iTTCA-Hybrid: Improved and robust identification of tumor T cell antigens by utilizing hybrid feature representation

2020 ◽  
Vol 599 ◽  
pp. 113747 ◽  
Author(s):  
Phasit Charoenkwan ◽  
Chanin Nantasenamat ◽  
Md Mehedi Hasan ◽  
Watshara Shoombuatong
Keyword(s):  
T Cell ◽  
Feature Representation ◽  
Robust Identification ◽  
T Cell Antigens

scholarly journals iTTCA-RF: a random forest predictor for tumor T cell antigens

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Shihu Jiao ◽  
Quan Zou ◽  
Huannan Guo ◽  
Lei Shi
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
Random Forest ◽  
Feature Representation ◽  
Feature Subset ◽  
Hybrid Features ◽  
Feature Selection Technique ◽  
Cell Antigen ◽  
Specificity And Sensitivity ◽  
T Cell Antigens

Abstract Background Cancer is one of the most serious diseases threatening human health. Cancer immunotherapy represents the most promising treatment strategy due to its high efficacy and selectivity and lower side effects compared with traditional treatment. The identification of tumor T cell antigens is one of the most important tasks for antitumor vaccines development and molecular function investigation. Although several machine learning predictors have been developed to identify tumor T cell antigen, more accurate tumor T cell antigen identification by existing methodology is still challenging. Methods In this study, we used a non-redundant dataset of 592 tumor T cell antigens (positive samples) and 393 tumor T cell antigens (negative samples). Four types feature encoding methods have been studied to build an efficient predictor, including amino acid composition, global protein sequence descriptors and grouped amino acid and peptide composition. To improve the feature representation ability of the hybrid features, we further employed a two-step feature selection technique to search for the optimal feature subset. The final prediction model was constructed using random forest algorithm. Results Finally, the top 263 informative features were selected to train the random forest classifier for detecting tumor T cell antigen peptides. iTTCA-RF provides satisfactory performance, with balanced accuracy, specificity and sensitivity values of 83.71%, 78.73% and 88.69% over tenfold cross-validation as well as 73.14%, 62.67% and 83.61% over independent tests, respectively. The online prediction server was freely accessible at http://lab.malab.cn/~acy/iTTCA. Conclusions We have proven that the proposed predictor iTTCA-RF is superior to the other latest models, and will hopefully become an effective and useful tool for identifying tumor T cell antigens presented in the context of major histocompatibility complex class I.

scholarly journals CD4 T Cell Antigens from Staphylococcus aureus Newman Strain Identified following Immunization with Heat-Killed Bacteria

2012 ◽  
Vol 19 (4) ◽  
pp. 477-489 ◽  
Author(s):  
Paulraj K. Lawrence ◽  
Bachra Rokbi ◽  
Nadège Arnaud-Barbe ◽  
Eric L. Sutten ◽  
Junzo Norimine ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
T Cell ◽  
Reverse Genetics ◽  
Vaccine Development ◽  
Protein A ◽  
Cd4 T Cell ◽  
Content Type ◽  
Intramammary Infections ◽  
T Cell Antigens ◽  
Ifn Γ

ABSTRACTStaphylococcus aureusis a commensal bacterium associated with the skin and mucosal surfaces of humans and animals that can also cause chronic infection. The emergence of antibiotic-resistant strains such as methicillin-resistantS. aureus(MRSA) and strains causing chronic intramammary infections (IMI) in cows results in severe human and livestock infections. Conventional approaches to vaccine development have yielded only a few noneffective vaccines against MRSA or IMI strains, so there is a need for improved vaccine development. CD4 T lymphocytes are required for promoting gamma interferon (IFN-γ) mediated immunoglobulin isotype switching in B lymphocytes to produce high-affinity IgG antibodies and IFN-γ-mediated phagocyte activation for an effective resolution of bacterial infection. However, the lack of known CD4 T cell antigens fromS. aureushas made it difficult to design effective vaccines. The goal of this study was to identifyS. aureusproteins recognized by immune CD4 T cells. Using a reverse genetics approach, 43 antigens were selected from theS. aureusNewman strain. These included lipoproteins, proteases, transcription regulators, an alkaline shock protein, conserved-domain proteins, hemolysins, fibrinogen-binding protein, staphylokinase, exotoxin, enterotoxin, sortase, and protein A. Screening of expressed proteins for recall T cell responses in outbred, immune calves identified 13 proteins that share over 80% sequence identity among MRSA or IMI strains. These may be useful for inclusion in a broadly protective multiantigen vaccine against MRSA or IMI.

Germ-line configuration of the T-cell receptor beta-chain gene in B-cell chronic lymphoproliferative disorders which co-express T-cell antigens

2009 ◽  
Vol 39 (5) ◽  
pp. 412-417 ◽  
Author(s):  
Fortunato Morabito ◽  
Angela Tassinari ◽  
Vincenzo Callea ◽  
Maura Brugiatelli ◽  
Maria Teresa Fierro ◽  
...  
Keyword(s):  
T Cell ◽  
T Cell Receptor ◽  
Germ Line ◽  
Cell Receptor ◽  
Lymphoproliferative Disorders ◽  
Chain Gene ◽  
Line Configuration ◽  
T Cell Antigens ◽  
T Cell Receptor Beta ◽  
Receptor Beta

scholarly journals Tpre, a new alloantigen encoded in the IgT-C region of chromosome 12, is expressed on bone marrow of nude mice, fetal T cell hybrids, and fetal thymus.

1983 ◽  
Vol 157 (2) ◽  
pp. 419-432 ◽  
Author(s):  
F L Owen
Keyword(s):  
Bone Marrow ◽  
T Cell ◽  
Bone Marrow Cells ◽  
Precursor Cell ◽  
Chromosome 12 ◽  
Cell Populations ◽  
Fetal Thymus ◽  
Cell Hybrids ◽  
T Cell Antigens ◽  
Adult Thymus

A new T cell alloantigen, Tpre, has been identified by monoclonal F.6.9.1 antibody. This antigen is encoded by a gene linked to the cluster of T cell antigens in the IgT-C region of chromosome 12 (Tthy, Tind, and Tsu). Tpre is distinct from Tthy, Tind, or Tsu because it is expressed on bone marrow cells of the AKR nustr/nustr, the thymus repopulating precursor cell in normal adult marrow, and normal fetal thymocytes. Several fetal and adult T cell hybrids express these antigens independently. Tpre and Tthy are expressed on largely overlapping cell populations in adult thymus.

scholarly journals Phenotype of recovering lymphoid cell populations after marrow transplantation.

1985 ◽  
Vol 161 (6) ◽  
pp. 1483-1502 ◽  
Author(s):  
K A Ault ◽  
J H Antin ◽  
D Ginsburg ◽  
S H Orkin ◽  
J M Rappeport ◽  
...  
Keyword(s):  
T Cell ◽  
B Cells ◽  
B Cell ◽  
Nk Cells ◽  
Cell Types ◽  
Lymphoid Cells ◽  
The Other ◽  
Hla Dr ◽  
T Cell Antigens ◽  
Leu 7

Four patients who received bone marrow transplants were studied sequentially during the posttransplant period to define the pattern of recovering lymphoid cell types. Three patients received T cell-depleted, HLA-matched marrow, and one received untreated marrow from an identical twin. Blood lymphoid cells were labeled with 25 different pairs of monoclonal antibodies. In each sample, one antibody was conjugated to fluorescein and one to phycoerythrin, thus allowing simultaneous assessment of the expression of the two markers using the fluorescence activated cell sorter. A total of 14 antibodies were used, routinely including HLE, Leu-M3, Leu-4, Leu-1, Leu-5, Leu-9, Leu-6, Leu-2, Leu-3, HLA-DR, Leu-7, Leu-11, Leu-15, and Leu-12. Other antibodies were used to further define some populations. This study has allowed us to define six distinct cell types that have appeared in all four patients by day 90 posttransplantation, and which account for 90-100% of all circulating lymphoid cells. These cell types are (a) T helper cells expressing Leu-1, Leu-4, Leu-9, Leu-5, Leu-3, and variable amounts of HLA-DR; (b) T suppressor cells expressing Leu-1, Leu-4, Leu-9, Leu-5, Leu-2, and variable amounts of HLA-DR; (c) B cells expressing Leu-12, B1, HLA-DR, IgD, and IgM, but none of the T cell antigens; (d) an unusual B cell phenotype (Leu-1 B) expressing all of the B cell markers, and also having low amounts of Leu-1, but none of the other T cell antigens; (e) natural killer (NK) cells expressing Leu-11, Leu-15, Leu-5 but none of the other T cell or B cell markers; (f) NK cells expressing Leu-11, Leu-15, Leu-5, and low levels of Leu-2. Both NK types also express Leu-7 on some, but not all cells. The relative frequencies of these cell types varied among the patients and with time, but the striking findings were the presence of relatively few mature T cells, large numbers of NK cells, and the preponderance of the unusual Leu-1 B cell over conventional B cells in all three patients who developed B cells. Sorting experiments confirmed the NK activity of the major NK cell phenotypes, and DNA analysis confirmed that all of the cells studied were of donor origin. In addition, analysis of Ig genes in one patient showed that the Leu-1 B cells were not clonally rearranged.(ABSTRACT TRUNCATED AT 400 WORDS)

The Phylogeny of T Cell Antigens

1986 ◽  
pp. 373-387 ◽  
Author(s):  
Margreet Jonker ◽  
Franciscus J. M. Nooij
Keyword(s):  
T Cell ◽  
T Cell Antigens

scholarly journals Human Mycobacterium tuberculosis CD8 T Cell Antigens/Epitopes Identified by a Proteomic Peptide Library

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e67016 ◽  
Author(s):  
David M. Lewinsohn ◽  
Gwendolyn M. Swarbrick ◽  
Meghan E. Cansler ◽  
Megan D. Null ◽  
Veena Rajaraman ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
T Cell ◽  
Cd8 T Cell ◽  
Peptide Library ◽  
T Cell Antigens

scholarly journals Human T-cell antigens defined by monoclonal antibodies. Absence of T65 on committed myeloid and erythroid progenitors

Blood ◽  
1980 ◽  
Vol 56 (5) ◽  
pp. 943-946 ◽  
Author(s):  
R Taetle ◽  
I Royston
Keyword(s):  
Bone Marrow ◽  
T Cell ◽  
Progenitor Cells ◽  
Peripheral Blood ◽  
Myelogenous Leukemia ◽  
Erythroid Progenitors ◽  
Normal Peripheral Blood ◽  
Human T Cell ◽  
Complement Dependent Cytotoxicity ◽  
T Cell Antigens

Abstract The complement-dependent cytotoxicity of monoclonal T-cell antibody (T101) for normal and abnormal hemopoietic progenitors was assessed. T101 demonstrated toxicity for normal T-colony-forming cells from peripheral blood and bone marrow. Cytotoxicity was absent for normal peripheral blood and bone marrow granulocytes/macrophage (CFU-C) and erythroid (BFU-E) progenitors. The antibody was also not toxic for peripheral blood blast progenitors from patients with acute myelogenous leukemia (AML). These studies indicate the absence of the antigen defined by T101 (T65) from normal progenitor cells and from blast progenitors in patients with AML. T101 may be used in the treatment of T-cell malignancies and in the prevention of graft-versus-host disease (GVHD) without damage to normal progenitor cells.

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