O melanoma maligno é uma forma de câncer com alto índice de morte devido, em parte, à falta de tratamentos eficazes e à sua tendência de formar metástases. Nosso grupo tem desenvolvido vetores virais para a transferência gênica de fatores anti-tumorais e, inicialmente, foi construído um vetor adenoviral, AdPG, no qual a expressão do transgene é controlada por p53, um supressor de tumor e fator de transcrição. Sendo que aproximadamente 90% dos casos de melanoma retêm p53 selvagem, foi proposto que isto pudesse ser utilizado como uma ferramenta para dirigir a expressão do transgene codificado pelo vetor AdPG, um mecanismo apoiado por resultados anteriores de nosso grupo. Por exemplo, a transdução de células B16 (melanoma de camundongo, p53-selvagem, deleção de p19Arf) com vetores AdPG portadores de p19Arf ou interferon-<font face=\"Symbol\">b (IFN<font face=\"Symbol\">b) resultou em morte celular maciça enquanto a transferência de apenas um destes fatores isolados não causou o mesmo efeito. O trabalho descrito aqui inclui dois avanços tecnológicos críticos em comparação com trabalhos anteriores do grupo. Primeiramente, os transgenes de interesse (eGFP, p19Arf e IFN<font face=\"Symbol\">b) foram inseridos num vetor adenoviral que apresenta o tripetídeo RGD na sua proteína fibra. Essa modificação no vetor permite a eficiente transdução de um amplo espectro de células alvos sem a dependência do receptor viral do adenovírus selvagem, CAR. Além disso, foi construído um vetor bicistrônico, que contém a combinação de ambos os genes terapêuticos, como forma de garantir a transferência dos dois fatores ao mesmo tempo para as células-alvo. A inclusão de p19Arf, um supressor de tumor e inibidor de MDM2, como um gene terapêutico deve complementar as atividades do p53 celular endógeno e, como consequência, atuar na promoção da expressão a partir do vetor e também na inibição da proliferação das células tumorais. Porém, a transferência de p19Arf sozinho acarretaria efeito somente nas células que foram transduzidas e, então, seu efeito seria limitado. Por este motivo, descreve-se, além do p19Arf, a utilização de IFN<font face=\"Symbol\">b, uma proteína secretada com funções anti-tumorais, incluindo inibição de angiogênese, indução de apoptose e ativação da resposta imunológica. A estratégia do projeto contemplou vários níveis relacionados ao mecanismo do processo de transferência, incluindo a eficiência da transdução, o mecanismo de controle da expressão dos transgenes e as atividades dos transgenes. Assim, foi proposto que a combinação de p19Arf e IFN<font face=\"Symbol\">b pudesse ser uma estratégia interessante para induzir morte no tumor primário e uma resposta imunológica contra as células metastáticas. Com este projeto, foi iniciada a construção destes novos vetores aprimorados para transferência gênica nas células de melanoma. / Malignant melanoma is a type of cancer with high death rates, in part, because of a lack of efficient treatments and its tendency to generate metastases. Our group has developed viral vectors for the gene transfer of anticancer factors and, initially, we constructed an adenoviral vector, AdPG, in which transgene expression is controlled by p53, a tumor suppressor and transcription factor. As 90% of melanoma cases maintain wild-type p53, it was proposed that this could be used as a tool to drive transgene expression encoded by the AdPG vector, as evidenced by previous studies from our group. For example, transduction of B16 cells (mouse melanoma, wild-type p53, p19Arf-null) with vectors encoding p19Arf or interferon-<font face=\"Symbol\">b (IFN<font face=\"Symbol\">b) resulted in massive death cell, while transfer of just one of these factors alone did not cause the same effect. The work described here includes two critical technologic advances in comparison with our previous work. First, transgenes of interest (eGFP, p19Arf and IFN<font face=\"Symbol\">b) were inserted into an adenoviral vector which presents the RGD tripeptide in its fiber. This vector modification allows efficient transduction in a wide range of target cells without dependence on the wild type adenovirus receptor, CAR. In addition, a bicistronic vector was constructed which contains the combination of both therapeutic genes, ensuring the transfer of both factors to the target cells at the same time. Use of p19Arf, a tumor suppressor and MDM2 inhibitor, as a therapeutic gene should complement endogenous p53 activities and, as a consequence, promote expression from the AdPG vector and inhibit tumor cell proliferation. However, p19Arf gene transfer alone should have an effect only in transduced cells and, therefore, its effect would be limited. For this reason, we describe, in addition to p19Arf, the application IFN<font face=\"Symbol\">b, a secreted protein with antitumor functions, including inhibition of angiogenesis, induction of apoptosis and activation of immunologic response. This strategy involves several mechanistic levels related with the gene transfer process, including transduction efficiency, control over transgene expression and transgene activity. Therefore, it was proposed that the combination of p19Arf and IFN<font face=\"Symbol\">b could be an interesting strategy to induce primary tumor death and an immunologic response against metastatic cells. In this project, the construction of new vectors optimized for gene transfer in melanoma cells was initiated.

La régulation de l’expression des gènes est critique pour l’adaptation des cellules à leur environnement et pour leur homéostasie. La transcription, qui représente une étape essentielle de l’expression des gènes, est contrôlée par plusieurs facteurs et cofacteurs. L’un de ces cofacteurs, TRRAP, correspond à la plus grosse sous-unité de deux complexes de remodelage de la chromatine, SAGA et TIP60. TRRAP interagit avec divers facteurs de transcription, tels que c-MYC et E2Fs et permet ainsi le recrutement de SAGA et TIP60 aux promoteurs des gènes. TRRAP est un membre d’une famille de kinases atypiques, les PIKKs. Des études antérieures ont défini la co-chaperonne TTT comme régulateur essentiel de la stabilité et l’activité des PIKKs. Contrairement aux autres PIKKs, TRRAP ne possède pas les résidus requis à son activité catalytique et représente donc la seule pseudo-kinase parmi les PIKKs. Bien que TTT interagit et stabilise TRRAP, son rôle sur l’activité de ce dernier reste inconnu. En utilisant un système de dégron inductible qui permet la dégradation rapide de protéines endogènes, nous avons démontré que TTT est requis pour l’assemblage de TRRAP dans ses complexes fonctionnels précédent son import nucléaire. De plus, à travers des analyses transcriptomiques, nous avons pu déterminer que TTT régule la transcription de plusieurs gènes TRRAP-dépendants dans des cellules de cancer colorectal. L’analyse du profile de fixation de TRRAP à l’échelle du génome grâce à la technique du CUT&RUN suivie d’un séquençage à haut débit (CUT&RUN-seq), a permis d’identifier les cibles directes de TRRAP, parmi lesquelles seule une fraction restreinte correspond à des cibles directes de MYC. Nous avons également découvert que TRRAP possède un rôle de répresseur direct sur la transcription d’une partie des gènes stimulés par l’interféron (ISGs) qui interviennent dans la réponse à l’interféron du système immunitaire innée. En outre, nos résultats suggèrent que TRRAP et sa co-chaperonne TTT participent à la tumorigenèse notamment en maintenant et régulant un programme transcriptionnel spécifique. / Gene expression regulation is critical for cells to adapt to external changes and maintain their homeostasis. Transcription is an essential step in gene expression and is controlled by numerous factors and cofactors. One such cofactor is TRRAP, the largest subunit of two distinct chromatin-modifying complexes, SAGA and TIP60. TRRAP interacts with a diverse range of transcription factors including c-MYC and E2Fs, and mediates the recruitment of SAGA and TIP60 to gene promoters. TRRAP is a member of the PIKK family of atypical kinases. Prior studies defined the TTT co-chaperone as an essential regulator of PIKK stability and activity. In contrast to its cognate kinases, TRRAP lacks catalytic residues and is the sole pseudokinase among PIKKs. Although TTT has been shown to stabilize and interact with TRRAP, the role of TTT on TRRAP function remains unknown. Using an inducible degron system that allows the rapid and acute depletion of endogenous proteins, we demonstrated that TTT is required to assemble TRRAP within its functional complexes prior its nuclear import. Additionally, through transcriptomic analyses we determined that TTT regulates a large number of TRRAP-dependent genes in colorectal cancer cells. Profiling of the genome-wide binding of TRRAP via CUT&RUN-seq identified the direct targets of TRRAP, of which only a small fraction overlaps with MYC targets. We also uncovered a direct inhibitory role of TRRAP on a subset of the interferon-stimulated genes, which mediate the interferon response in the innate immune system. Altogether, our data suggest that TRRAP and its chaperone TTT are involved in tumorigenesis through the maintenance of a specific transcriptional program.

Listeria monocytogenes (LM) and Salmonella enterica serovar Typhimurium (ST) are intracellular bacterial pathogens that cause invasive disease in immune-altered individuals, including the immunocompromised and pregnant women. The mechanisms that modulate innate immunity to intracellular infection, particularly during pregnancy, are not well-understood. Functional selectin ligands play critical roles in leukocyte recruitment during inflammation. Increased control of LM infection in functional selectin ligand-deficient (FtDKO) mice is associated with increased levels of circulating innate immune cells, despite defective leukocyte migration compared to WT mice. Adoptive transfer of WT and FtDKO bone marrow (BM) cells to irradiated WT and FtDKO recipients demonstrates that BM reconstitution and the increased neutrophil phenotype of FtDKO mice is independent of functional selectin ligand expression within the host environment. Thus, functional selectin ligand deficiency enhances inherent innate immune resistance to intracellular infection. We then examined the impact of pregnancy-associated immunological changes on maternal susceptibility to intracellular infections. ST infection in pregnant mice results in profound systemic infection, increased fetal loss and enhanced serum and placental expression of pro-inflammatory cytokines. Pregnant mice showed decreased ratios of pro-inflammatory Th17 cells relative to anti-inflammatory regulatory T cells (Tregs) when compared to non-pregnant mice during infection. Functional inactivation of Tregs in vivo restored control of infection and normal Th17-to-Treg ratios, and reduced fetal loss. These indicate that modulation of Th17 and Treg responses impacts maternal and fetal protection from ST infection. Lastly, we examined the roles of type I interferons (IFNs) in modulating innate immunity to intracellular infections during pregnancy. Type I IFN receptor deficiency (IFNAR-/-) enhances immunity to LM and ST in the non-pregnant state by limiting pathogen-induced leukocyte death. We show that pregnant IFNAR-/- mice infected with LM retain increased protection from infection relative to WT controls. In contrast, protection conferred by IFNAR deficiency against ST infection in the non-pregnant state is abrogated during pregnancy. Distinctive maternal responses to LM and ST are associated with differential regulation of leukocyte distribution and cytokine expression in maternal systemic and/or placental compartments. Taken together, modulation of key mechanisms involved in leukocyte recruitment, immune-regulation and cytokine signaling impact host susceptibility to intracellular infections.

As a foodborne pathogen, Listeria monocytogenes (Lm) encounters many barriers to invasion and dissemination in the host that may change the nature of host response. Lm has been most commonly studied using intravenous (i.v.) inoculation, however, a method that delivers a bolus of bacteria directly to the bloodstream. Thus, little is known about what systemic and local mediators are triggered during the natural course of infection and how these may impact susceptibility. Our laboratory used foodborne transmission of Lm in mice to assess whether the method of transmission and the specific organ microenvironment could affect infection-induced secretion of type I interferon or prostaglandin E2. Type I interferon is a pro-inflammatory effector secreted in response to viruses that has been proposed to paradoxically down-regulate innate immunity to intracellular bacteria. In contrast to i.v. infection, type I interferon was not detrimental to the immune response when Lm were acquired orally. In fact, most of the anti-inflammatory effects of type I interferon in the spleen were attributable to i.v. but not foodborne infection. Importantly however, downregulation of the receptor for interferon gamma (IFNGR1), previously ascribed to the type I interferon response, was found to be a consequence of infection and unrelated to type I interferon. In the liver, robust recruitment and activation of neutrophils (PMN) is thought to be required for initiation of Lm immunity. Prostaglandin E2 (PGE2) is a lipid mediator most commonly associated with pain and fever that has also been demonstrated to have anti-inflammatory or tolerogenic effects. It is unknown, however, whether foodborne infection induces PGE2 in the liver and if PGE2 then down-regulates PMN activities. Recruitment of PMN to the liver following foodborne infection was robust in both susceptible and resistant animals. Bone marrow PMN from each killed Lm ex vivo with similar efficiency, thus suggesting that if PMN were dysfunctional during the course of natural infection, they were responding to cues in the microenvironment. Accordingly, significantly more PGE2 was made ex vivo by cells from the livers of susceptible animals than from resistant animals. When PGE2 was applied to naïve PMN prior to exposure to Lm, it consistently dampened the killing efficiency of these cells, suggesting that this lipid better known for its pro-inflammatory roles might have anti-inflammatory effects during Lm infection. Overall, these studies indicate that mediators produced as a result of infection may have very different roles dependent on route of inoculation, timing, and the specific organ examined.

<p>Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation. We developed a novel multiplexed method for SNP genotyping based on four-color fluorophore tag-microarray minisequencing. This method allows simultaneous genotyping of 80 samples and up to 200 SNPs in any allele combination. In study I we set up the method for a panel of SNPs from genes in the type I interferon system, and applied it in study III. In study II we used the technique to genotype SNPs from the coding region of the mitochondrial genome. A panel of 150 SNPs was genotyped in 265 individuals representing nine different populations. We demonstrated that the multiplexed SNP genotyping method for mitochondrial DNA increases the power of forensic identification in combination with sequencing of the hypervariable region of mitochondrial DNA. </p><p>In study III we performed a genetic association study of SNPs in genes related to the type I Interferon system in Systemic Lupus Erythematosus (SLE). SLE is a chronic autoimmune inflammatory disease with a complex etiology. The SNPs were genotyped in DNA samples from Swedish, Finnish, and Icelandic patients with SLE, unaffected family members, and unrelated controls. The analysis identified SNPs in two genes, the tyrosine kinase 2 (TYK2) and interferon regulatory factor 5 (IRF5) genes that are highly associated with SLE with p-values <10^-7 for joint linkage and association. </p><p>Study IV describes the analysis of the TYK2 and IRF5 SNPs in a large Rheumatoid Arthritis (RA) sample cohort. We found that SNPs in the IRF5 gene were significantly associated with RA with a p-value = 0.00008. In contrast, we did not detect an association with SNPs in the TYK2 gene. These findings demonstrate that SLE and RA may have a common genetic background in the case of IRF5, while the TYK2 variants appear to be unique for SLE. </p>

Single nucleotide polymorphisms (SNPs) are the most common form of genetic variation. We developed a novel multiplexed method for SNP genotyping based on four-color fluorophore tag-microarray minisequencing. This method allows simultaneous genotyping of 80 samples and up to 200 SNPs in any allele combination. In study I we set up the method for a panel of SNPs from genes in the type I interferon system, and applied it in study III. In study II we used the technique to genotype SNPs from the coding region of the mitochondrial genome. A panel of 150 SNPs was genotyped in 265 individuals representing nine different populations. We demonstrated that the multiplexed SNP genotyping method for mitochondrial DNA increases the power of forensic identification in combination with sequencing of the hypervariable region of mitochondrial DNA. In study III we performed a genetic association study of SNPs in genes related to the type I Interferon system in Systemic Lupus Erythematosus (SLE). SLE is a chronic autoimmune inflammatory disease with a complex etiology. The SNPs were genotyped in DNA samples from Swedish, Finnish, and Icelandic patients with SLE, unaffected family members, and unrelated controls. The analysis identified SNPs in two genes, the tyrosine kinase 2 (TYK2) and interferon regulatory factor 5 (IRF5) genes that are highly associated with SLE with p-values &lt;10-7 for joint linkage and association. Study IV describes the analysis of the TYK2 and IRF5 SNPs in a large Rheumatoid Arthritis (RA) sample cohort. We found that SNPs in the IRF5 gene were significantly associated with RA with a p-value = 0.00008. In contrast, we did not detect an association with SNPs in the TYK2 gene. These findings demonstrate that SLE and RA may have a common genetic background in the case of IRF5, while the TYK2 variants appear to be unique for SLE.

O melanoma maligno é uma forma de câncer com alto índice de morte devido, em parte, à falta de tratamentos eficazes e à sua tendência de formar metástases. Nosso grupo tem desenvolvido vetores virais para a transferência gênica de fatores anti-tumorais e, inicialmente, foi construído um vetor adenoviral, AdPG, no qual a expressão do transgene é controlada por p53, um supressor de tumor e fator de transcrição. Sendo que aproximadamente 90% dos casos de melanoma retêm p53 selvagem, foi proposto que isto pudesse ser utilizado como uma ferramenta para dirigir a expressão do transgene codificado pelo vetor AdPG, um mecanismo apoiado por resultados anteriores de nosso grupo. Por exemplo, a transdução de células B16 (melanoma de camundongo, p53-selvagem, deleção de p19Arf) com vetores AdPG portadores de p19Arf ou interferon-<font face=\"Symbol\">b (IFN<font face=\"Symbol\">b) resultou em morte celular maciça enquanto a transferência de apenas um destes fatores isolados não causou o mesmo efeito. O trabalho descrito aqui inclui dois avanços tecnológicos críticos em comparação com trabalhos anteriores do grupo. Primeiramente, os transgenes de interesse (eGFP, p19Arf e IFN<font face=\"Symbol\">b) foram inseridos num vetor adenoviral que apresenta o tripetídeo RGD na sua proteína fibra. Essa modificação no vetor permite a eficiente transdução de um amplo espectro de células alvos sem a dependência do receptor viral do adenovírus selvagem, CAR. Além disso, foi construído um vetor bicistrônico, que contém a combinação de ambos os genes terapêuticos, como forma de garantir a transferência dos dois fatores ao mesmo tempo para as células-alvo. A inclusão de p19Arf, um supressor de tumor e inibidor de MDM2, como um gene terapêutico deve complementar as atividades do p53 celular endógeno e, como consequência, atuar na promoção da expressão a partir do vetor e também na inibição da proliferação das células tumorais. Porém, a transferência de p19Arf sozinho acarretaria efeito somente nas células que foram transduzidas e, então, seu efeito seria limitado. Por este motivo, descreve-se, além do p19Arf, a utilização de IFN<font face=\"Symbol\">b, uma proteína secretada com funções anti-tumorais, incluindo inibição de angiogênese, indução de apoptose e ativação da resposta imunológica. A estratégia do projeto contemplou vários níveis relacionados ao mecanismo do processo de transferência, incluindo a eficiência da transdução, o mecanismo de controle da expressão dos transgenes e as atividades dos transgenes. Assim, foi proposto que a combinação de p19Arf e IFN<font face=\"Symbol\">b pudesse ser uma estratégia interessante para induzir morte no tumor primário e uma resposta imunológica contra as células metastáticas. Com este projeto, foi iniciada a construção destes novos vetores aprimorados para transferência gênica nas células de melanoma. / Malignant melanoma is a type of cancer with high death rates, in part, because of a lack of efficient treatments and its tendency to generate metastases. Our group has developed viral vectors for the gene transfer of anticancer factors and, initially, we constructed an adenoviral vector, AdPG, in which transgene expression is controlled by p53, a tumor suppressor and transcription factor. As 90% of melanoma cases maintain wild-type p53, it was proposed that this could be used as a tool to drive transgene expression encoded by the AdPG vector, as evidenced by previous studies from our group. For example, transduction of B16 cells (mouse melanoma, wild-type p53, p19Arf-null) with vectors encoding p19Arf or interferon-<font face=\"Symbol\">b (IFN<font face=\"Symbol\">b) resulted in massive death cell, while transfer of just one of these factors alone did not cause the same effect. The work described here includes two critical technologic advances in comparison with our previous work. First, transgenes of interest (eGFP, p19Arf and IFN<font face=\"Symbol\">b) were inserted into an adenoviral vector which presents the RGD tripeptide in its fiber. This vector modification allows efficient transduction in a wide range of target cells without dependence on the wild type adenovirus receptor, CAR. In addition, a bicistronic vector was constructed which contains the combination of both therapeutic genes, ensuring the transfer of both factors to the target cells at the same time. Use of p19Arf, a tumor suppressor and MDM2 inhibitor, as a therapeutic gene should complement endogenous p53 activities and, as a consequence, promote expression from the AdPG vector and inhibit tumor cell proliferation. However, p19Arf gene transfer alone should have an effect only in transduced cells and, therefore, its effect would be limited. For this reason, we describe, in addition to p19Arf, the application IFN<font face=\"Symbol\">b, a secreted protein with antitumor functions, including inhibition of angiogenesis, induction of apoptosis and activation of immunologic response. This strategy involves several mechanistic levels related with the gene transfer process, including transduction efficiency, control over transgene expression and transgene activity. Therefore, it was proposed that the combination of p19Arf and IFN<font face=\"Symbol\">b could be an interesting strategy to induce primary tumor death and an immunologic response against metastatic cells. In this project, the construction of new vectors optimized for gene transfer in melanoma cells was initiated.

No description available.

No description available.

Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / Ying Fang / Porcine reproductive and respiratory syndrome virus (PRRSV) employs multiple functions to modulate host’s innate immune response, and several viral nonstructural proteins (nsps) are major players. In this dissertation, the research was mainly focused on identification and functional dissection of ORF1a-encoded nsps. PRRSV replicase polyproteins encoded by ORF1a region are predicted to be processed into at least ten nonstructural proteins. In chapter 2, these predictions were verified by using a panel of newly established antibodies specific to ORF1a-encoded nsps. Most predicted nsps (nsp1β, nsp2, nsp4, nsp7α, nsp7β and nsp8) were identified, and observed to be co-localized with de novo-synthesized viral RNA in the perinuclear region of the cell. Among all PRRSV proteins screened, nsp1β is the strongest type I interferon antagonist. In chapter 3, mutagenesis analysis of nsp1β was performed to knock down nsp1β’s IFN antagonist function. A highly conserved motif, GKYLQRRLQ, was determined to be critical for nsp1β’s ability to suppress IFN-β and reporter gene expression. Double mutations introduced in this motif, K130A/R134A (type 1 PRRSV) or K124A/R128A (type 2 PRRSV), improved PRRSV’s ability to stimulate the expression of IFN-α, IFN-β and ISG15. In addition to its critical roles involving in modulating host innate immune response, in the studies of Chapter 4, we demonstrated that PRRSV nsp1β functions as a transactivator to induce the -2/-1 ribosomal frameshifting in nsp2, which results in expression of two novel PRRSV proteins, nsp2TF and nsp2N. The conserved motif GKYLQRRLQ is also determined to be critical for the transactivation function of nsp1β. In chapter 5, the interferon antagonist, de-Ub and de-ISGylation activity of newly identified nsp2TF and nsp2N were evaluated. In vitro and in vivo characterization of three nsp2TF-deficient recombinant viruses indicated that all mutant viruses have improved ability to stimulate the innate immune response and provide improved protection in mutant virus-vaccinated animals. In summary, this study verified the previously predicted PRRSV pp1a processing products, further evaluated the function of nsp1β and nsp2-related proteins. These data obtained here will provide basic knowledge for future development of vaccines and control measurements.