response?
Key questions
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Effect of bacteria on epithelial barrier function is highly strain-dependent
Hill et al. Unpublished data
Permeability of the epitheliumleaky robust
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Secreted cytokine response to bacterial colonists varies widely
Hill et al. Unpublished data
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Network analysis reveals novel correlations between gene expression events
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Epithelial cytokines control AMP secretion
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BD-2 inhibits E. coli growth in vitro
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Pre-treatment with IL-1β supresses microbial growth
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Epithelial cytokines control AMP secretion
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Cytokine environment alters epithelial permeability
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A working hypothesis on bacterial-epithelial interactions during gut colonization
Many questions remain
● How do bacteria elicit distinct epithelial responses?
● How do we distinguish the initial response to bacteria from the response to cytokines induced by bacteria?
● Does the epithelial response to initial colonists shape the environment in ways that affect subsequent colonists?
● Does the epithelial response reflect microbial community composition?
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Extending the HIO platform for application to clinical
sample sets
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Necrotizing enterocolitis is a critical health challenge
There has been no improvement in NEC incidence or mortality in over 40 years
• Severe intestinal inflammation and necrosis
• Affects up to 0.5% of US newborns• 7-fold elevated risk among premature and
low birth weight infants
• In-hospital mortality of up to 30%• Lifelong complications and disability
among survivors
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NEC results from intestinal immaturity and aberrant microbial colonization
Neu, J. & Walker, W. A. Necrotizing enterocolitis. N. Engl. J. Med. 364, 255–64 (2011).
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NEC results from intestinal immaturity and aberrant microbial colonization
Neu, J. & Walker, W. A. Necrotizing enterocolitis. N. Engl. J. Med. 364, 255–64 (2011).
How do we study these
processes in human tissues?
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Extending the HIO platform for application to clinical sample sets
GOAL: Identify and characterize clinical E. coli strains with physiologically relevant effects on the immature intestinal epithelium
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Description of clinical isolates
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Elucidating the mechanistic connections between tissue response, E. coli genetics, and clinical outcomes
GOALS:- Evaluate effect of clinical E. coli isolates on HIO- Identify E. coli genetic factors that predict the HIO repsonse
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Elucidating the mechanistic connections between tissue response, E. coli genetics, and clinical outcomes
GOALS:- Evaluate effect of clinical E. coli isolates on HIO- Identify E. coli genetic factors that predict the HIO repsonse
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Elucidating the mechanistic connections between tissue response, E. coli genetics, and clinical outcomes
GOALS:- Evaluate effect of clinical E. coli isolates on HIO- Identify E. coli genetic factors that predict the HIO repsonse
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Screening distinct E. coli isolates for effects on epithelial barrier permeability in HIOs
Dr. Roberto Cieza
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Clinical E. coli isolates elicit distinct patterns of cytokine secretion
Dr. Roberto Cieza
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Correlating clinical status with HIO response
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Correlating epithelial barrier permeability with epithelial secretions
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A Web of Correlated Data
Ongoing work
● Sequence, assemble, and annotate genomes for all clinical isolates (Dr. Roberto Cieza)
● Correlate genomic features with HIO response and identify genes associated with barrier function and cytokine secretion
● Test role of specific bacterial and host genes in vitro (Molecular Koch’s postulates)
● Can we identify bacterial genes associated with epithelial barrier integrity?
● Are these bacterial genes associated with NEC risk in clinical populations?
...and the tools to test those correlations directly
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HIOs are a flexible and modular model system
:
Hill, DR and Spence, JR. CMGH. 2017
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Young LaboratoryVince YoungVeda YadagiriRoberto CiezaMaddie BarronSteph SpohnJhansi LeslieBrooke BonsBrie Koves
FundingNAMSED U19AI11648201MMMP Training grant T32-AI007528PTSP training grant CTSA UL1TR000433UMCGR Pilot & Feasibility Grant
Washington University in St. Louis
Phil TarrCarla Hall-Moore