Colorectal cancer in inflammatory bowel disease: a review of the role of gut microbiota and bacterial biofilms in disease pathogenesis

The risk of colorectal cancer (CRC) is increased in patients with inflammatory bowel disease (IBD), particularly in extensive ulcerative colitis (UC) and Crohn's colitis. Gut microbiota have been implicated in the pathogenesis of CRC via multiple mechanisms, including the release of reactive oxygen species and genotoxins, and induction of inflammation as well as activation of the immune response. Gut microbiota can enhance their carcinogenic and pro-inflammatory properties by organizing into biofilms, potentially making them more resistant to the host's immune system and to antibiotics. Colonic biofilms have the capacity to invade colonic tissue and accelerate tumorigenesis in tumor-prone models of mice. In the context of IBD, the prevalence of biofilms has been estimated to be up to 95%. Although the relationship between chronic inflammation and molecular mediators that contribute to IBD-associated CRC is well established, the role of gut microbiota and biofilms in this sequence is not fully understood. Because CRC can still arise in the absence of histologic inflammation, there is a growing interest in identifying chemopreventive agents against IBD-associated CRC. 5-aminosalicylates, commonly used in the treatment of UC, have antimicrobial and anti-carcinogenic properties that might have a role in the chemoprevention of CRC via the inhibition or modulation of carcinogenic gut microbiota and potentially biofilm formation. Whether biologics and other IBD-targeted therapies can decrease the progression towards dysplasia and CRC via mechanisms independent of inflammation is still unknown. Further research is warranted to identify potential new microbial targets of therapy for chemoprevention of dysplasia and CRC in IBD.

Enrichment of Bacteroides fragilis and enterotoxigenic Bacteroides fragilis in CpG island methylator phenotype-high colorectal carcinoma

OBJECTIVES

Data support that enterotoxigenic Bacteroides fragilis (ETBF) harbouring the Bacteroides fragilis toxin (bft) gene may promote colorectal tumourigenesis through the serrated neoplasia pathway. We hypothesized that ETBF may be enriched in colorectal carcinoma subtypes with high-level CpG island methylator phenotype (CIMP-high), BRAF mutation, and high-level microsatellite instability (MSI-high).

METHODS

Quantitative PCR assays were designed to quantify DNA amounts of Bacteroides fragilis, ETBF, and each bft gene isotype (bft-1, bft-2, or bft-3) in colorectal carcinomas in the Health Professionals Follow-up Study and Nurses' Health Study. We used multivariable-adjusted logistic regression models with the inverse probability weighting method.

RESULTS

We documented 4476 colorectal cancer cases, including 1232 cases with available bacterial data. High DNA amounts of Bacteroides fragilis and ETBF were positively associated with BRAF mutation (p ≤ 0.0003), CIMP-high (p ≤ 0.0002), and MSI-high (p < 0.0001 and p = 0.01, respectively). Multivariable-adjusted odds ratios (with 95% confidence interval) for high Bacteroides fragilis were 1.40 (1.06-1.85) for CIMP-high and 2.14 (1.65-2.77) for MSI-high, but 1.02 (0.78-1.35) for BRAF mutation. Multivariable-adjusted odds ratios for high ETBF were 2.00 (1.16-3.45) for CIMP-high and 2.86 (1.64-5.00) for BRAF mutation, but 1.09 (0.67-1.76) for MSI-high. Neither Bacteroides fragilis nor ETBF was associated with colorectal cancer-specific or overall survival.

DISCUSSION

The tissue abundance of Bacteroides fragilis is associated with CIMP-high and MSI-high, whereas ETBF abundance is associated with CIMP-high and BRAF mutation in colorectal carcinoma. Our findings support the aetiological relevance of Bacteroides fragilis and ETBF in the serrated neoplasia pathway.

The microbial landscape of colorectal cancer

Colorectal cancer (CRC) is a substantial source of global morbidity and mortality in dire need of improved prevention and treatment strategies. As our understanding of CRC grows, it is becoming increasingly evident that the gut microbiota, consisting of trillions of microorganisms in direct interface with the colon, plays a substantial role in CRC development and progression. Understanding the roles that individual microorganisms and complex microbial communities play in CRC pathogenesis, along with their attendant mechanisms, will help yield novel preventive and therapeutic interventions for CRC. In this Review, we discuss recent evidence concerning global perturbations of the gut microbiota in CRC, associations of specific microorganisms with CRC, the underlying mechanisms by which microorganisms potentially drive CRC development and the roles of complex microbial communities in CRC pathogenesis. While our understanding of the relationship between the microbiota and CRC has improved in recent years, our findings highlight substantial gaps in current research that need to be filled before this knowledge can be used to the benefit of patients.

Fecal transplant from vaginally seeded infants decreases intraabdominal adiposity in mice

Exposing C-section infants to the maternal vaginal microbiome, coined "vaginal seeding", partially restores microbial colonization. However, whether vaginal seeding decreases metabolic disease risk is unknown. Therefore, we assessed the effect of vaginal seeding of human infants on adiposity in a murine model. Germ-free mice were colonized with transitional stool from human infants who received vaginal seeding or control (placebo) seeding in a double-blind randomized trial. There was a reduction in intraabdominal adipose tissue (IAAT) volume in male mice that received stool from vaginally seeded infants compared to control infants. Higher levels of isoleucine and lower levels of nucleic acid metabolites were observed in controls and correlated with increased IAAT. This suggests that early changes in the gut microbiome and metabolome caused by vaginal seeding have a positive impact on metabolic health.

Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors

Colorectal cancer exhibits dynamic cellular and genetic heterogeneity during progression from precursor lesions toward malignancy. Analysis of spatial multi-omic data from 31 human colorectal specimens enabled phylogeographic mapping of tumor evolution that revealed individualized progression trajectories and accompanying microenvironmental and clonal alterations. Phylogeographic mapping ordered genetic events, classified tumors by their evolutionary dynamics, and placed clonal regions along global pseudotemporal progression trajectories encompassing the chromosomal instability (CIN+) and hypermutated (HM) pathways. Integrated single-cell and spatial transcriptomic data revealed recurring epithelial programs and infiltrating immune states along progression pseudotime. We discovered an immune exclusion signature (IEX), consisting of extracellular matrix regulators DDR1, TGFBI, PAK4, and DPEP1, that charts with CIN+ tumor progression, is associated with reduced cytotoxic cell infiltration, and shows prognostic value in independent cohorts. This spatial multi-omic atlas provides insights into colorectal tumor-microenvironment co-evolution, serving as a resource for stratification and targeted treatments.

The Role of the Gut Microbiome in Cancer: A Review, With Special Focus on Colorectal Neoplasia and Clostridioides difficile

The gut microbiome has coevolved with humans to aid in physiologic functions and prevent disease. An increasing prevalence of gut dysbiosis in modern society exists and has strong linkages to multiple disease processes common in the developed world. Mechanisms for microbiome-human interactions that impact host homeostasis include bacterial metabolite/toxin production, biofilm formation with mucous layer infiltration, and host immune system modulation. Most of this crosstalk occurs at the epithelial layer of the gut, and as such the role of these interactions in the induction of colorectal cancer-a highly prevalent disease globally and one undergoing significant epidemiologic shifts-is under increasing scrutiny. Although multiple individual gut bacteria have been hypothesized as possible driver organisms in the oncogenic process, no bacterium has been definitively identified as a causal agent of colorectal cancer, suggesting that host lifestyle factors, microbiome community interactions, and the mucosal and/or systemic immune response may play a critical role in the process. Recent evidence has emerged implicating the ubiquitous human pathogen Clostridioides difficile as a possible promoter of colorectal cancer through chronic toxin-mediated cellular changes. Although much remains to be defined regarding the natural history of infections caused by this pathogen and its potential for oncogenesis, it provides a strong model for the role of both individual bacteria and of the gut microbial community as a whole in the development of colorectal cancer.

Is neighborhood deprivation index a risk factor for Staphylococcus aureus infections?

BACKGROUND

We assessed the association between neighborhood area deprivation index (ADI) and community-onset (co) and hospital-onset (ho) Staphylococcus aureus infection.

METHODS

Demographic and clinical characteristics of patients admitted to 5 adult hospitals in the mid-Atlantic between 2016 and 2018 were obtained. The association of ADI with methicillin-resistant (MRSA) and methicillin-sensitive (MSSA) S aureus infections was assessed using logistic regression models adjusting for severity of illness and days of admission.

RESULTS

Overall, increasing ADI was associated with higher odds of co- and ho-MRSA and MSSA infection. In univariate analysis, Black race was associated with 44% greater odds of ho-MRSA infection (odds ratio [OR] 1.44; 95% CI 1.18-1.76) and Asian race (co-MRSA OR 0.355; Confidence Interval (CI) 0.240-0.525; co-MSSA OR 0.718; CI 0.557-0.928) and unknown race (co-MRSA OR 0.470; CI 0.365-0.606; co-MSSA OR 0.699; CI 0.577-0.848) was associated with lower odds of co-MSSA and co-MRSA infections. When both race and ADI were included in the model, Black race was no longer associated with ho-MRSA infections whereas Asian and unknown race remained associated with lower odds of co-MRSA and co-MSSA infection. In the multivariable logistic regression, ADI was consistently associated with increased odds of S aureus infection (co-MRSA OR 1.132; CI 1.064-1.205; co-MSSA OR 1.089; CI 1.030-1.15; ho-MRSA OR 1.29; CI 1.16-1.43: ho-MSSA OR 1.215; CI 1.096-1.346).

CONCLUSIONS

The area deprivation index is associated with community and hospital-onset MRSA and MSSA infections.

Subtle, persistent shaping of the gut microbiome by host genes: A critical determinant of host biology

Although environmental impacts on the host microbiome have been well studied, it is less certain whether and how host genetics impact the microbiome. This commentary discusses current literature supporting host genetic influences on resident species and pathogenic microbes. Mechanistic experimental studies are warranted to understand host gene-microbiome interplay.

Longitudinal Bile Acid Composition Changes Following Faecal Microbiota Transplantation for Clostridioides difficile Infection in Children With and Without Underlying Inflammatory Bowel Disease

BACKGROUND AND AIMS

Faecal microbiota transplant [FMT] is effective in treating recurrent Clostridioides difficile infection [CDI] and restores gut microbiota composition. This is unlikely to account for its entire mechanism of efficacy, as studies have shown that factors such as bile acids influence the risk of infection by affecting Clostridioides difficile germination. We therefore aimed to investigate longitudinal changes in the gut bile acid composition after FMT performed for recurrent CDI, in children with and without inflammatory bowel disease [IBD].

METHODS

Eight children received FMT; five had underlying IBD. Primary and secondary faecal bile acids were measured by liquid chromatography-mass spectrometry in recipients [pre-FMT and longitudinally post-FMT for up to 6 months] and donors.

RESULTS

Pre-FMT, recipients had higher primary and lower secondary bile acid proportions compared with donors. Post-FMT, there was a gradual increase of secondary and decrease of primary bile acids. Whereas gut bacterial diversity had been shown to be restored in all children shortly after FMT, normalisation of bile acids to donor levels occurred only by 6 months. In children with IBD, although microbiota diversity returned to pre-FMT levels within 6 months, secondary bile acids remained at donor levels.

CONCLUSIONS

The differences in bile acid profiles compared with gut bacterial diversity post-FMT suggests that interactions between the two may be more complex than previously appreciated and may contribute to FMT efficacy in different ways. This initial finding demonstrates the need to further investigate gut metabolites in larger cohorts, with longitudinal sampling to understand the mechanisms of FMT effectiveness.

Understanding the mechanisms and translational implications of the microbiome for cancer therapy innovation

The intersection of the microbiota and cancer and the mechanisms that define these interactions are a fascinating, rapidly evolving area of cancer biology and therapeutics. Here we present recent insights into the mechanisms by which specific bacteria or their communities contribute to carcinogenesis and discuss the bidirectional interplay between microbiota and host gene or epigenome signaling. We conclude with comments on manipulation of the microbiota for the therapeutic benefit of patients with cancer.

Gut colonization with an obesity-associated enteropathogenic microbe modulates the premetastatic niches to promote breast cancer lung and liver metastasis

Introduction

Obesity, an independent risk factor for breast cancer growth and metastatic progression, is also closely intertwined with gut dysbiosis; and both obese state and dysbiosis promote each other. Enteric abundance of Bacteroides fragilis is strongly linked with obesity, and we recently discovered the presence of B. fragilis in malignant breast cancer. Given that enterotoxigenic B. fragilis or ETBF, which secretes B. fragilis toxin (BFT), has been identified as a procarcinogenic microbe in breast cancer, it is necessary to examine its impact on distant metastasis and underlying systemic and localized alterations promoting metastatic progression of breast cancer.

Methods

We used syngeneic mammary intraductal (MIND) model harboring gut colonization with ETBF to query distant metastasis of breast cancer cells. Alterations in the immune network and cytokines/chemokines in the tumor microenvironment and distant metastatic sites were examined using flow cytometry, immunohistochemistry, and multiplex arrays.

Results

ETBF infection initiates a systemic inflammation aiding in the establishment of the premetastatic niche formation in vital organs via increased proinflammatory and protumorigenic cytokines like IL17A, IL17E, IL27p28, IL17A/F, IL6, and IL10 in addition to creating a prometastatic immunosuppressive environment in the liver and lungs rich in myeloid cells, macrophages, and T regulatory cells. It induces remodeling of the tumor microenvironment via immune cell and stroma infiltration, increased vasculogenesis, and an EMT-like response, thereby encouraging early metastatic dissemination ready to colonize the conducive environment in liver and lungs of the breast tumor-bearing mice.

Discussion

In this study, we show that enteric ETBF infection concomitantly induces systemic inflammation, reshapes the tumor immune microenvironment, and creates conducive metastatic niches to potentiate early dissemination and seeding of metastases to liver and lung tissues in agreement with the "seed and soil hypothesis." Our results also support the ETBF-induced "parallel model" of metastasis that advocates for an early dissemination of tumor cells that form metastatic lesions independent of the primary tumor load.

Abstract 3374: Circulating cell-free tumor DNA dynamics capture minimal residual disease with neoadjuvant immune checkpoint blockade plus chemoradiotherapy for patients with operable esophageal/gastroesophageal junction cancer

Introduction: There is a critical need to incorporate molecular assessments of minimal residual disease (MRD) during neoadjuvant immunotherapy, in order to identify individuals at high risk for disease recurrence based on analyses of circulating cell-free tumor DNA (ctDNA) landscapes. Here we employed longitudinal liquid biopsies to dynamically assess clinical outcomes with neoadjuvant immuno-chemoradiotherapy in patients with esophageal/gastroesophageal junction (E/GEJ) cancer.

Methods: We utilized targeted error-correction sequencing to perform high-depth ctDNA next-generation sequencing for 141 serial plasma and 32 matched white blood cell (WBC) DNA samples from 32 patients with operable stage II/III E/GEJ cancer that received neoadjuvant immune checkpoint blockade (ICB) with chemoradiotherapy prior to surgery (NCT03044613). ctDNA analyses were performed at baseline, post-ICB induction, after completion of chemoradiotherapy (pre-op), and post-operatively (post-op). Using a tumor-agnostic WBC DNA-informed panel NGS approach we determined the cellular origin of plasma variants, filtering out germline and clonal hematopoiesis (CH) variants and evaluated ctDNA clonal dynamics over time. Molecular MRD was evaluated post-ICB, pre-op and post-op and correlated with recurrence-free (RFS) and overall survival (OS).

Results: Twenty out of 32 patients had detectable ctDNA at any timepoint. Of the 12 patients with undetectable ctDNA, 9 had only CH- and/or germline-derived variants, while 3 patients had no detectable variants of any origin. ctDNA clearance post-ICB was correlated with tumor regression &gt;80% at the time of resection (Fischer’s exact p=0.04). The subset of patients that did not attain complete pathologic response was heterogeneous with respect to ctDNA dynamics; such that ctDNA clearance pre-op identified patients with longer OS despite residual tumor of &gt;0% at the time of resection (log rank p=0.06). Patients with undetectable ctDNA or ctDNA clearance pre-op had a longer RFS (log rank p=0.007) and OS (log rank p=0.03). Molecular MRD was associated with RFS and OS such that patients with ctDNA clearance post-op had longer RFS (log-rank p=0.007) and OS (log-rank p=0.017).

Conclusion: ctDNA clearance post-ICB, pre-op and post-op reflects differential clinical outcomes for patients with E/GEJ cancer receiving neoadjuvant immuno-chemoradiotherapy. Understanding ctDNA dynamics and their relationship with pathological response and long-term outcomes can help identify patients at higher risk for recurrence and open a therapeutic window for future intervention.

Citation Format: Blair V. Landon, Ronan J. Kelly, Ali H. Zaidi, Archana Balan, Jenna V. Canzoniero, Gavin Pereira, Zineb Belcaid, Russell K. Hales, K Ranh Voong, Richard J. Battafarano, Blair A. Jobe, Stephen C. Yang, Stephen Broderick, Jinny Ha, Kellie N. Smith, Elizabeth Thompson, Fyza Y. Shaikh, James R. White, Cynthia L. Sears, Eun J. Shin, Ali I. Amjad, Benny Weksler, Josephine L. Feliciano, Chen Hu, Vincent K. Lam, Valsamo Anagnostou. Circulating cell-free tumor DNA dynamics capture minimal residual disease with neoadjuvant immune checkpoint blockade plus chemoradiotherapy for patients with operable esophageal/gastroesophageal junction cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3374.

514. Association Between Antibiotic Exposure and Clinical Outcomes of Immune Checkpoint Inhibition

Background

Recent studies have suggested that antibiotic (ABX) use and resulting changes in the gut microbiome alter the efficacy of immune checkpoint inhibitors (ICIs) in cancer treatment, but detailed data are lacking. We performed a retrospective analysis of the impact of ABX timeframe of administration on overall survival (OS) and progression-free survival (PFS) in non-small cell lung cancer (NSCLC) patients treated with ICIs.

Methods

We assembled a cohort of stage IV NSCLC patients treated with ICIs at Johns Hopkins Medicine between 1/1/2013 and 12/31/2019 (n=154). Patient demographics, ICI and ABX (intravenous and/or oral, n=100) treatments, tumor characteristics, and progression and survival data was extracted from the electronic medical record (EMR) and verified by chart review. Progression was defined by radiological evidence or provider notes. Univariate analysis was performed with Kaplan-Meier curves with log-rank tests and multivariate analysis was performed with Cox regression.

Results

Demographic data indicated that most patients were white (n=109), smokers (n=130), and had Eastern Cooperative Oncology Group (ECOG) performance statuses of zero to one (n=128). The median age was 67 years old and slightly under half of patients (n=65) received ICIs as first line therapy. Analysis with Kaplan-Meier curves for OS and PFS revealed significantly worse OS for patients with exposure to any ABX vs. not exposed in the 2.8 years before to 4.8 years after ICI start (Median OS: 14 vs. 21.5 months, p = 0.019; Median PFS: 4.4 vs. 7.7 months, p = 0.24). ABX exposure in the 2 months before to 2 months after ICI start also negatively impacted OS (Median OS: 7.5 vs. 17.4 months, p = 0.05; Median PFS: 3.3 vs. 5.8 months, p = 0.39). Decreased OS with any ABX use in the 2.8 years before to 4.8 years after ICI start was supported by multivariate analysis controlling for age, race, ECOG performance status, tumor histology, prior lines of therapy, and prior treatment types (Adjusted Hazard Ratio: 2.0, 95% CI: 1.3-3.3).

Kaplan-Meier survival analysis of antibiotic exposure

Overall survival (A) and progression-free survival (B) in stage IV NSCLC patients treated with ICIs, with or without exposure to ABX in the 2.8 years before to 4.8 years after ICI start. P-values calculated with log-rank tests.

Conclusion

Our study indicates a negative association of ABX on OS of ICI-treated NSCLC patients in both a broad and narrow timeframe around ICI start. Further work defining ABX impact on therapeutic outcomes in a larger cohort of patients across multiple tumor types is ongoing.

Disclosures

Grant Wilson, BS, Infectious Diseases Society of America G.E.R.M. Grant: Grant/Research Support Cynthia L. Sears, MD, Bristol Myers Squibb: Grant/Research Support Fyza Shaikh, MD, PhD, Bristol Myers Squibb: Grant/Research Support.

Diet-Related and Gut-Derived Metabolites and Health Outcomes: A Scoping Review

We conducted a scoping review to map available evidence about the health impact of gut microbiota-derived metabolites. We searched PubMed and Embase for studies that assessed the health impact of ten metabolites on any health condition: deoxycholate or deoxycholic acid (DCA), lithocholate or lithocholic acid (LCA), glycolithocholate or glycolithocholic acid, glycodeoxycholate or glycodeoxycholic acid, tryptamine, putrescine, d-alanine, urolithins, N-acetylmannosamine, and phenylacetylglutamine. We identified 352 eligible studies with 168,072 participants. Most (326, 92.6%) were case-control studies, followed by cohort studies (14, 4.0%), clinical trials (8, 2.3%), and cross-sectional studies (6, 1.7%). Most studies assessed the following associations: DCA on hepatobiliary disorders (64 studies, 7976 participants), colorectal cancer (19 studies, 7461 participants), and other digestive disorders (27 studies, 2463 participants); LCA on hepatobiliary disorders (34 studies, 4297 participants), colorectal cancers (14 studies, 4955 participants), and other digestive disorders (26 studies, 2117 participants); putrescine on colorectal cancers (16 studies, 94,399 participants) and cancers excluding colorectal and hepatobiliary cancers (42 studies, 4250 participants). There is a need to conduct more prospective studies, including clinical trials. Moreover, we identified metabolites and conditions for which systemic reviews are warranted to characterize the direction and magnitude of metabolite-disease associations.

Abstract IA017: Microbiota drivers of colorectal cancer and their translation to prevention

Abundant data support that the microbiota, both communities and individual pathogenic bacteria, promote the development of colorectal cancer (CRC). More limited data support that CRC is initiated by specific bacteria or communities. This talk will focus on bacterial contributors to CRC pathogenesis, potential mechanisms, gaps in knowledge and potential approaches to enabling use of the colon microbiota and its members to advance CRC prevention. Improved approaches to prevention are particularly key to identify those at risk for early onset CRC that represents a global change in CRC epidemiology.

Citation Format: Cynthia L. Sears. Microbiota drivers of colorectal cancer and their translation to prevention [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr IA017.

Microbial metabolites damage DNA

Unexpected members of the gut microbiota produce diverse host cell genotoxins.

Murine fecal microbiota transfer models selectively colonize human microbes and reveal transcriptional programs associated with response to neoadjuvant checkpoint inhibitors

Human gut microbial species found to associate with clinical responses to immune checkpoint inhibitors (ICIs) are often tested in mice using fecal microbiota transfer (FMT), wherein tumor responses in recipient mice may recapitulate human responses to ICI treatment. However, many FMT studies have reported only limited methodological description, details of murine cohorts, and statistical methods. To investigate the reproducibility and robustness of gut microbial species that impact ICI responses, we performed human to germ-free mouse FMT using fecal samples from patients with non-small cell lung cancer who had a pathological response or nonresponse after neoadjuvant ICI treatment. R-FMT mice yielded greater anti-tumor responses in combination with anti-PD-L1 treatment compared to NR-FMT, although the magnitude varied depending on mouse cell line, sex, and individual experiment. Detailed investigation of post-FMT mouse microbiota using 16S rRNA amplicon sequencing, with models to classify and correct for biological variables, revealed a shared presence of the most highly abundant taxa between the human inocula and mice, though low abundance human taxa colonized mice more variably after FMT. Multiple Clostridium species also correlated with tumor outcome in individual anti-PD-L1-treated R-FMT mice. RNAseq analysis revealed differential expression of T and NK cell-related pathways in responding tumors, irrespective of FMT source, with enrichment of these cell types confirmed by immunohistochemistry. This study identifies several human gut microbial species that may play a role in clinical responses to ICIs and suggests attention to biological variables is needed to improve reproducibility and limit variability across experimental murine cohorts.

Western-Style Diet, pks Island-Carrying Escherichia coli, and Colorectal Cancer: Analyses From Two Large Prospective Cohort Studies

BACKGROUND & AIMS

Evidence supports a carcinogenic role of Escherichia coli carrying the pks island that encodes enzymes for colibactin biosynthesis. We hypothesized that the association of the Western-style diet (rich in red and processed meat) with colorectal cancer incidence might be stronger for tumors containing higher amounts of pks+E coli.

METHODS

Western diet score was calculated using food frequency questionnaire data obtained every 4 years during follow-up of 134,775 participants in 2 United States-wide prospective cohort studies. Using quantitative polymerase chain reaction, we measured pks+E coli DNA in 1175 tumors among 3200 incident colorectal cancer cases that had occurred during the follow-up. We used the 3200 cases and inverse probability weighting (to adjust for selection bias due to tissue availability), integrated in multivariable-adjusted duplication-method Cox proportional hazards regression analyses.

RESULTS

The association of the Western diet score with colorectal cancer incidence was stronger for tumors containing higher levels of pks+E coli (Pheterogeneity = .014). Multivariable-adjusted hazard ratios (with 95% confidence interval) for the highest (vs lowest) tertile of the Western diet score were 3.45 (1.53-7.78) (Ptrend = 0.001) for pks+E coli-high tumors, 1.22 (0.57-2.63) for pks+E coli-low tumors, and 1.10 (0.85-1.42) for pks+E coli-negative tumors. The pks+E coli level was associated with lower disease stage but not with tumor location, microsatellite instability, or BRAF, KRAS, or PIK3CA mutations.

CONCLUSIONS

The Western-style diet is associated with a higher incidence of colorectal cancer containing abundant pks+E coli, supporting a potential link between diet, the intestinal microbiota, and colorectal carcinogenesis.

Human Colon Cancer-Derived Clostridioides difficile Strains Drive Colonic Tumorigenesis in Mice

Defining the complex role of the microbiome in colorectal cancer and the discovery of novel, protumorigenic microbes are areas of active investigation. In the present study, culturing and reassociation experiments revealed that toxigenic strains of Clostridioides difficile drove the tumorigenic phenotype of a subset of colorectal cancer patient-derived mucosal slurries in germ-free ApcMin/+ mice. Tumorigenesis was dependent on the C. difficile toxin TcdB and was associated with induction of Wnt signaling, reactive oxygen species, and protumorigenic mucosal immune responses marked by the infiltration of activated myeloid cells and IL17-producing lymphoid and innate lymphoid cell subsets. These findings suggest that chronic colonization with toxigenic C. difficile is a potential driver of colorectal cancer in patients.

SIGNIFICANCE

Colorectal cancer is a leading cause of cancer and cancer-related deaths worldwide, with a multifactorial etiology that likely includes procarcinogenic bacteria. Using human colon cancer specimens, culturing, and murine models, we demonstrate that chronic infection with the enteric pathogen C. difficile is a previously unrecognized contributor to colonic tumorigenesis. See related commentary by Jain and Dudeja, p. 1838. This article is highlighted in the In This Issue feature, p. 1825.

Colon Tumors in Enterotoxigenic Bacteroides fragilis (ETBF)-Colonized Mice Do Not Display a Unique Mutational Signature but Instead Possess Host-Dependent Alterations in the APC Gene

Enterotoxigenic Bacteroides fragilis (ETBF) is consistently found at higher frequency in individuals with sporadic and hereditary colorectal cancer (CRC) and induces tumorigenesis in several mouse models of CRC. However, whether specific mutations induced by ETBF lead to colon tumor formation has not been investigated. To determine if ETBF-induced mutations impact the Apc gene, and other tumor suppressors or proto-oncogenes, we performed whole-exome sequencing and whole-genome sequencing on tumors isolated after ETBF and sham colonization of Apcmin/+ and Apcmin/+Msh2fl/flVC mice, as well as whole-genome sequencing of organoids cocultured with ETBF. Our results indicate that ETBF-induced tumor formation results from loss of heterozygosity (LOH) of Apc, unless the mismatch repair system is disrupted, in which case, tumor formation results from new acquisition of protein-truncating mutations in Apc. In contrast to polyketide synthase-positive Escherichia coli (pks+ E. coli), ETBF does not produce a unique mutational signature; instead, ETBF-induced tumors arise from errors in DNA mismatch repair and homologous recombination DNA damage repair, established pathways of tumor formation in the colon, and the same genetic mechanism accounting for sham tumors in these mouse models. Our analysis informs how this procarcinogenic bacterium may promote tumor formation in individuals with inherited predispositions to CRC, such as Lynch syndrome or familial adenomatous polyposis (FAP). IMPORTANCE Many studies have shown that microbiome composition in both the mucosa and the stool differs in individuals with sporadic and hereditary colorectal cancer (CRC). Both human and mouse models have established a strong association between particular microbes and colon tumor induction. However, the genetic mechanisms underlying putative microbe-induced colon tumor formation are not well established. In this paper, we applied whole-exome sequencing and whole-genome sequencing to investigate the impact of ETBF-induced genetic changes on tumor formation. Additionally, we performed whole-genome sequencing of human colon organoids exposed to ETBF to validate the mutational patterns seen in our mouse models and begin to understand their relevance in human colon epithelial cells. The results of this study highlight the importance of ETBF colonization in the development of sporadic CRC and in individuals with hereditary tumor conditions, such as Lynch syndrome and familial adenomatous polyposis (FAP).

Abstract 3052: Fusobacterial-dominant colorectal cancer biofilms are associated with high levels of the polyamine N1,N12-diacetylspermine

Background: Mucus-invasive colonic bacterial biofilms are dense, polymicrobial communities that are in direct contact with the epithelium. Prior data from our group has demonstrated that these invasive biofilms are prevalent in colorectal cancer, are directly tumorigenic in germ-free and specific pathogen-free ApcMin/+ mouse models, and are associated with enrichment of the polyamine N1,N12-diactylspermine (DAS) in patient samples. However, whether the composition of these biofilms impacts their pro-tumorigenic behavior and/or metabolism is presently unknown.

Methods: Carnoy’s-fixed CRC resections from 115 patients from the University of Malaya in Malaysia were stained with the all-bacterial EUB338 probe and screened for mucus-invasive biofilms (BF). All BF+ samples were subsequently stained with oligonucleotide probes targeting Bacteroidetes, Fusobacteria, Lachnospiraceae, and γ/β-Proteobacteria. Imaging was performed on a Zeiss780 confocal microscope with linear unmixing. Untargeted metabolomics was performed on 5-10 samples of each biofilm type using a Waters UPLC Xevo GS-XS quadrupole time-of-flight (QTOF) mass spectrometer. Five Fusobacterium nucleatum (Fn) strains derived from CRC cohorts were singly gavaged into germ-free ApcMin/+ mice and colons were harvested for tumors 11 wk later.

Results: Seventy-nine of 115 Malaysian tumors (69%) were BF+ using EUB338 staining. As with our prior US CRC cohort, BFs were more prevalent on the tumors proximal to the hepatic flexure (35/39, 90%) vs. those that were distal (44/76, 58%) (Chi-square p &lt; 0.001). Of the BF+ tumors (BF+T), 55% were polymicrobial (predominantly Bacteroidetes/Lachnospiraceae), 40% were polymicrobial with fusobacterial blooms, and 5% were Proteobacteria dominant. Untargeted metabolomics of BF- healthy biopsies, BF-T, and BF+T with various BF composition subtypes revealed a gradient in levels of the polyamine DAS, with BF+T with fusobacterial blooms having the highest levels (p = 0.055 vs. Proteo-dominant BF+T, p = 0.043 vs. polymicrobial BF+T, p = 0.015 vs. BF-T, p &lt; 0.001 vs. BF- healthy biopsies), suggesting that fusobacteria may drive proliferation and polyamine production in CRC tissues. However, inoculation of 5 different CRC-derived Fn strains including a strain isolated from a Malaysia CRC patient did not promote tumorigenesis in germ-free ApcMin/+ mice.

Conclusions: Fusobacterial-dominant biofilms are prevalent in a Malaysian CRC cohort and are associated with high levels of the polyamine N1,N12-diacetylspermine. However, F. nucleatum strains were not tumorigenic in germ-free ApcMin/+ mice, suggesting that the association between Fn, DAS, and tumorigenesis may require other bacteria in order to confer a procarcinogenic state.

Citation Format: Julia L. Drewes, Jessica Queen, Jada C. Domingue, Caroline R. Wensel, Yuping Cai, Jane Wanyiri, April C. Roslani, Jamuna Vadivelu, Caroline H. Johnson, Cynthia L. Sears. Fusobacterial-dominant colorectal cancer biofilms are associated with high levels of the polyamine N1,N12-diacetylspermine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3052.

Abstract 1973: Patients with operable esophageal cancer and improved responses to combined chemoradiotherapy and immunotherapy display distinct microbiome profiles enriched in multiple Bacteroides species

Background: Preclinical and clinical data indicate that neoadjuvant chemoradiotherapy (CRT) may prime an anti-tumor immunological response in esophageal cancer driven by intratumoral CD8+ T cells and PD-L1 expression. LAG-3 is also highly expressed in esophagogastric cancers. The microbiome, a novel and potentially modifiable, biomarker of IO response, has not yet been examined in the neoadjuvant setting in esophageal cancer and is the goal of our study.

Methods: Fecal samples were collected from patients with stage II/III esophageal or gastroesophageal junction carcinoma eligible for curative resection treated with the standard of care regimen of carboplatin paclitaxel (50mg/m2), radiation 50.4 Gy in 28 fractions and an Ivor-Lewis esophagectomy 6-10 weeks after last CRT and immunotherapy (IO) dose. Patients on arm A (n=11) received 2 cycles of induction with nivolumab plus 3 additional cycles on week 1, 3 and 5 of CRT. Patients on arm B (n=8) received nivolumab plus relatlimab on the same schedule (Clinical trial: NCT03044613). We examined longitudinal fecal samples from n=19 patients across both arms (n=90 samples) using 16S rRNA amplicon sequencing. Patients were classified based on pathological response: complete response (CR) and grades 1, 2, and 3 (G1, G2, G3) with increasing residual tumor visible in the resected specimen. Sequencing data was trimmed and filtered for contaminants, followed by high-resolution taxonomic assignment and normalization of reads across all samples. Analysis was performed using multiple metrics for alpha diversity and beta-diversity, with principal coordinates analysis/PERMANOVA, and pathway analysis using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt).

Results: Patients with improved response in the neoadjuvant setting (CR/G1 vs G2/G3) grouped in distinct clusters using Bray-Curtis (p &lt; 0.001). Patients with CR had higher alpha diversity, using both measures of richness and evenness, compared to patients with a G3 responses (p &lt; 0.03). Specifically, family Bacteroidaceae and genus Bacteroides were enriched in patients with CR vs G3 (p &lt; 0.02). At the species level, B. finegoldii, B. ovatus, and B. uniformis were enriched in patients with CR vs G3 (p &lt; 0.02). In contrast, genus Klebsiella and Clostridium termitidis were enriched in patients with a poor response, G3 (p &lt;0.001, both). Pathway analysis found two metabolic pathways enriched in patients with CR: secondary bile acid biosynthesis (p=0.005) and lysine biosynthesis (p=0.02).

Conclusions: Patients with operable esophageal cancer and improved responses to combined CRT and IO had distinct microbiome profiles enriched in multiple Bacteroides species. Further analyses and validation efforts are underway to confirm metabolomic pathways.

Citation Format: Fyza Y. Shaikh, James R. White, Ronan J. Kelly, Ali H. Zaidi, Jenna V. Canzoniero, Josephine L. Feliciano, Russell K. Hales, K Ranh Voong, Richard J. Battafarano, Blair A. Jobe, Stephen C. Yang, Stephen Broderick, Jinny Ha, Kellie N. Smith, Elizabeth Thompson, Eun J. Shin, Ali I. Amjad, Patrizia Guerrieri, Benny Weksler, Chen Hu, Valsamo Anagnostou, Vincent K. Lam, Cynthia L. Sears. Patients with operable esophageal cancer and improved responses to combined chemoradiotherapy and immunotherapy display distinct microbiome profiles enriched in multiple Bacteroides species [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1973.

Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses

Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, cost-effective approach for detecting exposure and response to microbial protein products. We designed and constructed a library of 95,601 56-amino acid peptide tiles spanning 14,430 proteins with "toxin" or "virulence factor" keyword annotations. We used PhIP-Seq to profile the antibodies of ∼1,000 individuals against this "ToxScan" library. In addition to enumerating immunodominant antibody epitopes, we studied the age-dependent stability of the ToxScan profile and used a genome-wide association study to find that the MHC-II locus modulates bacterial epitope selection. We detected previously described anti-flagellin antibody responses in a Crohn's disease cohort and identified an association between anti-flagellin antibodies and juvenile dermatomyositis. PhIP-Seq with the ToxScan library is thus an effective tool for studying the environmental determinants of health and disease at cohort scale.

Label-Free Vibrational and Quantitative Phase Microscopy Reveals Remarkable Pathogen-Induced Morphomolecular Divergence in Tumor-Derived Cells

Delineating the molecular and morphological changes that cancer cells undergo in response to extracellular stimuli is crucial for identifying factors that promote tumor progression. Label-free optical imaging offers a potentially promising route for retrieving such single-cell information by generating detailed visualization of the morphology and determining alterations in biomolecular composition. The potential of such nonperturbative morphomolecular microscopy for analyzing microbiota-cancer cell interactions has been surprisingly underappreciated, despite the growing evidence of the critical role of dysbiosis in malignant transformations. Here, using a model system of breast cancer cells, we show that label-free Raman microspectroscopy and quantitative phase microscopy can detect biomolecular and morphological changes in single cells exposed to Bacteroides fragilis toxin (BFT), a toxin secreted by enterotoxigenicB. fragilis. Remarkably, using machine learning to elucidate subtle, but consistent, cellular differences, we found that the morphomolecular differences between BFT-exposed and control breast cancer cells became more accentuated after in vivo passage, corroborating our findings that a short-term BFT exposure imparts a long-term effect on cancer cells and promotes a more invasive phenotype. Complementing more classical labeling techniques, our label-free platform offers a global detection approach with measurements representative of the overall cellular phenotype, paving the way for further investigations into the multifaceted interactions between the cancer cell and the microbiota.

Adult-Attained Height and Colorectal Cancer Risk: A Cohort Study, Systematic Review, and Meta-Analysis

BACKGROUND

The influence of anthropometric characteristics on colorectal neoplasia biology is unclear. We conducted a systematic review and meta-analysis to determine if adult-attained height is independently associated with the risk of colorectal cancer or adenoma.

METHODS

We searched MEDLINE, EMBASE, the Cochrane Library, and Web of Science from inception to August 2020 for studies on the association between adult-attained height and colorectal cancer or adenoma. The original data from the Johns Hopkins (Baltimore, MD) Colon Biofilm study was also included. The overall HR/OR of colorectal cancer/adenoma with increased height was estimated using random-effects meta-analysis.

RESULTS

We included 47 observational studies involving 280,644 colorectal cancer and 14,139 colorectal adenoma cases. Thirty-three studies reported data for colorectal cancer incidence per 10-cm increase in height; 19 yielded an HR of 1.14 [95% confidence interval (CI), 1.11-1.17; P < 0.001), and 14 engendered an OR of 1.09 (95% CI, 1.05-1.13; P < 0.001). Twenty-six studies compared colorectal cancer incidence between individuals within the highest versus the lowest height percentile; 19 indicated an HR of 1.24 (95% CI, 1.19-1.30; P < 0.001), and seven resulting in an OR of 1.07 (95% CI, 0.92-1.25; P = 0.39). Four studies reported data for assessing colorectal adenoma incidence per 10-cm increase in height, showing an overall OR of 1.06 (95% CI, 1.00-1.12; P = 0.03).

CONCLUSIONS

Greater adult attained height is associated with an increased risk of colorectal cancer and adenoma.

IMPACT

Height should be considered as a risk factor for colorectal cancer screening.

Next-generation sequencing: insights to advance clinical investigations of the microbiome

Next-generation sequencing (NGS) technology has advanced our understanding of the human microbiome by allowing for the discovery and characterization of unculturable microbes with prediction of their function. Key NGS methods include 16S rRNA gene sequencing, shotgun metagenomic sequencing, and RNA sequencing. The choice of which NGS methodology to pursue for a given purpose is often unclear for clinicians and researchers. In this Review, we describe the fundamentals of NGS, with a focus on 16S rRNA and shotgun metagenomic sequencing. We also discuss pros and cons of each methodology as well as important concepts in data variability, study design, and clinical metadata collection. We further present examples of how NGS studies of the human microbiome have advanced our understanding of human disease pathophysiology across diverse clinical contexts, including the development of diagnostics and therapeutics. Finally, we share insights as to how NGS might further be integrated into and advance microbiome research and clinical care in the coming years.

1001. Chronic Colonization with Toxigenic Clostridioides difficile Strains Drives Colonic Tumorigenesis in Mice

Background

Long-term effects of chronic and/or recurrent C. difficile infections (CDI) are not well understood, and any potential role of CDI in colorectal cancer (CRC) risk is presently unknown. While pursuing efforts to identify novel procarcinogenic microbes, we identified two mucosal slurries from CRC patients (3728T and 3752T) that were tumorigenic in germ-free (GF) Apc^Min/+ mice. Surprisingly, both of these CRC patient slurries were positive for C. difficile by 16S rRNA amplicon sequencing. Given the ability of other chronic infections to promote tumorigenesis (e.g., H. pylori), we hypothesized that chronic colonization with C. difficile could promote tumorigenesis in the colon.

Methods

A consortium of 30 bacterial isolates including a toxigenic tcdA+ tcdB+ C. difficile strain (CIm_3728T) was cultured from GF Apc^Min/+ mice gavaged with the 3728T slurry. This consortium was gavaged into additional GF Apc^Min/+ mice with or without C. difficile strains CIm_3728T, CIm_3752T (isolated from mice gavaged with the 3752T slurry), or isogenic tcdA/tcdB mutants of the M7404 R027 strain. Single cell RNA sequencing (scRNAseq), high dimensional (HD) flow cytometry, and fluorescence in situ hybridization (FISH) with EUB338 and Cd198 probes were performed on distal colons from mice gavaged with either complex CRC slurries or the 3728T isolates with CIm_3728T.

Results

C. difficile strains drove tumorigenesis of the 3728T isolate mixture (Fig. 1A,B). Tumorigenesis was associated with early procarcinogenic signaling and spatial changes including induction of Wnt signaling in colonic epithelial progenitor cells by scRNAseq, IL-17 induction in immune cells by HD flow cytometry, and bacterial biofilm invasion deep into epithelial crypts by FISH. Tumorigenesis correlated with chronic colonization with toxigenic strains of C. difficile and was toxin-dependent, as toxin mutant strains (M7404 tcdA-tcdB-) did not induce tumors.

Figure 1. C. difficile strains from CRC patients induce distal colonic tumorigenesis in germ-free (GF) ApcMin/+ mice.

A consortium of 30 bacteria, including C. difficile, were isolated from mice gavaged with the 3728T human CRC mucosal slurry. These isolates were then gavaged into additional GF ApcMin/+ mice, with or without C. difficile isolates from mice gavaged with the 3728T slurry or 3752T slurry. (A) Colonic tumor numbers in GF ApcMin/+ mice at 10 wk p.i. demonstrate that C. difficile (Cd) drives the tumorigenesis of this 30-member bacterial consortium. (B) Gross tumors can be observed in the colon of a representative mouse gavaged with the 3728T isolates with the CIm_3728T (top) or CIm_3752T (middle) strain of C. difficile but not in a mouse gavaged with the isolates lacking C. difficile (bottom).

Conclusion

Toxigenic C. difficile strains isolated from human CRC mucosal slurries were pro-carcinogenic in mice, suggesting that C. difficile is a potential driver of CRC. Given the public health burden of C. difficile, further studies are warranted to determine whether C. difficile infections (initial, recurrent, and chronic asymptomatic) increase CRC risk in patients.

Disclosures

Jada Domingue, PhD, AstraZeneca (Employee) James White, PhD, Personal Genome Diagnostics (Consultant) Patricia J. Simner, PhD, Accelerate Diagnostics (Grant/Research Support)Affinity Biosensors (Grant/Research Support)BD Diagnostics (Consultant, Grant/Research Support)GeneCapture (Consultant)OpGen, Inc (Consultant, Grant/Research Support)Shionogi, Inc (Consultant) Karen C. Carroll, MD, MeMed (Scientific Research Study Investigator)Meridian Diagnostics, Inc. (Grant/Research Support)Pattern Diagnostics (Advisor or Review Panel member)Scanogen, Inc. (Advisor or Review Panel member) Karen C. Carroll, MD, Pattern Diagnostics, Inc. (Individual(s) Involved: Self): Grant/Research Support; Scanogen, Inc. (Individual(s) Involved: Self): Consultant Cynthia L. Sears, MD, Bristol Myers Squibb (Grant/Research Support)Ferring (Advisor or Review Panel member)Janssen (Grant/Research Support)

Bacterial genotoxin accelerates transient infection-driven murine colon tumorigenesis

Chronic and low-grade inflammation associated with persistent bacterial infections has been linked to colon tumor development; however, the impact of transient and self-limited infections in bacterially-driven colon tumorigenesis has remained enigmatic. Here we report that UshA is a novel genotoxin in attaching/effacing (A/E) pathogens, which includes the human pathogens enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and their murine equivalent Citrobacter rodentium (CR). UshA harbors direct DNA digestion activity with a catalytic histidine-aspartic acid dyad. Injected via the Type III Secretion System (T3SS) into host cells, UshA triggers DNA damage and initiates tumorigenic transformation during infections in vitro and in vivo. Moreover, UshA plays an indispensable role in CR infection-accelerated colon tumorigenesis in genetically susceptible ApcMinΔ716/+ mice. Collectively, our results reveal that UshA, functioning as a bacterial T3SS-dependant genotoxin, plays a critical role in prompting transient and noninvasive bacterial infection-accelerated colon tumorigenesis in mice.

The Cancer Microbiome: Recent Highlights and Knowledge Gaps

Knowledge of the human microbiome, which is likely a critical factor in the initiation, progression, and prognosis of multiple forms of cancer, is rapidly expanding. In this review, we focus on recent investigations to discern putative, causative microbial species and the microbiome composition and structure currently associated with procarcinogenesis and tumorigenesis at select body sites. We specifically highlight forms of cancer, gastrointestinal and nongastrointestinal, that have significant bacterial associations and well-defined experimental evidence with the aim of generating directions for future experimental and translational investigations to develop a clearer understanding of the multifaceted mechanisms by which microbiota affect cancer formation. SIGNIFICANCE: Emerging and, for some cancers, strong experimental and translational data support the contribution of the microbiome to cancer biology and disease progression. Disrupting microbiome features and pathways contributing to cancer may provide new approaches to improving cancer outcomes in patients.

The Microbiome Colorectal Cancer Puzzle: Initiator, Propagator, and Avenue for Treatment and Research

The human gut microbiome has an ever-increasing role in the instigation and progression of colorectal cancer (CRC). Recent investigations have focused on identifying the key causative bacterial species and the composition and structure of the microbiome as a whole that ultimately lead to tumorigenesis in the colon. Understanding the bacterial mechanisms that promote CRC provides a rich area for the development of new screening modalities and therapeutics that may improve patient outcomes. This article reviews the various mechanisms that bacteria in the gut use to induce and/or promote tumor formation, discusses the application of the microbiome in the prevention and therapy of CRC, and provides directions for future research endeavors aiming to develop a more complete understanding of this complex phenomenon.

Bacterial-Driven Inflammation and Mutant BRAF Expression Combine to Promote Murine Colon Tumorigenesis That Is Sensitive to Immune Checkpoint Therapy

Colorectal cancer is multifaceted, with subtypes defined by genetic, histologic, and immunologic features that are potentially influenced by inflammation, mutagens, and/or microbiota. Colorectal cancers with activating mutations in BRAF are associated with distinct clinical characteristics, although the pathogenesis is not well understood. The Wnt-driven multiple intestinal neoplasia (MinApcΔ716/+) enterotoxigenic Bacteroides fragilis (ETBF) murine model is characterized by IL17-dependent, distal colon adenomas. Herein, we report that the addition of the BRAF V600E mutation to this model results in the emergence of a distinct locus of midcolon tumors. In ETBF-colonized BRAF V600E Lgr5 CreMin (BLM) mice, tumors have similarities to human BRAF V600E tumors, including histology, CpG island DNA hypermethylation, and immune signatures. In comparison to Min ETBF tumors, BLM ETBF tumors are infiltrated by CD8+ T cells, express IFNγ signatures, and are sensitive to anti-PD-L1 treatment. These results provide direct evidence for critical roles of host genetic and microbiota interactions in colorectal cancer pathogenesis and sensitivity to immunotherapy. SIGNIFICANCE: Colorectal cancers with BRAF mutations have distinct characteristics. We present evidence of specific colorectal cancer gene-microbial interactions in which colonization with toxigenic bacteria drives tumorigenesis in BRAF V600E Lgr5 CreMin mice, wherein tumors phenocopy aspects of human BRAF-mutated tumors and have a distinct IFNγ-dominant immune microenvironment uniquely responsive to immune checkpoint blockade.This article is highlighted in the In This Issue feature, p. 1601.

Self-reported Metabolic Risk Factor Associations with Adenomatous, Sessile Serrated, and Synchronous Adenomatous and Sessile Serrated Polyps

Studies have found a positive association between metabolic risk factors, such as obesity and diabetes, and adenomatous polyps (AP). However, fewer studies have assessed the association between sessile serrated polyps (SSP) or synchronous diagnosis of APs and SSPs (synch polyps). Study participants (N = 1,370; ages 40-85) undergoing screening colonoscopy were enrolled between August 2016 and February 2020. Self-reported metabolic risk factors, including diabetes, hypertension, hyperlipidemia, and overweight/obesity, were evaluated for associations with new diagnoses of APs, SSPs, and synch polyps at the present colonoscopy. Average participant age was 60.73 ± 8.63 (SD) years; 56.7% were female and 90.9% white. In an assessment of individual metabolic risk factors, adjusted for age, sex, race, and smoking status, increased body mass index (BMI; overweight or obese vs. normal BMI of <25 kg/m2) was associated with an increased odds for new onset of colon APs (P trend < 0.001) as was a diagnosis of diabetes [adjusted conditional OR (aCOR) = 1.59 (1.10-2.29)]. No associations were seen between the metabolic risk factors and onset of SSPs. Being obese or hypertensive each increased the odds of new onset of synch polyps with aCOR values of 2.09 (1.01-4.32) and 1.79 (1.06-3.02), respectively. Self-reported risk factors may help assess polyp type risk. Because SSPs and synch polyps are rare, larger studies are needed to improve our understanding of the contribution of these factors to polyp risk. These data lead us to hypothesize that differences in observed metabolic risk factors between polyp types reflect select metabolic impact on pathways to colorectal cancer. PREVENTION RELEVANCE: Self-reported medical history provides valuable insight into polyp risk, potentially enabling the use of larger retrospective studies of colonoscopy populations to assess knowledge gaps. More aggressive colonoscopy screening, critical to colorectal cancer prevention, may be considered in populations of individuals with metabolic risk factors and modifiable lifestyle risk factors.

G-protein coupled receptor 35 (GPR35) regulates the colonic epithelial cell response to enterotoxigenic Bacteroides fragilis

G protein-coupled receptor (GPR)35 is highly expressed in the gastro-intestinal tract, predominantly in colon epithelial cells (CEC), and has been associated with inflammatory bowel diseases (IBD), suggesting a role in gastrointestinal inflammation. The enterotoxigenic Bacteroides fragilis (ETBF) toxin (BFT) is an important virulence factor causing gut inflammation in humans and animal models. We identified that BFT signals through GPR35. Blocking GPR35 function in CECs using the GPR35 antagonist ML145, in conjunction with shRNA knock-down and CRISPRcas-mediated knock-out, resulted in reduced CEC-response to BFT as measured by E-cadherin cleavage, beta-arrestin recruitment and IL-8 secretion. Importantly, GPR35 is required for the rapid onset of ETBF-induced colitis in mouse models. GPR35-deficient mice showed reduced death and disease severity compared to wild-type C57Bl6 mice. Our data support a role for GPR35 in the CEC and mucosal response to BFT and underscore the importance of this molecule for sensing ETBF in the colon.

Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices

Meta-analysis is a practical and powerful analytic tool that enables a unified statistical inference across the results from multiple studies. Notably, researchers often report the results on multiple related markers in each study (eg, various α-diversity indices in microbiome studies). However, univariate meta-analyses are limited to combining the results on a single common marker at a time, whereas existing multivariate meta-analyses are limited to the situations where marker-by-marker correlations are given in each study. Thus, here we introduce two meta-analysis methods, multi-marker meta-analysis (mMeta) and adaptive multi-marker meta-analysis (aMeta), to combine multiple studies throughout multiple related markers with no priori results on marker-by-marker correlations. mMeta is a statistical estimator for a pooled estimate and its SE across all the studies and markers, whereas aMeta is a statistical test based on the test statistic of the minimum P-value among marker-specific meta-analyses. mMeta conducts both effect estimation and hypothesis testing based on a weighted average of marker-specific pooled estimates while estimating marker-by-marker correlations non-parametrically via permutations, yet its power is only moderate. In contrast, aMeta closely approaches the highest power among marker-specific meta-analyses, yet it is limited to hypothesis testing. While their applications can be broader, we illustrate the use of mMeta and aMeta to combine microbiome studies throughout multiple α-diversity indices. We evaluate mMeta and aMeta in silico and apply them to real microbiome studies on the disparity in α-diversity by the status of human immunodeficiency virus (HIV) infection. The R package for mMeta and aMeta is freely available at https://github.com/hk1785/mMeta.

Pathways to Leadership: Reflections of Recent Infectious Diseases Society of America (IDSA) Leaders During Conception and Launch of the Inclusion, Diversity, Access, and Equity Movement Within the IDSA

Opportunities for leadership in the specialty of infectious diseases (ID) have markedly increased over the last decade, including in newly recognized areas. Commensurate with the expansion of opportunities in ID, pathways to leadership positions within the Infectious Diseases Society of America (IDSA) are expanding as the Society seeks to advance the field for IDSA members. Acknowledging both the importance of diverse leaders to organizational success and shortfalls in diverse representation within IDSA leadership led to concentrated efforts to enhance transparency and opportunities for members to participate broadly in the work of IDSA. Herein, IDSA leaders reflect on their paths to IDSA leadership, hoping to help guide members seeking to partner with the Society. Features identified as important to individual success include mentorship, networking, participation in ID and IDSA volunteer experiences, passion for ID, and working with IDSA staff to advance the programs and initiatives of IDSA on behalf of members.

Comparative Analysis of Colon Cancer-Derived Fusobacterium nucleatum Subspecies: Inflammation and Colon Tumorigenesis in Murine Models

Fusobacteria are commonly associated with human colorectal cancer (CRC), but investigations are hampered by the absence of a stably colonized murine model. Further, Fusobacterium nucleatum subspecies isolated from human CRC have not been investigated. While F. nucleatum subspecies are commonly associated with CRC, their ability to induce tumorigenesis and contributions to human CRC pathogenesis are uncertain. We sought to establish a stably colonized murine model and to understand the inflammatory potential and virulence genes of human CRC F. nucleatum, representing the 4 subspecies, animalis, nucleatum, polymorphum, and vincentii. Five human CRC-derived and two non-CRC derived F. nucleatum strains were tested for colonization, tumorigenesis, and cytokine induction in specific-pathogen-free (SPF) and/or germfree (GF) wild-type and ApcMin/+ mice, as well as in vitro assays and whole-genome sequencing (WGS). SPF wild-type and ApcMin/+ mice did not achieve stable colonization with F. nucleatum, whereas certain subspecies stably colonized some GF mice but without inducing colon tumorigenesis. F. nucleatum subspecies did not form in vivo biofilms or associate with the mucosa in mice. In vivo inflammation was inconsistent across subspecies, whereas F. nucleatum induced greater cytokine responses in a human colorectal cell line, HCT116. While F. nucleatum subspecies displayed genomic variability, no distinct virulence genes associated with human CRC strains were identified that could reliably distinguish these strains from non-CRC clinical isolates. We hypothesize that the lack of F. nucleatum-induced tumorigenesis in our model reflects differences in human and murine biology and/or a synergistic role for F. nucleatum in concert with other bacteria to promote carcinogenesis. IMPORTANCE Colon cancer is a leading cause of cancer morbidity and mortality, and it is hypothesized that dysbiosis in the gut microbiota contributes to colon tumorigenesis. Fusobacterium nucleatum, a member of the oropharyngeal microbiome, is enriched in a subset of human colon tumors. However, it is unclear whether this genetically varied species directly promotes tumor formation, modulates mucosal immune responses, or merely colonizes the tumor microenvironment. Mechanistic studies to address these questions have been stymied by the lack of an animal model that does not rely on daily orogastric gavage. Using multiple murine models, in vitro assays with a human colon cancer cell line, and whole-genome sequencing analysis, we investigated the proinflammatory and tumorigenic potential of several F. nucleatum clinical isolates. The significance of this research is development of a stable colonization model of F. nucleatum that does not require daily oral gavages in which we demonstrate that a diverse library of clinical isolates do not promote tumorigenesis.

A Uniform Computational Approach Improved on Existing Pipelines to Reveal Microbiome Biomarkers of Nonresponse to Immune Checkpoint Inhibitors

PURPOSE

While immune checkpoint inhibitors (ICI) have revolutionized the treatment of cancer by producing durable antitumor responses, only 10%-30% of treated patients respond and the ability to predict clinical benefit remains elusive. Several studies, small in size and using variable analytic methods, suggest the gut microbiome may be a novel, modifiable biomarker for tumor response rates, but the specific bacteria or bacterial communities putatively impacting ICI responses have been inconsistent across the studied populations.

EXPERIMENTAL DESIGN

We have reanalyzed the available raw 16S rRNA amplicon and metagenomic sequencing data across five recently published ICI studies (n = 303 unique patients) using a uniform computational approach.

RESULTS

Herein, we identify novel bacterial signals associated with clinical responders (R) or nonresponders (NR) and develop an integrated microbiome prediction index. Unexpectedly, the NR-associated integrated index shows the strongest and most consistent signal using a random effects model and in a sensitivity and specificity analysis (P < 0.01). We subsequently tested the integrated index using validation cohorts across three distinct and diverse cancers (n = 105).

CONCLUSIONS

Our analysis highlights the development of biomarkers for nonresponse, rather than response, in predicting ICI outcomes and suggests a new approach to identify patients who would benefit from microbiome-based interventions to improve response rates.

Abstract PS19-02: Gut pathogen, Bacteroides fragilis promotes breast cancer liver and lung metastasis

Background: The last decade established significant contributions of microbiome to many organ specific cancers. Existence of distinct breast microbiota has been recently established but their biological impact in breast cancer progression remains elusive. A few recent studies suggested the existence of distinct breast microbiota and a shift in microbial community composition in diseased breast compared to normal breast however, their functional impact and underlying mechanisms are unknown. Present study was designed to examine the contribution of pro-carcinogenic bacteria in breast cancer initiation, progression and metastasis. Utilizing extensive data mining and metagenomic analyses, we discovered the presence of toxin producing enterotoxigenic Bacteroides fragilis (ETBF) in malignant breast. ETBF is a pro-carcinogenic bacteria known for its potential to initiate and/or promote colon cancer and its pathogenicity has been attributed to its unique toxin B. fragilis toxin (BFT)’.

Results: Using mammary intraductal model we discovered that ETBF can successfully colonize the breast confirmed by qPCR and Fluorescent in situ hybridization where it induces local inflammation, fibrosis and hyperproliferation of breast epithelial cells. Mice bearing gut ETBF infection exhibit significant circulating BFT confirmed by qPCR and ELISA and distinct morphological alterations in mammary gland as observed from whole breast mounting and histological evaluation. Gut colonization with ETBF rapidly induces hyperplasia in mammary glands with systemic and local breast inflammation validated by flow cytometry, immunohistochemistry and cytokine profiling. While no changes are observed in cell growth and clonogenicity upon BFT treatment, significant increase in migration and invasion potential and decreased adhesion of MCF10A and MCF7 cells are observed. BFT leads to prominent cytoskeletal reorganization, and increase in migration, invasion and stemness potential of breast cancer cells. Our results indicate that breast cancer cells exposed to BFT ensue to exhibit increase tumor growth, form multifocal tumors and show a striking increase in tumor-initiating cells upon in vivo limiting dilution in immunocompromised mice exhibiting retention of ‘BFT memory’ from the initial exposure. Mechanistically, RNA-sequencing shows enrichment of βcatenin and Notch pathway in secondary tumors derived from BFT-exposed breast cancer cells. Inhibitors of βcatenin and Notch axis abrogates BFT-induced migration and invasion potential indicating the functional importance of this axis. Intriguingly, gut colonization with ETBF at a physiologically relevant level strongly induces growth and metastatic progression of 4T1 tumor cells implanted in mammary ducts monitored by whole animal bioluminescent imaging. In vivo and ex vivo analyses of tumors and distant organs reveal a significant induction of lung and liver metastasis of breast cancer by ETBF while gut colonization with non-toxigenic Bacteroides fragilis (NTBF) does not exhibit any tumor-augmenting impact. We mechanistically evaluate the oncogenic impact of alpha bug ETBF on breast cancer progression and its role in promoting liver and lung metastasis using multiple mice models and multiple techniques including multi-color flow cytometry, immunohistochemistry, quantitative PCR, multiplexed ELISA, ex vivo functional assays and western blotting.

Conclusion: Collectively, these findings present the first evidence to show that gut colonization with Bacteroides fragilis rapidly induces inflammation, fibrosis and hyperplasia in the breast. In syngeneic breast cancer model, gut colonization with ETBF aggravates breast cancer progression and induces enhanced lung and liver metastasis via systemic immune modulation, cytokine synthesis and activation of pro-oncogenic pathways.

Citation Format: Sheetal Parida, Sumit Siddharth, Guannan Wang, Himavanth Gatla, Shaoguang Wu, Brian Ladle, Kathleen Gabrielson, Cynthia L Sears, Dipali Sharma. Gut pathogen, Bacteroides fragilis promotes breast cancer liver and lung metastasis [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS19-02.

Abstract PO008: The mouse colon modulates human microbes in transplantable murine tumor models after human fecal microbiota transfer (FMT)

While immune checkpoint inhibitors (ICIs) have revolutionized the treatment of many cancers by producing durable anti-tumor responses, only 10-30% of treated patients respond to the available immunotherapy drugs and the ability to predict response to treatment remains elusive. Preliminary studies suggest that the gut microbiome may be an independent, novel modulator of systemic anti-tumor responses to ICIs, initially through bacterial interaction with the immune system in gut-associated lymphoid tissue. Multiple mouse tumor models have been developed to further elucidate the mechanism(s); specifically, FMT of human stool from ICI responder versus non-responder patients into germ-free mice suggests that responder human microbiota can facilitate tumor and immune responses in murine transplantable tumor models. However, data about how the mouse colon modulates the human microbiota are limited or lacking. We hypothesized that only a subset of specific human microbiota establish in the mouse colon and that analysis of these microbes may provide insight into the specific microbial communities that mediate ICI responses. To test this hypothesis, we first selected two human patients who were a distinct ICI responder (R) and nonresponder (NR) and tested their fecal samples in GF mice using syngeneic transplantable tumor models employing B16F0 and MC38 tumor cell lines. While the human ICI responses were replicated in these models, it was notable that individual mouse tumor responses were highly variable. To identify sources of experimental variability, we performed 16S rRNA amplicon sequencing on the human stool samples, experimental inocula, and mouse fecal samples at multiple time points. Our data show that the inocula (alpha diversity, composition) for each experiment were similar to the pre-treatment human stool. However, only 40-50% of human microbes were able to engraft in the mouse colon, and the relative abundance in the inocula was not the primary indicator for species engraftment. When we compared microbes across multiple experiments using beta diversity metrics, each experiment largely contained a distinct set of bacteria. Further analysis is underway to detect longitudinal microbiome shifts, cage effects, and/or bacteria enriched in small (responding) versus large (non-responding) tumors. Our results show that the mouse colon significantly modulates human microbiota in mouse FMT models and mouse microbiota analyses in germ-free models may yield mechanistic insights into bacteria facilitating ICI responses.

Citation Format: Fyza Y. Shaikh, Joell J. Gills, James R. White, Fuad Mohammad, Courtney M. Stevens, Jarushka Naidoo, Drew M. Pardoll, Cynthia L. Sears. The mouse colon modulates human microbes in transplantable murine tumor models after human fecal microbiota transfer (FMT) [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO008.