bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract PR03: Metabolic control of Polycomb Repressive Complex 2 in Lung Disease and Lung Cancer
Authors: Bakhtiari Mojtaba , Byrd Aria L. , Chen Fan , Lukyanchuk Alexsandr , DuCote Tanner J. , Brainson Christine Fillmore
Published: December 2020

Dysregulated epigenetic control of lung lineage fate is believed to be a major driver of lung disease, including plasticity in lung cancer. Our laboratory has observed a marked decrease in Polycomb Repressive Complex 2 (PRC2) activity in bronchiolar epithelium of COPD patients, poorly differentiated adenocarcinomas and the majority of squamous cell carcinomas. Interestingly, the PRC2 methyltransferase EZH2 is still highly expressed in many of these tissues, suggesting a de-coupling of EZH2 and PRC2 activity. A mouse model of lineage switching from adenocarcinoma to squamous lung cancer clearly showed that loss of PRC2 activity was a catalyst to epigenetic reprogramming. This model also showed increased infiltration of neutrophils, which are known to produce large amounts of superoxide. Our current hypothesis is that oxidative stress, in part through neutrophil recruitment to lung tissue, drives the loss of PRC2 activity through metabolic changes. To support this hypothesis, we have shown that a redox-sensitive enzyme in the methionine pathway, cystathionine beta synthase (CBS), is expressed in COPD and lung cancer and modulates PRC2 activity. Enforced CBS expression drives global decrease in the PRC2-mediated histone marked, H3K27me3, and increased expression of genes expressed by basal cells of the lung, including KRT5, SOX2 and PD-L1. Furthermore, we have found that PRC2 activity can be stabilized through restriction of methionine levels or knock-down of CBS, leading to increased sensitivity of cells to chemotherapy and radiation treatments. PRC2-low epigenetic states can also be exploited – either pharmacological or genetic perturbation of EZH2 led to sensitivity to several classes of drugs, including immunotherapies. Our future studies include using Stable Isotope Resolved Metabolomics (SIRM) to understand how oxidative stress alters the methionine cycle and ultimately changes the stability and function of the PRC2 complex, and to use this information to design better therapeutic strategies. Work supported by AACR Innovation and Discovery Grant, American Cancer Society 133123-RSG-19-081-01-TBG and IRG-85-001-25, NCI R01 CA237643, NIGMS P20 GM121327-03, NIEHS T32 5T32ES007266-30, NCI T32 CA165990 and NHLBI F31 HL151111-01.

Citation Format: Mojtaba Bakhtiari, Aria L. Byrd, Fan Chen, Alexsandr Lukyanchuk, Tanner J. DuCote, Christine Fillmore Brainson. Metabolic control of Polycomb Repressive Complex 2 in Lung Disease and Lung Cancer [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PR03.
Abstract PR05: Loss of PRC2 or KMT2D-COMPASS generates two quasi-mesenchymal cell states with distinct metastatic abilities
Authors: Zhang Yun , Donaher Joana Liu , Das Sunny , Li Xin , Reinhardt Ferenc , Krall Jordan A. , Lambert Arthur W. , Thiru Prathapan , Keys Heather R. , Khan Mehreen , Hofree Matan , Wilson Molly M. , Yedier-Bayram Ozlem , Lack Nathan A. , Onder Tamer T. , Bagci-Onder Tugba , Tyler Michael , Tirosh Itay , Regev Aviv , Lees Jacqueline , Weinberg Robert A.
Published: December 2020

The epithelial-mesenchymal transition (EMT) is a key cell-biological program enabling carcinoma cell phenotypic plasticity. Accumulating evidence suggests EMT programs do not operate as a stereotypical program that functions as a binary switch, shifting cells from an epithelial (E) to a mesenchymal (M) state. Instead, EMT programs generate cells that enter into a series of intermediate states arrayed along the E-M phenotypic spectrum. At present, we still lack a coherent understanding of how carcinoma cells control their entrance into and residence in these various intermediate states, and which EMT intermediate state(s) favour the metastatic process. Here we characterize a new level of regulation of EMT, consisting of two chromatin-modifying complexes, PRC2 and KMT2D-COMPASS, that function as critical regulators to maintain stable residence of both normal and neoplastic cells in an epithelial state via regulating the downstream response of EMT-inducing signals. Dysfunction of either of these two complexes causes cells that were previously stably ensconced in an epithelial state to lapse into two distinct quasi-mesenchymal cell states with strongly differing metastatic abilities. These observations uncover a novel mechanism that regulates E-M plasticity, specifies which intermediate EMT state a cell will reside in, and thereby determines the metastatic ability of carcinoma cells.

Citation Format: Yun Zhang, Joana Liu Donaher, Sunny Das, Xin Li, Ferenc Reinhardt, Jordan A. Krall, Arthur W. Lambert, Prathapan Thiru, Heather R. Keys, Mehreen Khan, Matan Hofree, Molly M. Wilson, Ozlem Yedier-Bayram, Nathan A. Lack, Tamer T. Onder, Tugba Bagci-Onder, Michael Tyler, Itay Tirosh, Aviv Regev, Jacqueline Lees, Robert A. Weinberg. Loss of PRC2 or KMT2D-COMPASS generates two quasi-mesenchymal cell states with distinct metastatic abilities [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PR05.
Abstract A01: Fusobacterium nucleatum and clinicopathologic features of colorectal carcinoma: Results from the ColoCare Study
Authors: Eisele Yannick , Mallea Patrick M. , Gigic Biljana , Stephens W. Zac , Warby Christy A. , Buhrke Kate , Lin Tengda , Schrotz-King Petra , Hardikar Sheetal , Huang Lyen C. , Pickron T. Bartley , Scaife Courtney , Koelsch Torsten , Peoples Anita R. , Pletneva Maria A. , Bronner Mary , Schneider Martin , Ulrich Alexis B. , Swanson Eric A. , Toriola Adetunji T. , Hauner Hans , Round June , Ulrich Cornelia M. , Holowatyj Andreana N. , Ose Jennifer
Published: December 2020

Background: Fusobacterium nucleatum (Fn), an oral commensal involved in a wide spectrum of infections, has recently been implicated in colorectal cancer (CRC) etiology. However, the role of Fn in treatment-naïve CRC patients remains unclear. Therefore, we assessed whether Fn abundance is associated with clinicopathologic characteristics among treatment-naïve CRC patients enrolled in the prospective ColoCare Study.

Methods: Quantitative real-time PCR was used to amplify and detect Fn DNA in fecal samples collected prior to surgery from 105 patients. We utilized multivariable regression analysis to investigate associations between Fn abundance and sex, age at surgery, BMI, tumor stage, tumor grade, tumor site, infection with H. pylori, microsatellite instability, alcohol consumption, and smoking history by adjusting for sex, age at surgery, cohort, and BMI.

Results: Compared to patients with undetectable or low abundance of Fn, patients with higher abundance of Fn were more likely to be diagnosed with rectal cancer than colon cancer (Odds Ratio [OR] = 3.01, 95% CI 1.06-8.57 P=0.04). Categorizing the colon into right-sided (proximal) and left-sided (distal) showed that patients with a high abundance of Fn were also more likely to be diagnosed with rectal cancer compared to right-sided colon cancer (OR=5.32, 95% CI 1.23-22.98 P=0.03), thus suggesting an increasing risk of cancer diagnosis along the bowel towards the rectum.

Conclusion: Our study sheds light on the association of high abundance of Fn in fecal biospecimen with colorectal carcinogenesis, which may support future preventive or diagnostic measures.

Citation Format: Yannick Eisele, Patrick M. Mallea, Biljana Gigic, W. Zac Stephens, Christy A. Warby, Kate Buhrke, Tengda Lin, Petra Schrotz-King, Sheetal Hardikar, Lyen C. Huang, T. Bartley Pickron, Courtney Scaife, Torsten Koelsch, Anita R. Peoples, Maria A. Pletneva, Mary Bronner, Martin Schneider, Alexis B. Ulrich, Eric A. Swanson, Adetunji T. Toriola, Hans Hauner, June Round, Cornelia M. Ulrich, Andreana N. Holowatyj, Jennifer Ose. Fusobacterium nucleatum and clinicopathologic features of colorectal carcinoma: Results from the ColoCare Study [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 A01.
Abstract A05: Growth rate alterations of human colorectal cancer cells by 157 gut bacteria
Authors: Taddese Rahwa , Garza Daniel R. , Ruiter Lilian , Belzer Clara , Aalvink Steven , Nagtegaal Iris D. , Dutilh Bas E. , Boleij Annemarie
Published: December 2020

Several bacteria in the human gut microbiome have been associated with colorectal cancer (CRC) by high-throughput screens. In some cases, molecular mechanisms have been elucidated that drive tumorigenesis, including bacterial membrane proteins or secreted molecules that interact with the human cancer cells. For most gut bacteria, however, it remains unknown if they enhance or inhibit cancer cell growth. Here, we screened bacteria-free supernatants (secretomes) and inactivated cells of over 150 cultured bacterial strains for their effect on CRC cell growth. Five CRC cell lines and one noncancerous kidney cell line were selected based on their differences in mutational landscapes. We observed family-level and strain-level effects that often differed between bacterial cells and secretomes, suggesting that different molecular mechanisms are at play. Secretomes of Bacteroidaceae, Enterobacteriaceae, and Erysipelotrichaceae enhanced CRC cell growth, while most Fusobacteriaceae cells and secretomes inhibited growth, contrasting prior findings. For some bacterial families, strong cell line-dependent effects were obsevered, such as for Streptococcaceae and HT29 cells. In some bacteria, the presence of specific functional genes was associated with CRC cell growth rates, including the virulence genes TcdA in Clostridiales and FadA in Fusobacteriaceae, which both inhibited growth. Bacteroidaceae cells that enhanced growth were enriched for genes of the cobalamin synthesis pathway, while Fusobacteriaceae cells that inhibit growth were enriched for genes in ethanolamine utilization pathway. Together, our results reveal how different gut bacteria have wide-ranging effects on cancer cells, contribute a better understanding of the effects of the gut microbiome on the human host, and provide a valuable resource for identifying candidate target genes for potential microbiome-based diagnostics and treatment strategies.

Citation Format: Rahwa Taddese, Daniel R. Garza, Lilian Ruiter, Clara Belzer, Steven Aalvink, Iris D. Nagtegaal, Bas E. Dutilh, Annemarie Boleij. Growth rate alterations of human colorectal cancer cells by 157 gut bacteria [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 A05.
Abstract A07: The involvement of a type VII secretion system in the interactions between Streptococcus gallolyticus subspecies gallolyticus and colorectal cancer
Authors: Taylor John Culver , Rutherford Jacob , Nunez Maria , Xu Yi
Published: December 2020

Colorectal cancer (CRC) is the 2nd-3rd most common cancer worldwide and is a leading cause of cancer-related death. Increasing evidence suggests that the gut microbiome plays an important role in the development of CRC. One such organism of the gut microbiome that plays an important role in CRC is Streptococcus gallolyticus subspecies gallolyticus (Sgg). Previously, we reported that Sgg stimulates CRC cell proliferation in a β-catenin dependent manner. Using an azoxymethane-induced mouse model of CRC, we have also shown that Sgg-treated mice had significantly higher tumor burden in the colon compared to mice treated with saline or negative control bacteria, suggesting that Sgg actively promotes the development of CRC. The mechanism underlying Sgg’s role in CRC development, however, has yet to be elucidated. The type VII secretion system (T7SS), also called the Esx secretion system, is a specialized secretion system found primarily in Firmicutes and Actinobacteria and has been shown to play an important role in virulence in Staphylococcus aureus and Mycobacterium tuberculosis. Here, we examined the genome of Sgg and found that it encodes a putative T7SS (SggT7SS) highly similar to the T7SS in S. aureus with respect to sequence identity and gene organization. We further showed that the SggT7SS is functional. To investigate if the SggT7SS is involved in the connection between Sgg and CRC, we generated an Sgg mutant lacking the core components of the T7SS secretion machinery. Functional characterization of the mutant indicates that SggT7SS is intimately involved in the interactions between Sgg and CRC cells. Taken together, our results suggest that a T7SS system may be important in inducing specific host responses to Sgg in the context of CRC. Studies to further elucidate the activities of T7SS and its role in Sgg’s contribution to CRC are currently under way.

Citation Format: John Culver Taylor, Jacob Rutherford, Maria Nunez, Yi Xu. The involvement of a type VII secretion system in the interactions between Streptococcus gallolyticus subspecies gallolyticus and colorectal cancer [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 A07.
Abstract A09: Understanding the role of colorectal cancer-associated microbes in colorectal cancer
Authors: Ternes Dominik , Schmitz Martine , Grandmougin Léa , Tsenkova Mina , Koncina Eric , Ginolhac Aurélien , Karta Jessica , Kuhn Diana , Garcia Javier Ramiro , Greenhalgh Kacy , Wilmes Paul , Letellier Elisabeth , Haan Serge
Published: December 2020

Accumulating evidence suggests that dysbiosis, a state of pathologic imbalance in the human gut microbiome, is present in patients suffering from colorectal cancer (CRC). Several microbiome studies identified specific bacteria that are associated with CRC, among which Fusobacteria were shown to directly interact with cancer or immune cells of their host. However, only a limited number of CRC-associated microbes have been studied for host-microbial interactions; hence, the role of bacteria in the etiology of the disease remains unknown. Accordingly, our work aims at the development of a methodologic workflow for studying CRC-associated bacteria and their role in colon cancer tumor initiation and progression. In a first step, we identified CRC-associated bacteria that are enriched at the tumor site of CRC patients. Therefore, we used publicly available datasets and an in-house patient sample collection. Then, we predicted and optimized bacterial growth in silico by using a genome-scale metabolic reconstruction model combined with a constraint-based modeling approach. Finally, we implemented CRC-associated bacteria together with established primary CRC patient cultures into the microfluidics-based human-microbial crosstalk model (HuMiX). Our workflow allowed to analyze host-microbial interaction mechanisms of CRC-associated bacteria on a transcriptomic, proteomic, and metabolomic level.

Citation Format: Dominik Ternes, Martine Schmitz, Léa Grandmougin, Mina Tsenkova, Eric Koncina, Aurélien Ginolhac, Jessica Karta, Diana Kuhn, Javier Ramiro Garcia, Kacy Greenhalgh, Paul Wilmes, Elisabeth Letellier, Serge Haan. Understanding the role of colorectal cancer-associated microbes in colorectal cancer [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 A09.
Abstract A11: Betel nut chewing, oral Cyanobacteria, and exposure to cyanotoxins
Authors: Hernandez Brenda Y. , Zhu Xuemei , Sotto Patrick , Paulino Yvette
Published: December 2020

Betel nut from the Areca catechu palm tree, chewed alone or as a quid wrapped in Piper betle leaf, is the 4th most widely used addictive substance globally, primarily in parts of Asia and the Pacific. Betel nut chewing is an independent cause of cancers of the oral cavity and esophagus and has been linked to other malignancies. We evaluated 16S rRNA in oral cavity swabs and saliva obtained from 122 adults (64 current betel nut chewers, 37 former chewers, 21 never chewers) in Guam. Cyanobacteria was detected at 90-fold higher abundance in oral samples from current betel nut compared to both former and never chewers. Cyanobacteria was also the predominant bacterial taxa detected in Areca catechu nuts and Piper betle leaves.16S sequence data were evaluated using PICRUSt to predict gene families and to generate a composite metagenome. AntiSMASH 5.0 was used for the analysis of gene marker data corresponding to secondary metabolites. Cyanotoxins, including microcystins, nodularins, and cylindrospermopsin, as well as other secondary metabolites were identified as putative secondary metabolites. Subsets of oral and plant samples evaluated via ELISA confirmed the presence of these metabolites. The identification of these cyanotoxins in this population suggests their possible contribution to betel nut-associated carcinogenesis.

Citation Format: Brenda Y. Hernandez, Xuemei Zhu, Patrick Sotto, Yvette Paulino. Betel nut chewing, oral Cyanobacteria, and exposure to cyanotoxins [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 A11.
Abstract A21: Promotion of colorectal cancer by Streptococcus gallolyticus—a novel mechanism
Authors: Taylor John , Kumar Ritesh , Sarshekeh Amir , Davies Jennifer , Kopetz Scott , Xu Juan , Xu Yi
Published: December 2020

Streptococcus gallolyticus subsp. gallolyticus (Sgg) is an opportunistic gut pathobiont. It has a longstanding clinical association with colorectal cancer (CRC). We previously demonstrated that Sgg stimulates CRC cell proliferation and promotes tumor growth in mouse models of CRC (Kumar et al., 2017). Recent studies also indicated that Sgg induced an immune-tolerant environment in the mouse colon conductive for tumor development (Zhang et al., 2018). These results provide strong experimental support for Sgg being an active promoter of tumor development. The molecular mechanism underlying Sgg’s tumor promoting activity was unknown. We investigated the effect of Sgg on CRC cells by analyzing mass spectrometry proteomics data. We found that several types of collagen were upregulated in Sgg-treated cells compared to cells cultured in media only. The upregulation was further confirmed by RT-qPCR and Western blot. Transforming growth factor beta (TGFbeta) is a master regulator of the extracellular matrix. Therefore, we examined the effect of Sgg on the TGFbeta signaling pathway. The results showed that Sgg-treated cells had significantly higher level of phosphorylated Smad2. Sgg treatment also induced the expression of TGFbeta target genes. The effects of Sgg on CRC cells were significantly decreased in the presence of inhibitors for TGFbeta signaling. In addition, we observed that Sgg induced similar effects in mouse colon. Together, these results demonstrate that Sgg activates the TGFbeta signaling pathway in vitro and in vivo. Furthermore, we found that activation of TGFbeta by Sgg is mediated by specific Sgg genes. Deletion of these genes abolished the effect of Sgg on CRC cells in vitro and its ability to promote tumor growth in a mouse model of CRC. These results suggest that TGFbeta activation is a mechanism underlying Sgg’s contribution to tumor growth. Next, we tried to determine if these findings are relevant to CRC patients. Examination of tumor tissues from CRC patients revealed that Sgg-positive tumors exhibit significantly enhanced TGFbeta activity compared to Sgg-negative tumors, suggesting that Sgg-positivity correlates with stronger TGFbeta signaling activities in CRC patients. Taken together, our results highlight a previously unrecognized mechanism in which a colonic microbe activates the TGFbeta signaling pathway to promote the development of CRC. Studies to further delineate this novel mechanism are currently under way.

Citation Format: John Taylor, Ritesh Kumar, Amir Sarshekeh, Jennifer Davies, Scott Kopetz, Juan Xu, Yi Xu. Promotion of colorectal cancer by Streptococcus gallolyticus—a novel mechanism [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 A21.
Abstract A28: Concomitant use of antibiotics and immune checkpoint inhibitors in patients with solid neoplasms: Retrospective data from real-world settings
Authors: Kapoor Akhil , Noronha Vanita , Patil Vijay M. , Joshi Amit , Menon Nandini , Janu Amit , Prabhash Kumar
Published: December 2020

Background: The use of antibiotics is known to alter the gut microbiome and it is hypothesized that use of antibiotics may also alter the response to checkpoint inhibitors (CPI). As data are limited from real-world settings, we performed a retrospective audit of patients who received CPI along with concomitant antibiotics.

Patients and Methods: This study is a retrospective audit of prospectively collected database of patients who received CPI for advanced solid tumors in any line between August 2015 and November 2018 at Tata Memorial Hospital, Mumbai, India. Antibiotic use was recorded from two weeks before the start of CPI and concomitantly with CPI. All statistical calculations were performed using SPSS statistical software for Windows version 20.0.

Results: A total of 155 patients were identified to have received CPI during the study period, of which 70 (44%) patients received antibiotics. Median PFS in patients who received antibiotics was 1.7 months (95% CI: 1.1-2.3) against 3.6 months (95% CI: 2.3-4.8) for patients who did not receive antibiotics (p=0.912). Median OS in the patients who received antibiotics was 3.9 months (95% CI: 1.8-11.4) as compared to 9.2 months (95% CI: 4.2-12.3) for patients who did not receive antibiotics with a trend to significance with p=0.053 (HR-1.023; 95%CI: 1.00-1.04). Among the patients who received antibiotics, median OS for patients who received ≤10 days of antibiotics was 8.8 months (95% CI: 4.2-11.2) while for patients receiving >10 days of antibiotics, it was 2.8 months (95% CI: 1.2-4.4), p=0.025 (HR 2.0, 95% CI: 1.1-3.7).

Conclusions: This study shows that judicious use of antibiotics is required in patients on CPI or scheduled to be started on CPI.

Note: This abstract was not presented at the conference.

Citation Format: Akhil Kapoor, Vanita Noronha, Vijay M. Patil, Amit Joshi, Nandini Menon, Amit Janu, Kumar Prabhash. Concomitant use of antibiotics and immune checkpoint inhibitors in patients with solid neoplasms: Retrospective data from real-world settings [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 A28.
Abstract A29: Differential regulation of apoptosis and senescence by the miR-449 family microRNAs and its implications in tumor microenvironments of NSCLC
Authors: Cho Chun-Yu , Chung Shih-Ying , Chuang Shuang-En
Published: December 2020

MicroRNAs (miRNAs) play important roles in various biologic processes, and aberrant miRNA expression is one of the mechanisms of tumorigenesis. Previous studies indicate that oncogenic HPV infection interrupts the expression of tumor-suppressive miR-34a and contributes to the development of cervical cancer. In addition, the traditional Chinese medicine Gynostemma pentaphyllum (Thunb.) Makino may exert its pharmacologic effects through modifying the gut microbiota by regulating hepatic miR-34a expression. MiR-449 miRs are members of the tumor suppressor miR-34 family and are evolutionarily conserved. In this study, we demonstrated that, in lung cancer cells, ectopic expression of miR-449 family, including miR-449a, miR-449b, and miR-449c, decreased the levels of several G1 phase proteins including cyclin D1, cyclin D3, CDK4, and CDK6 via directly targeting their mRNA’s 3’-UTR. We also observed a differential induction of apoptosis vs. senescence by the miR-449 cluster. While miR-449a and miR-449c induced senescence, miR-449b induced apoptosis and sensitized cancer cells to apoptotic stimuli, such as serum deprivation. Interestingly, among this cluster miRNAs, only miR-449a could induce significant senescence-associated secretory phenotype (SASP), e.g., expression of IL-8, IL-6, IL-1b, and TNF-alpha. Moreover, we also found that miR-449a increased NF-kB phosphorylation at S276, but not phosphorylation site of S536, and promoted the expression of IL-8 mRNA. In this regard, the gut microbiota has been indicated to induce proinflammatory cytokines such as IL-8 to influence the outcomes of cancer patients. In addition to MRX34 (a miR-34a mimic) used in clinical trials, miR-449 family may also potentially become a new therapeutic candidate for NSCLC and other solid tumors’ treatment.

Citation Format: Chun-Yu Cho, Shih-Ying Chung, Shuang-En Chuang. Differential regulation of apoptosis and senescence by the miR-449 family microRNAs and its implications in tumor microenvironments of NSCLC [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 A29.
Abstract A32: Identifying actionable pathway malfunction scores with ML algorithm for omics data
Authors: Chebanov Dmitrii , Tatevosova Nadezhda , Mikhaylova Irina
Published: December 2020

Background: Driver mutations are traditionally considered as actionable biomarkers for targeted drugs, but the resistance and relapse effects often occur even when these events are precisely discovered. At the same time, primary DNA mutations can be only the triggers for cell malignancy and further development of the tumor occurs due to following pathways imbalance, which may be reflected in gene expression. The goal is to detect preaffected pathways that are most close to the oncogenic affected state, so during the treatment strategy planning we could consider these pathways as the next potential targets after nonresponse or relapse.

Methods: We took the data from TCGA Pan-Cancer Atlas on whole-exome sequencing and RNA expression for 33 cancers. Mutations were filtered based on their pathogenicity (1,2). The training set included data on mutations and corresponded RNA levels of 1821 cancer pathways-related genes (3). ML method-logistic regression, with 5-fold cross-validation with a test set, was realized on Python 3.7.

Results: Using gene expression data, 9 most common actionable events were predicted: oncogenic mutations affecting Ras, Raf, Ras/Raf/MEK, PI3K, CDK protein families, amplifications of EGFR, ERBB2, CDK4 genes, with an accuracy of 80% - 93%. Results were the probabilities of events: range 10-30% occurrence is shown.

Discussion: We considered the obtained molecular events probabilities as the scores of corresponding pathways’ malfunctions. For some molecular events, more than one-third of patients has >10% affected (unbalanced) pathway state. This approach after validation can be used in clinical research practice for patient cohorts risk stratification, or as additional reinforcement for drug companion tests.

References: 1. COSMIC; 2. Chakravarty et al., 2017a; 3. KEGG.

Citation Format: Dmitrii Chebanov, Nadezhda Tatevosova, Irina Mikhaylova. Identifying actionable pathway malfunction scores with ML algorithm for omics data [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 A32.
Abstract A35: Methanobrevibacter is associated with cervical dysplasia in Hispanics with HPV infections
Authors: Godoy-Vitorino Filipa , Romaguera Josefina
Published: December 2020

Bacteria have been extensively associated with several disease phenotypes. Archaea, a major neglected component of the microbiome, accounts for a relatively small percentage of the microbiota and has mostly been studied in the gastrointestinal tract. We hypothesized that dysbiosis in the genital tract included changes in both bacterial and archaeal organisms according to human papillomavirus infections and levels of dysplasia. We analyzed 62 patient samples from recruited patients coming for colposcopy clinics at the UPR and San Juan City clinics (Puerto Rico). From these, 52 were HPV positive and 10 were HPV negative and were stratified according to cytology results. From genomic DNA extracted from cervical swabs, we sequenced 16S rRNA genes and selected 10 patient samples for additional shotgun metagenomics. The patients were grouped in those without epithelial lesions, CIN 1 and CIN3. DNA data analyses were done with shotgun and QIIME. Analyses of the 16S rRNA reads revealed 16 archaeal OTUs, revealing an abundance of Methanobrevibacter associated with CIN3 lesions. Shotgun data revealed Methanosarcina to be dominant across all samples with higher dominance in patients without lesions and an increased dominance in Methanobrevibacter and Methanococcus in CIN3 lesions. No archaeal significant differences were found according to HPV risk (HPV infection); however, a significant decrease in Lactobacilli was associated with dysplasia. We found that archaea are commensals of the cervical mucosa and may contribute to dysbioses. Acetoclastic Methanosarcina are dominant across samples, and CIN3 lesions revealed a higher dominance of hydrogenotrophic methanogens such as Methanobrevibacter. The significance of these preliminary results may indicate that archaea cannot be taken out of the ecological context for future cervical cancer prevention strategies.

Grant support: Research reported in this abstract was partially supported by NIH National Institute on Minority Health and Health Disparities: RCMI Grant No. 2U54MD007600, an Institutional Development Award (IDeA) from the NIH National Institute of General Medical Sciences (Grant No. P20GM103475) and by the NIH/NIMHD Endowment program HiREC S21MD001830.

Citation Format: Filipa Godoy-Vitorino, Josefina Romaguera. Methanobrevibacter is associated with cervical dysplasia in Hispanics with HPV infections [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 A35.
Abstract A38: RNA-seq analysis identified candidate pathogens for prostate cancer
Authors: Ashida Shingo , Kawada Chiaki , Daibata Masanori , Inoue Keiji , Nakagawa Hidewaki
Published: December 2020

There is an abundance of evidence that chronic inflammation is linked to prostate cancer (PC), and pathogen infection is considered to be one of the possible causes for PC. Prostate infections by bacteria or viruses have been widely investigated. However, most of these studies have showed conflicting and controversial results. Most studies have focused on the PCR-based targeted detection of bacteria or viruses, and pathogen for PC remains to be found. To identify pathogen for PC, we investigated the transcriptomes of human prostate samples using whole-genome next-generation sequencing. The prostate specimens obtained by radical prostatectomy from 20 PC patients were sliced and divided into four sections. High-quality RNAs were extracted from the sections including PC. RNA-seq libraries were constructed according to the Illumina protocol and next-generation sequenced on a HiSeq 2000 instrument. To explore the potential of other pathogens being associated with PC, we performed de novo assembly of unmapped reads from the RNA-seq data from 20 PC samples. RNA-seq analysis identified four bacteria as candidate pathogens, which included Cutibacterium acnes, uncultured Chroococcidiopsis, Micrococcus luteus, and Moraxella osloensis. Among these candidate pathogens, Cutibacterium acnes was detected in 19 of 20 PC tissue samples by immunohistochemistry. We also performed PCR to detect other candidate pathogens (uncultured Chroococcidiopsis, Micrococcus luteus, and Moraxella osloensis) in PC samples for validation. Our findings provide further evidence of Cutibacterium acnes infections in human PCs as a promising pathogen for PC, and suggest that uncultured Chroococcidiopsis, Micrococcus luteus, and Moraxella osloensis could be novel candidate pathogens for PC. Further research is required and ongoing to clarify the molecular mechanisms underlying bacterial pathogenesis of PC.

Citation Format: Shingo Ashida, Chiaki Kawada, Masanori Daibata, Keiji Inoue, Hidewaki Nakagawa. RNA-seq analysis identified candidate pathogens for prostate cancer [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 A38.
Abstract A40: The SIAMCAT R package enables statistical and machine learning analyses for case-control microbiome datasets
Authors: Wirbel Jakob , Zych Konrad , Essex Morgan , Karcher Nicolai , Kartal Ece , Salazar Guillem , Bork Peer , Sunagawa Shinichi , Zeller Georg
Published: December 2020

Alterations in microbiome composition have been linked to many human diseases, including colorectal cancer or precancerous liver diseases. Findings from microbiome-association studies are increasingly explored as promising avenues for clinical applications due to their diagnostic or therapeutic potential. However, microbiome data complexity and the lack of integrated computational tools make it difficult to arrive at robust associations and predictive disease models. Here, we present the SIAMCAT R package as a modular and user-friendly toolbox for machine learning workflows, statistical analysis, and confounder detection for case-control microbiome datasets. Previously, we conducted a machine learning meta-analysis of colorectal cancer metagenomics studies (Wirbel, Pyl et al., Nat Med 2019) using the functionalities of SIAMCAT, which is now available to the wider community via Bioconductor. We showcase how SIAMCAT is a versatile tool by applying it to a large set of metagenomic datasets that have been processed with a wide variety of taxonomic and functional profiling tools. We furthermore demonstrate how SIAMCAT can help to detect confounding factors in microbiome association studies. By making stringent machine learning workflows and analysis pipelines available through a user-friendly and flexible interface, SIAMCAT will facilitate microbiome data analyses, biomarker discovery, and thus the translation of microbiome research to clinical applications, while simultaneously improving statistical rigor and safeguarding against common machine learning pitfalls.

Citation Format: Jakob Wirbel, Konrad Zych, Morgan Essex, Nicolai Karcher, Ece Kartal, Guillem Salazar, Peer Bork, Shinichi Sunagawa, Georg Zeller. The SIAMCAT R package enables statistical and machine learning analyses for case-control microbiome datasets [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 A40.
Abstract B03: E-cigarette vapor exposure skews competition between colonizing oral Streptococci to allow biofilm formation of S. mutans and activation of stress and survival pathways in the oral cavity
Authors: Caldwell Matthew , Valentin Alma Catala , Bernard Joshua , Moore Sean , Andl Claudia D.
Published: December 2020

E-cigarette (e-cig) use is rising, but much is unknown about the effects of its vapor. This vapor contains chemicals such as propylene glycol, a known antimicrobial, and nicotine, whose derivatives are carcinogenic. Here, we study the effects of vaping on resident bacteria of the oral cavity and on oral cell inflammation, which is linked to tumorigenesis. Streptococcus mutans, Streptococcus sanguinis, and Streptococcus gordonii species are significant residents in the oral cavity, with S. mutans the primary cause of dental caries. Growth and biofilm formation is enhanced upon exposure to traditional cigarette smoke in vitro. We aim to analyze the interplay between e-cigarette vapor and oral streptococci colonizing of the oral epithelium. S. mutans, S. sanguinis, and S. gordonii were treated using nicotine-free and 3mg nicotine vapor, as well as double-shot menthol freeze flavored 3mg nicotine vapor in a vape chamber designed to phenocopy physiologically relevant exposure. Next, we analyzed the effects on growth and biofilm formation. Nicotine-independent inhibition of growth occurred upon exposure in all three species. Interestingly, biofilm formation was enhanced in S. mutans while decreased in S. sanguinis and S. gordonii. Upon exposure to the same conditions in the vape chamber, oral epithelial cells showed activation of survival pathways, such as ERK 1/2, by Western blot. Upon coculturing of bacterial and oral epithelial cells at a multiplicity of infection of one for five hours exposed to the same conditions, we observed activation of survival and inflammatory pathways, by Western blot. The pioneer colonizers S. gordonii and S. sanguinis generally antagonize caries-causing S. mutans, which can become a predominant member of the community under appropriate conditions, leading to dental caries formation. The observed decrease in the biofilm formation of the commensals S. sanguinis and S. gordonii upon e-cig vapor exposure indicates the opportunistic colonization of S. mutans, whose biofilm-forming abilities increased. Following e-cig usage, dental caries, periodontitis, and eventually cancer in the oral epithelium may result from this dysbiosis of the microbiome in the oral cavity.

Citation Format: Matthew Caldwell, Alma Catala Valentin, Joshua Bernard, Sean Moore, Claudia D. Andl. E-cigarette vapor exposure skews competition between colonizing oral Streptococci to allow biofilm formation of S. mutans and activation of stress and survival pathways in the oral cavity [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 B03.
Abstract B25: Colorectal cancer-associated anaerobic bacteria proliferate in tumor spheroids and alter the microenvironment
Authors: Kasper Stephen H. , Morell-Perez Carolina , Wyche Thomas P. , Sana Theodore R. , Lieberman Linda A. , Hett Erik C.
Published: December 2020

Recent reports show that colorectal tumors contain microbiotas that are distinct from those that reside in a “normal” colon environment and that these microbiotas can contribute to cancer progression. Fusobacterium nucleatum is the most commonly observed species in the colorectal tumor microenvironment and reportedly influences disease progression through numerous mechanisms. However, a detailed understanding of the role of this organism in cancer progression is limited, in part due to challenges in maintaining F. nucleatum viability under standard aerobic cell culture conditions. Herein we describe the development of a 3-dimensional (3D) tumor spheroid model that can harbor and promote the growth of anaerobic bacteria. Bacteria-tumor cell interactions and metabolic crosstalk were extensively studied by measuring the kinetics of bacterial growth, cell morphology and lysis, cancer-related gene expression, and metabolomics. We observed that viable F. nucleatum assembles biofilm-like structures in the tumor spheroid microenvironment, whereas heat-killed F. nucleatum is internalized and sequestered in the cancer cells. Lastly, we use the model to coculture 28 Fusobacterium clinical isolates and demonstrate that the model successfully supports coculture with diverse fusobacterial species. This bacteria-spheroid coculture model enables mechanistic investigation of the role of anaerobic bacteria in the tumor microenvironment.

Citation Format: Stephen H. Kasper, Carolina Morell-Perez, Thomas P. Wyche, Theodore R. Sana, Linda A. Lieberman, Erik C. Hett. Colorectal cancer-associated anaerobic bacteria proliferate in tumor spheroids and alter the microenvironment [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 B25.
Abstract B34: The ALPK1/TIFA/NF-kB axis links a bacterial carcinogen to replication stress and DNA damage
Authors: Bauer Michael , Nascakova Zuzana , Mihai Anca , Müller Anne
Published: December 2020

Exposure of gastric epithelial cells to the bacterial carcinogen Helicobacter pylori causes DNA double-strand breaks. Here, we show that H. pylori-induced DNA damage occurs co-transcriptionally in S-phase cells that activate NF-kB signaling upon innate immune recognition of LPS biosynthetic intermediates, such as ADP-heptose, by the ALPK1/TIFA pathway. DNA damage is accompanied by replication fork stalling as determined by DNA fiber assay and can be observed also in gastric organoids derived from bariatric surgery patients. We link H. pylori-induced DNA damage to the formation of RNA/DNA hybrids (R-loops), as overexpression of the R-loop-processing enzyme RNAse H1 prevents DNA damage and replication stress. R-loops form in infected cells as a consequence of ADP-heptose/ALPK1/TIFA/NF-kB signaling. Factors associated with R-loop processing and prevention are recurrently mutated in gastric cancer. In summary, our results link bacterial infection and NF-kB-driven innate immune responses to DNA damage, replication stress, and carcinogenesis.

Citation Format: Michael Bauer, Zuzana Nascakova, Anca Mihai, Anne Müller. The ALPK1/TIFA/NF-kB axis links a bacterial carcinogen to replication stress and DNA damage [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 B34.
Abstract IA01: Molecular control of the gut microbiome to improve cancer chemotherapy
Authors: Redinbo Matthew
Published: December 2020

The diverse and complex communities of GI microbiota play important roles in human health, particularly with respect to cancer chemotherapy. We focused on systems where gut bacteria catalyze reactions that exert a profoundly negative impact on intestinal tissues and prove to be dose limiting for chemotherapy. The anticancer drug irinotecan is used to treat colon and pancreatic cancers and is eliminated as an inactivated drug-glucuronide by the phase II drug metabolism. Irinotecan’s dose-limiting toxicity is severe delayed diarrhea hypothesized to arise from the reactivation of the inactive irinotecan metabolite in the gut. We pinpointed the molecular basis of this reactivation to the beta-glucuronidase sugar-scavenging enzymes present in gut bacteria. We further developed potent, selective, and nonlethal inhibitors to bacterial beta-glucuronidase (GUS) enzymes and demonstrated that they prevented GI injury in mouse models of irinotecan-induced intestinal damage. Bacterial GUS inhibitors also prevent these sites of intestinal damage in mice treated with NSAIDs, which are glucuronidated and used to control cancer-related inflammation. We have since extended this work to the tyrosine kinase inhibitor regorafenib and to a probe-enabled activity-based proteomics pipeline to discover the enzymes driving the production of toxic metabolites. Together, our data demonstrate that enzyme targets in the GI microbiota can be inhibited to improve cancer care in a manner that can advance the promise of personalized medicine. Furthermore, our results shed significant light on the mammalian-microbial axes of chemical communication ongoing between two domains of life in the “higher-order” human superorganism.

Citation Format: Matthew Redinbo. Molecular control of the gut microbiome to improve cancer chemotherapy [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 IA01.
Abstract IA03: Control over colorectal tumor growth via bacteria-specific T-cell activation of the local immune response
Authors: Overacre-Delgoffe Abigail , Bumgarner Hannah , Hand Tim
Published: December 2020

Colorectal cancer (CRC) is a leading cause of cancer-related death and its incidence is on the rise, particularly in young people. Therapy for late-stage CRC is often ineffective, and colorectal tumors are most often detected at stage 3 or 4. Immunotherapy is revolutionizing the treatment of many types of cancer but is only effective for a very small subset of CRC patients. Thus, there is a tremendous need for improved therapies for CRC. Colorectal tumors grow from the intestinal epithelium and are therefore subject to interaction with the dense and diverse colonic microbiota. Indeed, CRC has been associated with shifts in the composition of the microbiota that effect inflammation and tumor growth. How the microbiota shapes the CRC immune microenvironment is not fully understood. In general, the microbiota can directly shape T-cell responses, directing the differentiation of CD4 T cells to develop into either regulatory (Treg) or effector (Th1, Th17, etc.) T cells. This is particularly true of those T cells local to the intestine that are often specific to antigens derived from intestinal bacteria. We became interested in how colonization with different bacterial taxa might affect the T-cell immune response and control over colorectal cancer. Using a mouse model of CRC, we show that colonization with a single bacterial taxon, after tumors have already developed, leads to a reduction in tumor burden and size. Bacteria-dependent tumor reduction depended upon CD4 T cells but not CD8 T cells as antibody depletion of CD4 T cells completely abrogated the effect. Accordingly, de novo bacterial colonization was associated with a colorectal tumor environment that possessed fewer Tregs, increased CD4 IFNgamma-producing T cells, and increased CD103+ dendritic cells. We also observed that colonized mice develop increased numbers of organized tertiary lymphoid structures that were adjacent to colonic tumor. Importantly, bacteria-specific CD4 T cells were commonly found in these tertiary lymphoid structures, as were bacteria. Our hypothesis is that microbiota-driven and T cell-dependent development of TLS structures leads to enhanced tumor antigen presentation and augmented antitumor immune responses. This work has the potential to inform CRC therapies via the rational modification of the local microbiota to support TLS formation and antitumor immunity.

Citation Format: Abigail Overacre-Delgoffe, Hannah Bumgarner, Tim Hand. Control over colorectal tumor growth via bacteria-specific T-cell activation of the local immune response [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 IA03.