Silander, OlinSulit, Arielle Kae2022-05-032022-08-252022-05-032022-08-252022http://hdl.handle.net/10179/17513Figures 1.1 & 4.8 are licensed Attribution 4.0 International (CC BY 4.0).Colorectal cancer (CRC) is a highly heterogeneous disease that manifests differently from patient to patient, making prognosis, management, and therapy more complex as no universal solution is available. With the advent of high throughput sequencing, descriptions of CRC tumors have moved from histopathological features and descriptions to molecular characterization, allowing for the subtyping of CRC into groups with similar characteristics. This inter-tumoral heterogeneity affects CRC development and patient response to treatments. Understanding the different mechanisms of CRC development and response to therapy is therefore crucial to personalized healthcare. The majority of CRC tumors do not have a familial background, suggesting the environment plays a large role in their development. Environmental factors include the microbiome, which has been shown previously to affect CRC development. However, the role of the microbiome has largely been overlooked in studies of the CRC subtyping and radiotherapy response in rectal cancer treatment. In this thesis, I show that bacteria in CRC may affect immune responses that drive CRC development in different subtypes, and radiotherapy response. I used RNA sequencing to revisit the consensus molecular subtypes (CMS) of CRCs and identified microbes that have possible contributions to their different characteristics. As microbes have been associated with differing responses to therapy, I also looked at their putative roles in radiotherapy response in a rectal cancer cohort. I first developed a computational pipeline that takes raw sequencing reads as input and yields host gene expression data, microbiome abundances and functional information. I then focused on two subtypes of CRC, CMS1 and CMS4. Analysis of host gene expression in these subtypes confirmed that their expression profiles are enriched in gene sets associated with immune responses. Analysis of the microbiome content found that lipopolysaccharides (LPS) from Fusobacterium periodonticum and Bacteroides fragilis in CMS1, and Porphyromonas asaccharolytica in CMS4 potentially affect the production of the immune infiltrates of their respective subtypes. F. periodonticum LPS enhanced cytokine production while LPS from the latter two bacteria suppressed cytokine production in peripheral blood mononuclear cells (PBMCs) in vitro. These data indicate possible roles of LPS from these microbes in CRC development via immune response. These also indicate possible roles of these molecules in CRC therapy. I also found that in complete responders of radiotherapy, there was an enrichment in host gene functions that are associated with complement activation, response to viruses, and B-cell activation, all of which indicated a link to immunotherapy responses triggered by radiotherapy. Furthermore, bacteria that had previous associations with immunotherapy responses were enriched in complete responders indicating a role in enhancement of these cytotoxic immune responses in radiosensitivity. Immune infiltrates have always been a crucial element in cancers, and the type of infiltrates can have conflicting effects on cancer development and therapeutic responses. In this work, I show that the types of bacterial molecules and how they interact between species can affect specific immune responses in CRC development, that dampening of immune responses in CRC is as crucial as inducing immunogenicity, and that specific bacteria also affect immune responses in a manner that may be similar to immunotherapy that will increase radiosensitivity. This work provides an initial look into mechanisms of how microbes interact with host immune responses affecting CRC development into two different subtypes, and radiosensitivity. It also provides initial experimental evidence for effects of LPS in CRC development and a possible mechanism of radiotherapy sensitivity to test in the laboratory.The AuthorColon (Anatomy)RectumCancerMicrobiologyImmunological aspectsThesis310507 Genetic immunology