Gut Microbiota-Derived Metabolites: Comparison
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Please note this is a comparison between Version 2 by Rita Xu and Version 1 by Alexander Visekruna.

The tumor microenvironment (TME) comprises various non-malignant cells and soluble factors that surround cancer cells and which have mostly a pro-tumorigenic role. Growing evidence indicates that commensal bacteria are involved in the pathogenesis and progression but also in the suppression of various human cancers.

  • tumor microenvironment (TME)
  • intratumoral microbiota
  • oncobiome
  • microbiota-derived metabolites

1. Introduction

Multiple lines of evidence suggest an essential role for the mutualistic interaction between intestinal microbiota and the host for the maturation of the immune system and maintenance of human health [1]. Long-lasting and parallel co-evolutionary processes have led to the establishment of a stable gut microbial ecology that exhibits reciprocal communication with the host [2]. The development of a protective immune system coincides with the expansion and alterations of the intestinal microbiota that, during the short weaning period, imprints the resistance or susceptibility to inflammatory processes later in life. This so-called “weaning reaction” is a central factor for the induction of Foxp3+ regulatory T cells (Tregs) in the gut and protection against diverse inflammatory and autoimmune diseases later in life [3]. Over the past decade, a number of studies have shown that the gut microbiota is not only essential for the mucosal tissue-associated development of the local immune system, but it also modulates the course of carcinogenesis and impacts treatment response [4[4][5],5], which may offer novel opportunities for the development of microbiota-based therapeutic strategies in the coming years. Emerging data demonstrate a complex interplay of bacterial and fungal molecules with cells of the tumor microenvironment (TME) across diverse cancer types [6,7][6][7]. There is evidence now that specific members of gut microbiota influence the treatment approaches, such as immune checkpoint inhibitors (ICI) and chimeric antigen receptor (CAR) T cell therapies [8,9,10,11][8][9][10][11]. The TME comprises various non-malignant cellular populations, such as tumor-infiltrating immune cells, fibroblasts and endothelial cells. Metabolic and transcriptomic alterations, induced by intercellular interactions, soluble factors and metabolites, frequently promote an immunosuppressive phenotype of immune cells, e.g., tumor-associated macrophages (TAMs), infiltrating myeloid-derived suppressor cells (MDSCs) and Tregs, which ultimately supports tumor progression and metastases [12]. Cancer and stroma cells commonly induce the expression of programmed cell death ligand 1 (PD-L1) that binds to programmed cell death 1 (PD-1) on T cells and leads to their exhaustion, a known phenomenon during cancer development and in chronic viral infections [13,14][13][14]. Recently, the antibodies targeting PD-L1, or its receptor PD-1, have revolutionized therapeutic options for the treatment of cancer patients [15,16][15][16]. Although ICI-based immunotherapy has greatly improved the overall survival among patients with metastatic melanoma, in other cancer types, only a small subset of patients responds to this treatment [17]. Remarkably, some commensal bacteria, such as Akkermansia muciniphila and Bifidobacterium longum, seem to augment anti-tumor immunity and enhance the effectiveness of ICI therapy [4,18,19,20,21][4][18][19][20][21]. Novel data suggest that the high diversity and richness of commensal bacteria synergize with ICI treatment and that exposure to antibiotics may result in worse outcomes among cancer patients [22,23][22][23].

2. The Intestinal Microbiota and Its Relation to Cancer Development and Cancer Immunotherapy

Progress in both basic cancer research in experimental animal models and translational oncology has essentially contributed to the current understanding of how gut commensal bacteria impact cancer development and targeted therapy for cancer. Mutual interactions between intestinal microbiota and host T cells seem to be a key factor that contributes substantially to a bacteria-primed immune reaction and the trafficking of intestinal and circulating T cells to tumor tissue that supports cancer therapy [28][24]. There is a growing awareness of the role of a “favorable” microbiota composition that correlates with an efficient response to ICI treatment in humans and mice [29][25]. Using a murine model of ICI therapy (anti-cytotoxic T-lymphocyte-associated protein-4 (CTLA-4) blockade), Vetizou et al. found that enhanced anti-cancer immunotherapy relies on the presence of Bacteroides fragilis or Bacteroides thetaiotaomicron within the gut microbiome [30][26]. Another study suggested a strong impact of the Bifidobacterium species on the infiltration of intratumoral CD8+ T cells, which resulted in enhanced efficacy of anti-PD-L1 immunotherapy. A subsequent report demonstrating the abundance of eight different commensal species with a better response to ICI therapy confirmed the association of Bifidobacterium longum and an augmented anti-PD-1 efficacy [31][27]. Importantly, the fecal microbiota transplantation (FMT) from human responders to ICI therapy led to reduced tumor growth, an increasing number of intratumoral CD8+ T cells and the enhanced efficacy of PD-1/PD-L1 blockade in mice [32,33,34][28][29][30]. Similarly, a recent study has revealed that a defined commensal consortium comprising 11 human bacteria that were derived from the feces of healthy human donors elicits CD8+ T cell responses and promotes anti-tumor effects in murine subcutaneous tumor models [35,36][31][32]. Interestingly, also “non-favorable” members of gut microbiota, such as Roseburia intestinalis and Ruminococcus obeum, have been recently identified [31][27]. Collectively, the composition of gut microbiota influences anti-cancer immune responses, tumor microenvironments and the clinical benefits of ICI therapy. Although commensal bacteria are capable of reshaping the functionality of cells surrounding the tumors and even of enhancing the efficacy of anti-tumor immunity, ourthe understanding of the impact of specific microbiota-derived species and their molecules on the tumor immune microenvironment is still limited. Several mechanisms have been suggested, potentially explaining how gut bacteria may influence anti-cancer immune surveillance and TMEs. The system effects of gut microbes can be mediated via the ligands of pattern recognition receptors that deliver adjuvant signals for the cells of innate immunity, such as dendritic cells and macrophages [37][33]. Additionally, cross-reactive anti-tumor T cell responses can be generated by specific T cells that recognize microbial antigens with high similarity in their structure to tumor neoantigens [38,39][34][35]. Finally, the host/microbiota interactions can be mediated through small molecules produced by commensal bacteria that can leave the bacterial community in the intestine and reach the TME via circulation [40,41,42,43][36][37][38][39]. Recent studies have demonstrated that gut microbiota-derived metabolites are capable of eliciting and strengthening T cell-mediated anti-tumor immunity [44,45][40][41].

3. The Oncobiome and Cancer

Reduced diversity or altered composition of the intestinal microbiome has been found to correlate with many chronic disorders, such as metabolic dysfunctions and cardiovascular, inflammatory and autoimmune diseases [46][42]. Generally, a more diverse gut microbiome has a positive effect on the functional diversity of the immune system, likely lowering the risk of developing cancer. For example, the diversity of the microbial community is an independent predictor of survival in cervical cancer [47][43]. It was observed that cancer patients with a high diversity of gut microbiota had increased tumor infiltration of Th1 and CTLs in various cancer types. Surprisingly, a novel study investigating the human tumor microbiome uncovered that intratumoral bacteria are present in various solid tumors, such as breast and ovarian cancer, lung and pancreatic tumor tissues, and even in tumors that have no direct communication with the external environment (e.g., glioblastoma or bone tumors) [6,48][6][44]. Diverse intracellular bacteria have been detected mostly in both cancer and the neighboring immune cells. The characterization of the tumor microbiome revealed that different tumor types have distinct bacterial compositions. Interestingly, at the phylum level, only two phyla (Firmicutes and Proteobacteria) have been mostly observed in the TME; however, the Proteobacteria to Firmicutes ratio seems to vary between cancer types. Furthermore, a high diversity was found for bacterial families, genera and species among various cancers [6]. Several mechanisms may be involved in the translocation and transport of bacteria to the TME during tumor development. A leaky and flexible vasculature may allow the entry of circulating bacteria and immune cells, such as macrophages, engulfing and transporting bacteria to tumor tissue. Currently, it is difficult to speculate whether intratumoral bacteria actively modulate the development of cancer or if bacteria appear at later stages in established tumors, where they can persist in certain niches. A very recent study suggests that the distribution of bacteria in the TME does not occur randomly. Instead, the presence of tumor-associated bacteria in immunosuppressive microniches points to a highly organized colonization of tumor tissues that affect the behavior of tumor and immune cells [49][45]. Intriguingly, it was postulated that the cell-associated members of the intratumoral microbiota could drive the migration of cancer cells and impact the cellular heterogeneity of the TME. Interestingly, the total bacterial load in tumors was negatively regulated with the expression of tumor suppression protein p53 [49][45]. OurThe better understanding of these effects may contribute to the development of alternative approaches to enhance the current cancer treatment efficacy by modulating the composition of the so-called oncobiome [50][46]. The presence of tumor-associated bacteria in colorectal carcinoma is probably easier to explain than in cancers that are not in close proximity to the intestinal microbiome. The processes that damage the integrity and function of the epithelial barriers in our body might compromise mucosal homeostasis, leading to microbial dysbiosis. Interestingly, intestinal bacteria and some oral bacteria have been found in colorectal cancer (CRC) samples. It was reported that Fusobacterium nucleatum, a common oral bacterium, can migrate to the colon, where it enriches in tumor tissue and impairs the therapeutic outcome and prognosis of radiotherapy and promotes colorectal carcinogenesis [51,52,53,54][47][48][49][50]. Transcriptional modification, induced by this invasive bacterium, has been related to the upregulation of signaling cascades triggered through the growth factor receptors, such as epidermal growth factor receptor (EGFR) and platelet-derived growth factor (PDGF), as well as NF-kB signaling, while pathways linked to the cell cycle, DNA damage repair and p53 signaling were downregulated. In cultured cancer cell spheroids treated with F. nucleatum, intestinal epithelial cells detached from the spheroid mass and infiltrated the surrounding collagen [49][45]. Notably, this member of the oral microbiota was also abundantly detected in breast and pancreatic tumor patient cohorts [55,56][51][52]. Furthermore, using advanced high-throughput 16S rRNA sequencing techniques, several studies have demonstrated that pancreatic tumor cohorts are enriched in Proteobacteria, which are normally found in duodenum tissues [57,58][53][54]. These findings suggest a retrograde bacterial translocation from the duodenum to the pancreatic duct. Of note, in both cancer types with high frequencies of K-Ras mutations, pancreatic adenocarcinoma (PDAC) and lung adenocarcinoma, the intratumoral microbiota promotes the development of cancer due to local microbiota-immune crosstalk and by modulating the tumor immune microenvironment [59,60,61][55][56][57]. Interestingly, not only bacteria but also pancreatic fungal mycobiome seem to promote oncogenesis. Mechanistically, the binding of glycans of the fungal wall to the mannose-binding lectin (MBL) accelerates oncogenic progression [62][58]. Following diagnosis, the actual five-year survival of PDAC patients is very low (approximately 9%). A recent study focusing on the tumor-associated microbiota in short-term survivors and long-term survivors offered new insights into a complex interaction between bacterial communities and the cells of the TME in PDAC. In the tumor tissue of long-term survivors, particularly three genera (Saccharopolyspora, Pseudoxanthomonas and Streptomyces) were enriched that were marginally present in short-term survivors. A strong correlation between these top-three genera and CD8+ and granzyme B+ densities was found for long-term survivors [63][59], suggesting that infiltration of the TME with CTLs, but also higher activity of these cells might be connected to a specific microbial signature within tumor tissue. Collectively, although it is premature to interpret the functional influence of the local microbiome composition within tumors, the targeted modulation of tumor-associated bacteria may affect the effectiveness of cancer treatment. It might be important to define a specific fraction of bacteria that belong to a “favorable oncobiome” with the potential to reshape tumor immune responses and “re-educate” the cells of the TME. In the future, such therapeutic approaches could be combined with established types of cancer immunotherapies, such as CAR-T cell or ICI therapy. The discovery of specific tumor-associated microbiome signatures in various human cancer types may also lead to the development of novel diagnostic tools to predict the effectiveness of cancer immunotherapies.

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