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.

A Procarcinogenic Colon Microbe Promotes Breast Tumorigenesis and Metastatic Progression and Concomitantly Activates Notch and β-Catenin Axes

The existence of distinct breast microbiota has been recently established, but their biological impact in breast cancer remains elusive. Focusing on the shift in microbial community composition in diseased breast compared with normal breast, we identified the presence of Bacteroides fragilis in cancerous breast. Mammary gland as well as gut colonization with enterotoxigenic Bacteroides fragilis (ETBF), which secretes B. fragilis toxin (BFT), rapidly induces epithelial hyperplasia in the mammary gland. Breast cancer cells exposed to BFT exhibit "BFT memory" from the initial exposure. Intriguingly, gut or breast duct colonization with ETBF strongly induces growth and metastatic progression of tumor cells implanted in mammary ducts, in contrast to nontoxigenic Bacteroides fragilis. This work sheds light on the oncogenic impact of a procarcinogenic colon bacterium ETBF on breast cancer progression, implicates the β-catenin and Notch1 axis as its functional mediators, and proposes the concept of "BFT memory" that can have far-reaching biological implications after initial exposure to ETBF. SIGNIFICANCE: B. fragilis is an inhabitant of breast tissue, and gut or mammary duct colonization with ETBF triggers epithelial hyperplasia and augments breast cancer growth and metastasis. Short-term exposure to BFT elicits a "BFT memory" with long-term implications, functionally mediated by the β-catenin and Notch1 pathways.This article is highlighted in the In This Issue feature, p. 995.

Glucosylceramide production maintains colon integrity in response to Bacteroides fragilis toxin-induced colon epithelial cell signaling

Enterotoxigenic Bacteroides fragilis (ETBF) is a commensal bacterium of great importance to human health due to its ability to induce colitis and cause colon tumor formation in mice through the production of B. fragilis toxin (BFT). The formation of tumors is dependent on a pro-inflammatory signaling cascade, which begins with the disruption of epithelial barrier integrity through cleavage of E-cadherin. Here, we show that BFT increases levels of glucosylceramide, a vital intestinal sphingolipid, both in mice and in colon organoids (colonoids) generated from the distal colons of mice. When colonoids are treated with BFT in the presence of an inhibitor of glucosylceramide synthase (GCS), the enzyme responsible for generating glucosylceramide, colonoids become highly permeable, lose structural integrity, and eventually burst, releasing their contents into the extracellular matrix. By increasing glucosylceramide levels in colonoids via an inhibitor of glucocerebrosidase (GBA, the enzyme that degrades glucosylceramide), colonoid permeability was reduced, and bursting was significantly decreased. In the presence of BFT, pharmacological inhibition of GCS caused levels of tight junction protein 1 (TJP1) to decrease. However, when GBA was inhibited, TJP1 levels remained stable, suggesting that BFT-induced production of glucosylceramide helps to stabilize tight junctions. Taken together, our data demonstrate a glucosylceramide-dependent mechanism by which the colon epithelium responds to BFT.

Charting the Path Forward: Development, Goals and Initiatives of the 2019 Infectious Diseases Society of America Strategic Plan

In October 2018, the Infectious Diseases Society of America (IDSA) Board of Directors (BOD) decided to develop a 2019 IDSA Strategic Plan. The IDSA BOD has invested in strategic planning at regular intervals as part of an ongoing process to review and to renew the vision and direction of IDSA. Herein, the 2018-2019 strategic planning process and outcomes are described. The 2019 IDSA Strategic Plan presents 4 key initiatives: (1) optimize the development, dissemination, and adoption of timely and relevant ID guidance and guidelines that improve the outcomes of clinical care; (2) quantify, communicate, and advocate for the value of ID physicians to increase professional fulfillment and compensation; (3) facilitate the growth and development of the ID workforce to meet emerging scientific, clinical, and leadership needs; and (4) develop and position a new tool to serve as the leading US benchmark to measure and drive national progress on antimicrobial resistance. The BOD looks forward to developing, implementing, assessing, and advancing the 2019 IDSA Strategic Plan working with member volunteers, Society partners, and IDSA staff.

Messengers from the microbiota

Microbiota produce inosine, a metabolite that modulates effector T cells and tumor immunity

Yogurt consumption and colorectal polyps

Diet modifies the risk of colorectal cancer (CRC), and inconclusive evidence suggests that yogurt may protect against CRC. We analysed the data collected from two separate colonoscopy-based case-control studies. The Tennessee Colorectal Polyp Study (TCPS) and Johns Hopkins Biofilm Study included 5446 and 1061 participants, respectively, diagnosed with hyperplastic polyp (HP), sessile serrated polyp, adenomatous polyp (AP) or without any polyps. Multinomial logistic regression models were used to derive OR and 95 % CI to evaluate comparisons between cases and polyp-free controls and case-case comparisons between different polyp types. We evaluated the association between frequency of yogurt intake and probiotic use with the diagnosis of colorectal polyps. In the TCPS, daily yogurt intake v. no/rare intake was associated with decreased odds of HP (OR 0·54; 95 % CI 0·31, 0·95) and weekly yogurt intake was associated with decreased odds of AP among women (OR 0·73; 95 % CI 0·55, 0·98). In the Biofilm Study, both weekly yogurt intake and probiotic use were associated with a non-significant reduction in odds of overall AP (OR 0·75; 95 % CI 0·54, 1·04) and (OR 0·72; 95 % CI 0·49, 1·06) in comparison with no use, respectively. In summary, yogurt intake may be associated with decreased odds of HP and AP and probiotic use may be associated with decreased odds of AP. Further prospective studies are needed to verify these associations.

Oral antibiotic use and chronic disease: long-term health impact beyond antimicrobial resistance and Clostridioides difficile

We recently reported an increased colon cancer risk associated with oral antibiotic use in a large United Kingdom population. This association between antibiotic exposure and cancer risk adds to a growing body of evidence that antibiotic use has unintended off-target long-term health consequences. This addendum highlights major studies linking antibiotic use and chronic disease in pediatric and adult populations. Microbiota dysbiosis is the key proposed mechanism underlying antibiotic:disease associations, resulting in alterations in gene expression, epigenetic modification, colonization by pathogenic bacteria, instigation of biofilms, and immune regulation and inflammation. These adverse outcomes of antibiotic exposure underscore the need for diagnostic and antibiotic stewardship, as well as the urgency for further development of non-antibiotic therapies for bacterial infections.

Intestinal Bacteria Maintain Adult Enteric Nervous System and Nitrergic Neurons via Toll-like Receptor 2-induced Neurogenesis in Mice

BACKGROUND & AIMS

The enteric nervous system (ENS) exists in close proximity to luminal bacteria. Intestinal microbes regulate ENS development, but little is known about their effects on adult enteric neurons. We investigated whether intestinal bacteria or their products affect the adult ENS via toll-like receptors (TLRs) in mice.

METHODS

We performed studies with conventional C57/BL6, germ-free C57/BL6, Nestin-creER^T2:tdTomato, Nestin-GFP, and ChAT-cre:tdTomato. Mice were given drinking water with ampicillin or without (controls). Germ-free mice were given drinking water with TLR2 agonist or without (controls). Some mice were given a blocking antibody against TLR2 or a TLR4 inhibitor. We performed whole gut transit, bead latency, and geometric center studies. Feces were collected and analyzed by 16S ribosomal RNA gene sequencing. Longitudinal muscle myenteric plexus (LMMP) tissues were collected, analyzed by immunohistochemistry, and levels of nitric oxide were measured. Cells were isolated from colonic LMMP of Nestin-creER^T2:tdTomato mice and incubated with agonists of TLR2 (receptor for gram-positive bacteria), TLR4 (receptor for gram-negative bacteria), or distilled water (control) and analyzed by flow cytometry.

RESULTS

Stool from mice given ampicillin had altered composition of gut microbiota with reduced abundance of gram-positive bacteria and increased abundance of gram-negative bacteria, compared with mice given only water. Mice given ampicillin had reduced colon motility compared with mice given only water, and their colonic LMMP had reduced numbers of nitrergic neurons, reduced neuronal nitric oxide synthase production, and reduced colonic neurogenesis. Numbers of colonic myenteric neurons increased after mice were switched from ampicillin to plain water, with increased markers of neurogenesis. Nestin-positive enteric neural precursor cells expressed TLR2 and TLR4. In cells isolated from the colonic LMMP, incubation with the TLR2 agonist increased the percentage of neurons originating from enteric neural precursor cells to approximately 10%, compared with approximately 0.01% in cells incubated with the TLR4 agonist or distilled water. Mice given an antibody against TLR2 had prolonged whole gut transit times; their colonic LMMP had reduced total neurons and a smaller proportion of nitrergic neurons per ganglion, and reduced markers of neurogenesis compared with mice given saline. Colonic LMMP of mice given the TLR4 inhibitor did not have reduced markers of neurogenesis. Colonic LMMP of germ-free mice given TLR2 agonist had increased neuronal numbers compared with control germ-free mice.

CONCLUSIONS

In the adult mouse colon, TLR2 promotes colonic neurogenesis, regulated by intestinal bacteria. Our findings indicate that colonic microbiota help maintain the adult ENS via a specific signaling pathway. Pharmacologic and probiotic approaches directed towards specific TLR2 signaling processes might be developed for treatment of colonic motility disorders related to use of antibiotics or other factors.

Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet

Translational microbiome science in humans has not yet fully realized its clinical potentials. The analyses by Poore et al. in Nature offer a strong foundation on which to begin to build microbial diagnostics to detect cancer.

Changes in Gut Microbiome after Bariatric Surgery Versus Medical Weight Loss in a Pilot Randomized Trial

BACKGROUND

Gut microbiota likely impact obesity and metabolic diseases. We evaluated the changes in gut microbiota after surgical versus medical weight loss in adults with diabetes and obesity.

METHODS

We performed 16S rRNA amplicon sequencing to identify the gut microbial composition at baseline and at 10% weight loss in adults with diabetes who were randomized to medical weight loss (MWL, n = 4), adjustable gastric banding (AGB, n = 4), or Roux-en-Y gastric bypass (RYGB, n = 4).

RESULTS

All participants were female, 75% reported black race with mean age of 51 years. At similar weight loss amount and glycemic improvement, the RYGB group had the most number of bacterial species (10 increased, 1 decreased) that significantly changed (p < 0.05) in relative abundance. Alpha-diversity at follow-up was significantly lower in AGB group compared to MWL and RYGB (observed species for AGB vs. MWL, p = 0.0093; AGB vs. RYGB, p = 0.0093). The relative abundance of Faecalibacterium prausnitzii increased in 3 participants after RYGB, 1 after AGB, and 1 after MWL.

CONCLUSIONS

At similar weight loss and glycemic improvement, the greatest alteration in gut microbiota occurred after RYGB with an increase in the potentially beneficial bacterium, F. prausnitzii. Gut microbial diversity tended to decrease after AGB and increase after RYGB and MWL. Future studies are needed to determine the impact and durability of gut microbial changes over time and their role in long-term metabolic improvement after bariatric surgery in adults with type 2 diabetes.

CLINICAL TRIAL REGISTRATION

NCTDK089557- ClinicalTrials.gov.

Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes

Most patients diagnosed with resected pancreatic adenocarcinoma (PDAC) survive less than 5 years, but a minor subset survives longer. Here, we dissect the role of the tumor microbiota and the immune system in influencing long-term survival. Using 16S rRNA gene sequencing, we analyzed the tumor microbiome composition in PDAC patients with short-term survival (STS) and long-term survival (LTS). We found higher alpha-diversity in the tumor microbiome of LTS patients and identified an intra-tumoral microbiome signature (Pseudoxanthomonas-Streptomyces-Saccharopolyspora-Bacillus clausii) highly predictive of long-term survivorship in both discovery and validation cohorts. Through human-into-mice fecal microbiota transplantation (FMT) experiments from STS, LTS, or control donors, we were able to differentially modulate the tumor microbiome and affect tumor growth as well as tumor immune infiltration. Our study demonstrates that PDAC microbiome composition, which cross-talks to the gut microbiome, influences the host immune response and natural history of the disease.

A Central Role for Lipocalin-2 in the Adaptation to Short-Bowel Syndrome Through Down-Regulation of IL22 in Mice

BACKGROUND & AIMS

In short-bowel syndrome (SBS), inadequate intestinal adaptation is responsible for the majority of complications, including sepsis, liver failure, and death. In this study, we sought to further delineate the adaptive response to identify potential therapeutic targets.

METHODS

We performed a 75% small-bowel resection (SBR) or sham operation on C57Bl/6J wild-type (WT), lipocalin-2 (LCN2)-/-, and interleukin 22 (IL22)-/- mice. Exogenous IL22 was administered to SBR WT mice. Cecal fecal matter from SBR WT and SBR LCN2-/- mice were transplanted into germ-free mice. Intestinal permeability, inflammation, proliferation, and the microbiome were evaluated 1 week after surgery. CD4+IL22+ laminal propria lymphocytes were sorted by flow cytometry. Naïve T cells were polarized to T-helper cells with or without LCN2.

RESULTS

A 75% SBR in a mouse re-creates the increased intestinal permeability, enterocyte proliferation, and intestinal dysbiosis seen in SBS. LCN2 expression increases after 75% SBR, and this increase can be abrogated with broad-spectrum antibiotic treatment. LCN2-/- mice have less intestinal inflammation, increased IL22 expression, and greater adaptation as evidenced by less intestinal permeability, increased carbohydrate enzyme expression, less weight loss, and less dysbiosis after 75% SBR than WT mice. The proinflammatory and anti-adaptive effects of LCN2 can be transferred to germ-free mice via a fecal transplant. Administration of exogenous IL22 improves adaptation and restores the normal microbiome after 75% SBR in WT mice.

CONCLUSIONS

LCN2 promotes inflammation and slows intestinal adaptation through changes in the microbiome and IL22 inhibition in a mouse SBS model. Strategies to reduce LCN2 may offer novel therapeutic approaches to enhance adaptation in SBS.

Abstract IA06: Colon cancer: Microbes and communities in microbiome translation

Intensive efforts are under way to understand how the colon microbiome contributes to the pathogenesis of colorectal cancer (CRC) and to determine if and how the microbiome can be utilized in the prevention and/or therapy of CRC. Both single microbes and microbial communities are proposed as contributors to human CRC. Among single microbes, attention to date has focused on enterotoxigenic Bacteroides fragilis (ETBF), (pks+) Escherichia coli, and Fusobacterium spp., although other candidates are emerging. Among communities, one aspect has been the potential contribution of mucus-invasive, dense mucosal microbial communities termed biofilms to CRC disease pathogenesis. This talk will review select concepts within ETBF’s and biofilm contribution to colon carcinogenesis. While ETBF exposure is common, the risk of colon carcinogenesis in an individual is unknown but potentially influenced by colonization state, B. fragilis toxin isotype secreted by ETBF, colon site, and the underlying genomic state of the colonic epithelial cells. With respect to colon biofilms, about 50% of human sporadic colon cancer, particularly in the right colon, display polymicrobial biofilms with marked tumor infiltration with bacteria whereas ~15% of normal colonoscopy biopsies also reveal polymicrobial biofilms. These polymicrobial biofilms are typically composed of Bacteroidetes and Lachnospiraceae with a subset of tumors, but not biopsies, also displaying Fusobacterium. Further, samples from biofilm-positive human colon cancers induce assembly of biofilms in the distal germ-free mouse colon within a week following inoculation and are procarcinogenic (JCI 129:1699, 2019). One of the common hereditary human colon cancers (familial adenomatous polyposis; APC+/−) also displays biofilms but dominated by two bacteria, (pks+) E. coli and ETBF. A mouse model of (pks+) E. coli and ETBF cocolonization exhibited accelerated tumor formation and mortality when cocolonized with the cancer-inducing bacteria, potentially by fostering increased microbial adherence, IL-17, changes in gene expression, and enhanced colonic epithelial cell DNA damage (Science 2018;359:592-97). Current directions of translational research will be presented.

Citation Format: Cynthia L. Sears. Colon cancer: Microbes and communities in microbiome translation [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr IA06.

Abstract A14: Meta-analysis improves identification of microbiome associations with antitumor response in melanoma, lung, and kidney cancer patients treated with checkpoint inhibitors

While immune checkpoint inhibitors (ICIs) have revolutionized the treatment of many cancers by producing durable antitumor responses, only 10-30% of treated patients respond and the ability to predict response to treatment remains elusive. Preliminary studies suggest the gut microbiome may be a novel biomarker for tumor response rates, including high alpha-diversity and a few specific bacterial species that associate with improved tumor responses to ICIs in melanoma, renal cell cancer (RCC), and non-small cell lung cancer (NSCLC). Despite these reports, the specific bacteria or bacterial communities helpful or harmful to ICI responses have been inconsistent across study populations and various malignancies, and further correlation with immune and mutational biomarkers is limited or lacking. We hypothesized that, by use of a larger sample size and a consistent computational approach, we would derive a clearer microbial profile that correlated with immunotherapeutic outcomes in more than one cancer type and in response to ICIs that target different immune checkpoints. To test this hypothesis, we have reanalyzed the available raw 16S rRNA amplicon and metagenomic sequencing data across five recently published studies (n=303) using Resphera Insight v2.2 and MetaPhlAn2, respectively, for taxonomic assignment. We used pathway prediction algorithms (PICRUSt) to examine functional characteristics enriched among responders and nonresponders, as well as effect of antibiotic usage and virulence factors using multiple reference databases. Our results confirm signals reported in each study, though some bacteria reported initially were not statistically significant after correction for false discovery rate. Likely, in part, because our analysis allows for comparison of individual species across cohorts, we were able to identify new bacterial signatures associated with clinical response or nonresponse. Further, these new results enabled us to re-evaluate and develop response and nonresponse indicator indexes. When our composite index was compared to an index assembled from the literature, some improvement occurred in a sensitivity and specificity analysis. Moreover, while lower alpha-diversity has been associated with disease states and higher alpha-diversity with healthy states, we found that alpha-diversity was not consistently predictive of response or nonresponse to ICIs. In summary, this bioinformatics platform improves on existing pipelines by standardizing critical preprocessing and downstream analysis tools, enabling comprehensive evaluations of taxonomic and functional signals across sequencing datasets. These analyses allow for identification of novel bacterial signatures associated with clinical responses that could potentially be used as biomarkers in patients undergoing treatment with checkpoint inhibitors. Results from these analyses will be validated in subsequent analyses of ICI therapy and clinical outcomes in our ongoing prospective cohorts.

Citation Format: Fyza T. Shaikh, James R. White, Joell G. Gills, Jarushka Naidoo, Evan Lipson, Drew M. Pardoll, Cynthia L. Sears. Meta-analysis improves identification of microbiome associations with antitumor response in melanoma, lung, and kidney cancer patients treated with checkpoint inhibitors [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr A14.

Abstract B13: Development of a low-cost method for collecting fecal samples in clinical trials

Although immune checkpoint inhibitors (ICIs) have shown promise in treating various cancers, fewer than half of patients with most tumor types experience a durable response. Thus, there is a need for biomarkers to better predict outcomes. Recent studies suggest that the presence of a handful of microbial species and greater alpha-diversity in the gut may serve as a biomarker for and might facilitate ICI responses. However, the specific bacteria, or bacterial communities, that associate with improved ICI responses vary across study populations, and the factors that contribute to these discrepant findings remain elusive. Thus, a standardized method by which biospecimens may be collected, transported, and stored for gut microbiome studies in the context of ICI therapy is needed. In this study, we evaluated a method for shipping fecal samples using a low-cost (&lt;$3.00) ThinPrep Pap Test® methanol-based preservative kit. Under an IRB-approved protocol, we recruited patients with melanoma, Merkel cell carcinoma, endometrial cancer, and non-small cell lung cancer who had experienced &gt;1 year of durable tumor response after ICI therapy. Patients were provided with stool collection kits and either asked to collect fecal samples at home within 48 hours of their clinic visit and store at 4°C (fresh) or asked to place stool in preservative and ship at ambient temperature to our laboratory (fixed). For fresh samples, a portion of each sample was frozen and another portion placed into preservative as a paired control. DNA was extracted using Zymo Quick-DNA™ Fecal/Soil Microbe kit. For fixed samples, methanol was removed by evaporation prior to DNA extraction. Microbial composition was analyzed with 16S rRNA amplicon sequencing with V1-V2 primers with 150bp paired-end sequencing using an Illumina platform. Among n=10 samples collected in clinic, fixed portions demonstrated decreased alpha-diversity and a uniform shift in beta-diversity compared to the paired frozen portions. In all fixed samples, Faecalibacterium and Roseburia relative abundance decreased with a corresponding increase in Bacteroides. Among a second set of n=11 samples that were placed in preservative by patients and then shipped to our laboratory, we analyzed the effects of shipping by comparing fresh stool samples and shipped fixed samples collected by the same patient within one month. The data revealed similar trends, suggesting that fixation, rather than shipping, drives the overall effect. We are currently verifying the relative abundance of specific bacterial species in both sets of samples using quantitative RT-PCR. Our data show that methanol-based preservation must be optimized prior to clinical utilization for accurate assessment. If optimized, we have identified a low-cost method to collect fecal samples that could be adopted in community practices and low-income areas. Ongoing work from our group includes optimization of processing procedures, ratio of fecal matter to preservative, and storage conditions.

Citation Format: Kimberly E. Peloza, Joell J. Gills, Fyza Y. Shaikh, James R. White, Sara Glass, Carisse Lansiquot, Courtney Stevens, William Assan, William H. Sharfman, Dung T. Le, Jarushka Naidoo, Evan J. Lipson, Drew M. Pardoll, Cynthia L. Sears. Development of a low-cost method for collecting fecal samples in clinical trials [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B13.

Abstract PR02: Bacteroides fragilis toxin induces epithelial-to-mesenchymal transition and stem-like phenotype in breast epithelial cells and concomitantly activates Notch1 and βcatenin axes

The last decade established significant contributions of the microbiome to many organ-specific cancers. 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. The present study examines the contribution of procarcinogenic bacteria in breast cancer initiation, growth, and progression. Extensive data mining and metagenomic analyses of existing datasets revealed the presence of toxin-producing Bacteroides fragilis in malignant breast. B. fragilis is a procarcinogenic bacteria known for its potential to initiate and promote colon cancer; its pathogenicity has been attributed to its unique toxin “BFT.” B. fragilis-infected mice exhibited a significant increase in circulating BFT and distinct morphologic alterations in mammary gland. In vitro, upon treatment with BFT, no changes were observed in cell growth and clonogenicity. However, significant increase in migration and invasion potential and decreased adhesion of MCF10A and MCF7 cells were observed. BFT-treated cells displayed acquisition of fibroblast-like appearance and increased formation of pseudopodia/microtentacles emanating from the cell membrane along with molecular markers of epithelial-to-mesenchymal transition. Decreased expression of epithelial marker, E-cadherin, along with elevated levels of mesenchymal markers, N-cadherin and vimentin, were observed. BFT also increased the expression of EMT-related transcription factors, Snail, Slug and Twist. BFT-treated cells attained stem cell-like phenotype, exhibiting an increased ability to form secondary and tertiary mammospheres and elevated expression of pluripotency-factors (Oct4, Nanog, and Sox2). Mechanistic studies showed that BFT induced expression and nuclear translocation of NICD (cleaved NOTCH) and β-catenin resulting in activation of downstream targets. Inhibition of Notch1 and β-catenin using γ-secretase and β-catenin inhibitors successfully inhibited functional effects of BFT. Mammary gland implantation and in vivo limiting dilution assays were utilized to corroborate the in vitro findings. BFT-pretreated MCF7 cells exhibit increased tumor growth and form multifocal tumors in mice. MCF10A-KRas cells, pretreated with BFT, also showed increased tumor progression and multifocal tumors in mice. In vivo limiting dilution assay using breast tumors from BFT-pretreated MCF7 cells exhibited a striking increase in tumor-initiating cells. Follow-up analyses of these tumors demonstrated increased migratory, invasive, and mammospheres-forming behavior, confirming that brief BFT exposure elicits long-term molecular changes. Collectively, these findings present the first in vitro and in vivo evidence to show that Bacteroides fragilis toxin induces EMT, invasion/migration and stem cell-like phenotype and leads to concomitant activation of Notch and β-catenin axes.

This abstract is also being presented as Poster A66.

Citation Format: Sheetal Parida, Shaoguang Wu, Nethaji Muniraj, Sumit Siddharth, Arumugam Nagaligam, Cynthia L. Sears, Dipali Sharma. Bacteroides fragilis toxin induces epithelial-to-mesenchymal transition and stem-like phenotype in breast epithelial cells and concomitantly activates Notch1 and βcatenin axes [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr PR02.

The Impact of Human Immunodeficiency Virus Infection on Gut Microbiota α-Diversity: An Individual-level Meta-analysis

BACKGROUND

Whether human immunodeficiency virus (HIV) infection impacts gut microbial α-diversity is controversial. We reanalyzed raw 16S ribosomal RNA (rRNA) gene sequences and metadata from published studies to examine α-diversity measures between HIV-uninfected (HIV-) and HIV-infected (HIV+) individuals.

METHODS

We conducted a systematic review and individual level meta-analysis by searching Embase, Medline, and Scopus for original research studies (inception to 31 December 2017). Included studies reported 16S rRNA gene sequences of fecal samples from HIV+ patients. Raw sequence reads and metadata were obtained from public databases or from study authors. Raw reads were processed through standardized pipelines with use of a high-resolution taxonomic classifier. The χ2 test, paired t tests, and generalized linear mixed models were used to relate α-diversity measures and clinical metadata.

RESULTS

Twenty-two studies were identified with 17 datasets available for analysis, yielding 1032 samples (311 HIV-, 721 HIV+). HIV status was associated with a decrease in measures of α-diversity (P < .001). However, in stratified analysis, HIV status was associated with decreased α-diversity only in women and in men who have sex with women (MSW) but not in men who have sex with men (MSM). In analyses limited to women and MSW, controlling for HIV status, women displayed increased α-diversity compared with MSW.

CONCLUSIONS

Our study suggests that HIV status, sexual risk category, and gender impact gut microbial community α-diversity. Future studies should consider MSM status in gut microbiome analyses.

Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer

Disrupted interactions between host and intestinal bacteria are implicated in colorectal cancer (CRC) development. However, activities derived from these bacteria and their interplay with the host are unclear. Here, we examine this interplay by performing mouse and microbiota RNA sequencing on colon tissues and 16S and small RNA sequencing on stools from germfree (GF) and gnotobiotic ApcMin Δ 850/+ ;Il10-/- mice associated with microbes from biofilm-positive human CRC tumor (BF+T) and biofilm-negative healthy (BF-bx) tissues. The bacteria in BF+T mice differentially expressed (DE) >2,900 genes, including genes related to bacterial secretion, virulence, and biofilms but affected only 62 host genes. Small RNA sequencing of stools from these cohorts revealed eight significant DE host microRNAs (miRNAs) based on biofilm status and several miRNAs that correlated with bacterial taxon abundances. Additionally, computational predictions suggest that some miRNAs preferentially target bacterial genes while others primarily target mouse genes. 16S rRNA sequencing of mice that were reassociated with mucosa-associated communities from the initial association revealed a set of 13 bacterial genera associated with cancer that were maintained regardless of whether the reassociation inoculums were initially obtained from murine proximal or distal colon tissues. Our findings suggest that complex interactions within bacterial communities affect host-derived miRNA, bacterial composition, and CRC development.IMPORTANCE Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the bacteria and bacterial transcriptome associated with microbes derived from biofilm-positive human cancers that promoted tumorigenesis in a murine model of CRC. The murine response to different microbial communities (derived from CRC patients or healthy people) was evaluated through RNA and microRNA sequencing. We identified a complex interplay between biofilm-associated bacteria and the host during CRC in mice. These findings may lead to the development of new biomarkers and therapeutics for identifying and treating biofilm-associated CRCs.

Oral antibiotic use and risk of colorectal cancer in the United Kingdom, 1989-2012: a matched case-control study

BACKGROUND

Microbiome dysbiosis predisposes to colorectal cancer (CRC), but a population-based study of oral antibiotic exposure and risk patterns is lacking.

OBJECTIVE

To assess the association between oral antibiotic use and CRC risk.

DESIGN

A matched case-control study (incident CRC cases and up to five matched controls) was performed using the Clinical Practice Research Datalink from 1989 to 2012.

RESULTS

28 980 CRC cases and 137 077 controls were identified. Oral antibiotic use was associated with CRC risk, but effects differed by anatomical location. Antibiotic use increased the risk of colon cancer in a dose-dependent fashion (p_trend <0.001). The risk was observed after minimal use, and was greatest in the proximal colon and with antibiotics with anti-anaerobic activity. In contrast, an inverse association was detected between antibiotic use and rectal cancers (p_trend=0.003), particularly with length of antibiotic exposure >60 days (adjusted OR (aOR), 0.85, 95% CI 0.79 to 0.93) as compared with no antibiotic exposure. Penicillins, particularly ampicillin/amoxicillin increased the risk of colon cancer (aOR=1.09 (1.05 to 1.13)), whereas tetracyclines reduced the risk of rectal cancer (aOR=0.90 (0.84 to 0.97)). Significant interactions were detected between antibiotic use and tumour location (colon vs rectum, p_interaction<0.001; proximal colon versus distal colon, p_interaction=0.019). The antibiotic-cancer association was found for antibiotic exposure occurring >10 years before diagnosis (aOR=1.17 (1.06 to 1.31)).

CONCLUSION

Oral antibiotic use is associated with an increased risk of colon cancer but a reduced risk of rectal cancer. This effect heterogeneity may suggest differences in gut microbiota and carcinogenesis mechanisms along the lower intestinal tract.

Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin

Objective: The human intestinal microbiome plays an important role in inflammatory bowel disease (IBD) and colorectal cancer (CRC) development. One of the first discovered bacterial mediators involves Bacteroides fragilis toxin (BFT, also named as fragilysin), a metalloprotease encoded by enterotoxigenic Bacteroides fragilis (ETBF) that causes barrier disruption and inflammation of the colon, leads to tumorigenesis in susceptible mice, and is enriched in the mucosa of IBD and CRC patients. Thus, targeted inhibition of BFT may benefit ETBF carrying patients. Design: By applying two complementary in silico drug design techniques, drug repositioning and molecular docking, we predicted potential BFT inhibitory compounds. Top candidates were tested in vitro on the CRC epithelial cell line HT29/c1 for their potential to inhibit key aspects of BFT activity, being epithelial morphology changes, E-cadherin cleavage (a marker for barrier function) and increased IL-8 secretion. Results: The primary bile acid and existing drug chenodeoxycholic acid (CDCA), currently used for treating gallstones, cerebrotendinous xanthomatosis, and constipation, was found to significantly inhibit all evaluated cell responses to BFT exposure. The inhibition of BFT resulted from a direct interaction between CDCA and BFT, as confirmed by an increase in the melting temperature of the BFT protein in the presence of CDCA. Conclusion: Together, our results show the potential of in silico drug discovery to combat harmful human and microbiome-derived proteins and more specifically suggests a potential for retargeting CDCA to inhibit the pro-oncogenic toxin BFT.

Impact of the microbiome on checkpoint inhibitor treatment in patients with non-small cell lung cancer and melanoma

The microbiome is increasingly recognized for its role in multiple aspects of cancer development and treatment, specifically in response to checkpoint inhibitors. While checkpoint inhibitors have revolutionized cancer treatment by producing durable anti-tumor responses, only a minority of patients respond to the available immunotherapy drugs and accurate, sensitive and specific microbiome predictors of response to treatment remain elusive. Additionally, the specific mechanisms linking the microbiome and host immunological responses remain unclear. In this review, we examine the evidence for the gut microbiome's association with anti-tumor responses to checkpoint inhibitors in the treatment of melanoma, non-small cell lung cancer, and renal cell carcinoma. Furthermore, we discuss the current evidence available from murine models seeking to explain the immunological mechanisms that may drive this process. While this work is promising in defining the impact of gut microbiota in cancer treatment, many unanswered questions indicate the need for additional human and experimental studies.