The effect of gender on Helicobacter pylori and gastric cancer

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2011.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student submitted PDF version of thesis.Includes bibliographical references.Gastric cancer is the 2nd leading cause of cancer death worldwide and the 4th most commonly diagnosed cancer worldwide. Helicobacter pylori infection is the major risk factor of gastric cancer, and as such, this bacterium has been classified as a type 1, or definite, carcinogen by the International Agency for Research on Cancer. H. pylori infects the gastric mucosa of more than half of the world's population and promotes gastric carcinogenesis by inducing chronic inflammation. Over decades of persistent H. pylori infection and chronic inflammation, the stomach goes through a well characterized pathological progression involving chronic gastritis, atrophy, intestinal metaplasia, dysplasia, and ultimately cancer. Interestingly, there are strong gender differences in the development of gastric cancer, as men are twice as likely to develop the disease than women. Given the importance of H. pylori and chronic inflammation in gastric carcinogenesis, this thesis investigated the role of gender in modulating host immune responses to H. pylori. The aims of this thesis explored 1) the effect of gender on H. pylori's ability to induce mutations and 2) the effect of estrogen and the anti-estrogen, Tamoxifen, on H. pyloriinduced gastric cancer. For the first aim, the gpt delta mouse model, a murine mutational analysis model, was used to study chronic infection with H. pylori. Increased frequency of point mutations was observed in infected female mice at 12 months post infection. These mutations were not observed in infected male mice. Further analysis revealed that H. pylori induced a greater immune response in female mice in this model, as measured by increased severity of gastric lesions, decreased bacterial counts and the higher levels of Th1 antibodies for H. pylori. The spectra of mutations pointed towards oxidative damage as the underlying cause of induction. This study revealed that gender differences in mutagenesis were mediated by the severity and duration of the immune response. In the second aim, 17[beta]-estradiol prevented the formation of gastric cancer in the INSGAS mouse model, which develops gastric cancer in a male-predominant manner. Unexpectedly, this study led to the discovery that Tamoxifen may act as an agonist in this model of gastric cancer, as it was able to prevent gastric cancer using mechanisms similar to 17[beta]- estradiol. Both compounds downregulated pathways associated with cellular movement and cancer. CXCL1, a murine homolog of IL-8, was downregulated by treatment at both local and systemic levels, which led to a decreased neutrophilic infiltrate. 17[beta]-estradiol and Tamoxifen mediated the disruption of a positive feedback loop coupling CXCL1 secretion with neutrophil recruitment, which dampened the activation of proinflammatory and oncogenic pathways, leading to protection against gastric cancer. In conclusion, these studies provide further insight into the role of gender modulation of host immune response in H. pylori-induced mutagenesis and carcinogenesis.by Alexander Sheh.Ph.D

Draft Genome Sequences of Eight Enterohepatic Helicobacter Species Isolated from Both Laboratory and Wild Rodents

The draft genome sequences of eight enterohepatic Helicobacter species, H. muridarum, H. trogontum, H. typhlonius, and five unnamed helicobacters, are presented here. Using laboratory mice pervasively infected with helicobacters, we characterized the presence of known virulence factors.National Institutes of Health (U.S.) (grant R01CA067529)National Institutes of Health (U.S.) (grant R01OD011141)National Institutes of Health (U.S.) (grant P01CA26731)National Institutes of Health (U.S.) (grant P30ES002109

Draft Genome Sequences of Six Enterohepatic Helicobacter Species Isolated from Humans and One from Rhesus Macaques

Draft genome sequences of seven enterohepatic Helicobacter species, H. bilis, H. canadensis, H. canis, H. cinaedi, H. winghamensis, H. pullorum, and H. macacae, are presented. These isolates were obtained from clinical patients and a nonhuman primate. Due to potential zoonotic risks, we characterized antibiotic resistance markers and Helicobacter virulence factors.National Institutes of Health (U.S.) (Department of Health and Human Services, under grant U54HG003067)National Human Genome Research Institute (U.S.)National Institutes of Health (U.S.) (Department of Health and Human Services, under grant R01CA067529)National Institutes of Health (U.S.) (Department of Health and Human Services, under grant R01OD011141)National Institutes of Health (U.S.) (Department of Health and Human Services, under grant P01CA26731)National Institutes of Health (U.S.) (Department of Health and Human Services, under grant P30ES002109

Draft Genome Sequences of Helicobacter pylori Strains Isolated from Regions of Low and High Gastric Cancer Risk in Colombia

The draft genome sequences of six Colombian Helicobacter pylori strains are presented. These strains were isolated from patients from regions of high and low gastric cancer risk in Colombia and were characterized by multilocus sequence typing. The data provide insights into differences between H. pylori strains of different phylogeographic origins.National Institutes of Health (U.S.) (grant P01CA028842)National Institutes of Health (U.S.) (grant P01CA026731)National Institutes of Health (U.S.) (grant P30ES002109

Chord Segmentation and Recognition using EM-Trained Hidden Markov Models

Automatic extraction of content description from commercial audio recordings has a number of important applications, from indexing and retrieval through to novel musicological analyses based on very large corpora of recorded performances. Chord sequences are a description that captures much of the character of a piece in a compact form and using a modest lexicon. Chords also have the attractive property that a piece of music can (mostly) be segmented into time intervals that consist of a single chord, much as recorded speech can (mostly) be segmented into time intervals that correspond to specific words. In this work, we build a system for automatic chord transcription using speech recognition tools. For features we use "pitch class profile" vectors to emphasize the tonal content of the signal, and we show that these features far outperform cepstral coefficients for our task. Sequence recognition is accomplished with hidden Markov models (HMMs) directly analogous to subword models in a speech recognizer, and trained by the same Expectation-Maximization (EM) algorithm. Crucially, this allows us to use as input only the chord sequences for our training examples, without requiring the precise timings of the chord changes— which are determined automatically during training. Our results on a small set of 20 early Beatles songs show frame-level accuracy of around 75% on a forced-alignment task

Helicobacter hepaticus Infection Promotes Hepatitis and Preneoplastic Foci in Farnesoid X Receptor (FXR) Deficient Mice

Farnesoid X receptor (FXR) is a nuclear receptor that regulates bile acid metabolism and transport. Mice lacking expression of FXR (FXR KO) have a high incidence of foci of cellular alterations (FCA) and liver tumors. Here, we report that Helicobacter hepaticus infection is necessary for the development of increased hepatitis scores and FCA in previously Helicobacter-free FXR KO mice. FXR KO and wild-type (WT) mice were sham-treated or orally inoculated with H. hepaticus. At 12 months post-infection, mice were euthanized and liver pathology, gene expression, and the cecal microbiome were analyzed. H. hepaticus induced significant increases hepatitis scores and FCA numbers in FXR KO mice (P<0.01 and P<0.05, respectively). H. hepaticus altered the beta diversity of cecal microbiome in both WT and FXR KO mice compared to uninfected mice (P<0.05). Significant upregulation of β-catenin, Rela, Slc10a1, Tlr2, Nos2, Vdr, and Cyp3a11 was observed in all FXR KO mice compared to controls (P<0.05). Importantly, H. hepaticus and FXR deficiency were necessary to significantly upregulate Cyp2b10 (P<0.01). FXR deficiency was also a potent modulator of the cecal microbiota, as observed by a strong decrease in alpha diversity. A significant decrease in Firmicutes, particularly members of the order Clostridiales, was observed in FXR KO mice (P<0.05 and FDR<5%, ANOVA). While FXR deficiency strongly affects expression of genes related to immunity and bile acid metabolism, as well as the composition of the microbiome; however, its deficiency was not able to produce significant histopathological changes in the absence of H. hepaticus infection.National Institutes of Health (U.S.) (NIH R01 OD011141)National Institutes of Health (U.S.) (NIH T32 OD010978)National Institutes of Health (U.S.) (NIH P30 ES002109)National Institutes of Health (U.S.) (P01 CA026731

Alterations in common marmoset gut microbiome associated with duodenal strictures

Chronic gastrointestinal (GI) diseases are the most common diseases in captive common marmosets (Callithrix jacchus). Despite standardized housing, diet and husbandry, a recently described gastrointestinal syndrome characterized by duodenal ulcers and strictures was observed in a subset of marmosets sourced from the New England Primate Research Center. As changes in the gut microbiome have been associated with GI diseases, the gut microbiome of 52 healthy, non-stricture marmosets (153 samples) were compared to the gut microbiome of 21 captive marmosets diagnosed with a duodenal ulcer/stricture (57 samples). No significant changes were observed using alpha diversity metrics, and while the community structure was significantly different when comparing beta diversity between healthy and stricture cases, the results were inconclusive due to differences observed in the dispersion of both datasets. Differences in the abundance of individual taxa using ANCOM, as stricture-associated dysbiosis was characterized by Anaerobiospirillum loss and Clostridium perfringens increases. To identify microbial and serum biomarkers that could help classify stricture cases, we developed models using machine learning algorithms (random forest, classification and regression trees, support vector machines and k-nearest neighbors) to classify microbiome, serum chemistry or complete blood count (CBC) data. Random forest (RF) models were the most accurate models and correctly classified strictures using either 9 ASVs (amplicon sequence variants), 4 serum chemistry tests or 6 CBC tests. Based on the RF model and ANCOM results, C. perfringens was identified as a potential causative agent associated with the development of strictures. Clostridium perfringens was also isolated by microbiological culture in 4 of 9 duodenum samples from marmosets with histologically confirmed strictures. Due to the enrichment of C. perfringens in situ, we analyzed frozen duodenal tissues using both 16S microbiome profiling and RNAseq. Microbiome analysis of the duodenal tissues of 29 marmosets from the MIT colony confirmed an increased abundance of Clostridium in stricture cases. Comparison of the duodenal gene expression from stricture and non-stricture marmosets found enrichment of genes associated with intestinal absorption, and lipid metabolism, localization, and transport in stricture cases. Using machine learning, we identified increased abundance of C. perfringens, as a potential causative agent of GI disease and intestinal strictures in marmosets.National Institutes of Health/[T32 OD010978]/NIH/Estados UnidosNational Institutes of Health/[P30-ES002109]/NIH/Estados UnidosUniversidad de Costa Rica/[803-C1-163]/UCR/Costa RicaUCR::Vicerrectoría de Investigación::Unidades de Investigación::Ciencias de la Salud::Centro de Investigación en Enfermedades Tropicales (CIET

Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

Modern scientific knowledge of how memory functions are organized in the human brain originated from the case of Henry G. Molaison (H.M.), an epileptic patient whose amnesia ensued unexpectedly following a bilateral surgical ablation of medial temporal lobe structures, including the hippocampus. The neuroanatomical extent of the 1953 operation could not be assessed definitively during H.M.’s life. Here we describe the results of a procedure designed to reconstruct a microscopic anatomical model of the whole brain and conduct detailed 3D measurements in the medial temporal lobe region. This approach, combined with cellular-level imaging of stained histological slices, demonstrates a significant amount of residual hippocampal tissue with distinctive cytoarchitecture. Our study also reveals diffuse pathology in the deep white matter and a small, circumscribed lesion in the left orbitofrontal cortex. The findings constitute new evidence that may help elucidate the consequences of H.M.’s operation in the context of the brain’s overall pathology

17 -Estradiol and Tamoxifen Prevent Gastric Cancer by Modulating Leukocyte Recruitment and Oncogenic Pathways in Helicobacter Pylori-Infected INS-GAS Male Mice

Helicobacter pylori infection promotes male-predominant gastric adenocarcinoma in humans. Estrogens reduce gastric cancer risk and previous studies demonstrated that prophylactic 17β-estradiol (E2) in INS-GAS mice decreases H. pylori-induced carcinogenesis. We examined the effect of E2 and Tamoxifen, on H. pylori-induced gastric cancer in male and female INS-GAS mice. After confirming robust gastric pathology at 16 weeks post-infection (WPI), mice were implanted with E2, Tamoxifen, both E2 and Tamoxifen, or placebo pellets for 12 weeks. At 28 WPI, gastric histopathology, gene expression and immune cell infiltration were evaluated, and serum inflammatory cytokines measured. After treatment, no gastric cancer was observed in H. pylori-infected males receiving E2 and/or Tamoxifen, while 40% of infected untreated males developed gastric cancer. E2, Tamoxifen and their combination significantly reduced gastric precancerous lesions in infected males compared to infected untreated males (P<0.001, 0.01 and 0.01, respectively). However, Tamoxifen did not alter female pathology regardless of infection status. Differentially expressed genes from males treated with E2 or Tamoxifen (n=363 and n=144, Q<0.05) associated highly with cancer and cellular movement, indicating overlapping pathways in the reduction of gastric lesions. E2 or Tamoxifen deregulated genes associated with metastasis (PLAUR and MMP10) and Wnt inhibition (FZD6 and SFRP2). Compared to controls, E2 decreased gastric mRNA (Q<0.05) and serum levels (P<0.05) of CXCL1, a neutrophil chemokine, leading to decreased neutrophil infiltration (P<0.01). Prevention of H. pylori-induced gastric cancer by E2 and Tamoxifen may be mediated by estrogen signaling and is associated with decreased CXCL1, decreased neutrophil counts and downregulation of oncogenic pathways

Draft genome sequences of novel campylobacter species isolated from nonhuman primates

Campylobacter species are being increasingly isolated and associated with disease in humans and animals. Here, we describe four draft genome sequences of Campylobacter species from nonhuman primates. These include Campylobacter troglodytis, isolated from wild chimpanzees, and two likely new Campylobacter species isolated from a lemur, common marmoset, and cotton-top tamarin.NIH (Grants T32-OD010978, P30-ES002109, R01-OD01141, and R01-CA067529