Understanding the role of colorectal cancer-associated bacteria in colorectal cancer

Doctoral thesis (2021)

Mounting evidence from 16S rRNA-based or metagenomic analyses suggests that dysbiosis, a state of pathological microbial imbalance, is prevalent in the gut of patients with CRC. Numerous microbial taxa ... [more ▼]

Mounting evidence from 16S rRNA-based or metagenomic analyses suggests that dysbiosis, a state of pathological microbial imbalance, is prevalent in the gut of patients with CRC. Numerous microbial taxa have been identified of which representative isolate cultures can interact with cancer cells, further triggering distinct disease pathways in animal models. Nevertheless, how these complex interrelationships of a dysbiotic microbiota may be involved in the pathogenesis of CRC remains a fundamental question and requires multifaceted mechanistic studies. This thesis moves beyond observational studies, it integrates novel experimental approaches for the study of the gut microbiome in colorectal cancer. It incorporates current knowledge in the field as well as interdisciplinary approaches. My work aims at contributing to an ecosystem-level mechanistic understanding of the CRC-associated microbiome in the initiation and progression of the disease. In detail, the objective of my work comprised an integrative approach of microbiome-CRC interaction studies. We revised current knowledge on, and studied the CRC-associated bacteria, in particular Fusobacterium nucleatum (Fn) and Gemella morbillorum (Gm). We assessed their direct and indirect effects on CRC cells, their interactions with immune cells, as well as their tumor-modulating potential in vitro, in silico, and in vivo. The results presented in this thesis comprise new findings on human microbial cross-talk of Fn with CRC. We identified formate as a potential fusobacterial oncometabolite, which enhanced cancer incidence and progression via increased cancer stemness signaling. Furthermore, we discovered immune-suppressive functions of Gm in the context of CRC. With my work in collaboration projects, I contributed to the development of two novel approaches in anti-cancer therapy: First, to the establishment of a personalized in vitro model (iHuMiX) for the study of microbe-host-immune interactions in anti-cancer therapy, and second, to the validation of an in silico workflow that uses metabolic rewiring strategies for network-based drug target predictions for CRC therapy. Taken together, this thesis work broadened the mechanistic understanding of CRC-associated microbes and it contributed to potential strategies for the development of an improved CRC therapy. [less ▲]

Microbiome in Colorectal Cancer: How to Getfrom Meta-omics to Mechanism?

in Trends in Microbiology (2020)

Mounting evidence from metagenomic analyses suggests that a state of pathological microbial imbalance or dysbiosis is prevalent in the gut of patients with colorectal cancer. Several bacterial taxa have ... [more ▼]

Mounting evidence from metagenomic analyses suggests that a state of pathological microbial imbalance or dysbiosis is prevalent in the gut of patients with colorectal cancer. Several bacterial taxa have been identified of which representative isolate cultures interact with human cancer cells in vitro and trigger disease path-ways in animal models. However, how the complex interrelationships in dysbiotic communities may be involved in cancer pathogenesis remains a crucial question.Here, we provide a survey of current knowledge of the gut microbiome in colorectal cancer. Moving beyond observational studies, we outline new experimental approaches for gaining ecosystem-level mechanistic understanding of the gut microbiome’s role in cancer pathogenesis [less ▲]

From meta-genomics to causality: Understanding the role of colon cancer-associated bacteria in colorectal cancer

Poster (2017, February 05)

The human gastrointestinal tract is home for trillions of bacteria that influence homeostasis and health in a complex biological system: the gut microbiome. Accumulating evidence suggests that a state of ... [more ▼]

The human gastrointestinal tract is home for trillions of bacteria that influence homeostasis and health in a complex biological system: the gut microbiome. Accumulating evidence suggests that a state of pathological imbalance in the microbiome (dysbiosis) is present in patients suffering from colorectal cancer (CRC). To date, microbiome studies identified specific bacteria being associated with dysbiosis in CRC. Some of these bacteria (e.g. Fusobacteria) directly or indirectly interact with cancer and immune cells of their host. However, current studies only focused on certain microbes in detail, hence, their role in the etiology of the disease remains elusive. Accordingly, my project investigates the role of CRC-associated bacteria in tumor initiation and progression while addressing the question: which and what kind of microbes interact with, favor, or can cause CRC? In a first step, we identified CRC-associated bacteria, enriched at the tumor site of Luxembourgish CRC patients. By using Fusobacterium nucleatum as our study model, we predicted and optimized bacterial growth (media) in silico by using a genome-scale metabolic reconstruction model for a constraint-based modelling approach. Next, we assessed bacterial growth and metabolism in the optimized growth medium by using flow cytometry and mass spectrometry. Finally, we co-cultured the bacteria together with primary patient-derived cultures in the recently developed, microfluidics-based, human-microbial cross-talk model (HuMiX) [1]. As part of our ongoing validations, we infected patient-derived, healthy and cancerous 3D colonic organoids with our bacterial candidate. This workflow enables us to analyze pro-tumorigenic capacities of CRC-associated bacteria on healthy and cancerous colonocytes. It will serve as a promising tool for future analysis of host-microbial interaction mechanisms of various CRC-associated bacteria on a transcriptomic, proteomic, and metabolomic level. [1] Shah P, Fritz JV, Glaab E, Desai MS, Greenhalgh K et al. (2016) A microfluidics-based in vitro model of the gastrointestinal human-microbe interface. Nature communications 7: 11535. [less ▲]

Hypoxia-responsive miR-210 promotes self-renewal capacity of colon tumor-initiating cells by repressing ISCU and by inducing lactate production

in Oncotarget (2016), 7(40), 97-114

Low oxygen concentrations (hypoxia) are known to affect the cellular metabolism and have been suggested to regulate a subpopulation of cancer cells with tumorigenic properties, the so-called tumor ... [more ▼]

Low oxygen concentrations (hypoxia) are known to affect the cellular metabolism and have been suggested to regulate a subpopulation of cancer cells with tumorigenic properties, the so-called tumor-initiating cells (TICs). To better understand the mechanism of hypoxia-induced TIC activation, we set out to study the role of hypoxia-responsive miRNAs in recently established colon cancer patientderived TICs. We were able to show that low oxygen concentrations consistently lead to the upregulation of miR-210 in different primary TIC-enriched cultures. Both stable overexpression of miR-210 and knockdown of its target gene ISCU resulted in enhanced TIC self-renewal. We could validate the tumorigenic properties of miR- 210 in in vivo experiments by showing that ectopic expression of miR-210 results in increased tumor incidence. Furthermore, enhanced miR-210 expression correlated with reduced TCA cycle activity and increased lactate levels. Importantly, by blocking lactate production via inhibition of LDHA, we could reverse the promoting effect of miR-210 on self-renewal capacity, thereby emphasizing the regulatory impact of the glycolytic phenotype on colon TIC properties. Finally, by assessing expression levels in patient tissue, we could demonstrate the clinical relevance of the miR-210/ISCU signaling axis for colorectal carcinoma. Taken together, our study highlights the importance of hypoxia-induced miR-210 in the regulation of colon cancer initiation. [less ▲]