No description available.

Xie Tong. / "May 2004." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2004. / Includes bibliographical references (p. 113-126). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

acase@tulane.edu / Next generation sequencing (NGS) is a relatively new technology that has revolutionized the way scientists discover and investigate pathogens. It has been estimated that a staggering one in every five cancers worldwide is linked to an infectious agent. An understanding of the pathogen biology as well as the interactions with the host will lead to better therapies and outcomes for patients suffering from pathogen-associated malignancies. Despite the promise for this phenomenon through NGS-based approaches, we are still in the infancy of sequence analysis and are unable to fully appreciate the potential of NGS. To facilitate data mining, an automated computational pipeline for the simultaneous analysis of pathogen and host transcripts called RNA CoMPASS was developed. Using RNA CoMPASS to investigate a variety of sequencing datasets over the years, substantial bacterial contamination have been routinely identified in human-derived RNA-seq datasets that likely arose from environmental sources. Based on this analysis, a need for more stringent sequencing and analysis protocols to investigate sequence-based microbial signatures in clinical samples is crucial. NGS-based approaches were utilized to investigate the role of Epstein-Barr virus (EBV) in the pathogenesis of gastric carcinoma. A comprehensive assessment of the virome of various brain tissue samples was also performed, with the notion that an NGS-based detection method would be unbiased, sensitive, specific, and accurate. Taken together, these studies provide a framework for using NGS technology to study oncogenic pathogens and bring awareness to contamination issues within sequencing datasets. / 1 / Michael J Strong

Epstein-Barr Virus (EBV) has two states of infection, latent and lytic. During the latent state the viral genome remains stable in cells as episomes and replicates with cellular DNA. During the lytic cycle the viral DNA becomes amplified and packaged in newly formed virions. An unsolved problem is whether newly replicated EBV DNA produced upon lytic cycle activation is associated with histones, and if so, whether these histones are acetylated. This question has biological significance as knowing the chromatin structure of genes is important in determining their function and expression profile. Our hypothesis is that newly synthesized EBV lytic DNA is associated with histones and the histone tails are selectively acetylated. To investigate our hypothesis we performed chromatin immunoprecipitation (ChIP) in HH514-16 cells, a Burkitts Lymphoma cell line, during latent and lytic replication. We used quantitative PCR (qPCR) to detect the relative concentration of DNA among the different samples. We tested three different variables: type of inducing agent, duration of treatment, and different regulatory regions in the genome of Epstein-Barr Virus. We found that in cells induced into the lytic cycle with Trichostatin A (TSA), a histone deacetylase inhibitor (HDACi), association of newly replicated EBV DNA with acetylated histone 3 (H3) increased ~ 6-10 fold. This increase in association was greatest 72 hrs after treatment. Furthermore, activation of lytic viral replication in HH514-16 cells using a different inducing agent, Azacytidine (AZC), which is known to function as a DNA methyltransferase inhibitor, increased binding of H3 with viral DNA ~8 fold. However, unlike TSA, AZC increased the acetylation state of histones bound to newly synthesized viral DNA only ~ 2 fold. Changing the regulatory region of the EBV genome analyzed in qPCR did not affect our results. Our results suggest that newly replicated viral DNA is associated with histones, a fraction of which are acetylated. The degree of acetylation likely depends on the agent used to induce the lytic cycle. H3 is highly acetylated when an HDACi is used and less acetylated when AZC is used. Our study provides new insight on the epigenetic profile of newly replicated viral DNA during the lytic cycle. It remains to be determined whether histones are packaged together with viral genomes into virions and whether the chromatin state of virion DNA affects gene expression after the virus enters uninfected cells.

Nasopharyngeal carcinoma (NPC) is a common cancer in Southeast Asia. While external radiotherapy is the mainstay of treatment, adjuvant chemotherapy is required in advanced disease. Current chemotherapy heavily relies on cisplatin and docetaxel. The disease relapse rate is relatively high with poor survival chance for recurrent or metastatic disease. Development of novel therapeutic strategies against the disease is clearly needed. Bortezomib and suberoylanilide hydroxamic acid are respectively classified as proteasome inhibitor and histone deacetylase inhibitor. Bortezomib and SAHA induce apoptosis in various cancers including renal cell carcinoma, hepatoma and mantle cell lymphoma. However, the effect of bortezomib and SAHA on NPC cells was not mentioned. We sought to study the molecular and cellular effects of the bortezomib and SAHA on NPC cells hoping to look for drug alternatives in NPC treatment. Since SAHA reactivates EBV in NPC cells, the combined effect of bortezomib and SAHA on EBV lytic cycle was also evaluated. NPC proliferation was assessed by MTT assay. 5 EBV-positive NPC cell lines authenticated by Short Tandem Repeats (STR) profiling were used as most NPC in Chinese contains EBV. Isobologram and combination index analysis confirmed that the anti-proliferative effect on NPC mediated by the drug combination was synergistic. 30 nM bortezomib and 5μM SAHA were chosen for further studies on apoptosis because the synergism of the drugs was maximal at these concentrations. NA and C666-1 were chosen for further studies because C666-1 was the only NPC cell line that consistently harboured native NPC and the combination index was lowest in NA among the rest of the NPC cell lines. Bortezomib led to apoptosis in NPC cells. The effect was more pronounced after the addition of SAHA as evidenced by greater TUNEL positive population and earlier cleavage of poly ADP ribose polymerase (PARP). In previous cancer studies, ROS induction was commonly suggested pathways of bortezomib and SAHA’s antiproliferative effects. Staining with dichlorofluorescein diacetate (DCFH-DA) revealed enhanced reactive oxygen species (ROS) level in cells treated with both drugs. At the same time, addition of N-acetyl cysteine, a ROS scavenger, markedly reduced their effect on cytotoxicity. SAHA is known for its effect on EBV lytic cycle induction. Yet, the addition of bortezomib diminished SAHA-induced viral load, lytic protein expression and EBV infectivity. The expression of Latent Membrane Protein 1 (LMP1) was much lower in NPC treated with both drugs than in NPC treated with SAHA alone, which would reduce NF-κB activation. This, together with reduced EBNA1 expression upon treatment with both drugs, would theoretically reduce oncogenic activity. In conclusion, bortezomib and SAHA induced ROS-driven apoptosis of NPC in a synergistic manner and bortezomib inhibited SAHA-induced EBV lytic cycle. It suggests that bortezomib and SAHA are potential drug candidates for the treatment of nasopharyngeal carcinoma. / published_or_final_version / Paediatrics and Adolescent Medicine / Master / Master of Research in Medicine

Effective control of chronic viral infections may require the generation of polyfunctional T cells (PFCs) which are capable of producing multiple cytokines and possess cytotoxic function. In this study, I investigate (i) whether PFCs play an important role in the long term immune control of a persistent human virus, Epstein-Barr virus (EBV), (ii) the relationship between the development of immunodominance and functionality during the evolution of the anti-viral T cell responses, and (iii) whether PFCs can be generated in patients with EBV-associated haemophagocytic lymphohistiocytosis (HLH). To tackle the first question, I established a 9-color flow cytometry assay to characterize the co-expression of four cytokines (interferon-f [IFN-[], macrophage inflammatory protein 1-] [MIP1-[], tumour necrosis factor-] [TNF- ] and interleukin-2 [IL-2]) and degranulation marker (CD107a) by both EBV lytic and latent peptide-specific CD4+ and CD8+ T cells in 20 healthy long term viral carriers. Two patients with EBV-associated post-transplant lymphoproliferative disorder (PTLD) were studied for comparison. Both CD4+ and CD8+ PFCs were readily generated in the long term carriers with the immunodominant EBV proteins apparently stimulating higher proportions of PFCs than the subdominant viral proteins. The PFCs producing greater amount of cytokines per cell than the single functional T cells. In contrast, EBV-specific PFCs were hardly generated in the patients with PTLD. To investigate the relationship between the development of immunodominance and functionality, I performed a longitudinal study of CD4+ and CD8+ T cell responses in 10 children with infectious mononucleosis (IM) and 4 asymptomatic individuals (AS) with primary EBV infection from the time of diagnosis to one year post-infection. Viral peptide-specific T cells were examined for the co-expression of three cytokines (IFN-t, TNF-T and IL-2), perforin and CD107a upon stimulation with overlapping peptide pools of lytic and latent proteins, respectively. PBMC viral loads were reduced gradually in both IM and AS subjects. Whilst lytic and latent peptide-specific PFCs were still detectable at the acute stage of infection, they showed an increase in functionality over time in response to peptide pools of immunodominant proteins. From acute to persistent infection stage, the CD8+ T cell responses shifted from reactivities against the lytic peptides to those against the latent EBNA3A and 3B peptides with concurrent increase in functionality. Change in CD4+ T cell responses is less obvious, apparently from reactivities towards broad range to EBNA1 peptides. Finally, we found that two patients with the life-threatening EBV-associated haemophagocytic lymphohistiocytosis (HLH) had very high viral loads at the onset of disease. The clinical symptoms improved and viral loads were gradually reduced by the immunosuppressive drug therapy. Interestingly, EBV lytic and latent peptide-specific PFCs could be subsequently generated post-treatment with sustained resolution of clinical symptoms and clearance of plasma viral loads . In conclusion, lytic and latent peptide-specific CD4+ and CD8+ PFCs may confer long term immune control to EBV. The PFCs may be generated concurrent with the establishment of immunodominance hierarchy during the evolution of viral-specific T cell responses. Long term polyfunctional T cell responses to EBV can be formed in patients with EBV-associated HLH. / published_or_final_version / Paediatrics and Adolescent Medicine / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / toc / Anatomy / Doctoral / Doctor of Philosophy

published_or_final_version / Microbiology / Master / Master of Philosophy

published_or_final_version / Microbiology / Master / Master of Philosophy

No description available.