Faculty Bibliography

Motivation/UNASSIGNED:Shotgun DNA sequencing provides sensitive detection of all 182 HPV types in tissue and body fluid. However, existing computational methods either produce false positives misidentifying HPV types due to shared sequences among HPV, human, and prokaryotes, or produce false negative since they identify HPV by assembled contigs requiring large abundant of HPV reads. Results/UNASSIGNED:We designed HPViewer with two custom HPV reference databases masking simple repeats and homology sequences respectively and one homology distance matrix to hybridize these two databases. It directly identified HPV from short DNA reads rather than assembled contigs. Using 100,100 simulated samples, we revealed that HPViewer was robust for samples containing either high or low number of HPV reads. Using 12 shotgun sequencing samples from respiratory papillomatosis, HPViewer was equal to VirusTAP, and Vipie and better than HPVDetector with the respect to specificity and was the most sensitive method in the detection of HPV types 6 and 11. We demonstrated that contigs-based approaches had disadvantages of detection of HPV. In 1,573 sets of metagenomic data from 18 human body sites, HPViewer identified 104 types of HPV in a body-site associated pattern and 89 types of HPV co-occurring in one sample with other types of HPV. We demonstrated HPViewer was sensitive and specific for HPV detection in metagenomic data. Availability/UNASSIGNED:HPViewer can be accessed at https://github.com/yuhanH/HPViewer/. Contact/UNASSIGNED:Zhiheng.pei@nyumc.org. Supplementary information/UNASSIGNED:Supplementary data are available at Bioinformatics online.

BACKGROUND:Dysbiosis of the oral microbiome can lead to local oral disease and potentially to cancers of the head, neck, and digestive tract. However, little is known regarding exogenous factors contributing to such microbial imbalance. RESULTS:We examined the impact of alcohol consumption on the oral microbiome in a cross-sectional study of 1044 US adults. Bacterial 16S rRNA genes from oral wash samples were amplified, sequenced, and assigned to bacterial taxa. We tested the association of alcohol drinking level (non-drinker, moderate drinker, or heavy drinker) and type (liquor, beer, or wine) with overall microbial composition and individual taxon abundance. The diversity of oral microbiota and overall bacterial profiles differed between heavy drinkers and non-drinkers (α-diversity richness p = 0.0059 and β-diversity unweighted UniFrac p = 0.0036), and abundance of commensal order Lactobacillales tends to be decreased with higher alcohol consumption (fold changes = 0.89 and 0.94 for heavy and moderate drinkers, p trend = 0.005 [q = 0.064]). Additionally, certain genera were enriched in subjects with higher alcohol consumption, including Actinomyces, Leptotrichia, Cardiobacterium, and Neisseria; some of these genera contain oral pathogens, while Neisseria can synthesize the human carcinogen acetaldehyde from ethanol. Wine drinkers may differ from non-drinkers in microbial diversity and profiles (α-diversity richness p = 0.048 and β-diversity unweighted UniFrac p = 0.059) after controlling for drinking amount, while liquor and beer drinkers did not. All significant differences between drinkers and non-drinkers remained after exclusion of current smokers. CONCLUSIONS:Our results, from a large human study of alcohol consumption and the oral microbiome, indicate that alcohol consumption, and heavy drinking in particular, may influence the oral microbiome composition. These findings may have implications for better understanding the potential role that oral bacteria play in alcohol-related diseases.

Importance/UNASSIGNED:Case-control studies show a possible relationship between oral bacteria and head and neck squamous cell cancer (HNSCC). Prospective studies are needed to examine the temporal relationship between oral microbiome and subsequent risk of HNSCC. Objective/UNASSIGNED:To prospectively examine associations between the oral microbiome and incident HNSCC. Design, Setting, and Participants/UNASSIGNED:This nested case-control study was carried out in 2 prospective cohort studies: the American Cancer Society Cancer Prevention Study II Nutrition Cohort (CPS-II) and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). Among 122 004 participants, 129 incident patient cases of HNSCC were identified during an average 3.9 years of follow-up. Two controls per patient case (n = 254) were selected through incidence density sampling, matched on age, sex, race/ethnicity, and time since mouthwash collection. All participants provided mouthwash samples and were cancer-free at baseline. Exposures/UNASSIGNED:Oral microbiome composition and specific bacterial abundances were determined through bacterial 16S rRNA gene sequencing. Overall oral microbiome composition and specific taxa abundances were compared for the case group and the control group, using PERMANOVA and negative binomial generalized linear models, respectively, controlling for age, sex, race, cohort, smoking, alcohol, and oral human papillomavirus-16 status. Taxa with a 2-sided false discovery rate (FDR)-adjusted P-value (q-value) <.10 were considered significant. Main Outcomes and Measures/UNASSIGNED:Incident HNSCC. Results/UNASSIGNED:The study included 58 patient cases from CPS-II (mean [SD] age, 71.0 [6.4] years; 16 [27.6%] women) and 71 patient cases from PLCO (mean [SD] age, 62.7 [4.8] years; 13 [18.3%] women). Two controls per patient case (n = 254) were selected through incidence density sampling, matched on age, sex, race/ethnicity, and time since mouthwash collection. Head and neck squamous cell cancer cases and controls were similar with respect to age, sex, and race. Patients in the case group were more often current tobacco smokers, tended to have greater alcohol consumption (among drinkers), and to be positive for oral carriage of papillomavirus-16. Overall microbiome composition was not associated with risk of HNSCC. Greater abundance of genera Corynebacterium (fold change [FC], 0.58; 95% confidence interval [CI], 0.41-0.80; q = .06) and Kingella (FC, 0.63; 95% CI, 0.46-0.86; q = .08) were associated with decreased risk of HNSCC, potentially owing to carcinogen metabolism capacity. These findings were consistent for both cohorts and by cohort follow-up time. The observed relationships tended to be stronger for larynx cancer and for individuals with a history of tobacco use. Conclusions and Relevance/UNASSIGNED:This study demonstrates that greater oral abundance of commensal Corynebacterium and Kingella is associated with decreased risk of HNSCC, with potential implications for cancer prevention.

Background: Russell Body Gastritis (RBG) is considered to be a rare histologic finding that has an unclear pathogenesis and an unpredictable clinical outcome. We sought to clarify the frequency and significance of RBG by assessing their associated histology and relationship with the local microbiome. Design: We reviewed all 220 gastric biopsies over a 2-month period at 1 institution for the presence and density of Russell bodies (RB). In biopsies with RB, the quantity of RB was manually counted using light microscopy at 200x magnification in every biopsy level (3068 sections) and the sectional area was estimated using a 1x1 mm grid overlay. RB density was calculated by dividing the total quantity of RB in all sections by the total sectional area. 48 additional patients, which corresponded to an extra 100 histologic biopsies, were consented at the same visit for an extra gastric biopsy for 16S rRNA sequencing, and these microbiome profiles were correlated with the highest RB density per patient. Results: Russell bodies (RB) were frequent in gastric biopsies (43% of all gastritides) and the RB density significantly increased with more severe gastritides (p<0.001, n=320). The gastric microbiome globally differed in beta diversity between RB-positive and RB-negative cases by unweighted and weighted principal component analysis (p=0.03, p=0.007, n=48, respectively). In particular, Helicobacter and Streptococcus were significantly enriched in gastritis with RB and their abundances correlated with RB density (p=0.0002, r=0.51; p=0.009, r=0.37, n=48, respectively). Protonpump inhibitor (PPI) use reduced RB density per unit abundance of Streptococcus (p=0.0021, n=48). H. pylori abundance significantly correlated with RB density and two Streptococcus species (an unclassified Streptococcal species and S. anginosus) significantly correlated with RB density in H. pylori-negative gastritis (p=0.009, n=36, r=0.36; p=0.0025, n=36, r=0.51, respectively). 7 H. pylorinegative patients were followed for 1 year and variation in Streptococcus abundance reflected RB density (p=0.085, n=7). Conclusions: RB are common within the inflamed gastric mucosa and gastritis with RB is associated with Helicobacter and Streptococcus enrichment and consequent global shifts in the gastric microbiome. PPI dampens RB production, presumably through anti-inflammatory effects. Gastritis with RB might represent a reactive humoral response to bacteria within the gastric microbiome. Streptococcus species may influence chronic gastritis

Background/UNASSIGNED:The majority of patients diagnosed with oropharyngeal squamous cell cancer (OPSCC) are due to HPV infection. At present, there are no reliable tests for screening HPV in patients with OPSCC. The objective of this study was to assess the Cobas® HPV Test on oral rinse specimens as an early, non-invasive tool for HPV-related OPSCC. Methods/UNASSIGNED:Oral rinse specimens were collected from 187 patients (45 with OPSCC, 61 with oral cavity SCC (OCSCC) and 81 control patients who had benign or malignant thyroid nodules) treated at MSKCC. The Cobas® HPV Test was used to detect 14 high-risk HPV types in these samples. Performance of the HPV Test was correlated with p16 tumor immunohistochemistry as gold standard. Results/UNASSIGNED:91.1% of the oropharynx cancer patients had p16 positive tumors compared to 3.3% of oral cavity cancer. Of the 81 control patients, 79 (97.5%) had no HPV in their oral rinse giving a specificity of the HPV test of 98%. For the combined oral cavity oropharynx cancer cohort, the sensitivity, specificity, positive predictive value and negative predictive value of the HPV Test were 79.1%, 90.5%, 85.0% and 86.4% respectively when p16 immunohistochemistry was used as the reference. Conclusion/UNASSIGNED:The Cobas® HPV Test on oral rinse is a highly specific and potentially sensitive test for oropharyngeal cancer and may be a potentially useful screening test for early oropharyngeal cancer. Impact/UNASSIGNED:We describe an oral rinse test for the detection of HPV related oropharyngeal cancer.

Bacteria may play a role in esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), although evidence is limited to cross-sectional studies. In this study, we examined the relationship of oral microbiota with EAC and ESCC risk in a prospective study nested in two cohorts. Oral bacteria were assessed using 16S rRNA gene sequencing in prediagnostic mouthwash samples from n = 81/160 EAC and n = 25/50 ESCC cases/matched controls. Findings were largely consistent across both cohorts. Metagenome content was predicted using PiCRUST. We examined associations between centered log-ratio transformed taxon or functional pathway abundances and risk using conditional logistic regression adjusting for BMI, smoking, and alcohol. We found the periodontal pathogen Tannerella forsythia to be associated with higher risk of EAC. Furthermore, we found that depletion of the commensal genus Neisseria and the species Streptococcus pneumoniae was associated with lower EAC risk. Bacterial biosynthesis of carotenoids was also associated with protection against EAC. Finally, the abundance of the periodontal pathogen Porphyromonas gingivalis trended with higher risk of ESCC. Overall, our findings have potential implications for the early detection and prevention of EAC and ESCC. Cancer Res; 77(23); 6777-87. ©2017 AACR.

BACKGROUND: Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize and infer relationships between mucosal T cells, the host tissue environment, and microbial communities in patients with IBD who will serve as basis for mechanistic studies on human IBD. METHODS: We characterized mucosal CD4 T cells using flow cytometry, along with matching mucosal global gene expression and microbial communities data from 35 pinch biopsy samples from patients with IBD. We analyzed these data sets using an integrated framework to identify predictors of inflammatory states and then reproduced some of the putative relationships formed among these predictors by analyzing data from the pediatric RISK cohort. RESULTS: We identified 26 predictors from our combined data set that were effective in distinguishing between regions of the intestine undergoing active inflammation and regions that were normal. Network analysis on these 26 predictors revealed SAA1 as the most connected node linking the abundance of the genus Bacteroides with the production of IL17 and IL22 by CD4 T cells. These SAA1-linked microbial and transcriptome interactions were further reproduced with data from the pediatric IBD RISK cohort. CONCLUSIONS: This study identifies expression of SAA1 as an important link between mucosal T cells, microbial communities, and their tissue environment in patients with IBD. A combination of T cell effector function data, gene expression and microbial profiling can distinguish between intestinal inflammatory states in IBD regardless of disease types.

Background: The two most common types of esophageal cancer, esophageal adenocarcinoma (EAC) and squamous cell carcinoma (ESCC), are highly fatal. The human microbiota have been suggested to play a role in esophageal cancer etiology, although the evidence is limited to small, cross-sectional studies. We hypothesized that the oral microbiota, which shape the esophageal microbiota, may be causative agents in esophageal carcinogenesis. Methods: We conducted a prospective study nested in two large U.S. cohorts: ACS CPS-II and NCI-PLCO. Oral bacteria were assessed in pre-diagnostic mouth-wash samples collected from cases and controls (n=81/160 EAC and n=25/50 ESCC cases/matched controls), using 16S rRNA gene sequencing. We compared overall microbial composition between cases and controls using permutational multivariate analysis of variance (PERMANOVA) of UniFrac distances, and we examined associations between centered log-ratio transformed taxon abundances and cancer risk using conditional logistic regression. Metagenome functional content was predicted from taxonomic composition using PiCRUST. Results: Overall microbial composition did not differ between EAC cases and matched controls or ESCC cases and matched controls, adjusting for matching factors (age, sex, race, cohort, time to diagnosis/selection), BMI, smoking, and alcohol intake (all p>0.40). The periodontal pathogens Tannerella forsythia and Porphyromonas gingivalis were nominally associated with increased risk for EAC (OR [95% CI] = 1.21 [1.01, 1.46], p=0.04) and ESCC (OR [95% CI] = 1.3 [0.96, 1.77], p=0.09), respectively. Conversely, genus Neisseria, previously shown to be depleted by cigarette smoking, was associated with protection against EAC (OR [95% CI] = 0.88 [0.8, 0.97], p=0.01). Other species associated with EAC risk (p<0.05) included Corynebacterium durum, Prevotella nanceiensis, and Streptococcus pneumoniae (inversely associated with EAC), and Actinomyces cardiffensis, Selenomonas oral taxon 134, and Veillonella oral taxon 917 (positively associated with EAC). Other species associated with ESCC risk (p<0.05) included Aggregatibacter paraphrophilus (inversely associated with ESCC) and Prevotella nanceiensis, Bergeyella oral taxon 322, and Neisseria weaveri (positively associated with ESCC). Analysis of inferred metagenomes revealed that bacterial carotenoid biosynthesis was associated with protection against EAC (OR [95% CI] = 0.84 [0.7, 1.0], p=0.05). Conclusions: Our findings from this prospective study suggest that specific bacterial pathogens may play a causal role in esophageal cancer, while members of the healthy oral microbiota may protect against carcinogenesis. Unique microbial profiles may contribute to each of the distinct esophageal cancer types, EAC and ESCC. Oral microbiota manipulation may be a future strategy for preventing this highly fatal disease