Trillions of microbes line the gastrointestinal tract to form the gut microbiome, a symbiotic organ whose supportive functions include energy production, immune homeostasis, and defense against pathogens. Disturbances to gut microbial composition, in turn, drive the pathogenesis of various metabolic, inflammatory, and carcinogenic diseases. Much effort has been dedicated to elucidating environmental triggers of gut dysbiosis, not the least of which is the consumption of medications. Antibiotics eradicate keystone commensals and enhance pathogenic behaviors of persisting pathobionts, whose resistance mechanisms can have off-target effects on human physiology and treatment response. Recent evidence indicates that the spectrum of antimicrobial compounds that disturb the gut microbiome extends far beyond traditional antibiotics, and includes commonly prescribed cardiovascular, neuropsychiatric, metabolic, and cancer medications. Although the capacity of non-antibiotic pharmaceuticals to induce gut dysbiosis is well appreciated, their impact on gut microbial function has not been studied systematically. Bacterial multi-omic profiling offers a cost-effective, high-throughput approach to understanding bacterial genetic responses to chemical perturbations, and how these functional changes might reciprocally impact relevant human phenotypes. Our laboratory, which houses a personal strain biobank of over 30,000 gut bacterial isolates spanning over 400 taxa, has established scalable pipelines for bacterial genomic and transcriptomic profiling that are readily applicable to diverse non-model gut microbes. We applied these methodologies to healthy fecal samples and bacterial isolates to elucidate strain-level responses to common pharmaceuticals with known gut microbiome associations. We first performed a gut microbiota transcriptomic screen of 19 representative fecal isolates against 20 top-prescribed orally delivered medications. Computational analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed induction of pathways associated with metabolism and multidrug resistance, including upregulation of efflux machinery by lipid-lowering drugs, antidepressants and cardiovascular medications. We discovered many bacterial responses with clinical significance, which we computationally validated using clinical metagenomic datasets. Most importantly, we showed that statin-mediated overexpression of the AcrAB-TolC efflux pump generates collateral toxicity in dietary retinol and secondary bile acids, resulting in depletion of pump-containing Bacteroidales species from patient microbiomes. We next performed the first comprehensive screen for antimicrobial activity in cancer drugs by exposing three healthy fecal samples to a panel of 41 first-line cancer therapeutics. Using 16S-genomic profiling, we identified several members of the targeted kinase inhibitor (TKI) class that induced gut dysbiosis, including first-line hepatocellular carcinoma (HCC) treatment sorafenib. We profiled natural bacterial isolates exposed to different TKI HCC treatments, and again observed transcriptional induction of conserved multidrug efflux pumps. Adaptive evolution assays identified Resistance-Nodulation-Division (RND) efflux pumps as effectors of TKI resistance. Remarkably, we demonstrated that acquired TKI resistance in evolved Bacteroidales lineages generated strain-specific cross-resistances and collateral sensitivities to several unrelated antibiotics. Collectively, our work demonstrates the importance of profiling xenobiotic impacts on the gut microbial resistome, as bacterial adaptations to pharmaceutical toxicities can feed back onto microbiome communities and the human host to affect health outcomes.

Simple Summary Gene therapy is a novel approach to treat diseases by introducing corrective genetic information into target cells. Adeno-associated virus vectors are the most frequently applied gene delivery tools for in vivo gene therapy and are also studied as part of innovative anticancer strategies. Here, we report on the natural preference of AAV2 vectors for hepatocellular carcinoma (HCC) compared to nonmalignant liver cells in mice and human tissue. This preference in transduction is due to the improved intracellular processing of AAV2 vectors in HCC, resulting in significantly more vector genomes serving as templates for transcription in the cell nucleus. Based on this natural tropism for HCC, novel therapeutic strategies can be designed or existing therapeutic approaches can be strengthened as they currently result in only a minor improvement of the poor prognosis for most liver cancer patients. Abstract Although therapeutic options are gradually improving, the overall prognosis for patients with hepatocellular carcinoma (HCC) is still poor. Gene therapy-based strategies are developed to complement the therapeutic armamentarium, both in early and late-stage disease. For efficient delivery of transgenes with antitumor activity, vectors demonstrating preferred tumor tropism are required. Here, we report on the natural tropism of adeno-associated virus (AAV) serotype 2 vectors for HCC. When applied intravenously in transgenic HCC mouse models, similar amounts of vectors were detected in the liver and liver tumor tissue. In contrast, transduction efficiency, as indicated by the level of transgene product, was moderate in the liver but was elevated up to 19-fold in mouse tumor tissue. Preferred transduction of HCC compared to hepatocytes was confirmed in precision-cut liver slices from human patient samples. Our mechanistic studies revealed that this preference is due to the improved intracellular processing of AAV2 vectors in HCC, resulting, for example, in nearly 4-fold more AAV vector episomes that serve as templates for gene transcription. Given this background, AAV2 vectors ought to be considered to strengthen current—or develop novel—strategies for treating HCC.

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Yau Mei-sze. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (leaves 96-112). / Abstracts in English and Chinese. / Abstract / Abstract (Chinese Version) / Acknowledgements / List of Abbreviations / Table of Contents / List of Tables / List of Figures / Chapter Chapter 1 --- Introduction / Chapter Chapter 2 --- Literature Review / Chapter 2.1 --- Hepatocellular Carcinoma / Chapter 2.2 --- Epidermal Growth Factor Receptor / Chapter 2.2.1 --- Activation of Epidermal Growth Factor Receptor / Chapter 2.2.2 --- Epidermal Growth Factor Receptor Signaling Pathways / Chapter 2.2.3 --- Expression Level and Patient Survival / Chapter 2.2.4 --- Epidermal Growth Factor Receptor Activity and Tumor Cell Growth / Chapter 2.2.5 --- Epidermal Growth Factor Receptor Activity and Radiation / Chapter 2.3 --- "Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor, ZD1839" / Chapter 2.3.1 --- Tumor Cell Growth Control Activities of ZD1839 / Chapter 2.3.2 --- Factors Affecting the Tumor Cell Growth Control Activities of ZD1839 / Chapter 2.3.3 --- Radiosensitization Activities of ZD1839 / Chapter 2.3.4 --- Factors Affecting the Radiosensitization Activities of ZD1839 / Chapter 2.4 --- Study Objectives / Chapter Chapter 3 --- Materials and Methods / Chapter 3.1 --- ZD1839 / Chapter 3.2 --- Cell lines and Cell Culture / Chapter 3.3 --- Immunoblot Analysis / Chapter 3.3.1 --- Total Protein Extraction / Chapter 3.3.2 --- Protein Amount Determination / Chapter 3.3.3 --- Protein Separation / Chapter 3.3.4 --- Blotting / Chapter 3.3.5 --- Antibody Labeling / Chapter 3.3.6 --- Detection of Antibody Binding / Chapter 3.4 --- Cytotoxicity Assay / Chapter 3.5 --- Nucleotide sequence analysis / Chapter 3.5.1 --- Total RNA Extraction / Chapter 3.5.2 --- RNA Amount Determination / Chapter 3.5.3 --- Reverse Transcription - Polymerase Chain Reaction (RT-PCR) / Chapter 3.5.3.1 --- Reverse Transcription / Chapter 3.5.3.2 --- High Fidelity Polymerase Chain Reaction / Chapter 3.5.4 --- Purification of PCR Product / Chapter 3.5.5 --- Cycle Sequencing Reaction / Chapter 3.5.6 --- DNA Precipitation and Sequencing / Chapter 3.6 --- Clonogenic Assay / Chapter 3.7 --- Immunohistochemical Analysis / Chapter Chapter 4 --- Results / Chapter 4.1 --- Immunoblot Analysis / Chapter 4.2 --- Cytotoxicity Assay / Chapter 4.2.1 --- Effect of ZD 1839 on cell morphology / Chapter 4.2.2 --- Effect of ZD 1839 on cell growth / Chapter 4.3 --- Nucleotide sequence analysis / Chapter 4.3.1 --- RNA Concentration of HCC cells / Chapter 4.3.2 --- Sequencing of TK domain within EGFR / Chapter 4.3.3 --- Sequencing of TK domain within HER2 / Chapter 4.4 --- Clonogenic assay / Chapter 4.4.1 --- Effects of ZD 1839 pre-treatment on radiation response / Chapter 4.4.2 --- Effects of ZD 1839 continuous treatment on radiation response / Chapter 4.5 --- Immunohistochemical Analysis / Chapter Chapter 5 --- Discussion / Chapter 5.1 --- Important Findings / Chapter 5.2 --- EGFR Expression of HCC Cells / Chapter 5.3 --- Cytotoxicity of ZD1839 on HCC Cell Lines / Chapter 5.4 --- Factors Affecting the Cytotoxicity of ZD1839 / Chapter 5.4.1 --- Effect of EGFR Expression on ZD1839 Cytotoxicity / Chapter 5.4.2 --- Effect of EGFR Mutations on ZD 1839 Cytotoxicity / Chapter 5.4.3 --- Effect of HER2 Expression on ZD1839 Cytotoxicity / Chapter 5.4.4 --- Effect of HER2 Mutations on ZD 1839 Cytotoxicity / Chapter 5.5 --- Radiation Response ofHCC Cell Lines upon ZD1839 Treatment / Chapter 5.6 --- Factors Affecting Radiation Response of ZD1839-treated HCC Cell Lines / Chapter 5.6.1 --- Effect of Growth Arrest on Radiation Response of HCC Cell Lines / Chapter 5.6.2 --- Other Factors Affecting Radiation Response of HCC Cell Lines / Chapter Chapter 6 --- Conclusion / References

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Primary hepatic malignant tumors (PHMT) represent an important cause of death of dogs at the Laboratório de Patologia Veterinária of the Universidade Federal de Santa Maria (LPV-UFSM). Based in this information, the prevalence and epidemiological and immunohistochemical aspects of PHMT were reviewed in dogs necropsied in a 48-year period (1965-2012). Out of those7,373 dogs, 64 died due to PHMT, which corresponds to 0.9% of the dogs dying from any cause in the period; 7.8% of dogs which deaths were caused by tumors in general; and 33.5% of all dogs dying from hepatic tumors (primary and metastatic). Out of the 64 cases of PHMT, 51 were reviewed histologically and evaluated by immunohistochemistry; from these cases, 46 were carcinomas (36 cholangiocarcinomas, 9 hepatocellular carcinomas and one hepatocholangiocarcinoma) and five were sarcomas (5 hemangiosarcomas). In those dogs in which the age was possible determined, 64.7% (cholangiocarcinomas) and 77.8% (hepatocellular carcinomas) were old. At necropsy examination cholangiocarcinomas were characterized mainly by a multinodular pattern (83.3%) while hepatocellular carcinomas occurred both as massive (44.4%) or multinodular (44.4%) distribution. Extra-hepatic metastasis occurred respectively in 77.8% and 33.3% of the cases of cholangiocarcinomas and hepatocellular carcinomas; metastatic cholangiocarcinomas affected mainly the lungs (52.8%), lymph nodes (50%) and peritoneum (19.4%). Ascites (22.2%) and icterus (22.2%) were observed frequently associated to both tumors. Histologically, most part of the cholangiocarcinomas (86.1%) and of the hepatocellular carcinomas (55.6%) presented respectively a tubular or trabecular type. Immunohistochemistry revealed that the majority (63.9%) of cholangiocarcinomas was positive for CK7 and none was marked for Hep Par 1. The majority (55.6%) of the hepatocellular carcinomas revealed positive reaction for Hep Par 1 and none was marked for CK7. The results presented here demonstrated a very high prevalence of PHMT, especially cholangiocarcinomas, in the dog. The necropsy, histological and immunohistochemical findings reported might be useful to help veterinary pathologists in the diagnosis of this common form of cancer in dogs of the Rio Grande do Sul, Brazil. / Os tumores hepáticos malignos primários (THMP) representam uma importante causa de morte de cães na rotina do Laboratório de Patologia Veterinária da Universidade Federal de Santa Maria (LPV-UFSM). Diante disso, a prevalência e os aspectos epidemiológicos, anatomopatológicos e imuno-histoquímicos dos THMP em cães foram estudados. De 7.373 cães necropsiados entre 1965 e 2012 (48 anos), 64 morreram de THMP. Esse número corresponde a 0,9% das causas de morte de cães, 7,8% das causas de morte de cães por tumores em geral e 33,5% das causas de morte de cães por tumores hepáticos. Desses 64 casos de THMP, 51 foram revistos histologicamente e avaliados imuno-histoquimicamente, dos quais 46 eram carcinomas (colangiocarcinomas [n=36], carcinomas hepatocelulares [n=9] e hepatocolangiocarcinoma [n=1]) e cinco eram sarcomas (hemangiossarcomas [n=5]). Dos cães com colangiocarcinomas e carcinomas hepatocelulares em que a idade estava disponível nos protocolos, 64,7% e 77,8% eram idosos, respectivamente. Na necropsia, colangiocarcinomas caracterizaram-se principalmente por ocorrerem em um padrão multinodular (83,3%), enquanto carcinomas hepatocelulares ocorreram tanto de forma massiva (44,4%) quanto multinodular (44,4%). Metástases extra-hepáticas foram vistas em 77,8% e 33,3% dos casos de colangiocarcinomas e carcinoma hepatocelulares, respectivamente, e em relação aos colangiocarcinomas afetaram principalmente pulmões (52,8%), linfonodos (50%) e peritônio (19,4%). Ascite (22,2%) e icterícia (22,2%) foram achados associados ocasionalmente com ambos os tumores. Na histologia, a maior parte dos colangiocarcinomas (86,1%) e dos carcinomas hepatocelulares (55,6%) tinha padrão tubular e trabecular, respectivamente. Na imuno-histoquímica, a maioria (63,9%) dos colangiocarcinomas demonstrou imunomarcação para CK7 e nenhum imunomarcou para Hep Par 1. A maioria (55,6%) dos carcinomas hepatocelulares demonstrou imunomarcação para Hep Par 1 e nenhum imunomarcou para CK7. Os resultados aqui apresentados demonstram uma alta prevalência de THMP, principalmente colangiocarcinomas, e servem para auxiliar, através dos achados de necropsia, histologia e imuno-histoquímica, patologistas veterinários no diagnóstico dessa forma tão comum de câncer em cães da Região Central do RS, Brasil.

Indiana University-Purdue University Indianapolis (IUPUI) / MicroRNAs are small RNA molecules that regulate expression of genes involved in development, cell differentiation, proliferation and death. It has been estimated that in eukaryotes, approximately 0.5 to 1% of predicted genes encode a microRNA, which in humans, regulate at least 30% of genes at an average of 200 genes per miRNA. Some microRNAs are tissue-specific, while others are ubiquitously expressed. In liver, a few microRNAs have been identified that regulate specialized functions. The best known is miR-122, the most abundant liver-specific miRNA, which regulates cholesterol biosynthesis and other genes of fatty acid metabolism; it also regulates the cell cycle through inhibition of cyclin G1. To discover other miRNAs with relevant function in liver, we characterized miRNA profiles in normal tissue and identified miR-709. Our data indicates this is a highly abundant hepatic miRNA and is dysregulated in an animal model of type 2 diabetes. To understand its biological role, miR-709 gene targets were identified by analyzing the transcriptome of primary hepatocytes transfected with a miR-709 mimic. The genes identified fell within four main categories: cytoskeleton binding, extracellular matrix attachment, endosomal recycling and fatty acid metabolism. Thus, similar to miR-122, miR-709 downregulates genes from multiple pathways. This would be predicted, given the abundance of the miRNA and the fact that the estimated number of genes targeted by a miRNA is in the hundreds. In the case of miR-709, these suggested a coordinated response during cell proliferation, when cytoskeleton remodeling requires substantial changes in gene expression. Consistently, miR-709 was found significantly upregulated in an animal model of hepatocellular carcinoma. Likewise, in a mouse model of liver regeneration, mature miR-709 was increased. To study the consequences of depleting miR-709 in quiescent and proliferating cells, primary hepatocytes and hepatoma cells were cultured with antagomiRs (anti-miRs). The presence of anti-miR-709 caused cell death in proliferating cells. Quiescent primary hepatocytes responded by upregulating miR-709 and its host gene, Rfx1. These studies show that miR-709 targets genes relevant to cystokeleton structural genes. Thus, miR-709 and Rfx1 may be needed to facilitate cytoskeleton reorganization, a process that occurs after liver injury and repopulation, or during tumorigenesis.

published_or_final_version / Pathology / Master / Master of Philosophy