Gut Microbes’ Impact on Oncogenic Drivers: Location Matters

Recent work by Kadosh et al., 2020Kadosh E. Snir-Alkalay I. Venkatachalam A. May S. Lasry A. Elyada E. Zinger A. Shaham M. Vaalani G. Mernberger M. et al.The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic.Nature. 2020; (Published online July 29, 2020)https://doi.org/10.1038/s41586-020-2541-0Crossref Scopus (50) Google Scholar suggests that mutant p53 activity in gut epithelia is influenced by local production of microbial metabolites. The switch of p53 from tumor suppressor to oncogene is location-dependent and is impacted by microbially derived gallic acid. Recent work by Kadosh et al., 2020Kadosh E. Snir-Alkalay I. Venkatachalam A. May S. Lasry A. Elyada E. Zinger A. Shaham M. Vaalani G. Mernberger M. et al.The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic.Nature. 2020; (Published online July 29, 2020)https://doi.org/10.1038/s41586-020-2541-0Crossref Scopus (50) Google Scholar suggests that mutant p53 activity in gut epithelia is influenced by local production of microbial metabolites. The switch of p53 from tumor suppressor to oncogene is location-dependent and is impacted by microbially derived gallic acid. The impact of microbes within tumors and within the gut is increasingly being recognized in the field of cancer—both in their potential contributions to carcinogenesis (Sears and Garrett, 2014Sears C.L. Garrett W.S. Microbes, microbiota, and colon cancer.Cell Host Microbe. 2014; 15: 317-328Abstract Full Text Full Text PDF PubMed Scopus (428) Google Scholar), as well as in modulating therapeutic response (Gopalakrishnan et al., 2018Gopalakrishnan V. Spencer C.N. Nezi L. Reuben A. Andrews M.C. Karpinets T.V. Prieto P.A. Vicente D. Hoffman K. Wei S.C. et al.Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.Science. 2018; 359: 97-103Crossref PubMed Scopus (1403) Google Scholar; Zitvogel et al., 2017Zitvogel L. Daillère R. Roberti M.P. Routy B. Kroemer G. Anticancer effects of the microbiome and its products.Nat. Rev. Microbiol. 2017; 15: 465-478Crossref PubMed Scopus (183) Google Scholar). The characterization of these microbes has been greatly facilitated via next-generation sequencing (NGS) approaches, with microbial signatures now identified within tumors across cancer types (Poore et al., 2020Poore G.D. Kopylova E. Zhu Q. Carpenter C. Fraraccio S. Wandro S. Kosciolek T. Janssen S. Metcalf J. Song S.J. et al.Microbiome analyses of blood and tissues suggest cancer diagnostic approach.Nature. 2020; 579: 567-574Crossref PubMed Scopus (100) Google Scholar), offering new diagnostic and therapeutic opportunities. Insights are being gained into the mechanisms through which these microbes may positively or negatively impact carcinogenesis and therapeutic response (Bullman et al., 2017Bullman S. Pedamallu C.S. Sicinska E. Clancy T.E. Zhang X. Cai D. Neuberg D. Huang K. Guevara F. Nelson T. et al.Analysis of Fusobacterium persistence and antibiotic response in colorectal cancer.Science. 2017; 358: 1443-1448Crossref PubMed Scopus (404) Google Scholar; Geller et al., 2017Geller L.T. Barzily-Rokni M. Danino T. Jonas O.H. Shental N. Nejman D. Gavert N. Zwang Y. Cooper Z.A. Shee K. et al.Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine.Science. 2017; 357: 1156-1160Crossref PubMed Scopus (384) Google Scholar; Pushalkar et al., 2018Pushalkar S. Hundeyin M. Daley D. Zambirinis C.P. Kurz E. Mishra A. Mohan N. Aykut B. Usyk M. Torres L.E. et al.The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression.Cancer Discov. 2018; 8: 403-416Crossref PubMed Scopus (277) Google Scholar; Riquelme et al., 2019Riquelme E. Zhang Y. Zhang L. Montiel M. Zoltan M. Dong W. Quesada P. Sahin I. Chandra V. San Lucas A. et al.Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes..Cell. 2019; 178: 795-806.e12Abstract Full Text Full Text PDF PubMed Scopus (231) Google Scholar), including associations with oncogenic drivers such as p53 (Greathouse et al., 2018Greathouse K.L. White J.R. Vargas A.J. Bliskovsky V.V. Beck J.A. von Muhlinen N. Polley E.C. Bowman E.D. Khan M.A. Robles A.I. et al.Interaction between the microbiome and TP53 in human lung cancer.Genome Biol. 2018; 19: 123Crossref PubMed Scopus (73) Google Scholar). These mechanisms, however, are incompletely understood and more research is clearly needed. Microbes are known to produce a multitude of metabolites that can impact host physiology and may also impact carcinogenesis as well as therapy response (Zitvogel et al., 2017Zitvogel L. Daillère R. Roberti M.P. Routy B. Kroemer G. Anticancer effects of the microbiome and its products.Nat. Rev. Microbiol. 2017; 15: 465-478Crossref PubMed Scopus (183) Google Scholar). Additionally, microbial diversity and composition differs substantially based on the location within the gut—thus, the local impact of microbially produced metabolites and other microbial mechanisms may be context dependent. A recent manuscript by Kadosh and colleagues published in Nature illustrates this point, demonstrating the impact of microbial metabolites on activity of mutant p53 at different locations within the gut (Kadosh et al., 2020Kadosh E. Snir-Alkalay I. Venkatachalam A. May S. Lasry A. Elyada E. Zinger A. Shaham M. Vaalani G. Mernberger M. et al.The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic.Nature. 2020; (Published online July 29, 2020)https://doi.org/10.1038/s41586-020-2541-0Crossref Scopus (50) Google Scholar). Using murine and organoid models of carcinogenesis, Kadosh and colleagues demonstrated dichotomous activity of mutant p53 as a tumor suppressor versus an oncogene in two different locations within the gut. Importantly, this was influenced by metabolites produced by the local gut microbiota, with divergent activities of mutant p53 in the proximal versus distal gut. This was associated with different levels of the metabolite gallic acid. In these studies, the group used two mouse models to study the impact of mutant p53 on gut tumorigenesis: CKIα mice, in which dysplasia was measured via immunohistochemistry (IHC), and ApcMin/+ mice, in which discrete intestinal tumors were formed. Initially, the authors observed dysplasia in the jejunum and ileum of mice with CKIα and wild-type p53 conditionally deleted from the gut epithelium (CKIαΔgut, p53Δgut), while mice with a p53 R172H mutation (p53R172H) demonstrated dysplasia confined only to the ileum. A similar effect was seen in ApcMin/+ mice whose tumors were primarily in the jejunum with sparing of the colon with wild-type p53 (p53WT) while mutated p53R172H acted as a tumor suppressor in the jejunum but oncogenic in the colon. These effects were then shown to be secondary to dysregulation of the WNT pathway through IHC analysis of WNT target genes. This initial signal demonstrated mutant p53’s action to be spatially dependent in vivo, acting as a tumor suppressor in the proximal gut and as an oncogene in the distal gut. The above spatial relationship, while compelling, does not speak to the source of this observed heterogeneity. Differences in dysplasia by cell type were then studied in ex vivo organoid models of ileal and jejunal cells. The authors noted that p53R172H as well as common mutations in human cancers p53R175H and p53273H exhibited tumor suppressive function in both CKIα and APC organoid models regardless of the sources of those organoids (jejunal versus ileal). This suggests the demonstrated mutated p53 tumor suppressor function regardless of cell type in vitro. In vivo factors, such as the gut microbiota, were then considered the possible causative factor. The group then returned to the in vivo murine model and demonstrated that treatment of mice with antibiotics (with resulting depletion of the gut microbiota confirmed with 16 s sequencing) was associated with restored tumor suppressor function of mutant p53R172H in the distal gut, whereas mice with conditional knockout of mutant p53 continued to demonstrate dysplasia in the proximal and distal gut. It was again confirmed that this tumor suppressive effect was associated with loss of WNT-dependent hyperproliferation. To study more precisely the action of the distal gut microbiome causing this switch, the authors’ attention moved to potentially causative metabolomics in the distal gut. To do this, they studied jejunal CKIαKOp53R172H organoids with a screen for metabolites with known potential impact on tumorogenesis via epigenetic modulation of gene expression. In these studies, the presence of high concentrations of gallic acid was associated with increased proliferative capacity of the organoids—and this was only true in the CKIαKOp53R17H organoids. Notably, hyperproliferative potential of the organoids was lost when gallic acid was removed from the media. The group then brought this back to in vivo models, demonstrating markedly higher levels of gallic acid in the ileum versus the jejunum along with differential expression of the bacterial enzyme shikimate dehydrogenase, which is involved in gallic acid production. Treatment with exogenous gallic acid was associated with highly proliferative epithelia in the jejunum with lesions of high-grade dysplasia in the mutant p53 background (but not with the wild-type p53 background), suggesting that this is mediated through mutant p53. This appeared to be mediated at least in part via gallic acid’s impact on TCF-4-chromatin association and H3K4me3 modification at genomic WNT promoters in jejunal enterocytes harboring mutant p53 (Figure 1). Together, these data galvanize the concept that gut microbes can have a profound impact on carcinogenesis and also highlight the plasticity of cancer-associated genes such as p53 and their influence from the local microenvironment. Second, it highlights that functional aspects of microbial environments are likely to have a dominant role via impact of metabolites and other factors on host physiology in health and disease. Thus, it is critical as we move forward as a field to focus on functional aspects of gut microbiota and their impact, rather than solely focusing on taxonomy. Nonetheless limitations exist with our current understanding, and further research exploring such associations and the mechanisms behind this are critically needed. Research studies in pre-clinical models such as the one performed by Kadosh et al. are important, though the relevance of such findings in patients needs to be carefully understood before bringing forward therapeutic approaches (such as targeting gallic acid). Though such research and reductionist approaches in genetically engineered mouse models are helpful in elucidating potential mechanisms, interactions in human organisms are far more complex with multiple potential confounders. Nonetheless, such studies, coupled with human subjects research, are paramount in developing next generation strategies for cancer care. J.A.W. is supported by the NIH ( 1 R01 CA219896-01A1 ), U.S-Israel Binational Science Foundation ( 201332 ), the Melanoma Research Alliance ( 4022024 ), American Association for Cancer Research Stand Up To Cancer ( SU2C-AACR-IRG-19-17 ), Department of Defense ( W81XWH-16-1-0121 ), MD Anderson Cancer Center Multidisciplinary Research Program Grant , Andrew Sabin Family Fellows Program , and MD Anderson Cancer Center’s Melanoma Moon Shots Program . J.A.W. is a member of the Parker Institute for Cancer Immunotherapy at MD Anderson Cancer Center. J.A.W. is an inventor on a US patent application (PCT/US17/53.717) submitted by the University of Texas MD Anderson Cancer Center that covers methods to enhance immune checkpoint blockade responses by modulating the microbiome. J.A.W. reports compensation for speaker’s bureau and honoraria from Imedex, Dava Oncology, Omniprex, Illumina, Gilead, PeerView, Physician Education Resource, MedImmune, and Bristol-Myers Squibb. J.A.W. serves as a consultant/advisory board member for Roche/Genentech, Novartis, AstraZeneca, GlaxoSmithKline, Bristol-Myers Squibb, Merck, Biothera Pharmaceuticals, and Microbiome DX. J.A.W. also receives research support from GlaxoSmithKline, Roche/Genentech, Bristol-Myers Squibb, and Novartis.