Metagenomics and personalized medicine

Abstract

The microbiome is a complex community of Bacteria, Archaea, Eukarya, and viruses that infect humans and live in our tissues. It contributes the majority of genetic information to our metagenome and, consequently, influences our resistance and susceptibility to diseases, especially common inflammatory diseases, such as type 1 diabetes, ulcerative colitis, and Crohn's disease. Here we discuss how host-gene-microbial interactions are major determinants for the development of these multifactorial chronic disorders and, thus, for the relationship between genotype and phenotype. We also explore how genome-wide association studies (GWAS) on autoimmune and inflammatory diseases are uncovering mechanism-based subtypes for these disorders. Applying these emerging concepts will permit a more complete understanding of the etiologies of complex diseases and underpin the development of both next-generation animal models and new therapeutic strategies for targeting personalized disease phenotypes.

Figure 1. Perfect Storms for Developing Crohn's Disease and Type 1 Diabetes

A series of overlapping events and phenotypes driven by metagentic and environmental processes that, in sum, contribute to the development and pathogenesis of type 1 diabetes (left) and Crohn’s disease (right).

Figure 1. Perfect Storms for Developing Crohn's Disease and Type 1 Diabetes

A series of overlapping events and phenotypes driven by metagentic and environmental processes that, in sum, contribute to the development and pathogenesis of type 1 diabetes (left) and Crohn’s disease (right).

Figure 2. Refining the Relationship between Genotype and Phenotype in Complex Inflammatory Diseases

(a) Traditionally a disease is considered as a single phenotype, with genes or loci conferring risk to two diseases shown as overlapping in a Venn diagram. (b) We propose a new view of the genotype-phenotype relationship in which different sets of loci are responsible for mechanistically distinct subtypes of diseases, and the sum of these subtypes constitutes the overall diagnosis. Here two disease subtypes are indicated for simplicity, but many such sub-types may exist, and sets of overlapping risk loci may be associated with these multiple mechanistically distinct disease phenotypes.

Figure 3. The Iterative Redefinition of Mechanism-based Disease Subtypes

Here we present a conceptual work flow for breaking a broad disease diagnosis into its component sub-types by the iterative application of genetics and mechanistic studies. One output would be therapeutics based on disease sub-type and patient stratification into groups more likely to respond to a given therapy or preventive strategy. The box shows specific challenges for this process for type 1 diabetes and Crohn’s disease.

Figure 4. Microbe Plus Gene Interactions Determine Inflammatory Bowel Disease Phenotypes

(a) Two recent studies analyzed the capacity of two different strains of murine norovirus, MNV strain CR6 versus MNV strain CW3, to trigger phenotypes when orally inoculated into mice with a mutation in the Crohn's disease risk gene Atg16L1 (Cadwell et al., 2010; Cadwell et al., 2008). This mutation results in decreased expression of Atg16L1 protein (hypomorphic, Atg16L1^HM). Even though MNV CW3 and MNV CR6 are closely related, they have different effects on intestinal pathology in Atg16L1^HM mice. Some of these interactions are observed only when mice are fed the chemical dextran sodium sulfate (DSS). (b) Two other studies analyzed the capacity of two different species of Bacteroides to trigger phenotypes in combination with mutations in the IL-10 receptor and T cell expression of a dominant negative form of the TGFβ-receptor (dnKO mice) (Bloom et al., 2011; Kang et al., 2008). dnKO mice are cured of their spontaneous colitis by treatment with antibiotics, but oral feeding of 'cured' mice with fecal contents or specific bacteria re-induce disease. Even though Bacteroides thetaiotaomicron and Bacteroides sp. TP5 are closely related, they induce different forms of inflammation when fed to antibiotic-cured dnKO mice. In the same studies dysbiosis (Box 1) with increases in the numbers of Enterobacteriaceae was noted in dnKO mice prior to curing the mice with antibiotics. However, E. coli inoculation did not trigger the pathologies seen with either Bacteroides species.

Figure 4. Microbe Plus Gene Interactions Determine Inflammatory Bowel Disease Phenotypes

(a) Two recent studies analyzed the capacity of two different strains of murine norovirus, MNV strain CR6 versus MNV strain CW3, to trigger phenotypes when orally inoculated into mice with a mutation in the Crohn's disease risk gene Atg16L1 (Cadwell et al., 2010; Cadwell et al., 2008). This mutation results in decreased expression of Atg16L1 protein (hypomorphic, Atg16L1^HM). Even though MNV CW3 and MNV CR6 are closely related, they have different effects on intestinal pathology in Atg16L1^HM mice. Some of these interactions are observed only when mice are fed the chemical dextran sodium sulfate (DSS). (b) Two other studies analyzed the capacity of two different species of Bacteroides to trigger phenotypes in combination with mutations in the IL-10 receptor and T cell expression of a dominant negative form of the TGFβ-receptor (dnKO mice) (Bloom et al., 2011; Kang et al., 2008). dnKO mice are cured of their spontaneous colitis by treatment with antibiotics, but oral feeding of 'cured' mice with fecal contents or specific bacteria re-induce disease. Even though Bacteroides thetaiotaomicron and Bacteroides sp. TP5 are closely related, they induce different forms of inflammation when fed to antibiotic-cured dnKO mice. In the same studies dysbiosis (Box 1) with increases in the numbers of Enterobacteriaceae was noted in dnKO mice prior to curing the mice with antibiotics. However, E. coli inoculation did not trigger the pathologies seen with either Bacteroides species.

Figure 5. A Metagenetic View of Developing Normal and Pathological Immune Responses

This flow-chart depicts stages in the development of normal immune responses or auto-immune and inflammatory diseases at which metagenetic interactions (i.e., gene-gene and gene-microbe interactions) might play a determining role. 'Microbial products' refers to molecules that interact with host innate immune sensors and initiate inflammation.