Peptides generated from cellular protein degradation via the ubiquitin-proteasome pathway are presented on MHC class I as a means for the immune system to monitor polypeptides being synthesized by cells. For CD8 + T cells to prevent the spread of an incipient infection, it appears essential they should be able to sense foreign polypeptides being synthesized as soon as possible. A prompt detection of viral proteins is of great importance for the success of an adaptive immune response. Defective ribosomal products (DRiPs) have been postulated as a preferential source which would allow for a rapid presentation of peptides derived from the degradation of all newly synthesized proteins. Although this hypothesis is intellectually appealing there is lack of experimental data supporting a mechanism that would prioritize presentation from DRiPs. In this dissertation I describe a series of experiments that probe the DRiPs hypothesis by assessing the contribution to class I presentation of model epitopes derived from DRiPs or from functional proteins. The results show that even at the early stages after mRNA synthesis DRiPs do not account for a significant fraction of the class I presented peptides. These observations suggest that the currently widespread model whereby a mechanism exists which selectively allows for DRiPs to preferentially contribute to class I antigen presentation, is incorrect. Rather, properly folded functional proteins can significantly contribute to class I antigen presentation as they are normally turned over by the ubiquitin-proteasome pathway.

INTRODUÇÃO: O penfigoide bolhoso é uma doença autoimune, vesicobolhosa com incidência de 0,2 a 1,4 por 100.000 hab. Sua fisiopatologia caracteriza-se pela ação de autoanticorpos na junção dermoepidérmica dos hemidesmossomos, promovendo a formação de bolhas subepidérmicas na pele e mucosas. Estudos vêm sendo publicados demonstrando a associação de penfigoide com alelos do sistema HLA classe II em diferentes populações do mundo, entretanto não há dados sobre a população brasileira, uma das mais heterogêneas do mundo. PACIENTES E MÉTODOS: O grupo de estudo incluiu 17 pacientes brasileiros com diagnóstico confirmado de PB de um hospital na cidade de São Paulo, sudeste do Brasil. O DNA foi extraído a partir de sangue periférico utilizando kits Qiagen (QIAamp DNA Mini Kit®) e a tipagem HLA loci A, B, C, DR e DQ foi realizada por meio de PCR e a amplificação utilizando o oligonucleótido de sequência específica (SSO) contido nos kits LABType®. O grupo controle foi composto por um banco de dados de 297 doadores falecidos da cidade de São Paulo. Este banco de dados é parte do Sistema de Transplantes da Secretaria de Saúde do Governo do Estado de São Paulo. RESULTADOS: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira, com risco relativo de 8,31 (2,46 a 28,16), 3,76 (1,81 a 7,79), 3,57 (1,53 a 8,33) e 4,02 (1,87 a 8,64), respectivamente (p < 0,005). O nível de significância estatística foi ajustado utilizando a correção de Bonferroni, dependendo das frequências fenotípicas avaliadas para HLA de classe I (A, B e C) e classe II (DRB1, DQB1 e DQA1). DISCUSSÃO: Os dados indicam que pacientes brasileiros com PB apresentam a mesma predisposição genética ligada ao HLA-DQB1*03:01 relatado anteriormente em caucasianos e indivíduos iranianos e o estudo apresenta três novos alelos (C *17, DQA1*01:03 e DQA1* 05:05) envolvidos na fisiopatologia da PB. CONCLUSÕES: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira / BACKGROUND: Bullous pemphigoid (BP) is an autoimmune disease with bullous vesicles and an incidence of 0.2 to 1.4 per 100,000 inhabitants. Its pathophysiology is characterized by the action of autoantibodies on hemidesmosomes at the dermalepidermal junction, promoting subepidermal blister formation in the skin and mucous membranes. Many studies have been published demonstrating the association of pemphigoid with HLA class II system alleles in different populations, however there are no data on the Brazilian population, one of the most heterogeneous in the world. PATIENTS AND METHODS: The study group included 17 Brazilian patients with a confirmed diagnosis of BP from a hospital in Sao Paulo city, southeast Brazil. DNA was extracted from peripheral blood using Qiagen kits (QIAamp DNA Mini Kit®) and HLA A, B, C, DR and DQ typing was performed using PCR and amplification using Sequence-Specific Oligonucleotide (SSO) contained in LABType® kits. The control group was composed of a database of 297 deceased donors from the city of São Paulo. This database is part of the Transplants State System of the Government\'s Health Secretary from the State of Sao Paulo. RESULTS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population, with relative risks of 8.31 (2.46 to 28.16), 3.76 (1.81 to 7.79), 3.57 (1.53 to 8.33), and 4.02 (1.87 to 8.64), respectively (p < 0.005). The statistical significance level was adjusted using the Bonferroni correction depending on the phenotypic frequencies evaluated for HLA class I (A, B and C) and class II (DRB1, DQB1 and DQA1). DISCUSSION: Our data indicate that Brazilian patients with BP present the same genetic predisposition linked to HLA-DQB1*03:01 previously reported in Caucasian and Iranian individuals and our study introduces three new alleles (C*17, DQA1*01:03 and DQA1*05:05) involved in the pathophysiology of BP. CONCLUSIONS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population

INTRODUÇÃO: O penfigoide bolhoso é uma doença autoimune, vesicobolhosa com incidência de 0,2 a 1,4 por 100.000 hab. Sua fisiopatologia caracteriza-se pela ação de autoanticorpos na junção dermoepidérmica dos hemidesmossomos, promovendo a formação de bolhas subepidérmicas na pele e mucosas. Estudos vêm sendo publicados demonstrando a associação de penfigoide com alelos do sistema HLA classe II em diferentes populações do mundo, entretanto não há dados sobre a população brasileira, uma das mais heterogêneas do mundo. PACIENTES E MÉTODOS: O grupo de estudo incluiu 17 pacientes brasileiros com diagnóstico confirmado de PB de um hospital na cidade de São Paulo, sudeste do Brasil. O DNA foi extraído a partir de sangue periférico utilizando kits Qiagen (QIAamp DNA Mini Kit®) e a tipagem HLA loci A, B, C, DR e DQ foi realizada por meio de PCR e a amplificação utilizando o oligonucleótido de sequência específica (SSO) contido nos kits LABType®. O grupo controle foi composto por um banco de dados de 297 doadores falecidos da cidade de São Paulo. Este banco de dados é parte do Sistema de Transplantes da Secretaria de Saúde do Governo do Estado de São Paulo. RESULTADOS: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira, com risco relativo de 8,31 (2,46 a 28,16), 3,76 (1,81 a 7,79), 3,57 (1,53 a 8,33) e 4,02 (1,87 a 8,64), respectivamente (p < 0,005). O nível de significância estatística foi ajustado utilizando a correção de Bonferroni, dependendo das frequências fenotípicas avaliadas para HLA de classe I (A, B e C) e classe II (DRB1, DQB1 e DQA1). DISCUSSÃO: Os dados indicam que pacientes brasileiros com PB apresentam a mesma predisposição genética ligada ao HLA-DQB1*03:01 relatado anteriormente em caucasianos e indivíduos iranianos e o estudo apresenta três novos alelos (C *17, DQA1*01:03 e DQA1* 05:05) envolvidos na fisiopatologia da PB. CONCLUSÕES: Os resultados mostram que os alelos HLA C*17, DQB1*03:01, DQA1*01:03 e DQA1*05:05 estão associados com o aparecimento da doença na população brasileira / BACKGROUND: Bullous pemphigoid (BP) is an autoimmune disease with bullous vesicles and an incidence of 0.2 to 1.4 per 100,000 inhabitants. Its pathophysiology is characterized by the action of autoantibodies on hemidesmosomes at the dermalepidermal junction, promoting subepidermal blister formation in the skin and mucous membranes. Many studies have been published demonstrating the association of pemphigoid with HLA class II system alleles in different populations, however there are no data on the Brazilian population, one of the most heterogeneous in the world. PATIENTS AND METHODS: The study group included 17 Brazilian patients with a confirmed diagnosis of BP from a hospital in Sao Paulo city, southeast Brazil. DNA was extracted from peripheral blood using Qiagen kits (QIAamp DNA Mini Kit®) and HLA A, B, C, DR and DQ typing was performed using PCR and amplification using Sequence-Specific Oligonucleotide (SSO) contained in LABType® kits. The control group was composed of a database of 297 deceased donors from the city of São Paulo. This database is part of the Transplants State System of the Government\'s Health Secretary from the State of Sao Paulo. RESULTS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population, with relative risks of 8.31 (2.46 to 28.16), 3.76 (1.81 to 7.79), 3.57 (1.53 to 8.33), and 4.02 (1.87 to 8.64), respectively (p < 0.005). The statistical significance level was adjusted using the Bonferroni correction depending on the phenotypic frequencies evaluated for HLA class I (A, B and C) and class II (DRB1, DQB1 and DQA1). DISCUSSION: Our data indicate that Brazilian patients with BP present the same genetic predisposition linked to HLA-DQB1*03:01 previously reported in Caucasian and Iranian individuals and our study introduces three new alleles (C*17, DQA1*01:03 and DQA1*05:05) involved in the pathophysiology of BP. CONCLUSIONS: Our findings show that alleles HLA C*17, DQB1*03:01, DQA1*01:03 and DQA1*05:05 are associated with the onset of the disease in the Brazilian population

This thesis is comprised of studies of proteins involved in class I and class II major histocompatibility complex (MHC) antigen procressing. In class I MHC processing, structural and functional studies were conducted of an aminopeptidase, ERAP1, that mediates the final step in antigen processing to understand how it is particularly suitable for cleavage of antigenic peptides for class I MHC presentation. In the class II MHC antigen presentation pathway, structural studies were conducted to characterize a fluorogenic peptide that can be used to understand peptide loading events in vivo and in real time. Also structural studies of class II MHC and peptide complexes were conducted to understand the nature of an unique C-terminal secondary structure element exhibited by an HIV derived peptide in the peptide binding groove of class II MHC. The studies discussed in this thesis provide insights into the proteins involved in the class I and class II MHC antigen presentation pathway. The endoplasmic reticulum (ER) aminopeptidase, ERAP1, is a 941 amino acid member of the M1 family of zinc metalloaminopeptidases. Unlike other aminopeptidases, ERAP1 has a length and C-terminal preference for its substrates. Interestingly, ERAP1 has been shown to trim antigenic peptides to lengths of 8 or 9 amino acids long. This length matches the length required to bind into the peptide binding groove of class I MHC molecules. In addition, ERAP1 is upregulated in the ER of cells treated with interferon gamma (IFN-γ). Knock-down of ERAP1 by siRNA results in less overall antigenic presentation during IFN-γ treatment, although the knock-down does not affect all class I MHC epitopes equally. Knock-out studies show that ERAP1 effects the antigen repertoire at the cell surface. These and other data implicate ERAP1 as an important player in class I MHC antigen presentation. A chapter of this thesis will describe the crystallographic work describing the structures of ERAP1 with an aminopeptidase inhibitor, bestatin, and ERAP1 without an inhibitor that suggest possible peptide binding site in ERAP1 that will allow it to generate suitable substrates for a subset of class I MHC alleles. Class II MHC plays a key role in the immune response by presenting antigenic peptides on CD4+ cytotoxic cell surfaces for T-cell response. The binding of peptides onto the MHC is an important step in creating an immune response. Structures of peptide bound MHC class II show conserved side chain binding pockets within the overall peptide-binding groove. In HLA-DR1, a common human class II MHC, the P1 pocket shows a preference for large hydrophobic side chains. Development of environmentally sensitive peptide analogs, that can bind into the class II MHC the same way as native peptides, can assist in visualizing the antigen binding process. A chapter in this thesis describes the crystallographic work showing that (4-DAPA)-HA can be used to study antigen-presenting processes in a cell by visualizing the changes in fluorescence of the synthesized peptide upon antigen loading. Crystallographic analysis of MHC class II, HLA-DR1, in complex with HIV gag-derived peptide, GagP16(PEVIPMFSALSEGATP), and superantigen, SEC3- 3B2, reveals the conventional polyproline conformation up to MHC binding pocket residue, P9, while the C-terminus of GagP16 adopts an unusual β- hairpin loop structure. Additionally, interactions between the leucine at P8 (LeuP8) and other residues on the loop such as ThrP16 and AlaP14 of the hairpin loop, was observed. Importantly, GagP16 requires the last 4 amino acids (P13-P16), which is part of the hairpin loop, for T-cell recognition. Understanding what dictates the C-terminal hairpin loop and the interaction motif of HLA-DR1/GagP16 complex with its TCR will provide insights on why it is important for T cell activation. A chapter in this thesis discusses the structural investigation conducted to understand the determinants of the loop at the C-terminus of GagP16 using designed peptides. It will also discuss work involving HLA-DR1 with the T cell receptor, AC25, that was cloned from T cells that are specific to HLA-DR1 in complex with the GagP16 peptide.

Indiana University-Purdue University Indianapolis (IUPUI) / Background: Bacterial adherence to the acquired dental pellicle, important in caries, is mediated by receptor-adhesin interactions such as Streptococcus mutans antigen I/II (I/II). Ten I/II epitopes from the A, V, P and C regions were chosen to determine their reactivity in human saliva. Underlying the body’s ability to immunologically respond to bacteria that lead to caries are the human leukocyte antigen (HLA) genes, specifically HLA class II (HLA-II) genes that control antigen presentation. Previous studies suggested that a specific HLA biomarker group (HLA-DRB1*04) may have differential control of immune responses to I/II. However, it was not known whether secretory IgA (SIgA) responses to the selected epitopes from HLA-DRB1*04 positive subjects were different compared to their non-biomarker counterparts (negative), or across other caries factors, since no study to date had thus assessed these questions. Methods: Per IRB approval, the study population was divided into age, sex and race matched DRB1*04 positive (n=16) and negative groups (n=16). SIgA-epitope (and whole cell) reactivity was determined using ELISA. Other caries factors were measured. Subjects received a clinical exam by a trained examiner. ix Differences between DRB1*04 positive and negative groups were examined using a two-sided, two-sample t-test. Results: DRB1*04 positive subjects had numerically, but not statistically, higher reactivity to 9 out of 10 epitopes, the exception being residues 834-853 from the V and P regions of I/II across multiple measures. Though statistically insignificant, DRB1*04 positive subjects also exhibited 25-30 μg mL-1 less total IgA (TIgA) than negative counterparts. All clinical caries data proved inconclusive when comparing groups, likely due to exogenous factors and sample size. Conclusion: DRB1*04 positive subjects showed a trend toward lower TIgA. Moreover, they also showed a lower SIgA response across multiple measures to 834-853, the I/II V and P region epitope. This region forms a sort of functional epicenter involved in collaboration between domains along the entire I/II antigen, and governs the region involved in initial attachment to the acquired dental pellicle. This region may be involved in an in vivo discontinuous conformationally specific immunogenic epitope that serves as an HLA-II binding motif which remains elusive.