Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.
Antigens, Neoplasm ; metabolism ; Data Analysis ; Databases, Genetic ; Humans ; Immunotherapy ; Mutation ; genetics ; Neoplasms ; genetics ; immunology ; Tumor Suppressor Protein p53 ; genetics ; Urinary Bladder Neoplasms ; genetics

OBJECTIVETo measure the expression of lymphocyte function-associated antigen-3 (CD58) in childhood B-lineage acute lymphoblastic leukemia (B-ALL) and to explore the feasibility of CD58 as an indicator for minimal residual disease (MRD) detection in childhood B-ALL.

METHODSEighty-seven children diagnosed with B-ALL between January 2014 and September 2014 were enrolled, and 20 hospitalized children who had no tumor or blood disease and had normal bone marrow cell morphology served as the control group. The expression features of CD58 in bone marrow samples from the two groups (at diagnosis, on day 15 of induction chemotherapy) were analyzed by four-color flow cytometry (FCM). Quantitative real-time polymerase chain reaction (qRT-PCR) and FCM were used to detect MRD in B-ALL patients on day 33 of induction chemotherapy.

RESULTSThe mean fluorescence intensity of CD58 expression in the 87 B-ALL cases (91±33) was significantly higher than that in the 20 controls (14±6) (P<0.01); CD58 was over-expressed in 44 of the B-ALL cases. In the B-ALL children, the expression of CD58 on day 15 of induction chemotherapy (105±22) was not significantly different from that at diagnosis (107±26) (P>0.05). In the 44 B-ALL patients with CD58 over-expression, FCM showed 9 MRD(+) cases and 35 MRD(-) cases, while qRT-PCR showed 11 MRD(+) cases and 33 MRD(-) cases; 42 cases (95%) showed consistent results of the two tests, so there was no significant difference between the two methods in detecting MRD (P>0.05).

CONCLUSIONSCD58 is over-expressed and stable in children with B-ALL, and it can be considered as an indicator for MRD detection in childhood B-ALL.

Adolescent ; CD58 Antigens ; analysis ; Cell Lineage ; Child ; Child, Preschool ; Feasibility Studies ; Female ; Humans ; Induction Chemotherapy ; Infant ; Male ; Neoplasm, Residual ; diagnosis ; Precursor B-Cell Lymphoblastic Leukemia-Lymphoma ; drug therapy ; immunology

Serum levels of soluble MHC class I-related chain A (sMICA) are related with the prognosis of various types of cancer; however, few studies on the prognostic value of sMICA in hepatocellular carcinoma (HCC) have been reported. In this study, we retrospectively investigated the relationship between sMICA levels and clinical features of advanced HCC, and we assessed the prognostic value of sMICA in advanced HCC. Furthermore, the relationship of serum sMICA levels and natural killer group 2, member D (NKG2D) expression on natural killer (NK) cells was also evaluated. We detected sMICA levels in the serum of 60 advanced HCC patients using enzyme-linked immunosorbent assay (ELISA) and measured expression levels of NKG2D on NK cells using flow cytometry. We found that serum sMICA levels in HCC patients were in the range of 0.10-6.21 ng/mL. Chi-square analyses showed that sMICA level was significantly related with only tumor size. Survival analysis showed that a high sMICA level was significantly related with poor prognosis among HCC patients. Multivariate analyses indicated that sMICA was an independent prognostic factor. In addition, the levels of CD56+NKG2D+ NK cells were within the range of 11.2%-55.4%, and correlation analyses indicated that sMICA level was negatively correlated with the level of NKG2D+ NK cells. Our results suggest that serum sMICA levels may be an independent prognostic factor for advanced HCC.
Adult ; Carcinoma, Hepatocellular ; blood ; immunology ; pathology ; Female ; Histocompatibility Antigens Class I ; blood ; Humans ; Killer Cells, Natural ; immunology ; metabolism ; Liver Neoplasms ; blood ; immunology ; pathology ; Male ; Middle Aged ; Multivariate Analysis ; NK Cell Lectin-Like Receptor Subfamily K ; metabolism ; Neoplasm Staging ; Retrospective Studies ; Survival Rate ; Tumor Burden

OBJECTIVETo verify the obtained immunogenic membrane antigens candidate of pancreatic cancer in the performed research.

METHODSPancreatic cancer cell line SW1990 membrane protein underwent immunoblot with serum IgG purified from clinically collected sera of 66 pancreatic cancer patients. Number 3 and number 8 positive dots of immunoblot were identified by MALDI-TOF mass spectrometry and peptide mass fingerprinting matching. The candidate membrane antigens were further validated in cell lines by RT-PCR, real-time PCR and Western blot, and their different expression level of gene and protein in pancreatic cancer cell lines were contrastly studied.

RESULTSNumber 3 and number 8 positive dots were identified as: voltage-dependent anion channel (VDAC3) and catechol-o-methyltransferase (COMT). RT-PCR, real-time PCR and Western blot showed that gene and protein of VDAC3 and COMT were expressed in the pancreatic cancer cell line SW1990, AsPc and P3 respectively.

CONCLUSIONVDAC3 and COMT might be the candidate immunogenic membrane antigens of human pancreatic cancer, and their gene and protein are differently expressed in the pancreatic cancer cell line SW1990, AsPc and P3.

Antigens, Neoplasm ; analysis ; Cell Line, Tumor ; Humans ; Pancreatic Neoplasms ; immunology ; Proteomics

This study was purposed to explore the feasibility of simultaneous analysis of telomere length and cell surface antigen by multicolor Flow-FISH to assess minimal residual disease (MRD) in leukemia. The telomere length in 34 leukemia patients versus 20 normal controls was compared by using Flow-FISH, and the relationship between telomere length and therapeutic effect and prognosis was analyzed preliminarily. As for those patients with follow-up samples, the changes of telomere length combined with surface antigen in different courses of disease were observed by multicolor Flow-FISH. The results indicated that the telomere length of de novo patients was significantly shorter than that of controls except the patients in chronic myeloid leukemia-chronic phase (CML-CP). The shorter telomere, the lower complete remission (CR) rates were observed in acute leukemia cases and the shorter duration of CP before onset of blast phase (BP) occurred in CML cases. The acute leukemia patients showed longer telomere and fewer cells expressed the related antigen after CR. The telomere length of cases with continued CR remained at normal level during remission, and there was no increased expression of the specific antigen. However, the telomere of relapsed cases shortened again after relapse with elevated specific antigen expression. In the relapsed cases, the telomere of related antigen positive cells shortened ahead of telomere length change of the whole cells and morphologic change of bone marrow cells. It is concluded that analysis of telomere length by flow-FISH manifests the significance for monitoring disease conditions, estimating prognosis and guiding therapy in all kinds of leukemia. The simultaneous analysis of telomere length and cell surface antigen by multicolor flow-FISH may monitor abnormal clone or clonal evolution to predict recurrence more sensitively and specifically, and may provide a promising and widely applicable method for monitoring MRD in leukemia.
Adolescent ; Adult ; Aged ; Antigens, Surface ; analysis ; Female ; Flow Cytometry ; Humans ; In Situ Hybridization, Fluorescence ; Leukemia ; genetics ; immunology ; Male ; Middle Aged ; Neoplasm, Residual ; genetics ; immunology ; Recurrence ; Remission Induction ; Telomere ; genetics ; Young Adult

OBJECTIVETo study the clinicopathologic characteristics of thymic epithelial tumors and to evaluate the diagnostic reproducibility and clinical relevance of the 2004 WHO histologic classification system.

METHODSThe morphology and immunophenotype of 52 cases of thymic epithelial tumor were reviewed. The tumors were classified according to the new WHO classification system and the clinical data were analyzed.

RESULTSOf the 52 cases studied, 45 were thymomas and 7 were thymic carcinomas. Amongst the 45 cases of thymoma, 6 (13.4%) were type A, 15 (33.3%) were type AB, 4 (8.9%) were type B1, 9 (20.0%) were type B2, 9 (20.0%) were type B3 and 2 (4.4%) were metaplastic thymoma. Amongst the 7 cases of thymic carcinoma, 6 were squamous cell carcinomas and 1 was neuroendocrine carcinoma. The commonest presentations were cough and chest pain. Some cases were incidentally discovered by routine physical examination. Thirteen cases (25.0%) of thymoma were associated with myasthenia gravis. CT scan showed that 49 cases (94.2%) were located in the anterior mediastinum. All cases of type A, AB and B1 thymoma and most cases of B2 thymoma appeared as well-defined homogeneous mass, whereas a few cases of type B2 thymoma and most cases of type B3 thymoma and thymic carcinoma were poorly demarcated and heterogeneous. According to Masaoka staging system, 20 cases (41.7%) belonged to stage I, 15 cases (31.3%) stage II, 11 cases (22.9%) stage III and 2 cases (4.1%) stage IV. The histologic subtypes of thymic epithelial tumors significantly correlated with the clinical stages (chi(2) = 32.5, P < 0.01).

CONCLUSIONSThe 2004 revision of WHO histologic classification system for thymic epithelial tumors shows a high degree of reproducibility. Correlation with the radiologic, clinical and prognostic parameters is helpful in determining the management strategy for individual patients.

Adult ; Aged ; Antibodies, Monoclonal ; analysis ; Antigens, CD20 ; metabolism ; CD5 Antigens ; metabolism ; Carcinoma, Neuroendocrine ; classification ; diagnostic imaging ; metabolism ; pathology ; Carcinoma, Squamous Cell ; classification ; diagnostic imaging ; metabolism ; pathology ; Female ; Follow-Up Studies ; Humans ; Keratins ; immunology ; Male ; Middle Aged ; Myasthenia Gravis ; Neoplasm Recurrence, Local ; Neoplasm Staging ; Prognosis ; Radiotherapy, Adjuvant ; Retrospective Studies ; Thymoma ; classification ; diagnostic imaging ; metabolism ; pathology ; Thymus Neoplasms ; classification ; diagnostic imaging ; metabolism ; pathology ; Tomography, X-Ray Computed

OBJECTIVETo separate the cell subpopulation with high tumorigenic ability and study the biological characteristics of this subpopulation in laryngeal carcinoma cells.

METHODSHuman laryngeal carcinoma cells were obtained by primary tissue culture technique. CD44 and CD133 molecules were used as markers to isolate the CD44(+), CD133(+), CD44(+)CD133(+) and CD44(+)CD133(-) cell subpopulations from the laryngeal carcinoma cells by flow cytometry. A nude mouse tumor xenograft model was developed for the study of the tumorigenic effects of the different cell populations. 1 x 10(6), 1 x 10(5), 1 x 10(4) and 1 x 10(3) cells were injected into the left flank of the mice, respectively. The mice were observed for palpable tumor formation and were sacrificed at 4 weeks later to assess the tumor formation rate, tumor volume and tumor weight. Boyden chamber migration assay was used to determine the migration ability and immunochemistry was used to detect the expression of stem cell antigen SCA-1 and beta1-integrin. Semi-quantities RT-PCR and Western blot analysis were performed to detect the expression level of Bmi-1 in the different cell subpopulations.

RESULTSThe growth of subcutaneous tumors in nude mice showed that a tumor can be generated with 1 x 10(3) CD44(+)CD133(+) cells. When the same dose of 1 x 10(6) CD44(+)CD133(+) cells was injected into the mice, both the average weight and volume of the tumors were significantly higher than those generated from other cell subpopulations. Boyden chamber migration assay showed that the invasion ability of CD44(+)CD133(+) cells was significantly higher than that of other cell subsets. The results of immunochemical analysis showed an abundant expression of stem cell antigen SCA-1 and beta1-integrin in the CD44(+)CD133(+) cells. Semi-quantitative RT-PCR and Western blot analysis provided strong evidence that the Bmi-1 expression in CD44(+)CD133(+) and CD133(+) cells was very significantly higher than that in CD44(+), CD44(+)CD133(-) and control cells (P < 0.01).

CONCLUSIONOur findings demonstrate that CD44(+)CD133(+) subset cells in laryngeal carcinoma posses some biological characteristics of tumor stem cells, which may be the original cells of laryngeal carcinoma and may become a new target of tumor therapy.

AC133 Antigen ; Animals ; Antigens, CD ; analysis ; Antigens, Ly ; metabolism ; Cell Adhesion ; Gene Expression Regulation, Neoplastic ; Glycoproteins ; analysis ; Humans ; Hyaluronan Receptors ; analysis ; Integrin beta1 ; metabolism ; Laryngeal Neoplasms ; immunology ; metabolism ; pathology ; Male ; Membrane Proteins ; metabolism ; Mice ; Mice, Inbred BALB C ; Mice, Nude ; Neoplasm Transplantation ; Nuclear Proteins ; genetics ; metabolism ; Peptides ; analysis ; Polycomb Repressive Complex 1 ; Proto-Oncogene Proteins ; genetics ; metabolism ; RNA ; metabolism ; Repressor Proteins ; genetics ; metabolism ; Tumor Burden ; Tumor Cells, Cultured

OBJECTIVETo investigate the expression of prostate stem cell antigen (PSCA) in human pancreatic carcinoma and explore its role in the oncogenesis of pancreatic cancer.

METHODSA pancreatic carcinoma tissue microarray was constructed, which contained 10 normal adult pancreas tissues, 12 chronic pancreatitis tissues and 78 pancreatic carcinomas. Immunohistochemistry was employed to detect the expression of PSCA, and the relation between PSCA expression and the clinicopathological factors of pancreatic carcinoma was analyzed.

RESULTSThe positivity rate of PSCA in pancreatic carcinoma was 79.5% (62/78), and PSCA staining was more intense in the malignant cells than in the benign cells (chi2=15.81, P<0.005) and chronic pancreatitis tissues (chi2=11.33, P<0.005). No obvious association was found between PSCA expression and the other variables of pancreatic carcinoma (including gender, age at surgery, tumor grade, and TNM stages).

CONCLUSIONThe expression of PSCA can be related to the development of pancreatic cancer, but not to the clinicopathological factors of the tumor.

Adult ; Aged ; Antigens, Neoplasm ; genetics ; metabolism ; Carcinoma, Ductal ; immunology ; metabolism ; Female ; GPI-Linked Proteins ; genetics ; metabolism ; Humans ; Male ; Middle Aged ; Neoplasm Proteins ; genetics ; metabolism ; Pancreatic Neoplasms ; immunology ; metabolism ; Tissue Array Analysis ; methods

As a part of our ongoing search for a safe and efficient anti-tumor vaccine, we attempted to determine whether the molecular nature of certain tumor antigens would influence immune responses against tumor cells. As compared with freeze-thawed or formaldehyde-fixed tumor antigens, heat-denatured tumor antigens elicited profound anti-tumor immune responses and greatly inhibited the growth of live tumor cells. The heat-denatured tumor antigens induced a substantial increase in the anti-tumor CTL response in the absence of any adjuvant material. This response appears to be initiated by strong activation of the antigen-presenting cells, which may recognize heat-denatured protein antigens. Upon recognition of the heat-denatured tumor antigens, macrophages and dendritic cells were found to acutely upregulate the expression of co-stimulatory molecules such as B7.2, as well as the secretion of inflammatory cytokines such as IL-12 and TNF-alpha. The results of this study indicate that heat-denatured tumor extracts might elicit protective anti-tumor adaptive immune responses and also raise the possibility that a safe and efficient adjuvant-free tumor vaccine might be developed in conjunction with a dendritic cell-based tumor vaccine.
Adjuvants, Immunologic ; Animals ; Antibodies, Neoplasm/immunology ; Antibody Specificity/immunology ; Antigens, Neoplasm/immunology ; Cancer Vaccines/*immunology ; Cell Line, Tumor ; Cell Proliferation ; Cytokines/biosynthesis ; Cytotoxicity, Immunologic/immunology ; Dendritic Cells/immunology ; *Hot Temperature ; Immunity, Cellular/immunology ; Immunization ; Immunologic Memory/immunology ; Macrophages, Peritoneal/immunology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Neoplasms/*immunology/*pathology ; Survival Analysis ; T-Lymphocytes, Cytotoxic/immunology

BACKGROUND: The aberrant, leukemia-associated antigen expression patterns allow us to discriminate leukemic blasts from normal precursor cells. Our major goal was to determine a guideline for the detection of minimal residual disease using CD20+/CD34+ and myeloid Ag+/CD19+ combination in the bone marrow of acute leukemia in complete remission (CR) after chemotherapy. METHODS: Bone marrow samples from 117 patients with acute leukemia in complete remission after chemotherapy and from 22 healthy controls were immunophenotyped by triple staining and measured by flow cytometry. RESULTS: The CD20+/CD34+ cells in the large lymphocyte gate (R1) ranged from 0% to 3.24% (0.8+/-0.82%, P=0.000) in CD20+/CD34+ B-lineage ALL CR (N=31), from 0.03% to 4.2% (0.7+/-0.83%, P=0.000) in CD20-/CD34- B-lineage ALL CR (N=66), from 0.1% to 0.96% (0.45+/-0.32%, P=0.016) in T-ALL CR (N=10), and from 0.02% to 0.48% (0.18+/-0.15%, P=0.776) in AML CR (N=10). The CD13,33+/CD19+ cells in R1 gate ranged from 0% to 2.69% (0.37+/-0.48%, P<0.001) in CD13,33+/CD19+ B-lineage ALL CR (N=31), from 0% to 1.8% (0.31+/-0.28%, P<0.001) in CD13,33-/CD19+B-lineage ALL CR (N=65), from 0.02% to 0.64% (0.29+/-0.22%, P=0.071) in T-ALL CR (N=9), and from 0% to 0.17% (0.07+/-0.09%, P=0.341) in AML CR (N=3). CONCLUSIONS: Using an immunophenotypic method for the detection of early relapse or minimal residual disease of B-lineage ALL bone marrow in CR after chemotherapy, different cutoff values should be applied according to antigen combination and gating. When the proportion of aberrant antigen combination was less than 5% in large lymphocyte gate, the results should be interpreted with caution.
Acute Disease ; Antigens, CD/*metabolism ; Antigens, CD19/metabolism ; Antigens, CD20/metabolism ; Antigens, CD34/metabolism ; Antigens, Differentiation, Myelomonocytic/analysis/metabolism ; Bone Marrow Cells/*classification/metabolism ; Flow Cytometry ; Hematopoietic Stem Cells/classification/metabolism ; Humans ; Immunophenotyping ; Leukemia/*diagnosis/drug therapy ; Leukemia, Myeloid, Acute/diagnosis/drug therapy ; Neoplasm, Residual ; Remission Induction ; Tumor Markers, Biological/immunology