Protein-protein interactions play an important role in nearly all processes of the living cells and the function of many proteins is dependent on their specific interactions with other biomolecules. A reliable tool to modulate these interactions would be invaluable for the development of molecules suitable for diagnostics, medicine, and biotechnology. In this work, we aimed to study the specificity of interactions in the model system of Interferon gamma receptor 1 (IFNgR1) and its natural ligand Interferon gamma (IFNg), important in innate immunity. We searched for mutations within the interferon receptor molecule IFNgR1 to modulate (increase as well as decrease) its affinity to IFNg by in silico analysis of the existing crystal structures of the complex between IFNgR1 and IFNg. We modeled amino acid substitutions and gauged how they influenced the interaction using empirical force field implemented in software FoldX. All selected promising IFNgR1 variants were expressed in Escherichia coli, purified to homogeneity, characterized, and kinetics of their interactions with IFNg was measured by Surface Plasmon Resonance (SPR). The first set of IFNgR1 variants included mutations on the interface of the IFNg/IFNgR1 complex. According to our SPR measurements, the affinity of most of these receptor...

Hepatitis C virus (HCV) infection is a leading cause of cirrhosis and hepatocellular carcinoma. The degree of fibrosis progression and treatment-related outcomes are critically dependent on the age of the infected individual. Progressive ageing is associated with a decline in the efficacy of adaptive immune system function. T-lymphocytes from aged subjects demonstrate multiple phenotypic and functional changes, including telomere shortening. Short telomeres are associated with poor proliferative capacity, pro-inflammatory responses and increased mortality in clinical studies. This research aimed to study telomere length changes in T-lymphocytes in chronic HCV infection and its relationship to clinical endpoints. Further, the intracellular signalling changes in T-lymphocytes with short telomeres were studied in subjects with chronic HCV. Short CD4+ T-lymphocyte telomeres were associated with the presence of severe hepatic fibrosis independent of other known factors. Telomere length was associated with blood markers of hepatic damage and dysfunction as well as histological markers of inflammation and fibrosis. Further, on prospective follow-up, short CD4+ telomere length at enrolment predicted progression to clinical endpoints of hepatic decompensation, development of hepatocellular carcinoma and death. Short CD4+ telomere length predicted a failure to respond to anti-viral treatment for HCV infection. Unexpectedly, subjects with non-viraemic HCV had short CD8+ telomere length. Liver biopsy tissue from a cohort of subjects with non-viraemic HCV was studied and demonstrated significant inflammation or fibrosis in most. To study the IFN-α signalling pathway in cells with short telomeres, I utilised the phospho-histone γ-H2AX, a downstream signal from short telomeres. CD8+ T-lymphocytes expressing γ-H2AX had the form and function of cells with end-stage differentiation. γ-H2AX+ cells had a pro-inflammatory cytokine secretion profile with high expression of IFN-γ and low IL-2. Further γ-H2AX+ cells were unable to respond to exogenous IFN-α by phosphorylating Stat1. This failure was attributable to a post-receptor defect. T-lymphocyte telomere length changes in HCV may underpin the effect of age on clinical and treatment-related outcome. Short telomeres are associated with intracellular signalling defects which may explain the failure to respond to anti-viral therapy.

SMAC mimetic compounds (SMCs) are small molecule antagonists of the Inhibitor of Apoptosis (IAP) family of proteins. Binding of SMCs to the IAPs results in the sensitization of cancer cells to apoptosis in the presence of death ligands, such as tumour necrosis factor alpha (TNFα). I hypothesize that type I interferon (IFN) stimulation in cancer cells and in immune cells leads to the production of TNFα, which can then synergize with SMCs to kill cancer cells. The combined treatment of SMC and IFNα induces tumour regression in mice, and this effect is completely abrogated upon treatment with TNFα-neutralizing antibody. The synergistic effects are mediated by tumour cells and by contribution of immune cells, particularly macrophages and dendritic cells, as the systemic depletion of phagocytic innate immune cells results in an increase in tumour volume following combination treatment. The characterization of immune cell contribution will aid in the translation of the SMC combination therapy into clinical applications for the treatment of cancer.

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Tsang Sai Leong. / Thesis submitted in: December 2004. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 96-104). / Abstracts in English and Chinese. / Abstract (in Chinese) --- p.(i) / Abstract --- p.(iii) / Table of contents --- p.(v) / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- The interferon --- p.1 / Chapter 1.1.1 --- About type I IFN --- p.1 / Chapter 1.1.2 --- IFN α/β receptor and signal transduction --- p.3 / Chapter 1.1.3 --- IFN induction --- p.3 / Chapter 1.1.4 --- Functions --- p.4 / Chapter 1.1.5 --- MuIFN α subtypes --- p.8 / Chapter 1.1.6 --- Gene expression --- p.9 / Chapter 1.2 --- Aim of study: Functions and gene expression --- p.9 / Chapter Chapter 2 --- Materials and Methods / Chapter 2.1 --- Materials --- p.15 / Chapter 2.1.1 --- "Cell line, bacterial strain, virus strain and plasmid vector" --- p.15 / Chapter 2.1.2 --- Chemicals --- p.20 / Chapter 2.1.3 --- "Culture media, buffer and other solutions" --- p.20 / Chapter 2.1.4 --- Reagents and nucleic acids --- p.21 / Chapter 2.1.5 --- Reaction kits --- p.22 / Chapter 2.1.6 --- Solutions --- p.22 / Chapter 2.1.7 --- Major equipments --- p.24 / Chapter 2.1.8 --- Primers used --- p.24 / Chapter 2.2 --- Methods --- p.26 / Chapter 2.2.1 --- "Cloning of MuIFN αl2, MuIFN αl and MuIFN α4 from L929 genomic DNA and their subcloning into pEGFP-Nl mammalian expression vector" --- p.26 / Chapter 2.2.1.1 --- PCR of MuIFN αl2 --- p.26 / Chapter 2.2.1.2 --- Gel purification of MuIFN αl2 PCR product --- p.26 / Chapter 2.2.1.3 --- Ligation of MuIFN αl2 PCR product into pGEM-T vector --- p.26 / Chapter 2.2.1.4 --- Sequencing of clones which were positive in PCR screening --- p.26 / Chapter 2.2.1.5 --- Subcloning of the gene from pGEM-T vector to pEGFP-Nl --- p.28 / Chapter 2.2.1.6 --- Construction of expression vectors for MuIFN αl and MuIFN a4 gene --- p.28 / Chapter 2.2.2 --- Preparation ofplasmid DNA --- p.29 / Chapter 2.2.3 --- Preparation of cell culture medium --- p.30 / Chapter 2.2.4 --- Production of recombinant MuIFN α (rMuIFN α) --- p.30 / Chapter 2.2.5 --- Production of native MuIFN α by polyI：polyC induction --- p.31 / Chapter 2.2.6 --- Influenza A virus strain A/NWS/33 preparation and titration --- p.31 / Chapter 2.2.7 --- Virus infection in Influenza A virus challenge assay --- p.32 / Chapter 2.2.8 --- Cell culture techniques --- p.32 / Chapter 2.2.9 --- "MTT cell proliferation assay of JCS cell line, for measuring MuIFN α anti-proliferation activity" --- p.33 / Chapter 2.2.10 --- Quantitative analysis of MuIFN α --- p.34 / Chapter 2.2.11 --- Flow cytofluorometric analysis of cell cycle of MuIFN α treated JCS cells by propidium iodide staining --- p.34 / Chapter 2.2.12 --- FACS study on the effect of MuIFN α on MHC-I up-regulation in JCS cells --- p.35 / Chapter 2.2.13 --- FACS study on the effect of MuIFN α on MHC-I up-regulation on primary macrophages from Balb/c mice --- p.35 / Chapter 2.2.14 --- Anti-viral activity by transfection of MuIFN α gene --- p.36 / Chapter 2.2.15 --- Sequencing of MuIFN al2 coding region from genomic DNA of L929 and JCS cell lines --- p.37 / Chapter 2.2.16 --- "RNA extraction from L929 cell lines, with or without Influenza A virus infection or polyI:polyC induction" --- p.37 / Chapter 2.2.17 --- RNA extraction from tissues of Balb/c mouse --- p.38 / Chapter 2.2.18 --- Reverse transcription --- p.39 / Chapter 2.2.19 --- Polymerase Chain Reaction (PCR) --- p.39 / Chapter Chapter 3 --- Results / Chapter 3.1 --- Overview --- p.40 / Chapter 3.2 --- "Subcloning of MuIFN α 12, MuIFN αl and MuIFN α4 coding sequences into the pEGFP-Nl vector" --- p.40 / Chapter 3.3 --- The growth inhibitory effect of different MuIFN α subtypes on murine myeloid leukemia cell line JCS --- p.41 / Chapter 3.4 --- Quantitation of MuIFN α subtype samples --- p.50 / Chapter 3.5 --- Cell cycle analysis of MuIFN α treated JCS cells --- p.50 / Chapter 3.6 --- FACS analysis of the effect of different MuIFN α subtypes on MHC-I expression in JCS cell line --- p.57 / Chapter 3.7 --- FACS analysis of the effect of different MuIFN α subtypes on MHC-I expression in primary macrophages in Balb/c mice --- p.65 / Chapter 3.8 --- Effect of MuIFN α subtype transgenes on L929 cells challenged with Influenza A virus --- p.72 / Chapter 3.9 --- Sequencing of MuIFN αl2 coding region from genomic DNA of L929 and JCS cell line --- p.78 / Chapter 3.10 --- "MuIFN αl2 expression in untreated, Influenza A virus infected or polyl:polyC induced L929 cells" --- p.78 / Chapter 3.11 --- Detection of MuIFN α12 transcripts in tissues of the 8-10 week untreated Balb/c mice --- p.85 / Chapter Chapter 4 --- Discussion --- p.89 / Chapter 4.1 --- Overview --- p.89 / Chapter 4.2 --- rMuIFN α 12 has anti-proliferative and apoptotic effects on JCS cell line --- p.89 / Chapter 4.3 --- "Up-regulation of MHC-I expression in JCS cells and primary macrophages by rMuIFN αl2, rMuIFN αl, rMuIFN α4 and mixed type I IFN" --- p.91 / Chapter 4.4. --- Transfection of MuIFN α12 gene could induce anti-viral state in L929 cell line --- p.91 / Chapter 4.5 --- Gene regulation of MuIFN al2 in L929 cells infected with Influenza A virus or induced by polyI:polyC --- p.92 / Chapter 4.6 --- Gene expression of MuIFN αl2 in different tissues of Balb/c mice --- p.94 / Conclusion --- p.95 / Reference List --- p.96 / List of figures: / Fig. 1.1 The 3D structure of recombinant human interferon alpha (HuIFN α) subtype 2B --- p.11 / Fig. 1.2 Current model of lFN induction --- p.12 / Fig. 1.3 Activation of RNase L --- p.13 / Fig. 2.1 Graphical map of plasmid vector pEGFP-Nl --- p.17

Interferons comprise a class of structurally related proteins which exert several regulatory effects in responsive cells. These effects include the establishment of an antiviral state, the inhibition of cellular proliferation and the alteration of different immune reactions. In particular, the IFN:s rapidly augment the lytic activity of the natural killer (NK) cells. In the present thesis, some of the functional and molecular mechanisms by which IFN:s act on NK cells and other leucocytes are studied. A good correlation is found between the ability of different tumor cell lines to induce IFN production among peripheral blood lymphocytes and their sensitivity to NK cell cytotoxicity, indicating that IFN might regulate the activity of NK cells through a positive feed-back mechanism. When studying the interaction between the NK cells and two target cell lines it is demonstrated that the two cell lines are not recognized by the same receptors. The augmentation of NK cell cytotoxicity by IFN is shown to involve both alteration of receptor structures on the NK cell and enhancement of steps in their lytic machinery. The effects of IFN on the synthesis of individual proteins is then studied by two-dimensional electrophoresis. It is demonstrated that IFN-a and IFN-ß within 1.5 hours induce the synthesis of nine proteins (Mf80, 75, 62, 58, 53, 38, 36, 33 and 30 kD) in human lymphocytes. Tne induction is dependent on a rapid de novo RNA synthesis, which is initiated less than 30 minutes after the addition of IFN. The expression of the nine proteins is well correlated to the development of augmented NK cell cytotoxicity. Four of the proteins (Mr 80, 62, 38 and 33 kD) are found to be expressed in a panel of ten hematopoetic and two anchorage-dependent cell lines, whereas the remaining proteins seem to be expressed in leucocytes only. IFN induce the synthesis of the same proteins in both purified large granular lymphocytes (responsible for the main NK cell activity in man), T cells and monocytes, demonstrating that the augmentation of NK cell activity does not involve the formation of unique 1NK-cel11 specific proteins. Rather, the augmentation of the lytic activity of both NK cells, cytotoxic T cells and monocytes seem to involve common stages in their lytic mechanisms. In contrast to IFN-a and IFN-ß, IFN-y, does not induce any detectable proteins in either NK cells or T cells. This lack of effect of IFN-y on the protein synthesis is not a general phenomenon, since the effects of IFN-a and IFN-y are similar 1n a glioma cell line. These results demonstrate that there exists at least one pathway to augment the NK cell cytotoxicity which does not involve the increased synthesis of the nine IFN-a/IFN-ß inducible proteins and indicates that either these proteins are mainly involved in other effects of IFN, or that the augmentation by IFN-a/IFN-ß and IFN-y involve different pathways. When the effects of IFN-a on the synthesis of membrane-associated proteins is studied, it is demonstrated that only the 80 kD IFN-a inducible protein is associated with the cell membrane. In addition, IFN-a seems to induce three additional, me mb rane-as so ci a ted proteins (Mr 94, 76 and 66 kD) which are not detected in whole cell lysates. / <p>Diss. (sammanfattning) Umeå : Umeå universitet, 1985, härtill 5 uppsatser.</p> / digitalisering@umu

Thesis (M.Sc.). / Written for the Dept. of Microbiology and Immunology. Title from title page of PDF (viewed 2008/05/14). Includes bibliographical references.

Orientador: Raquel Mantuaneli Scarel Caminaga / Banca: Elisa Maria Aparecida Giro / Banca: Paula Cristina Trevilatto / Resumo: A doença periodontal (DP) em indivíduos com Síndrome de Down (SD) se desenvolve com alta prevalência, precocemente, de modo rápido e generalizado em comparação com indivíduos não-sindrômicos. Foi demonstrado que portadores da SD apresentam resposta imune diminuída em relação aos cromossomicamente normais. O objetivo desta pesquisa foi investigar diferenças nos parâmetros clínicos periodontais e níveis de expressão dos genes Interferon-gama (IFNG), Interferon-gama receptor 1 (IFNGR1), Interferon-gama receptor 2 (IFNGR2), Interferon-alfa (IFNA), Interferon-alfa receptor 1 (IFNAR1), Interferon-alfa receptor 2 (IFNAR2), Janus-quinase 1 (JAK1), Transdutor de sinal e ativador da transcrição 1 (STAT1) e Fator de regulação de interferon 1 (IRF1) em indivíduos com SD que apresentam ou não DP e em indivíduos cromossomicamente normais. Fizeram parte deste estudo 80 indivíduos entre 7 e 57 anos de idade subdivididos em 4 grupos: SD com DP (A); indivíduos com SD sem DP (B); indivíduos não-sindrômicos (Controle) com DP (C) e indivíduos Controle sem DP (D). A expressão gênica foi investigada por meio de quantificação relativa utilizando a técnica da Reação em Cadeia da Polimerase (PCR) em Tempo Real. Para o índice sangramento à sondagem (SS) não houve diferença entre os grupos A e 21 C. A periodontite crônica localizada foi o tipo prevalente tanto entre indivíduos com SD como Controle. Considerando os parâmetros clínicos, não foram encontradas diferenças na periodontite crônica localizada entre os indivíduos com SD e Controle, assim como para a periodontite crônica generalizada. Com relação à análise genética, observou-se que indivíduos dos grupos com SD em relação aos grupos cromossomicamente normais (A+B-C+D) tiveram uma expressão de IFNG semelhante ao observado entre indivíduos do grupo... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Periodontal disease (PD) in individuals with Down Syndrome (DS) has an early, quickly and widespread onset and high prevalence when compared with individuals without the Syndrome. Only poor oral hygiene does not explain the severe periodontal destruction seen in DS patients. It has been shown that DS patients have a weaker immune response than people with normal number of chromosomes. The aim of this study was to investigate differences in periodontal clinical parameters and the expression levels of the genes Interferon-gamma (IFNG), Interferon-gamma receptor 1 (IFNGR1), Interferon-gamma receptor 2 (IFNGR2), interferon-alpha (IFNA), interferon-alpha receptor 1 (IFNAR1), Interferon-alpha receptor 2 (IFNAR2), Janus-kinase 1 (JAK1), Signal transducers and activators of transcription 1 (STAT1) and Interferon regulatory factor 1 (IRF1) in DS patients with and without periodontal disease in comparison with chromossomically normal individuals. A total of 80 individuals aged 7 to 57 years participated in this study and were divided into 4 groups: DS with PD (A); DS without PD (B); individuals without DS (control) with PD (C) and individuals without DS (control) and without PD (D). A quantitative RT-qPCR was used to investigate gene expression. There was no difference between groups A and C regarding the bleeding on probing 25 (BOP) index. The most prevalent type of periodontitis seen in this study was the localized chronic periodontitis, both in individuals with and without DS. Considering the clinical parameters, localized and generalized chronic periodontitis did not differ between individuals with and without DS. Regarding genetic analysis, individuals of the groups with DS in relation to the groups without DS (A+B-C+D) showed an IFNG expression similar to that seen among the individuals of groups control with PD (C-D). However, individuals... (Complete abstract click electronic access below) / Mestre

The complexity of melanoma is pronounced at many levels, whereby both environmental influences and genetic predisposition are involved and interact. Embedded within this complexity is heterogeneity, a defining characteristic of this malignancy. The rearrangement of genomic material on chromosomes 1p, 6q, 9p or 10q, 11q and 17q has been frequently reported during the development and progression of cutaneous malignant melanoma (CMM), suggesting several putative tumour suppressor genes and oncogenes in these regions. The genomic complexity of chromosome 9p21 in melanoma development is well documented. This region encodes a potent cyclin-dependent kinase inhibitor CDKN2/INK4A/p16 as a tumour suppressor gene (TSG) that is frequently inactivated in melanomas. Functional evidence suggested the presence of additional TSG loci in the 9p21-22 chromosome region (Parris et al., 1999). In pursuit of identifying novel TSG(s), our previous group’s collaborative research provided experimental evidence that suggests IFNA1 as a candidate TSG for melanoma development. Therefore, the aim of this work was to provide a further functional validation of such tumour-suppressive activity in CMM. Firstly, I have successfully subcloned IFNA1 cDNA into pcDNA3 expression vector and established a panel of stably IFNA1-expressing clones. Subsequently, I have assessed their tumourigenicity in soft agar by measuring the colony-forming ability of each transfected clone. Expression analyses of IFNA1, at both post-transcriptional and translational levels, were also carried out. I have also demonstrated a strong correlation between anchorage-independent growth in soft agar and IFNA1 expression in qRT-PCR. The antiproliferative and pro-apoptotic effects of IFNα have been widely documented, however, the precise mechanisms that trigger and potentiate this behaviour are not completely known. Based on previous findings, I have investigated whether IFNA1 exerts its antitumoural activity through apoptosis. I was able to demonstrate a moderate relationship between anchorage-independent growth in soft agar and the apoptotic levels in the transfected clones. Although unpersuasive and inconclusive, the results seemed encouraging since this study was carried out using only the highly tumourigenic malignant melanoma UACC903 cell line.

Interferon regulatory factor 1 (IRF-1), the founding member of IRF family, is a nuclear transcription factor first described as a transcription factor that binds to the upstream region of interferon induced genes following viral infection. In addition, IRF-1 has been reported to be involved in cell growth regulation, induction of apoptosis, immune responses, post-transcriptional modification, and cell transformation by oncogenes. Thus, IRF-1 shows accumulative evidence supporting the theory that IRF-1 functions as a tumour suppressor. However, we still lack the knowledge in the regulation and function behind IRF-1 and many other tumour suppressors due to the lack of synthetic tools that can aid in understanding the mechanism of cancer biology. Here we described the creation of synthetic tools that can be applied to study the role of a transcription factor(s) in cancer biology. Firstly, we described the creation, using recombineering technology, of universal bacterial artificial chromosome (BAC) targeting vector. This targeting vector, carry a cre-conditioned STOP cassette that can be targeted at a desired specific area. The resulted targeting vector can aid the generation of mice models with a conditioned knock-in subtle mutation(s). The resulted cre-conditioned mice models are an essential tool for any outstanding research project in cancer biology. Secondly, we described the development of Flp-In System™ from Invitrogen; the system can ease the generation of isogenic stable mammalian expression cell lines. Using this system, we created two isogenic stable cell lines expressing wild-type IRF-1 and a mutant that abolish IRF-1 DNA binding ability (W11R). Both cell lines were investigated using microarray analysis revealing new IRF-1 target genes. We reported the up-regulation of expected standard interferon regulatory genes such as, interleukin-24 (IL-24) and interferon regulatory factor-2 binding protein-2 (IRF2BP2) and the up-regulation of standard apoptotic genes such as, early growth response-1 (EGR-1) and prostate transmembrane protein, androgen induced-1 (PMEPA1) confirming the role of IRF-1 as a tumour suppressor. However, we also reported the up-regulation of secreted phosphoprotein-1 (SPP1) and SH3 and PX domains-2A (SH3PXD2A) which are matricellular protein produced by cancer cells playing a role in cellular adhesion, invasion, tumour growth progression and metastasis. Thus, we proposed a new biological role of IRF-1 in cellular movement. Thirdly, we described the development of a synthetic stable reporter cell line which can report IRF-1 transcriptional activity; such reporter cell line can be used once large scale screening is needed. The created stable reporter cell line was used to screen a kinase inhibitor library which has revealed C3 as an IRF-1 modifier. The newly identified IRF-1 modifier regulates IRF-1 transcriptional activity by inhibiting platelet-derived growth factor receptor (PDGFR) and/or vascular endothelial growth factor receptor (VEGFR) tyrosine kinase. Finally, we validated the synthetic Flp-In System™ by testing the system using a novel oncoprotein model. We have developed a stable cell line that overexpresses an oncoprotein named Anterior Gradient 2 (AGR-2). We have found that AGR-2 can attenuate IRF-1 protein levels dependent of p53. In addition, AGR-2 has been identified as a cellular survivor factor during unfolding protein response. In conclusion, this study descried the creation and the validation of synthetic tools: synthetic cassette for cre-conditioned mice creation, the Flp-In System™ for isogenic stable cell line creation, and IRF-1 reporter cell line for high throughput screening. All synthetic tools were validated and used to investigate IRF-1, a transcription factor that plays a role in cancer and immune system.