Em diversos tipos de neoplasias já foi demonstrado que diferenças no perfil do infiltrado imune tumoral têm relação com prognóstico e resposta ao tratamento. Esta relação aparece intimamente correlacionada ao perfil de expressão imunoistoquímica do tumor. A presença de linfócitos T citotóxicos(CTLs) no microambiente do tumor sugere uma característica biológica crucial para a modulação da resposta imunológica antitumoral. Por outro lado, as células T regulatórias (Tregs) são importantes na manutenção da homeostase imune, em virtude da sua capacidade em inibir a resposta imunológica. Defeitos na função ou uma diminuição do número das Tregs tem sido documentado em doenças auto-imunes, ao passo que no câncer esta população ainda pode ser mais bem estudada. Sendo estabelecido que o câncer pode ser promovido e / ou agravado pela inflamação e infecções e considerando que a superexpressão de componentes do controle da resposta inflamatória específicos de Tregs e CTLs podem representar um potente mecanismo para o processo de progressão e/ou regressão de carcinoma papilífero de tireoide (CPT), o objetivo deste estudo foi identificar e caracterizar as Tregs e CTLs , bem como avaliar e investigar a relação e o papel dessas células implicado na patogênese da resposta imune em pacientes acometidos com CPT associado ou não com a presença de Tireoidite de Hashimoto (TH), relacionando-as com fatores prognósticos clínico-patológicos. Foram selecionados 36 casos estratificados em 3 grupos (12 casos em cada grupo): CPTS correspondeu aos casos de CPT sem associação com quadro de tireoidite, CPTL aos casos de CPT associados á tireoidite linfocitica (CPTL) e CPTH, casos aonde o CPT estava associado á tireoidite de Hashimoto (CPTH) os quais foram submetidos á técnica de imunoistoquímica para os marcadores CD4, CD8, CD25, CD56, FOXP3 e Gran B e os resultados avaliados pelo método quantitativo. Os dados clínicos foram obtidos dos prontuários médicos. As leituras das células marcadas foram feitas nas regiões de carcinoma papilífero (denominadas intratumorais), nas áreas de parênquima tireoidiano de interface ao tecido neoplásico (denominadas peritumorais) e em áreas subsequentes de tecido tireoidiano normal (denominadas distantes). O número de células T do infiltrado 9 inflamatório foi expresso pela média aritmética da contagem das células dos cinco campos distintos em cada área. Foram feitas análise de variância de Medidas Repetidas Modelo Mixto e calculado o coeficiente de correlação de Pearson para as variáveis CD4 com CD8 e FOXP3 com GranB. Adicionalmente, apesar da avaliação dos CPT divididos segundo seus parâmetros clínico-patológicos não ter se apresentado significante, verificamos que em CPTH as imunovariáveis CD4 e FOXP3 (marcadores para Tregs) apresentaram maior marcação em tumores > 4,1 cm. Nesse mesmo grupo CD8 e Gran B (marcadores para CTLs) se apresentaram com maior imunomarcação em tumores não metastáticos, de estádio menor e sem recorrência. No geral, o infiltrado de células imunes entre os grupos CPTH, CPTL e CPTS, apresentou-se com diferentes densidades entre as áreas estudadas (intratumoral, peritumoral e distante). Linfócitos infiltrando o tecido de forma difusa (CPTS e CPTL) ou em agregados linfoides (CPTH) foram mais abundantes em áreas peritumorais e distantes e a proporção das células CD4+ e CD8+ variou substancialmente entre os grupos, de maneira que todos apresentaram correlação positiva (CPTH r=0,67; CPTL r=0,7 e CPTS r=0,35) crescente entre as variáveis. Em conclusão, estes resultados indicam que nos CPTs o microambiente imune parece ter uma relação com carcterísticas patológicas de progressão do tumor. Nosso estudo mostrou que em CPTH a densidade do infiltrado tumoral e peritumoral por linfócitos Tregs e T citotóxicos está inversamente relacionada. Corroborando com a importância do microambiente imune na evolução dos CPTs, os Tregs exerceram atividade pró-tumoral, favorecendo tumores mais agressivos e os CTLs, atividade antitumoral, favorecendo características de menor agressividade. / It has already been shown that differences in tumoral immune infiltrate profile are related to prognosis and response to treatment in several types of neoplasias. This relationship is closely correlated to the tumor immunohistochemical expression profile. The presence of cytotoxic T lymphocytes (CTLs) in the tumor microenvironment suggests a crucial biological feature for the modulation of the antitumor immune response. On the other hand, regulatory T cells (Tregs) are important in maintaining immune homeostasis, because of their ability to inhibit the immune response. Defects in function or a decrease in the number of Tregs has been documented in autoimmune diseases, nevertheless in cancer this population may still be better studied. With the establishment that cancer can be promoted and / or aggravated by inflammation and infections and considering that overexpression of components of the inflammatory response specific for Tregs and CTLs may represent a potent mechanism for the progression and / or regression of thyroid papilary carcinoma (CPT). The objective of this study was to identify and characterize the Tregs and CTLs, as well as to evaluate and investigate the relationship and the role of these cells involved in the pathogenesis of the immune response in patients with CPT associated or not with the presence of Hashimoto\'s thyroiditis (HT) besides relating them to clinical-pathological prognostic factors. Thirty-six stratified cases were selected in 3 groups (12 cases per group): CPTS corresponded to TLC without thyroiditis association, CPTL to cases of TLC with lymphocytic thyroiditis associated (CPTL) and CPTH was considered cases which CPT was associated to Hashimoto thyroiditis (CPTH). These three groups were submitted to the immunohistochemical technique for the CD4, CD8, CD25, CD56, FOXP3 and Gran B markers and the results was evaluated by the quantitative method. Clinical data were obtained from medical records. Stained cells readings were made in the regions of papillary carcinoma (termed intratumoral area), in the areas of the thyroid parenchyma interface to the neoplastic tissue (termed peritumoral) and in subsequent areas of normal (distal) thyroid tissue. The number of T cells of the inflammatory infiltrate was expressed by the arithmetic mean of cells counted in five distinct fields. The variance analysis of Mixed Model Repeated 11 Measurements and the Pearson correlation coefficient for the CD4 and CD8 and FOXP3 variables with GranB were calculated. In addition, although the CPT divided according to clinical-pathological parameters did not present a significant difference, we found that the CD4 and FOXP3 immunoglobulins (Tregs markers) showed higher marking in tumors> 4.1cm. In this same group, CD8 and Gran B (markers for CTLs) presented a higher immunolabeling in nonmetastatic tumors, in smaller stage and in cases without recurrence. In general, the infiltrate of immune cells between the CPTH, CPTL and CPTS groups, presented different densities between the studied areas (intratumoral, peritumoral and distant). Lymphocytes infiltrating diffuse tissue (CPTS and CPTL) or lymphoid aggregates (CPTH) were more abundant in peritumoral and distal areas and the proportion of CD4 + and CD8 + cells varied substantially between groups, so that all groups presented positive correlation (CPTH r = 0.67, CPTL r = 0.7 and CPTS r = 0.35), increasing among the variables. In conclusion, these results indicate that in the CPTs the immune microenvironment seems to have a relation with pathological characteristics of tumor progression. Our study showed that in CPTH the density of tumor and peritumoral infiltrate by Tregs and T cells is inversely related. Corroborating with the importance of the immune microenvironment in the evolution of CPTs, Tregs exerted pro-tumor activity, favoring more aggressive tumors. While CTLs exerted an antitumor activity, favoring characteristics of lower aggressiveness.

Em diversos tipos de neoplasias já foi demonstrado que diferenças no perfil do infiltrado imune tumoral têm relação com prognóstico e resposta ao tratamento. Esta relação aparece intimamente correlacionada ao perfil de expressão imunoistoquímica do tumor. A presença de linfócitos T citotóxicos(CTLs) no microambiente do tumor sugere uma característica biológica crucial para a modulação da resposta imunológica antitumoral. Por outro lado, as células T regulatórias (Tregs) são importantes na manutenção da homeostase imune, em virtude da sua capacidade em inibir a resposta imunológica. Defeitos na função ou uma diminuição do número das Tregs tem sido documentado em doenças auto-imunes, ao passo que no câncer esta população ainda pode ser mais bem estudada. Sendo estabelecido que o câncer pode ser promovido e / ou agravado pela inflamação e infecções e considerando que a superexpressão de componentes do controle da resposta inflamatória específicos de Tregs e CTLs podem representar um potente mecanismo para o processo de progressão e/ou regressão de carcinoma papilífero de tireoide (CPT), o objetivo deste estudo foi identificar e caracterizar as Tregs e CTLs , bem como avaliar e investigar a relação e o papel dessas células implicado na patogênese da resposta imune em pacientes acometidos com CPT associado ou não com a presença de Tireoidite de Hashimoto (TH), relacionando-as com fatores prognósticos clínico-patológicos. Foram selecionados 36 casos estratificados em 3 grupos (12 casos em cada grupo): CPTS correspondeu aos casos de CPT sem associação com quadro de tireoidite, CPTL aos casos de CPT associados á tireoidite linfocitica (CPTL) e CPTH, casos aonde o CPT estava associado á tireoidite de Hashimoto (CPTH) os quais foram submetidos á técnica de imunoistoquímica para os marcadores CD4, CD8, CD25, CD56, FOXP3 e Gran B e os resultados avaliados pelo método quantitativo. Os dados clínicos foram obtidos dos prontuários médicos. As leituras das células marcadas foram feitas nas regiões de carcinoma papilífero (denominadas intratumorais), nas áreas de parênquima tireoidiano de interface ao tecido neoplásico (denominadas peritumorais) e em áreas subsequentes de tecido tireoidiano normal (denominadas distantes). O número de células T do infiltrado 9 inflamatório foi expresso pela média aritmética da contagem das células dos cinco campos distintos em cada área. Foram feitas análise de variância de Medidas Repetidas Modelo Mixto e calculado o coeficiente de correlação de Pearson para as variáveis CD4 com CD8 e FOXP3 com GranB. Adicionalmente, apesar da avaliação dos CPT divididos segundo seus parâmetros clínico-patológicos não ter se apresentado significante, verificamos que em CPTH as imunovariáveis CD4 e FOXP3 (marcadores para Tregs) apresentaram maior marcação em tumores > 4,1 cm. Nesse mesmo grupo CD8 e Gran B (marcadores para CTLs) se apresentaram com maior imunomarcação em tumores não metastáticos, de estádio menor e sem recorrência. No geral, o infiltrado de células imunes entre os grupos CPTH, CPTL e CPTS, apresentou-se com diferentes densidades entre as áreas estudadas (intratumoral, peritumoral e distante). Linfócitos infiltrando o tecido de forma difusa (CPTS e CPTL) ou em agregados linfoides (CPTH) foram mais abundantes em áreas peritumorais e distantes e a proporção das células CD4+ e CD8+ variou substancialmente entre os grupos, de maneira que todos apresentaram correlação positiva (CPTH r=0,67; CPTL r=0,7 e CPTS r=0,35) crescente entre as variáveis. Em conclusão, estes resultados indicam que nos CPTs o microambiente imune parece ter uma relação com carcterísticas patológicas de progressão do tumor. Nosso estudo mostrou que em CPTH a densidade do infiltrado tumoral e peritumoral por linfócitos Tregs e T citotóxicos está inversamente relacionada. Corroborando com a importância do microambiente imune na evolução dos CPTs, os Tregs exerceram atividade pró-tumoral, favorecendo tumores mais agressivos e os CTLs, atividade antitumoral, favorecendo características de menor agressividade. / It has already been shown that differences in tumoral immune infiltrate profile are related to prognosis and response to treatment in several types of neoplasias. This relationship is closely correlated to the tumor immunohistochemical expression profile. The presence of cytotoxic T lymphocytes (CTLs) in the tumor microenvironment suggests a crucial biological feature for the modulation of the antitumor immune response. On the other hand, regulatory T cells (Tregs) are important in maintaining immune homeostasis, because of their ability to inhibit the immune response. Defects in function or a decrease in the number of Tregs has been documented in autoimmune diseases, nevertheless in cancer this population may still be better studied. With the establishment that cancer can be promoted and / or aggravated by inflammation and infections and considering that overexpression of components of the inflammatory response specific for Tregs and CTLs may represent a potent mechanism for the progression and / or regression of thyroid papilary carcinoma (CPT). The objective of this study was to identify and characterize the Tregs and CTLs, as well as to evaluate and investigate the relationship and the role of these cells involved in the pathogenesis of the immune response in patients with CPT associated or not with the presence of Hashimoto\'s thyroiditis (HT) besides relating them to clinical-pathological prognostic factors. Thirty-six stratified cases were selected in 3 groups (12 cases per group): CPTS corresponded to TLC without thyroiditis association, CPTL to cases of TLC with lymphocytic thyroiditis associated (CPTL) and CPTH was considered cases which CPT was associated to Hashimoto thyroiditis (CPTH). These three groups were submitted to the immunohistochemical technique for the CD4, CD8, CD25, CD56, FOXP3 and Gran B markers and the results was evaluated by the quantitative method. Clinical data were obtained from medical records. Stained cells readings were made in the regions of papillary carcinoma (termed intratumoral area), in the areas of the thyroid parenchyma interface to the neoplastic tissue (termed peritumoral) and in subsequent areas of normal (distal) thyroid tissue. The number of T cells of the inflammatory infiltrate was expressed by the arithmetic mean of cells counted in five distinct fields. The variance analysis of Mixed Model Repeated 11 Measurements and the Pearson correlation coefficient for the CD4 and CD8 and FOXP3 variables with GranB were calculated. In addition, although the CPT divided according to clinical-pathological parameters did not present a significant difference, we found that the CD4 and FOXP3 immunoglobulins (Tregs markers) showed higher marking in tumors> 4.1cm. In this same group, CD8 and Gran B (markers for CTLs) presented a higher immunolabeling in nonmetastatic tumors, in smaller stage and in cases without recurrence. In general, the infiltrate of immune cells between the CPTH, CPTL and CPTS groups, presented different densities between the studied areas (intratumoral, peritumoral and distant). Lymphocytes infiltrating diffuse tissue (CPTS and CPTL) or lymphoid aggregates (CPTH) were more abundant in peritumoral and distal areas and the proportion of CD4 + and CD8 + cells varied substantially between groups, so that all groups presented positive correlation (CPTH r = 0.67, CPTL r = 0.7 and CPTS r = 0.35), increasing among the variables. In conclusion, these results indicate that in the CPTs the immune microenvironment seems to have a relation with pathological characteristics of tumor progression. Our study showed that in CPTH the density of tumor and peritumoral infiltrate by Tregs and T cells is inversely related. Corroborating with the importance of the immune microenvironment in the evolution of CPTs, Tregs exerted pro-tumor activity, favoring more aggressive tumors. While CTLs exerted an antitumor activity, favoring characteristics of lower aggressiveness.

Hypoxia is a common feature of solid tumors and one of the hallmarks of tumor microenvironment. Tumor hypoxia plays an important role in angiogenesis, malignant progression, metastatic development, chemo-radio resistance and favours immune evasion by the emergence of tumor variants with increased survival and anti-apoptotic potential. There is very little work done on the impact of tumor hypoxia on the regulation of tumor susceptibility to the lysis induced by cytotoxic antitumor response. Therefore, we asked whether hypoxia confers tumor resistance to cytotoxic T lymphocyte (CTL)-mediated killing. We demonstrated that exposure of target cells to hypoxia has an inhibitory effect on the CTL-mediated autologous target cell lysis. Such inhibition was not associated with an alteration of CTL reactivity and tumor target recognition. We also showed that the concomitant hypoxic induction of Signal transducer and activator of transcription 3 (STAT3) phosphorylation on tyrosine 705 residue (pSTAT3) and hypoxia inducible factor 1 alpha (HIF-1α) is functionally linked to the alteration of Non small cell lung carcinoma (NSCLC) target susceptibility to CTL-mediated killing. We also showed that hypoxia-induced resistance of lung tumor to CTL-mediated lysis was associated with autophagy induction in target cells. Inhibition of autophagy resulted in impairment of pSTAT3 (via inhibition Src kinase) and restoration of hypoxic tumor cell susceptibility to CTL-mediated lysis. Moreover, in vivo inhibition of autophagy by hydroxychloroquine (HCQ) in B16F10 tumor bearing mice and mice vaccinated with TRP2 peptide dramatically increased tumor growth inhibition. Collectively, the current study establishes a novel functional link between hypoxia-induced autophagy and the regulation of antigen specific T cell lysis and points to a major role of autophagy in the control of in vivo tumor growth.Finally, as resistance of tumor targets to killer cells is likely to be regulated by multiple factors, we further aimed to identify the microRNA's regulated by hypoxia in NSCLC and melanoma and their putative involvement in the regulation of tumor susceptibility to antigen-specific CTL-mediated killing. MicroRNA-210 (miR-210) was significantly induced in a HIF-1α dependent manner in NSCLC and melanoma cells and miR-210 was expressed in hypoxic zones of human NSCLC tissues. Moreover, we demonstrated that hypoxia-induced miR-210 regulates tumor cell susceptibility to CTL-mediated lysis in part by suppressing PTPN, HOXA1 and TP53I11 expression indicating that miR-210 plays a potential role in the regulation of anti-tumor immune response.

De nombreuses études ont montré que les enfants traités précocement ne sont pas capables de développer une réponse à médiation cellulaire contre le VIH [1]. Cependant, le rebond viral observé après la rémission prolongée du cas du « bébé du Mississippi » pose de nombreuses questions quant à la capacité de ces enfants à développer une réponse immunitaire VIH spécifique malgré une suppression virale à long terme [2, 3]. Nous avons étudié cinq cas ayant un profil similaire au « bébé du Mississippi » qui ont été identifiés précédemment [4]. L’objectif de ce projet était de déterminer si les enfants traités précocement développent une réponse immunitaire à médiation cellulaire contre le VIH qui est quantitativement et/ou qualitativement différente de celle retrouvée chez les enfants traités plus tard. Cette étude a permis de montrer que l’amplitude et la diversité des réponses LTC des enfants traités précocement est plus faible que celle observée chez des enfants traités plus tard ou non traités. / Several studies have shown early treated children are not able to develop a cell-mediated response [1]. However, the viral rebound after prolonged remission in the case of the "Mississippi baby" raises many questions about the ability of these children to develop a specific immune response despite HIV viral suppression in the long term [2, 3]. We currently have five cases with a similar profile to the "Mississippi baby" that were identified previously [4]. The objective of this project is to determine whether early treated children develop an immune cell-mediated response against HIV that is quantitatively and/or qualitatively different from that found in children treated later. This study showed that the magnitude and diversity of CTL responses of children treated early is lower than that observed in children treated later if possible.

No description available.

L’hypoxie est une caractéristique commune des tumeurs solides et l’une des spécificités du micro environnement tumoral. L’hypoxie tumorale joue un rôle important dans l’angio génèse, la progression maligne, le développement de métastases, la chimio/radio-résistance et favorise l’échappement au système immunitaire du fait de l’émergence de variant tumoraux avec un potentiel de survie et de résistance à l’apoptose augmenté. Cependant, très peu de travaux ont étudié l’impact de l’hypoxie tumorale sur la régulation de la susceptibilité des tumeurs à la lyse induite par la réponse immune cytotoxique. Nous nous sommes donc demandé si l’hypoxie pouvait conférer aux tumeurs une résistance à la lyse induite par les lymphocytes T cytotoxiques (CTL). Nous avons démontré que l’exposition de cellules cibles tumorales à l’hypoxie possédait un effet inhibiteur sur la lyse de ces cellules tumorales par des CTL autologues. Cette inhibition n’est pas associée à des altérations de la réactivité de CTL ou de la reconnaissance des cellules cibles. Cependant, nous avons montré que l’induction hypoxique concomitante de la phosphorylation de STAT3 (pSTAT3) au niveau de la tyrosine 705 et du facteur HIF-1α (Hypoxia Inducible Factor-1 alpha) est liée fonctionnellement à l’altération de la susceptibilité de cellules tumorales bronchiques non à petites cellules (NSCLC) à la mort induite par les CTL. Nous avons aussi montré que la résistance de cellules tumorales bronchiques à la lyse CTL induite par l’hypoxie était associée à une induction d’autophagie dans les cellules cibles. En effet, l’inhibition de l’autophagie empêche la phosphorylation de STAT3 (via l’inhibition de la kinase Src) et restaure la susceptibilité des cellules tumorales hypoxiques à la lyse induite par les CTL. De plus, l’inhibition in vivo de l’autophagie par l’hydroxychloroquine (HCQ) dans le modèle murin portant la tumeur B16F10 and chez les souris vaccinée avec le peptide TRP2 augmente de façon drastique l’inhibition de la croissance tumorale. Collectivement, cette étude établit un nouveau lien fonctionnel entre l’autophagie induite par l’hypoxie et la régulation de la lyse induite par les cellules T spécifique d’antigènes et souligne le rôle majeur de l’autophagie dans le contrôle de la croissance tumorale in vivo.Finalement, étant donné que le la résistance tumorale à la lyse induite par les cellules tueuses est très probablement régulée par de multiples facteurs, nous avons aussi eu pour but d’identifier les micro-ARNs (miRs) régulés par l’hypoxie dans des modèles de NSCLC et de mélanome et leur implication putative dans la régulation de la susceptibilité tumorale à la lyse induite par les cellules T spécifique d’antigènes. Le micro-ARN 210 (miR-210) est ainsi significativement induit de manière dépendante de HIF-1α dans des cellules de NSCLC et de mélanome, et miR-210 est exprimé dans les zones hypoxiques de tissus issus de NSCLC. De plus, nous avons démontré que l’induction de miR-210 par l’hypoxie régule la susceptibilité tumorale à la lyse induite par les CTL en partie grâce à l’inhibition de l’expression de PTPN, HOXA1 et TP53I11, indiquant que miR-210 joue un rôle potentiel dans la régulation de la réponse immune antitumorale. / Hypoxia is a common feature of solid tumors and one of the hallmarks of tumor microenvironment. Tumor hypoxia plays an important role in angiogenesis, malignant progression, metastatic development, chemo-radio resistance and favours immune evasion by the emergence of tumor variants with increased survival and anti-apoptotic potential. There is very little work done on the impact of tumor hypoxia on the regulation of tumor susceptibility to the lysis induced by cytotoxic antitumor response. Therefore, we asked whether hypoxia confers tumor resistance to cytotoxic T lymphocyte (CTL)-mediated killing. We demonstrated that exposure of target cells to hypoxia has an inhibitory effect on the CTL-mediated autologous target cell lysis. Such inhibition was not associated with an alteration of CTL reactivity and tumor target recognition. We also showed that the concomitant hypoxic induction of Signal transducer and activator of transcription 3 (STAT3) phosphorylation on tyrosine 705 residue (pSTAT3) and hypoxia inducible factor 1 alpha (HIF-1α) is functionally linked to the alteration of Non small cell lung carcinoma (NSCLC) target susceptibility to CTL-mediated killing. We also showed that hypoxia-induced resistance of lung tumor to CTL-mediated lysis was associated with autophagy induction in target cells. Inhibition of autophagy resulted in impairment of pSTAT3 (via inhibition Src kinase) and restoration of hypoxic tumor cell susceptibility to CTL-mediated lysis. Moreover, in vivo inhibition of autophagy by hydroxychloroquine (HCQ) in B16F10 tumor bearing mice and mice vaccinated with TRP2 peptide dramatically increased tumor growth inhibition. Collectively, the current study establishes a novel functional link between hypoxia-induced autophagy and the regulation of antigen specific T cell lysis and points to a major role of autophagy in the control of in vivo tumor growth.Finally, as resistance of tumor targets to killer cells is likely to be regulated by multiple factors, we further aimed to identify the microRNA’s regulated by hypoxia in NSCLC and melanoma and their putative involvement in the regulation of tumor susceptibility to antigen-specific CTL-mediated killing. MicroRNA-210 (miR-210) was significantly induced in a HIF-1α dependent manner in NSCLC and melanoma cells and miR-210 was expressed in hypoxic zones of human NSCLC tissues. Moreover, we demonstrated that hypoxia-induced miR-210 regulates tumor cell susceptibility to CTL-mediated lysis in part by suppressing PTPN, HOXA1 and TP53I11 expression indicating that miR-210 plays a potential role in the regulation of anti-tumor immune response.

Το καρκίνωμα εκ πλακώδους επιθηλίου ή πλακώδες καρκίνωμα (ΠΚ) του δέρματος είναι ο δεύτερος πιο συχνός καρκίνος του δέρματος και εμφανίζεται συνήθως σε έδαφος ακτινικής υπερκεράτωσης (ΑΚ). Τα νεοπλασματικά κύτταρα εκφράζουν μια ποικιλία αντιγόνων προσελκύοντας με αυτό τον τρόπο λεμφοκύτταρα, τα διηθούντα τον όγκο λεμφοκύτταρα (Tumor Ιnfiltrating Lymphocytes-TILs) στο μικροπεριβάλλον του όγκου. Με βάση το ανοσοφαινοτυπικό τους προφίλ η πλειοψηφία των TILs εκφράζει το μόριο CD3 και αφορά σε Τ-λεμφοκύτταρα. Αυτά με την σειρά τους διαχωρίζονται σε CD8+ Τ-κυτταροτοξικά λεμφοκύτταρα και CD4+ Τ-λεμφοκύτταρα. Η έκφραση του δείκτη CD25+ επιτρέπει τον διαχωρισμό των CD4+ λεμφοκυττάρων σε δύο επιπλέον υποομάδες, τα T-επικουρικά (CD4+/CD25-) και τα Τ-ρυθμιστικά (CD4+/CD25+) κύτταρα. Ο πιο αξιόπιστος δείκτης για την ανίχνευση των Τ-ρυθμιστικών κυττάρων (Tregs) θεωρείται ο Forkhead box P3 (Foxp3). Ο αυξημένος αριθμός των TILs έχει συσχετισθεί με την πρόγνωση και τη θεραπευτική αντιμετώπιση σε μια ποικιλία νεοπλασμάτων, περιλαμβανομένων και καρκίνων του δέρματος όπως το μελάνωμα. Η μεθοδολογία αξιολόγησης της λεμφοκυτταρικής διήθησης, ωστόσο, δεν έχει ακόμα αποσαφηνισθεί και ποικίλλει στα διάφορα είδη νεοπλασμάτων. Στα πλαίσια της παρούσας διπλωματικής εργασίας η ανίχνευση των Τ-λεμφοκυττάρων έγινε με ανοσοϊστοχημική μέθοδο με τη χρήση των κατάλληλων αντισωμάτων (CD3, CD4, CD8, Foxp3). Η παρουσία των κυττάρων αξιολογήθηκε με τη χρήση φωτονικού μικροσκοπίου με δυο διαφορετικά ημιποσοτικά συστήματα βαθμολόγησης για όλους τους μελετηθέντες Τ-κυτταρικούς υποπληθυσμούς καθώς και με ένα τρίτο σύστημα ποσοτικής καταμέτρησης για τα Τregs. Σκοπός ήταν να γίνει σύγκριση των μεθόδων ώστε να βρεθεί η καταλληλότερη μεθοδολογία αξιολόγησης της λεμφοκυτταρικής διήθησης στο πλακώδες καρκίνωμα του δέρματος, να υπολογιστεί ο αριθμός των Tregs στις μελετούμενες οντότητες χρησιμοποιώντας το βέλτιστο σύστημα βαθμολόγησης και να αναζητηθούν διαφορές στην πυκνότητα των λεμφοκυτταρικών υποπληθυσμών μεταξύ των οντοτήτων, οι οποίες μπορεί να έχουν παθογενετική ή θεραπευτική κλινική σημασία. / Squamous cell carcinoma (SCC) of the skin is the second most common skin cancer. It usually develops in a background of actinic keratosis (AK). Neoplastic cells express a variety of antigens, attracting lymphocytes in the tumor microenvironment (Tumor Ιnfiltrating Lymphocytes-TILs). Based on the immunophenotypic profile, the majority of TILs expresses the CD3 molecule, so they are T-lymphocytes. These in turn are divided into CD8+ cytotoxic T-lymphocytes and CD4+ T-lymphocytes. The expression of CD25 enables the separation of CD4+ lymphocytes in two further subgroups, the T-helper (CD4+/CD25-) and T-regulatory (CD4+/CD25+) cells. The most reliable marker for the detection of T-regulatory cells (Tregs) is considered to be the Forkhead box P3 (Foxp3). The increased number of TILs is associated with prognosis and treatment in a variety of tumors, including skin cancers, such as melanoma. The evaluation methology of lymphocytic infiltration, however, is not yet clarified and varies in different types of tumors. In the context of this thesis, the detection of T-lymphocytes was performed by immunohistochemistry using the appropriate antibodies (CD3, CD4, CD8, Foxp3). The presence of the cells was evaluated using light microscopy with two different semiquantitative scoring systems, for all the T-lymphocyte subpopulations, as well as with a third system of quantification of Tregs. The purpose was to compare the methods in order to find the most suitable methodology for the evaluation of the lymphocytic infiltration in squamous cell carcinoma of the skin, to evaluate the number of Tregs in the studied entities using the best method and examine for differences in the density of lymphocyte subpopulations.

Cytotoxic T-lymphocytes (CTLs) are important components of the adaptive immune system and function by scanning the intracellular environment so as to detect and de-stroy infected cells. CTL responses play a major role in controlling virus-infected cells such as in HIV or influenza and cells infected with intracellular bacteria such as in tuberculosis. To do so they require the antigens to be presented to them, which is fulfilled by the major histocompatibility complex (MHC), commonly known as human leukocyte antigen or HLA molecules in humans. Recognition of antigenic peptides to Class-1 HLA molecules is a prerequisite for triggering CTL immune responses. Individuals differ significantly in their ability to respond to an infection. Among the factors that govern the outcome of an infection, HLA polymorphism in the host is one of the most important. Despite a large body of work on HLA molecules, much remains to be understood about the relationship between HLA diversity and disease susceptibility. High complexity arises due to HLA allele polymorphism, extensive antigen cross-presentability, and host-pathogen heterogeneity. A given allele can recognize a number of different peptides from various pathogens and a given peptide can also bind to a number of different individuals. Thus, given the plurality in peptide-allele pairs and the large number of alleles, understanding the differences in recognition profiles and the implications that follow for disease susceptibilities require mathematical modelling and computational analysis. The main objectives of the thesis were to understand heterogeneity in antigen presentation by HLA molecules at different scales and how that heterogeneity translates to variations in disease susceptibilities and finally the disease dynamics in different populations. Towards this goal, first the variations in HLA alleles need to be characterized systematically and their recognition properties understood. A structure-based classification of all known HLA class-1 alleles was therefore attempted. In the process, it was also of interest to see if understanding of sub-structures at the binding grooves of HLA molecules could help in high confidence prediction of epitopes for different alleles. Next, the goal was to understand how HLA heterogeneity affect disease susceptibilities and disease spread in populations. This was studied at two different levels. Firstly, modelling the HLA genotypes and CTL responses in different populations and assessing how they recognized epitopes from a given virus. The second approach involved modelling the disease dynamics given the predicted susceptibilities in different populations. Influenza H1N1 infection was used as a case study. The specific objectives addressed are: (a) To develop a classification scheme for all known HLA class-1 alleles that can explain epitope recognition profiles and further to dissect the physic-chemical features responsible for differences in peptide specificities, (b) A statistical model has been derived from a large dataset of HLA-peptide complexes. The derived model was used to identify the interdependencies of residues at different peptide and thereby, rationalize the HLA class-I allele binding specificity at a greater detail, (c) To understand the effect of HLA heterogeneity on CTL mediated disease response. A model of HLA genotypes for different populations was required for this, which was constructed and used for estimating disease response to H1N1 via the prediction of epi-topes and (d) To model disease dynamics in different populations with the knowledge of the CTL response-grouping and to evaluate the effect of heterogeneity on different vaccination strategies. Each of the four objectives listed above are described subsequently in chapters 2 to 5, followed by Chapter 6 which summarises the findings from the thesis and presents future directions. Chapter 1 presents an introduction to the importance of the function of HLA molecules, describes structural bioinformatics as a discipline and the methods that are available for it. The chapter also describes different mathematical modelling strategies available to study host immune responses. Chapter 2 describes a novel method for structure-based hierarchical classification of HLA alleles. Presently, more than 2000 HLA class-I alleles are reported, and they vary only across peptide-binding grooves. The polymorphism they exhibit, enables them to bind to a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern due to multiplicity in their associations. Thus, a powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. The study reports a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification with 7 supergroups was derived, each further categorized to yield a total of 72 groups. An independent clustering scheme based only on the similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explains the basis for the observed clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues that contribute to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants. The results are presented in an interactive web- server http://proline.iisc.ernet.in/hlaclassify. In Chapter 3, the knowledge of structural features responsible for generating peptide recognition specificities are first analysed and then utilized for predicting T-cell epi-topes for any class-1 HLA allele. Since identification of epitopes is critical and central to many of the questions in immunology, a study of several HLA-peptide complexes is carried out at the structural level and factors are identified that discriminate good binder peptides from those that do not. T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics, critically dependent on experimentally obtained training data. Analysis of the training set from IEDB for several alleles indicate that sampling of the peptide space is extremely sparse covering only a tiny fraction of all possible nonamer space, and also heavily skewed, thus restricting the range of epitope prediction. A new epitope prediction method is therefore developed. The method has four distinct modules, (a) structural modelling, estimating statistical pair-potentials and constraint derivation, (b) implicit modelling and interaction profiling, (c) binding affinity prediction through feature representation and (d) use of graphical models to extract peptide sequence signatures to predict epitopes for HLA class I alleles . HLaffy is a novel and efficient epitope prediction method that predicts epitopes for any HLA Class-1 allele, by estimating binding strengths of peptide-HLA complexes which is achieved through learning pair-potentials important for peptide binding. It stands on the strength of mechanistic understanding of HLA-peptide recognition and provides an estimate of the total ligand space for each allele. The method is made accessible through a webserver http://proline.biochem.iisc.ernet.in/HLaffy. In chapter 4, the effect of genetic heterogeneity on disease susceptibilities are investigated. Individuals differ significantly in their ability to respond to an infection. Among the factors that govern the outcome of an infection, HLA polymorphism in the host is one of the most important. Despite a large body of work on HLA molecules, much remains to be understood about how host HLA diversity affects disease susceptibilities. High complexity due to polymorphism, extensive cross-presentability among HLA alleles, host and pathogen heterogeneity, demands for an investigation through computational approaches. Host heterogeneity in a population is modelled through a molecular systems approach starting with mining ‘big data’ from literature. The in-sights derived through this is used to investigate the effect of heterogeneity in a population in terms of the impact it makes on recognizing a pathogen. A case study of influenza virus H1N1 infection is presented. For this, a comprehensive CTL immunome is defined by taking a consensus prediction by three distinct methods. Next, HLA genotypes are constructed for different populations using a probabilistic method. Epidemic incidences in general are observed to correlate with poor CTL response in populations. From this study, it is seen that large populations can be classified into a small number of groups called response-types, specific to a given viral strain. Individuals of a response type are expected to exhibit similar CTL responses. Extent of CTL responses varies significantly across different populations and increases with increase in genetic heterogeneity. Overall, the study presents a conceptual advance towards understanding how genetic heterogeneity influences disease susceptibility in individuals and in populations. Lists of top-ranking epitopes and proteins are also derived, ranked on the basis of conservation, antigenic cross-reactivity and population coverage, which pro- vide ready short-lists for rational vaccine design (flutope). Next, in Chapter 5, the effect of genetic heterogeneity on disease dynamics has been investigated. A mathematical framework has been developed to incorporate the heterogeneity information in the form of response-types described in the previous chap-ter. The spread of a disease in a population is a complex process, controlled by various factors, ranging from molecular level recognition events to socio-economic causes. The ‘response-typing’ described in the previous chapter allows identification of distinct groups of individuals, each with a different extent of susceptibility to a given strain of the virus. 3 different approaches are used for modelling: (i) an SIR model where different response types are considered as partitions of each S, I and R compartment. Initially SIR models are developed, such that the S compartment is sub-divided into further groups based on the ‘response-types’ obtained in the previous chapter. This analysis shows an effect in infection sweep time, i.e., how long the infection stays in the population. A stochastic model incorporates the environmental noise due to random variation in population influx, due to birth, death or migration. The system is observed to show higher stability in the presence of genetic heterogeneity. As the contagion spreads only through direct host to host contact. The topology of the contact network, plays major role in deciding the extent of disease dynamics. An agent based computational framework has been developed for modelling disease spread by considering spatial distribution of the agents, their movement patterns and resulting contact probabilities. The agent-based model (ABM) incorporates the temporal patterns of contacts. The ABM is based on a city block model and captures movement of individuals parametrically. A new concept of system ‘characteristic time’ has been introduced in context of a time-evolving network. ‘Characteristic time’ is the minimum time required to ensure, every individual is connected to all other individuals, in the time aggregated contact network. For any given temporal system, disease time must exceed ‘characteristic time’ in order to spread throughout the population. Shorter ‘characteristic time’ of the system is suggestive of faster spread of the disease. A disease spread network is constructed which shows how the disease spreads from one infected individual to others in the city, given the contact rules and their relative susceptibilities to that viral strain. A high degree of population heterogeneity is seen to results in longer disease residence time. Susceptible individuals preferentially get infected first thereby exposing more susceptible individuals to the disease. Vaccination strategies are derived from the model, which indicates that vaccinating only 20% of the agents, who are hub nodes or highly central nodes and who also have a high degree to susceptible agents, lead to high levels of herd immunity and can confer protection to the rest of the population. Overall, the thesis has provided biologically meaningful classification of all known HLA class-1 alleles and has unravelled the physico-chemical basis for their peptide recognition specificities. The thesis also presents a new algorithm for estimating pep-tide binding affinities and consequently predicting epitopes for all alleles. Finally the thesis presents a conceptual advance in relating HLA diversity to disease susceptibilities and explains how different populations can respond differently to a given infection. A case study with the influenza H1N1 virus identified populations who are most susceptible and those who are least susceptible, in the process identifying important epitopes and responder alleles, providing important pointers for vaccine design. The influence of heterogeneity and response-typing on disease dynamics is also presented for influenza H1N1 infection, which has led to the rational identification of effective vaccination strategies. The methods and concepts developed here are fairly generic and can be adapted easily for studying other infectious diseases as well. Three new web-resources, a) HLAclassify, b) HLaffy and c) Flutope have been developed, which host pre-computed results as well as allow interactive querying to an user to perform analysis with a specific allele, peptide or a pathogenic genome sequence.

Tumor-induced immunosuppression can occur by multiple mechanisms, each posing a significant obstacle to immunotherapy. Evidence presented in this dissertation suggests that aberrant cytokine signaling, as a result of altered metabolism of Chronic Lymphocytic Leukemia (CLL) cells, confers a selective advantage for tumor survival and growth. Cells from CLL patients with aggressive disease (as indicated by high-risk cytogenetics) were found to exhibit prolongation in Interferon (IFN)-induced STAT3 phosphorylation, and increased levels of reactive oxygen species (ROS) in these cells reflected these signaling processes. Changes in the relative balance of phospho-STAT3 and phospho-STAT1 levels, in response to combinations of IL-2 + Toll-like receptor (TLR)-7 agonist + phorbol esters, as well as IFN, were associated with the immunosuppressive and immunogenic states of CLL cells. In addition, immunosuppressive leukemic cells were found to express high levels of proteins with O-linked N-acetylglucosamine (O-GlcNAc) modifications, due to increased metabolic activity through the Hexosamine Biosynthetic Pathway (HBP), which caused impaired intracellular signaling responses and affected disease progression. A conclusion of the studies presented here is that the intrinsic immunosuppressive properties of leukemic cells may be overcome by agents such as Resveratrol that target metabolic pathways of these cells.

Tumor-induced immunosuppression can occur by multiple mechanisms, each posing a significant obstacle to immunotherapy. Evidence presented in this dissertation suggests that aberrant cytokine signaling, as a result of altered metabolism of Chronic Lymphocytic Leukemia (CLL) cells, confers a selective advantage for tumor survival and growth. Cells from CLL patients with aggressive disease (as indicated by high-risk cytogenetics) were found to exhibit prolongation in Interferon (IFN)-induced STAT3 phosphorylation, and increased levels of reactive oxygen species (ROS) in these cells reflected these signaling processes. Changes in the relative balance of phospho-STAT3 and phospho-STAT1 levels, in response to combinations of IL-2 + Toll-like receptor (TLR)-7 agonist + phorbol esters, as well as IFN, were associated with the immunosuppressive and immunogenic states of CLL cells. In addition, immunosuppressive leukemic cells were found to express high levels of proteins with O-linked N-acetylglucosamine (O-GlcNAc) modifications, due to increased metabolic activity through the Hexosamine Biosynthetic Pathway (HBP), which caused impaired intracellular signaling responses and affected disease progression. A conclusion of the studies presented here is that the intrinsic immunosuppressive properties of leukemic cells may be overcome by agents such as Resveratrol that target metabolic pathways of these cells.