A Rare Transporter Associated with Antigen Processing Polymorphism Overpresented in HLAlow Colon Cancer Reveals the Functional Significance of the Signature Domain in Antigen Processing

Metastatic axillary lymph node ratio (LNR) is prognostically superior to pN staging in patients with breast cancer--results for 804 Chinese patients from a single institution

The number of axillary lymph nodes involved and retrieved are important prognostic factors in breast cancer. The purpose of our study was to investigate whether the lymph node ratio (LNR) is a better prognostic factor in predicting disease-free survival (DFS) for breast cancer patients as compared with pN staging. The analysis was based on 804 breast cancer patients who had underwent axillary lymph node dissection between 1999 and 2008 in Sun Yat-Sen University Cancer Center. Optimal cutoff points of LNR were calculated using X-tile software and validated by bootstrapping. Patients were then divided into three groups (low-, intermediate-, and high-risk) according to the cutoff points. Predicting risk factors for relapse were performed according to Cox proportional hazards analysis. DFS was estimated using the Kaplan-Meier method and compared by the log-rank test. The 5-year DFS rate decreased significantly with increasing LNRs and pN. Univariate analysis found that the pT , pN, LNR, molecule type, HER2, pTNM stage and radiotherapy well classified patients with significantly different prognosis. By multivariate analysis, only LNR classification was retained as an independent prognostic factor. Furthermore, there was a significant prognostic difference among different LNR categories for pN2 category, but no apparent prognostic difference was seen between different pN categories in any LNR category. Therefore, LNR rather than pN staging is preferable in predicting DFS in node positive breast cancer patients, and routine clinical decision-making should take the LNR into consideration.

The genotype of the transporter associated with antigen processing gene affects susceptibility to colorectal cancer in Japanese

OBJECTIVE

Although colorectal cancer (CRC) is one of the most frequent malignancies in Japan, the associated genetic factors remain to be elucidated. Functional loss of the transporter associated with antigen processing (TAP) 1 gene induces carcinogenesis. We investigated whether single nucleotide polymorphisms (SNPs) in the TAP1 gene (rs735883) are associated with susceptibility to CRC in a Japanese population.

METHODS

The study participants were 143 cases and 243 clinical controls. After extracting DNA from their peripheral blood cells, genotyping was conducted by the polymerase chain reaction-restriction fragment length polymorphism method.

RESULTS

Participants with a mutated allele had an increased risk for CRC. The adjusted odds ratios for the C/T, T/T, and the mutation type (C/T + T/T) compared to that of wild type (C/C) were 2.27 [95 % confidence interval (CI), 1.43-3.67], 1.95 (95 % CI, 0.88-4.30), and 2.22 (95 % CI, 1.42-3.55), respectively. Furthermore, a significant trend in the rate of cases was observed with an increasing number of mutated alleles (P for trend = 0.0068).

CONCLUSIONS

The genotype of the TAP1 gene is associated with susceptibility to CRC.

Novel insights into the molecular mechanisms of HLA class I abnormalities

Alterations in the MHC class I surface antigens represent one mechanism of tumor cells to escape from natural or immunotherapy-induced antitumor immune responses. In order to restore MHC class I expression, knowledge about the underlying molecular mechanisms of MHC class I defects in different tumor types is required. In most cases, abnormalities of MHC class I expression are reversible by cytokines suggesting a deregulation rather than structural abnormalities of members of the antigen-processing and presentation machinery (APM). The impaired expression of APM components could be controlled at the epigenetic, transcriptional and/or posttranscriptional level. Furthermore, a direct link between altered transcription factor binding, interferon signal transduction and MHC class I APM component expression has been shown, which might be further associated with cell cycle progression. This information will not only give novel insights into the (patho) physiology of the antigen-processing and presenting pathway, but will help in the future to design effective T cell-based immunotherapies.

The mechanism of ABC transporters: general lessons from structural and functional studies of an antigenic peptide transporter

The shuttling of substrates across a cellular membrane frequently requires a specialized ATP-binding cassette (ABC) transporter, which couples the energy of ATP binding and hydrolysis to substrate transport. Due to its importance in immunity, the ABC transporter associated with antigen processing (TAP) has been studied extensively and is an excellent model for other ABC transporters. The TAP protein pumps cytosolic peptides into the endoplasmic reticulum for loading onto class I major histocompatibility complex (MHC) for subsequent immune surveillance. Here, we outline a potential mechanism for the TAP protein with supporting evidence from bacterial transporter structures. The similarities and differences between TAP and other transporters support the notion that ABC transporters in general have adapted around a universal transport mechanism.

Functionally important interactions between the nucleotide-binding domains of an antigenic peptide transporter

The transporter associated with antigen processing (TAP), an ABC transporter, pumps cytosolic peptides into the endoplasmic reticulum, where the peptides are loaded onto class I MHC molecules for presentation to the immune system. Transport is fueled by the binding of ATP to two cytosolic nucleotide-binding domains (NBDs) and ATP hydrolysis. We demonstrate biochemically that there are two electrostatic interactions across the interface between the two TAP NBDs and that these interactions are important for peptide transport. Notably, disrupting these interactions by mutagenesis does not greatly alter the ATP hydrolysis rate in an isolated NBD model system, suggesting that the interactions function at alternative stages in the transport cycle. The data support the general model for ABC transporters in which the NBDs form a tight, closed conformation during transport. Our results are discussed in relation to other ABC transporters that do or do not conserve potential interacting residues of opposite charges at the homologous positions.

Immunologic markers of cancer progression and prognosis

During the past decade, significant progress has been made in understanding the interactions between the immune system and cancer. The re-emergence of cancer immunosurveillance and immunoediting concepts has provided an understanding of several immunologic markers that are associated with cancer progression and prognosis. Recent studies have attempted to define the critical role of tumor infiltration by lymphocytes as a reflection of a tumor-related immune response. More recently, there has been an improved ability to demonstrate distinct subsets of tumor-infiltrating lymphocytes (TILs) in different tumor compartments. Several of these studies indicate that the presence of TILs may be associated with improved clinical outcome in several human cancers. However, this improved clinical outcome is dependent upon the intratumoral balance and quality of TILs, or infiltration of regulatory T cells or myeloid-derived suppressor cells. Immunologic markers have an important role in demonstrating intermediate end points of a therapeutic intervention and ultimately may be useful in predicting clinical outcomes. These markers are important to the development of successful immunotherapy strategies in cancer.

Genetic variation of antigen processing machinery components and association with cervical carcinoma

The antigen processing machinery (APM) plays an important role in immune recognition of virally infected and transformed cells. Defective expression of several APM components is associated with progression and clinical outcome in cervical carcinoma. Genetic variation in the genes encoding APM components is known to be associated with risk of occurrence of several malignancies. However, only limited evidence exists supporting the role of single nucleotide polymorphisms (SNPs) in APM components in cervical carcinoma. We have therefore investigated the occurrence of APM component SNP genotypes and haplotypes in cervical carcinoma. Thirteen coding SNPs in the LMP2, LMP7, TAP1, TAP2, and ERAP1 genes were genotyped in 127 cervical carcinoma patients and 124 controls. Individual genotype and allele distributions were assessed by single-marker analysis. Effects of various SNP combinations were estimated by haplotype construction and subsequent haplotype interaction analysis. Significant haplotypes were modeled on disease risk. Allele distributions at the LMP7-145, TAP2-651, ERAP1-127, and ERAP1-730 loci differed significantly between cases and controls with the major allele at the LMP7 and TAP2 loci and the minor allele at both ERAP1 loci associated with increased cervical carcinoma risk. A combination of the two haplotypes spanning these loci was associated with a three-fold increased risk (OR = 3.024; P << 0.001); approximately 12% of all cervical carcinoma occurrences were attributable to this combination. Our data indicate that combined genetic variation in the TAP2, LMP7, and ERAP1 genes is associated with increased cervical carcinoma risk.

Upregulation of antigen-processing machinery components at mRNA level in acute lymphoblastic leukemia cells after CD40 stimulation

The development of immunotherapy in hematologic malignancies has been observed in the last few years. One of the approaches is the use of cancer vaccines based on leukemia-derived dendritic cells (DC). Recent studies from our laboratory and other laboratories have shown that CD40 stimulation improves leukemia cells immunogenicity and generates an antitumor immune response. The design of future cancer vaccines requires the knowledge concerning the function of dendritic cells including antigen processing. The aim of our present study was the assessment of antigen-processing machinery (APM) components in acute lymphoblastic leukemia (ALL) cells before and after CD40 stimulation at messenger RNA (mRNA) level. Twenty-five children with ALL were enrolled into the study. Leukemic cells were stimulated (or not) with CD40L and IL-4. Elements of the antigen-processing machinery (MB1, LMP2, LMP7, LMP10, TAP1, TAP2, calnexin, calreticulin, tapasin, ERp57, zeta, delta) were determined by real-time PCR technique. The expression of important costimulatory and adhesion molecules considered as DC markers (CD40, CD54, CD80, CD83, CD86) were determined at the mRNA (PCR) and protein (flow cytometry) levels. The following are the results of our study: (1) We noted an upregulation of all costimulatory and adhesion molecules at the mRNA and protein levels in ALL cells after the culture; (2) the significant rise in expression of nearly all APM components after CD40 stimulation was observed. This confirms specific stimulation of the antigen-processing system in ALL cells by CD40L. Future work should focus on the clinical significance of these findings for immunotherapy in leukemias.

Prediction of the deleterious nsSNPs in ABCB transporters

The non-synonymous SNPs (nsSNPs) in coding regions, neutral or deleterious, could lead to the alteration of the function or structure of proteins. We have developed the computational models to analyze the deleterious nsSNPs in the transporters and predict ones in ABCB (ATP-binding cassette B) transporters of interest. The RPLS (ridge partial least square) and LDA (linear discriminant analysis) methods were applied to the problem, by training on a selection of datasets from a specified source, i.e., human transporters. The best combination of datasets and prediction attributes was ascertained. The prediction accuracy of the theoretical RPLS model for the training and testing sets is 84.8% and 80.4%, respectively (LDA: 84.3% and 80.4%), which indicates the models are reasonable and may be helpful for pharmacogenetics studies.

Catalytic site modifications of TAP1 and TAP2 and their functional consequences

The transporter associated with antigen processing (TAP), a member of the ATP binding cassette (ABC) family of transmembrane transporters, transports peptides across the endoplasmic reticulum membrane for assembly of major histocompatibility complex class I molecules. Two subunits, TAP1 and TAP2, are required for peptide transport, and ATP hydrolysis by TAP1.TAP2 complexes is important for transport activity. Two nucleotide binding sites are present in TAP1.TAP2 complexes. Compared with other ABC transporters, the first nucleotide binding site contains non-consensus catalytic site residues, including Asp(668) in the Walker B region of TAP1 (in place of a highly conserved glutamic acid), and Gln(701) in the switch region of TAP1 (in place of a highly conserved histidine). At the second nucleotide binding site, a glutamic acid (TAP2 Glu(632)) follows the Walker B motif, and the switch region contains a histidine (TAP2 His(661)). We found that alterations at Glu(632) and His(661) of TAP2 significantly reduced peptide translocation and/or TAP-induced major histocompatibility complex class I surface expression. Alterations of TAP1 Asp(668) alone or in combination with TAP1 Gln(701) had only small effects on TAP activity. Thus, the naturally occurring Asp(668) and Gln(701) alterations of TAP1 are likely to contribute to attenuated catalytic activity at the first nucleotide binding site (the TAP1 site) of TAP complexes. Due to its enhanced catalytic activity, the second nucleotide binding site (the TAP2 site) appears to be the main site driving peptide transport. A mechanistic model involving one main active site is likely to apply to other ABC transporters that have an asymmetric distribution of catalytic site residues within the two nucleotide binding sites.

HLA-B44 polymorphisms at position 116 of the heavy chain influence TAP complex binding via an effect on peptide occupancy

A single residue polymorphism distinguishes HLA-B*4402(D116) from HLA-B*4405(Y116), which was suggested to allow HLA-B*4405 to acquire peptides without binding to tapasin-TAP complexes. We show that HLA-B*4405 is not inherently unable to associate with tapasin-TAP complexes. Under conditions of peptide deficiency, both allotypes bound efficiently to TAP and tapasin, and furthermore, random nonamer peptides conferred higher thermostability to HLA-B*4405 than to HLA-B*4402. Correspondingly, under conditions of peptide sufficiency, more rapid peptide-loading, dissociation from TAP complexes, and endoplasmic reticulum exit were observed for HLA-B*4405, whereas HLA-B*4402 showed greater endoplasmic reticulum retention and enhanced tapasin-TAP binding. Together, these studies suggest that position 116 HLA polymorphisms influence peptide occupancy, which in turn determines binding to tapasin and TAP. Relative to HLA-B*4405, inefficient peptide loading of HLA-B*4402 is likely to underlie its stronger tapasin dependence for cell surface expression and thermostability, and its enhanced susceptibility to pathogen interference strategies.