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1.
BMC Infect Dis ; 21(1): 111, 2021 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-33485302

RESUMO

BACKGROUND: T cells play an important role in the prognosis of hepatitis B virus (HBV) infection, and are involved in the seroconversion of a patient from HBsAb negative to positive. To compare the T-cell receptor ß-chain variable region (TcRBV) complementarity-determining region 3 (CDR3) in subjects with or without hepatitis B surface antigen (HBsAg) convert to hepatitis B surface antibody (HBsAb), the TcRBV was determined using high throughput sequencing (HTS). METHODS: The clonotype and diversity of CDR3 in peripheral blood mononuclear cells of subjects with resolved acute hepatitis B (AHB, HBsAb+, HBsAg-) (n = 5), chronic hepatitis B (CHB, HBsAb-, HBsAg+) (n = 5), and healthy controls (HC, HBsAb-, HBsAg-) (n = 3) were determined and analyzed using HTS (MiSeq). RESULTS: The overlapping rate of CDR3 clones of any two samples in AHB group was 2.00% (1.74% ~ 2.30%), CHB group was 1.77% (1.43% ~ 2.61%), and HC group was 1.82% (1.62% ~ 2.12%), and there was no significant difference among the three groups by Kruskal-Wallis H test. However, among the top 10 cumulative frequencies of clonotypes, only the frequency of clonotype (TcRBV20-1/BD1/BJ1-2) in AHB group was lower than that of HC group (P < 0.001). Moreover, exclude the 10 top clonotypes, there are 57 markedly different frequency of clones between AHB and CHB groups (18 clones up, 39 clones down), 179 (180-1) different clones between AHB and HC groups, and 134 different clones between CHB and HC groups. With regard to BV and BJ genotypes, there was no significant different frequency among the groups. Furthermore, there was no significant difference in the diversity of TcRBV CDR3 among the three groups (P > 0.05). CONCLUSIONS: Thus, there are 57 TcRBV clonotypes that may be related to HBsAg seroconversion of AHB subjects, but the diversity of TcRBV CDR3 is not significantly related to the HBsAb positive status.


Assuntos
Regiões Determinantes de Complementaridade/genética , Hepatite B/imunologia , Receptores de Antígenos de Linfócitos T alfa-beta/genética , Linfócitos T/imunologia , Adulto , Feminino , Hepatite B/sangue , Anticorpos Anti-Hepatite B/sangue , Antígenos de Superfície da Hepatite B/sangue , Vírus da Hepatite B/imunologia , Hepatite B Crônica/genética , Hepatite B Crônica/imunologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Leucócitos Mononucleares/imunologia , Masculino , Pessoa de Meia-Idade , Soroconversão , Adulto Jovem
2.
Mol Immunol ; 127: 112-123, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32961421

RESUMO

A highly diverse repertoire of T cell antigen receptors (TCR) is created in the thymus by recombination of gene segments and the insertion or deletion of nucleotides at the junctions. Using next-generation TCR sequencing we define here the features of recombination and selection in the human TCRα and TCRß locus, and show that a strikingly high proportion of the repertoire is shared by unrelated individuals. The thymic TCRα nucleotide repertoire was more diverse than TCRß, with 4.1 × 106 vs. 0.81 × 106 unique clonotypes, and contained nonproductive clonotypes at a higher frequency (69.2% vs. 21.2%). The convergence of distinct nucleotide clonotypes to the same amino acid sequences was higher in TCRα than in TCRß repertoire (1.45 vs. 1.06 nucleotide sequences per amino acid sequence in thymus). The gene segment usage was biased, and generally all individuals favored the same genes in both TCRα and TCRß loci. Despite the high diversity, a large fraction of the repertoire was found in more than one donor. The shared fraction was bigger in TCRα than TCRß repertoire, and more common in in-frame sequences than in nonproductive sequences. Thus, both biases in rearrangement and thymic selection are likely to contribute to the generation of shared repertoire in humans.


Assuntos
Impressão Genômica , Linfócitos T/imunologia , Timo/citologia , Sequência de Bases , Células Clonais , Regiões Determinantes de Complementaridade/genética , Feminino , Variação Genética , Humanos , Lactente , Recém-Nascido , Masculino , Mutagênese Insercional , Probabilidade , Receptores de Antígenos de Linfócitos T alfa-beta/genética , Recombinação Genética/genética
3.
PLoS Biol ; 18(9): e3000821, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32886672

RESUMO

As a novel alternative to established surface display or combinatorial chemistry approaches for the discovery of therapeutic peptides, we present a method for the isolation of small, cysteine-rich domains from bovine antibody ultralong complementarity-determining regions (CDRs). We show for the first time that isolated bovine antibody knob domains can function as autonomous entities by binding antigen outside the confines of the antibody scaffold. This yields antibody fragments so small as to be considered peptides, each stabilised by an intricate, bespoke arrangement of disulphide bonds. For drug discovery, cow immunisations harness the immune system to generate knob domains with affinities in the picomolar to low nanomolar range, orders of magnitude higher than unoptimized peptides from naïve library screening. Using this approach, knob domain peptides that tightly bound Complement component C5 were obtained, at scale, using conventional antibody discovery and peptide purification techniques.


Assuntos
Anticorpos/química , Dissulfetos/isolamento & purificação , Domínios de Imunoglobulina , Fragmentos de Peptídeos/isolamento & purificação , Domínios e Motivos de Interação entre Proteínas , Animais , Anticorpos/imunologia , Anticorpos/metabolismo , Afinidade de Anticorpos , Formação de Anticorpos , Especificidade de Anticorpos , Antígenos/genética , Antígenos/imunologia , Linfócitos B/fisiologia , Bovinos , Complemento C5/química , Complemento C5/genética , Complemento C5/imunologia , Regiões Determinantes de Complementaridade/química , Regiões Determinantes de Complementaridade/genética , Regiões Determinantes de Complementaridade/imunologia , Dissulfetos/química , Dissulfetos/imunologia , Mapeamento de Epitopos/métodos , Humanos , Imunização , Domínios de Imunoglobulina/genética , Modelos Moleculares , Fragmentos de Peptídeos/genética , Fragmentos de Peptídeos/imunologia , Domínios e Motivos de Interação entre Proteínas/genética
4.
Proc Natl Acad Sci U S A ; 117(36): 22341-22350, 2020 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-32855302

RESUMO

Conformational diversity and self-cross-reactivity of antigens have been correlated with evasion from neutralizing antibody responses. We utilized single cell B cell sequencing, biolayer interferometry and X-ray crystallography to trace mutation selection pathways where the antibody response must resolve cross-reactivity between foreign and self-proteins bearing near-identical contact surfaces, but differing in conformational flexibility. Recurring antibody mutation trajectories mediate long-range rearrangements of framework (FW) and complementarity determining regions (CDRs) that increase binding site conformational diversity. These antibody mutations decrease affinity for self-antigen 19-fold and increase foreign affinity 67-fold, to yield a more than 1,250-fold increase in binding discrimination. These results demonstrate how conformational diversity in antigen and antibody does not act as a barrier, as previously suggested, but rather facilitates high affinity and high discrimination between foreign and self.


Assuntos
Anticorpos , Diversidade de Anticorpos/genética , Autoantígenos , Rearranjo Gênico do Linfócito B/genética , Mutação/genética , Animais , Anticorpos/química , Anticorpos/genética , Anticorpos/metabolismo , Afinidade de Anticorpos/genética , Autoanticorpos/química , Autoanticorpos/genética , Autoanticorpos/metabolismo , Autoantígenos/química , Autoantígenos/metabolismo , Regiões Determinantes de Complementaridade/genética , Imunidade Humoral/genética , Camundongos , Modelos Moleculares , Conformação Proteica , Hipermutação Somática de Imunoglobulina/genética
5.
Science ; 369(6507): 1119-1123, 2020 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-32661058

RESUMO

Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti-SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53-neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)-binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.


Assuntos
Anticorpos Neutralizantes/química , Anticorpos Antivirais/química , Formação de Anticorpos , Betacoronavirus/imunologia , Regiões Determinantes de Complementaridade/química , Infecções por Coronavirus/prevenção & controle , Cadeias Pesadas de Imunoglobulinas/química , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Anticorpos Neutralizantes/genética , Anticorpos Neutralizantes/imunologia , Anticorpos Antivirais/genética , Anticorpos Antivirais/imunologia , Sítios de Ligação , Regiões Determinantes de Complementaridade/genética , Regiões Determinantes de Complementaridade/imunologia , Infecções por Coronavirus/genética , Infecções por Coronavirus/imunologia , Cristalografia por Raios X , Humanos , Cadeias Pesadas de Imunoglobulinas/genética , Cadeias Pesadas de Imunoglobulinas/imunologia , Pneumonia Viral/imunologia , Domínios Proteicos , Vacinas Virais/química , Vacinas Virais/genética , Vacinas Virais/imunologia
6.
Proc Natl Acad Sci U S A ; 117(24): 13659-13669, 2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32482872

RESUMO

T cell maturation and activation depend upon T cell receptor (TCR) interactions with a wide variety of antigenic peptides displayed in a given major histocompatibility complex (MHC) context. Complementarity-determining region 3 (CDR3) is the most variable part of the TCRα and -ß chains, which govern interactions with peptide-MHC complexes. However, it remains unclear how the CDR3 landscape is shaped by individual MHC context during thymic selection of naïve T cells. We established two mouse strains carrying distinct allelic variants of H2-A and analyzed thymic and peripheral production and TCR repertoires of naïve conventional CD4+ T (Tconv) and naïve regulatory CD4+ T (Treg) cells. Compared with tuberculosis-resistant C57BL/6 (H2-Ab) mice, the tuberculosis-susceptible H2-Aj mice had fewer CD4+ T cells of both subsets in the thymus. In the periphery, this deficiency was only apparent for Tconv and was compensated for by peripheral reconstitution for Treg We show that H2-Aj favors selection of a narrower and more convergent repertoire with more hydrophobic and strongly interacting amino acid residues in the middle of CDR3α and CDR3ß, suggesting more stringent selection against a narrower peptide-MHC-II context. H2-Aj and H2-Ab mice have prominent reciprocal differences in CDR3α and CDR3ß features, probably reflecting distinct modes of TCR fitting to MHC-II variants. These data reveal the mechanics and extent of how MHC-II shapes the naïve CD4+ T cell CDR3 landscape, which essentially defines adaptive response to infections and self-antigens.


Assuntos
Regiões Determinantes de Complementaridade/imunologia , Antígenos de Histocompatibilidade Classe II/imunologia , Receptores de Antígenos de Linfócitos T/imunologia , Linfócitos T Reguladores/imunologia , Tuberculose/genética , Alelos , Animais , Linfócitos T CD4-Positivos/imunologia , Regiões Determinantes de Complementaridade/química , Regiões Determinantes de Complementaridade/genética , Antígenos de Histocompatibilidade Classe II/genética , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Receptores de Antígenos de Linfócitos T/química , Receptores de Antígenos de Linfócitos T/genética , Baço/imunologia , Linfócitos T Reguladores/química , Tuberculose/imunologia
7.
Nat Commun ; 11(1): 3126, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32561710

RESUMO

Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases.


Assuntos
Regiões Determinantes de Complementaridade/genética , Biologia Computacional/métodos , RNA-Seq , Conjuntos de Dados como Assunto , Estudos de Viabilidade , Humanos , Receptores de Antígenos de Linfócitos B/genética
8.
BMC Cardiovasc Disord ; 20(1): 253, 2020 05 27.
Artigo em Inglês | MEDLINE | ID: mdl-32460698

RESUMO

BACKGROUND: This study aims to investigate the T-cell receptor (TCR) repertoire in patients with acute coronary syndrome (ACS). METHODS: The TCR repertoires of 9 unstable angina patients (UA), 14 acute myocardial infarction patients (AMI) and 9 normal coronary artery (NCA) patients were profiled using high-throughput sequencing (HTS). The clonal diversity of the TCR repertoires in different groups was analyzed, as well as the frequencies of variable (V), diversity (D) and joining(J) gene segments. RESULTS: ACS patients including UA and AMI, showed reduced TCRß diversity than NCA patients. ACS patients presented higher levels of clonal expansion. The clonotype overlap of complementarity determining region 3(CDR3) was significantly varied between different groups. A total of 10 V genes and 1 J gene were differently utilized between ACS and NCA patients. We identified some shared CDR3 amino acid sequences that were presented in ACS but not in NCA patients. CONCLUSIONS: This study revealed the distinct TCR repertoires in patients with ACS and demonstrated the presence of disease associated T-cell clonotypes. These findings suggested a role of T cells in ACS and provided a new way to explore the mechanisms of ACS.


Assuntos
Síndrome Coronariana Aguda/genética , Angina Instável/genética , Genes Codificadores dos Receptores de Linfócitos T , Sequenciamento de Nucleotídeos em Larga Escala , Infarto do Miocárdio/genética , Linfócitos T/imunologia , Síndrome Coronariana Aguda/diagnóstico , Síndrome Coronariana Aguda/imunologia , Idoso , Angina Instável/diagnóstico , Angina Instável/imunologia , Estudos de Casos e Controles , China , Regiões Determinantes de Complementaridade/genética , Feminino , Genes Codificadores da Cadeia beta de Receptores de Linfócitos T/genética , Humanos , Região Variável de Imunoglobulina , Masculino , Pessoa de Meia-Idade , Infarto do Miocárdio/diagnóstico , Infarto do Miocárdio/imunologia
9.
Scand J Immunol ; 92(2): e12912, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32458431

RESUMO

Immune processes in liver transplantation remain poorly understood. Acute allograft rejection in liver transplantation is a kind of T cell-mediated inflammatory disease accompanied by inflammatory cell infiltration. However, the effect of acute allograft rejection on the immunological characteristics of TCRs in peripheral blood mononuclear cell is unknown. In this study, we characterized the pattern of the human T cell receptor beta chain (TRB) and immunoglobulin heavy chain (IGH) complementarity-determining region 3 (CDR3) repertoires via high-throughput sequencing in 11 acute allograft rejection (AG) cases, 23 patients with stable allograft liver function (ST) who had liver transplantation performed and 20 healthy controls (HC). The diversity of TRB-CDR3 was significantly reduced in the AG group compared with the ST group and healthy controls (HC). The CDR3 and N-addition length distribution were not significantly different between the AG and ST groups. However, N-addition length distribution was significantly changed compared to HC. It seemed that AG used more short N-additions and healthy people used more long N-additions in TRB-CDR3 repertoire. Our findings suggested that the TRB-CDR3 region of AG had distinctive V gene use compared with that of HC. The characteristics of ST seemed to be in between those of AG and HC although the difference is not significant. Cluster analysis showed that the TRB repertoire could not effectively distinguish AG from ST. This research might give to a better understanding of the immune process of liver transplantation.


Assuntos
Regiões Determinantes de Complementaridade/imunologia , Rejeição de Enxerto/imunologia , Cadeias Pesadas de Imunoglobulinas/imunologia , Transplante de Fígado , Receptores de Antígenos de Linfócitos T alfa-beta/imunologia , Adulto , Regiões Determinantes de Complementaridade/genética , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Cadeias Pesadas de Imunoglobulinas/genética , Masculino , Pessoa de Meia-Idade , Receptores de Antígenos de Linfócitos T alfa-beta/genética
10.
Mol Immunol ; 120: 23-31, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32045771

RESUMO

Acne is a common chronic inflammatory skin disease, and the inflammation immune response runs through all stages of acne lesions. In this study, we use a combination of multiplex-PCR and high-throughput sequencing technologies to analyze T cell receptor ß chain CDR3 (complementarity-determining region 3) in peripheral blood isolated from severe acne patients. Once compared with healthy controls, we propose to identify acne-relevant CDR3 peptides. Our results reveal that the diversity of T cell receptor ß chain (TRB) CDR3 sequences in the peripheral blood of the severe acne vulgaris (SA) group differed from that of the control group. In addition, we find 10 TRB CDR3 sequences, amino acid sequences and V-J combinations with significantly different expressions between the SA group and the non-acne (NA) group (P < 0.0001). These findings may contribute to a better understanding of the role of immunity in the pathogenesis of acne and may serve as biomarkers for evaluating risk or prognosis of severe acne disease in future.


Assuntos
Acne Vulgar/genética , Acne Vulgar/imunologia , Regiões Determinantes de Complementaridade/genética , Genes Codificadores da Cadeia beta de Receptores de Linfócitos T , Adolescente , Sequência de Aminoácidos , Sequência de Bases , Variação Genética , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Reação em Cadeia da Polimerase Multiplex , Análise de Sequência de DNA , Análise de Sequência de Proteína , Adulto Jovem
11.
Proc Natl Acad Sci U S A ; 117(8): 4320-4327, 2020 02 25.
Artigo em Inglês | MEDLINE | ID: mdl-32047037

RESUMO

The prognosis of chronic lymphocytic leukemia (CLL) depends on different markers, including cytogenetic aberrations, oncogenic mutations, and mutational status of the immunoglobulin (Ig) heavy-chain variable (IGHV) gene. The number of IGHV mutations distinguishes mutated (M) CLL with a markedly superior prognosis from unmutated (UM) CLL cases. In addition, B cell antigen receptor (BCR) stereotypes as defined by IGHV usage and complementarity-determining regions (CDRs) classify ∼30% of CLL cases into prognostically important subsets. Subset 2 expresses a BCR with the combination of IGHV3-21-derived heavy chains (HCs) with IGLV3-21-derived light chains (LCs), and is associated with an unfavorable prognosis. Importantly, the subset 2 LC carries a single-point mutation, termed R110, at the junction between the variable and constant LC regions. By analyzing 4 independent clinical cohorts through BCR sequencing and by immunophenotyping with antibodies specifically recognizing wild-type IGLV3-21 and R110-mutated IGLV3-21 (IGLV3-21R110), we show that IGLV3-21R110-expressing CLL represents a distinct subset with poor prognosis independent of IGHV mutations. Compared with other alleles, only IGLV3-21*01 facilitates effective homotypic BCR-BCR interaction that results in autonomous, oncogenic BCR signaling after acquiring R110 as a single-point mutation. Presumably, this mutation acts as a standalone driver that transforms IGLV3-21*01-expressing B cells to develop CLL. Thus, we propose to expand the conventional definition of CLL subset 2 to subset 2L by including all IGLV3-21R110-expressing CLL cases regardless of IGHV mutational status. Moreover, the generation of monoclonal antibodies recognizing IGLV3-21 or mutated IGLV3-21R110 facilitates the recognition of B cells carrying this mutation in CLL patients or healthy donors.


Assuntos
Cadeias lambda de Imunoglobulina/genética , Leucemia Linfocítica Crônica de Células B/genética , Receptores de Antígenos de Linfócitos B/imunologia , Linfócitos B/imunologia , Estudos de Coortes , Regiões Determinantes de Complementaridade/genética , Regiões Determinantes de Complementaridade/imunologia , Predisposição Genética para Doença , Humanos , Cadeias Pesadas de Imunoglobulinas/genética , Cadeias Pesadas de Imunoglobulinas/imunologia , Cadeias lambda de Imunoglobulina/imunologia , Leucemia Linfocítica Crônica de Células B/imunologia , Mutação Puntual , Receptores de Antígenos de Linfócitos B/genética
12.
Life Sci ; 248: 117457, 2020 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-32092334

RESUMO

AIMS: Multiple surgical procedures and anesthesia increase the risk of the development in children. However, the influence of such exposures on the developing childhood immunity organs is rarely reported. MATERIALS AND METHODS: High-throughput sequencing of T-cell receptor (TCR) repertoires (TCRseq) from rhesus monkeys' thymus was performed to investigate whether anesthetics could induce de novo antigen recognition via TCR or TCR development impairments. KEY FINDINGS: No significant difference between sevoflurane and control groups regarding VJ gene combinations and diversity of V and J gene was seen, nor was there an obvious change in similar average number of Complementarity Determining Region 3 (CDR3) aa clonotypes. Our analysis of Rank abundance, Gini coefficient, Simpson index, Normalized Shannon Diversity Entropy (NSDE), Morisita-Horn Similarity Index (MHSI) and Bhattacharyya Distance (BD) indicated there is no difference in TCR diversity and similarity. SIGNIFICANCE: These results suggest early events in thymic T cell development and repertoire generation are not abnormality after multiple sevoflurane exposure during childhood. The stabilization of the immune repertoires suggested the safety of sevoflurane in host immune response in children.


Assuntos
Anestésicos Inalatórios/farmacologia , Regiões Determinantes de Complementaridade/genética , Receptores de Antígenos de Linfócitos T/genética , Sevoflurano/farmacologia , Linfócitos T/efeitos dos fármacos , Timo/efeitos dos fármacos , Animais , Animais Recém-Nascidos , Regiões Determinantes de Complementaridade/classificação , Feminino , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Sequenciamento de Nucleotídeos em Larga Escala , Macaca mulatta , Masculino , Receptores de Antígenos de Linfócitos T/classificação , Receptores de Antígenos de Linfócitos T/imunologia , Linfócitos T/citologia , Linfócitos T/imunologia , Timo/citologia , Timo/imunologia , Recombinação V(D)J/imunologia
13.
J Immunol Methods ; 476: 112679, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31655052

RESUMO

Development of mechanism-driven biomarkers for immune checkpoint inhibitors (ICIs) in cancer immunotherapy requires sensitive and efficacious assays to identify tumor antigen (Ag)-specific T cells. We demonstrated the concept for a sensitive method to determine Ag-reactive T cell clones based on clonal expansion using model neoantigens (NeoAgs) rather than cytokine production. Sequential increase in T cell clonal frequencies following Ag stimulation was detected by next generation sequencing (NGS) of T cell receptor ß (TCR ß) complementarity-determining region 3 (CDR3), with a higher sensitivity than that of enzyme-linked immunospot (ELISPOT) by 100-fold. The TCRß CDR3 sequences could represent useful markers to track dynamic changes during immunotherapy. The TCRß NGS-based method could represent a novel platform both for the development of new biomarkers as well as several therapeutic options.


Assuntos
Antígenos de Neoplasias/imunologia , Células Clonais/imunologia , Regiões Determinantes de Complementaridade/genética , Epitopos , Genes Codificadores da Cadeia beta de Receptores de Linfócitos T , Sequenciamento de Nucleotídeos em Larga Escala , Linfócitos T/imunologia , Idoso , Separação Celular/métodos , ELISPOT , Feminino , Humanos , Neoplasias Pulmonares/imunologia , Sensibilidade e Especificidade
14.
Oncogene ; 39(8): 1773-1783, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31740784

RESUMO

Focusing on highly specific aspects of the immune response is likely to answer a number of basic questions, and in some cases even resolve basic contradictions, in cancer immunology. For example, there are many cases, where chronic inflammation is associated with cancer development, and many other cases where an immune response represents an anticancer process. In this study, using bioinformatics algorithms, we examined the chemical relationships between the amino acid sequences of the complementarity-determining region-3 (CDR3) represented by immune receptors associated with lower grade glioma and isocitrate dehydrogenase-1 (IDH1) mutants. In particular, we developed a chemical complementarity scoring approach to classify tumors based on the complementarity of CDR3s and mutant IDH1 amino acids, relying on net charge per residue and hydropathy parameters. There was a strong correlation between the increased survival in low-grade glioma (LGG) and complementarity of IDH1 mutants to the CDR3 domain of the T-cell receptor beta chain (TRB). Similar results were obtained for TRB CDR3s and NRAS mutants in melanoma. Furthermore, the clear connection between increased survival rates and immune receptor-IDH1 mutant complementarities may also, partially, explain the better LGG prognosis for patients with IDH1 mutants.


Assuntos
Regiões Determinantes de Complementaridade/genética , Regiões Determinantes de Complementaridade/metabolismo , Glioma/genética , Glioma/patologia , Isocitrato Desidrogenase/genética , Isocitrato Desidrogenase/metabolismo , Mutação , Regulação Neoplásica da Expressão Gênica , Humanos , Estimativa de Kaplan-Meier , Gradação de Tumores
15.
Mol Cell Proteomics ; 19(2): 278-293, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31767621

RESUMO

Human antibody response studies are largely restricted to periods of high immune activity (e.g. vaccination). To comprehensively understand the healthy B cell immune repertoire and how this changes over time and through natural infection, we conducted immune repertoire RNA sequencing on flow cytometry-sorted B cell subsets to profile a single individual's antibodies over 11 months through two periods of natural viral infection. We found that 1) a baseline of healthy variable (V) gene usage in antibodies exists and is stable over time, but antibodies in memory cells consistently have a different usage profile relative to earlier B cell stages; 2) a single complementarity-determining region 3 (CDR3) is potentially generated from more than one VJ gene combination; and 3) IgG and IgA antibody transcripts are found at low levels in early human B cell development, suggesting that class switching may occur earlier than previously realized. These findings provide insight into immune repertoire stability, response to natural infections, and human B cell development.


Assuntos
Linfócitos B/imunologia , Regiões Determinantes de Complementaridade/genética , Imunoglobulina A/imunologia , Imunoglobulina G/imunologia , Infecções por Picornaviridae/imunologia , Rhinovirus , Proteína C-Reativa/análise , Humanos , Switching de Imunoglobulina , Contagem de Leucócitos , Masculino , Pessoa de Meia-Idade , Infecções por Picornaviridae/sangue , Infecções por Picornaviridae/genética , Análise de Sequência de RNA
16.
Immunogenetics ; 72(1-2): 109-118, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31811313

RESUMO

Upon recognition of peptide-MHC complexes by T cell receptors (TCR), the cognate T cells expand and differentiate into effector T cells to generate protective immunity. Despite the fact that any immune response generates a diverse set of TCR clones against a particular epitope, only a few clones are highly expanded in any immune response. Previous studies observed that the highest frequency clones usually control viral infections better than subdominant clones, but the reasons for this dominance among T cell clones are still unclear. Here, we used publicly available TCR amino acid sequences to study which factors determine whether a response becomes immunodominance (ID) per donor; we classified the largest T cell clone as the epitope-specific dominant clone and all the other clones as subdominant responses (SD). We observed a distinctively hydrophobic CDR3 in ID responses against a dominant epitope from influenza A virus, compared to the SD responses. The common V-J combinations were shared between ID and SD responses, suggesting that the biased V-J recombination events are restricted by epitope specificity; thus, the immunodominance is not directly determined by a bias combination of V and J genetic segments. Our findings reveal a close similarity of global sequence properties between dominant and subdominant clones of epitope-specific responses but detectable distinctive amino acid enrichments in ID. Taken together, we believe this first comparative study of immunodominant and subdominant TCR sequences can guide further studies to resolve factors determining the immunodominance of antiviral as well as tumor-specific T cell responses.


Assuntos
Regiões Determinantes de Complementaridade/genética , Epitopos Imunodominantes/genética , Receptores de Antígenos de Linfócitos T/genética , Sequência de Aminoácidos , Linfócitos T CD8-Positivos/imunologia , Regiões Determinantes de Complementaridade/metabolismo , Bases de Dados Factuais , Epitopos/genética , Epitopos/imunologia , Epitopos de Linfócito T/imunologia , Humanos , Imunidade Celular , Epitopos Imunodominantes/imunologia , Ativação Linfocitária , Dados de Sequência Molecular , Receptores de Antígenos de Linfócitos T/imunologia , Recombinação V(D)J/genética
17.
J Exp Med ; 217(2)2020 02 03.
Artigo em Inglês | MEDLINE | ID: mdl-31704807

RESUMO

Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.


Assuntos
Vacinas contra a AIDS/imunologia , Linfócitos B/imunologia , Infecções por HIV/imunologia , Infecções por HIV/prevenção & controle , HIV-1/imunologia , Vacinação , Produtos do Gene env do Vírus da Imunodeficiência Humana/imunologia , Animais , Anticorpos Neutralizantes/imunologia , Linhagem da Célula/genética , Linhagem da Célula/imunologia , Células Cultivadas , Regiões Determinantes de Complementaridade/genética , Feminino , Anticorpos Anti-HIV/imunologia , Infecções por HIV/virologia , HIV-1/química , Sequenciamento de Nucleotídeos em Larga Escala , Cadeias Pesadas de Imunoglobulinas/genética , Macaca mulatta , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Análise de Célula Única , Hipermutação Somática de Imunoglobulina
18.
Immunology ; 159(4): 373-383, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-31821535

RESUMO

The anti-tumor immune response is considered to be due to the T-cell receptor (TCR) binding to tumor antigens, which can be either wild-type, early stem cell proteins, presumably foreign to a developed immune system; or mutant peptides, foreign to the immune system because of a mutant amino acid (aa) or otherwise somatically altered aa sequence. Recently, very large numbers of TCR complementarity-determining region-3 (CDR3) aa sequences obtained from tumor specimens have become available. We developed a novel algorithm for assessing the complementarity of tumor mutant peptides and TCR CDR3s, based on the retrieval of TCR CDR3 aa sequences from both tumor specimen and patient blood exomes and by using an automated process of assessing CDR3 and mutant aa electrical charges. Results indicated many instances where high electrostatic complementarity was associated with a higher survival rate. In particular, our approach led to the identification of specific genes contributing significantly to the complementary, TCR CDR3-mutant aa. These results suggest a novel approach to tumor immunoscoring and may lead to the identification of high-priority neo-antigen, peptide vaccines; or to the identification of ex vivo stimulants of tumor-infiltrating lymphocytes.


Assuntos
Algoritmos , Antígenos de Neoplasias/química , Neoplasias da Mama/genética , Regiões Determinantes de Complementaridade/química , Neoplasias Pulmonares/genética , Complexo Receptor-CD3 de Antígeno de Linfócitos T/química , Neoplasias Cutâneas/genética , Sequência de Aminoácidos , Aminoácidos , Antígenos de Neoplasias/genética , Antígenos de Neoplasias/imunologia , Sítios de Ligação , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/imunologia , Neoplasias da Mama/mortalidade , Regiões Determinantes de Complementaridade/genética , Regiões Determinantes de Complementaridade/imunologia , Exoma , Feminino , Expressão Gênica , Humanos , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/imunologia , Neoplasias Pulmonares/mortalidade , Masculino , Mutação , Prognóstico , Ligação Proteica , Complexo Receptor-CD3 de Antígeno de Linfócitos T/genética , Complexo Receptor-CD3 de Antígeno de Linfócitos T/imunologia , Projetos de Pesquisa , Neoplasias Cutâneas/diagnóstico , Neoplasias Cutâneas/imunologia , Neoplasias Cutâneas/mortalidade , Eletricidade Estática , Taxa de Sobrevida , Linfócitos T/imunologia , Linfócitos T/patologia
20.
Arthritis Res Ther ; 21(1): 295, 2019 12 19.
Artigo em Inglês | MEDLINE | ID: mdl-31856905

RESUMO

BACKGROUND: CD4+ T cells play critical roles in the pathogenesis of IgG4-related disease (IgG4-RD). The aim of this study was to investigate the TCR repertoire of peripheral blood CD4+ T cells in IgG4-RD. METHODS: The peripheral blood was collected from six healthy controls and eight IgG4-RD patients. TCR ß-chain libraries of CD4+ T cells were constructed by 5'-rapid amplification of cDNA ends (5'-RACE) and sequenced by Illumina Miseq platform. The relative similarity of TCR repertoires between samples was evaluated according to the total frequencies of shared clonotypes (metric F), correlation of frequencies of shared clonotypes (metric R), and total number of shared clonotypes (metric D). RESULTS: The clonal expansion and diversity of CD4+ T cell repertoire were comparable between healthy controls and IgG4-RD patients, while the proportion of expanded and coding degenerated clones, as an indicator of antigen-driven clonal expansion, was significantly higher in IgG4-RD patients. There was no significant difference in TRBV and TRBJ gene usage between healthy controls and IgG4-RD patients. The complementarity determining region 3 (CDR3) length distribution was skewed towards longer fragments in IgG4-RD. Visualization of relative similarity of TCR repertoires by multi-dimensional scaling analysis showed that TCR repertoires of IgG4-RD patients were separated from that of healthy controls in F and D metrics. We identified 11 IgG4-RD-specific CDR3 amino acid sequences that were expanded in at least 2 IgG4-RD patients, while not detected in healthy controls. According to TCR clonotype networks constructed by connecting all the CDR3 sequences with a Levenshtein distance of 1, 3 IgG4-RD-specific clusters were identified. We annotated the TCR sequences with known antigen specificity according to McPAS-TCR database and found that the frequencies of TCR sequences associated with each disease or immune function were comparable between healthy controls and IgG4-RD patients. CONCLUSION: According to our study of CD4+ T cells from eight IgG4-RD patients, TCR repertoires of IgG4-RD patients were different from that of healthy controls in the proportion of expanded and coding degenerated clones and CDR3 length distribution. In addition, IgG4-RD-specific TCR sequences and clusters were identified in our study.


Assuntos
Linfócitos T CD4-Positivos/metabolismo , Regiões Determinantes de Complementaridade/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Doença Relacionada a Imunoglobulina G4/genética , Receptores de Antígenos de Linfócitos T alfa-beta/genética , Adulto , Idoso , Linfócitos T CD4-Positivos/imunologia , Células Clonais/imunologia , Células Clonais/metabolismo , Análise por Conglomerados , Feminino , Redes Reguladoras de Genes/genética , Redes Reguladoras de Genes/imunologia , Humanos , Doença Relacionada a Imunoglobulina G4/imunologia , Masculino , Pessoa de Meia-Idade , Receptores de Antígenos de Linfócitos T alfa-beta/imunologia
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