NIH/NCI – Modulating Intestinal Microbiota to Enhance Protective Immune Responses against Cancer (R01, R21 Clinical Trial Not Allowed)

March 12, 2019 by School of Medicine Webmaster

The following description is from the R01 version of this FOA.

The purpose of this Funding Opportunity Announcement (FOA) is to support research which can elucidate mechanism(s) of action by which gut microbes inhibit or enhance anti-tumor immune responses. Thus, research projects should be focused on delineating how specific microbes or their metabolites target host immune responses to prevent colitis-associated or sporadic tumor formation.

This FOA will utilize the NIH Research Project Grant (R01) mechanism and is suitable for projects where proof-of-principle of the proposed methodology has already been established and supportive preliminary data are available.

This FOA runs in parallel with an FOA of identical scientific scope, PAR-19-199, which utilizes the Exploratory/Developmental Grant (R21) mechanism.


Growing evidence indicates an important role for the gut microbiome in maintaining epithelial integrity, regulating anti-tumor immunity, and suppressing chronic inflammatory processes in the colon and distal tissues. Several studies have demonstrated that altering the commensal microbiota by administration of beneficial microbes can modify both innate and adaptive immune responses and thereby prevent the development of colitis-associated and sporadic colon cancer in susceptible animal models. The efficacy of these probiotic microbes is often species- and strain-specific and thus requires an understanding and selection of specifically targeted host-microbe interactions to elicit a desirable outcome. Furthermore, our current level of understanding of the molecular mechanisms and signaling pathways that mediate these protective effects is very limited. Therefore, the goal of this concept is to promote basic and applied research that will identify and validate effective strains or combination of strains of beneficial microbes, or their metabolic products, that may enhance anti-tumor immune responses in the host.

Dynamics of altered intestinal microbiota and mucosal immunity in cancer patients

Inflammatory bowel diseases (IBDs) including ulcerative colitis and Crohn’s disease are believed to arise from an inappropriate immune response directed toward the commensal microbiota. IBD-related colon cancer patients often carry distinct gut microbiota that is different from healthy individuals. For example, specific commensals including Bifidobacteriumand Lactobacillus are consistently diminished and a higher presence of Fusobacterium nucleatum and Enterobacteriaceae was found in these patients. While it remains unclear if such shifts in microbial composition play a causal or consequential role in the development of colon cancer, the changes are frequently accompanied with inflammatory lesions that cross the single layer of gut epithelium. This breach in gut barrier challenges intestinal immune cells with an array of microbial ligands that induce inflammatory responses. For example, intestinal plasma cells release large quantities of high-affinity immunoglobulin A (IgA) antibodies that defend against the colonization and persistence of pathobionts in the intestine. Further, barrier disruption can lead to naïve CD4(+) T cell polarization to regulatory T cells that secrete the anti-inflammatory cytokines IL-10 and TGFβ which protect the colonic epithelium from inflammation-induced tissue damage, but which can also establish a tumor permissive immune environment. In addition, several types of myeloid-lineage cells (macrophages, dendritic cells, mast cells, and neutrophils) are induced to express inflammatory cytokines as part of an initial wound-healing response in the colon. These early immune responses to altered mucosal barrier function and microbial interactions are key to maintaining tissue homeostasis and the subsequent prevention of tumor formation at sites of barrier disruption.

Specific gut microbes are critical to induce protective immune responses

The importance of commensal gut microbiota in shaping systemic anti-tumor immune responses has been demonstrated by their effects on immunotherapy efficacy using PD-1/PD-L1 inhibitors. Similarly, the requirement for commensal microbes in inducing intestinal IgA has been confirmed in a germ-free animal model. A recent study adopting fluorescence-activated cell sorting (FACS) combined with 16S rRNA gene sequencing revealed that T-cell-dependent IgA antibodies specifically bind epitopes on colitogenic bacteria in the intestine and thereby can be used to identify microbes associated with the development of intestinal disease. It has also been shown that T-cell-dependent IgAs are not detectable in mice deficient in Th17 cells, suggesting that these T helper cells are essential to the generation of high-affinity and pathogen-neutralizing IgAs. In addition, circulating naïve T cells can be differentiated to Th17 cells in the gut only in the presence of specific intestinal microbes such as Bifidobacterium adolescentis in humans and segmented filamentous bacteria in mice. It was recently shown that a subset of microbe-induced intestinal Th17 cells do not provoke intestinal inflammation, which is contradictory to the traditionally conceived pro-inflammatory role of Th17 cells. These alternative actions of intestinal Th17 cells suggest that they may acquire a non-inflammatory and IgA producing phenotype from microbial signals that support T-cell-dependent IgA development in the colon. Further research on how specific gut microbiota promote host protective immune responses is needed to delineate mechanisms of microbial action in cancer prevention.

Beneficial effects of microbes enhancing the secretion of IL-10 in the intestine may arise from inducible Foxp3+ROR(γt)+ Treg cells

Establishing tolerance to microbial antigens is important to avoid states of chronic inflammation in the GI tract.  In the intestinal lamina propria, regulatory T (Treg) cells are able to suppress microbiome-induced inflammatory responses through the production and action of IL-10. Studies showed that about 80% of Treg cells in the intestine co-express the retinoic acid-related orphan receptor-γt (RORγt) together with forkhead box P3 (Foxp3) that is a signature transcription factor for Treg cells. Foxp3+ROR(γt)+ Treg cells are capable of producing IL-10 and also possess an enhanced suppressive capacity against inflammation compared to the circulating Foxp3+Treg cells observed in the colitis model. Thus, it is likely that the Foxp3+ROR(γt)+ Treg cells may be induced to hinder the inflammatory insults caused by microbiota-derived antigens in the gut. Importantly, the development of the protective Foxp3+RORγt+ Treg cells has been shown to be dependent on the presence of a variety of commensal bacteria including L. rhamnosus. While these findings are intriguing, it remains to be investigated if the stimulatory effects of intestinal microbes on the IL-10 cytokine release are involved with reduced risk of developing cancer.

Specific Research Objectives

The intestine is densely populated by commensal bacteria and thus sophisticated and novel techniques are likely required to characterize the immune-modulating properties of component microbes. Recently, animal models of colon cancer with genetic modifications of the inflammatory response have been developed to analyze molecular events of immune cells in the presence or absence of specific microbes of interest. In addition, several microbially-derived metabolites have been demonstrated to modulate anti-tumor immune responses through their interactions with immune cell membrane and cytoplasmic receptors. Microbial metabolism in the intestine can also have indirect effects on tumor immune responses, for example by producing secondary bile acids from cholesterol, which inhibits hepatocyte production of chemokines that direct a protective natural killer T cell response against developing liver tumors.  Thus, state-of-the-art metabolomic, molecular, and bioinformatic techniques may now be combined with cancer models to establish a physiological role for commensal microbes in tumor immunology. The efficient utilization of metagenomic databases to infer the capacity of microbial communities can expedite research that tests predictions of gut microbial associations with host immune responses. Bioinformatic approaches may also be used to identify patterns of microbial and immunological changes that can generate unique fingerprints and taxonomic associations of cancer risk.

Applications submitted to this FOA should be focused on delineating how specific microbes or their metabolites target host immune responses to prevent colitis-associated or sporadic tumor formation. Concentration, timing, and duration of the administered beneficial microbes may alter its effectiveness and thus those parameters should be rigorously addressed in the application.

The following are relevant but not all-inclusive examples for this FOA:

  • Determine how Lactobacilli species inhibit colon cancer and if its anti-tumor activity requires the induction of T-cell-dependent IgA;
  • Examine how commensal microbiota such as Bifidobacterium breve or Bacteroides fragilis influence differentiation of naïve T cells to distinct Th17 subsets that suppress or enhance tumor formation;
  • Evaluate the role of colonic Foxp3+RORγt+ Treg cells in mediating the anti-inflammatory effects of E. coli Nissle 1917 to prevent colon cancer;
  • Determine how specific gut microbiota modulates mucosal immune responses against cancer in the lung;
  • Determine how specific gut microbiota modulates mucosal immune responses against cancer in the lung;
  • Examine how short chain fatty acid production from Butyrivibrio fibrisolvens affects anti-tumor immune functions; and
  • Examine how microbial bile acid metabolism modulates immune responses in liver and colon tumors.

Deadlines:  June 10, 2019; November 6, 2019; June 10, 2020; November 6 2020; June 10, 2021; November 8, 2021 (letters of intent due 30 days prior to deadline)


Filed Under: Funding Opportunities