Research Proposal - Understanding how changes in gut-microbiota composition drive autoimmunity and regulatory B-cells

Hypothesis proposed: in healthy individuals, subtle changes in the gut-microbiota,
induced for example in response to infection, induce low-grade inflammation,
necessary for the generation of Bregs preventing unwanted, excessive inflammation.
Major aims of this project;
1. Examine relationship between fecal microbiome composition, changes in
Bregs and non-Bregs number and function, and disease severity in SLE
patients (pre and post treatment), using high-throughput 16S ribosomal DNA
(rDNA) targeted gene sequencing
2. Utilisation of in vivo models to understand microbiota-driven mechanisms.
Proposed workflow;
1. Examine microbiota in SLE patient studies. Patient material obtained at
UCL/UCLH (peripheral blood and matching fecal samples from SLE patients).
Cohort 1 will consist of 200 patients at varying stages of disease and
treatment. Cohort 2 will consist of around 30 newly diagnosed patients - both
cohorts evaluated every 3 months. This study will;
a. Determine microbiome stability, composition and metabolome (using a
combination of 16S rDNA sequence analysis with sub-divisions of
patient groups selected for shotgun metagenomics (in collaboration with
Francois Balloux, Professor of Computational Systems Biology, UCL)
b. Peripheral blood phenotyping looking at function and phenotype of
patients' peripheral blood regulatory B cells (via IL-10 expression,
activation and maturation markers, and antibody production) and
nonregulatory (Th1, Th17) subsets. Functional assays (against
Th1/Th17 cells) will determine cellular efficacy.
c. Fecal IgAhi bacteria phenotyping using 16S rDNA sequence analysis
2. Using in vivo models to understand microbiota-driven mechanisms. Main goal
- to determine whether the presence of individual/combinations of bacteria can
influence the incidence and severity of SLE and whther the presence of the
same/other bacteria is required for the development of a Breg response in vivo.
Using information from the previous step, bacteria will be selected that show
associations to disease severity/absence. This study will;
a. Compare microbiota between mouse and human systems to establish
translatability
b. Compare immunological parameters (Th1, Th17 and Bregs)
c. Show whether transplant/deletion of particular bacterial species (mouse or human) can exacerbate or attenuate disease.