{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,11,11]],"date-time":"2023-11-11T00:35:59Z","timestamp":1699662959005},"reference-count":31,"publisher":"Impact Journals, LLC","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Oncoscience"],"published-print":{"date-parts":[[2023,11,10]]},"DOI":"10.18632\/oncoscience.590","type":"journal-article","created":{"date-parts":[[2023,11,10]],"date-time":"2023-11-10T14:33:55Z","timestamp":1699626835000},"page":"59-66","source":"Crossref","is-referenced-by-count":0,"title":["An immunoinformatics assessment of the cancer testis antigen, DDX53, as a potential early esophageal cancer antigen"],"prefix":"10.18632","volume":"10","author":[{"given":"Peter","family":"Cheng","sequence":"first","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Konrad J.","family":"Cios","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mallika","family":"Varkhedi","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vayda R.","family":"Barker","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle","family":"Yeagley","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrea","family":"Chobrutskiy","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Oregon Health and Science University Hospital, Portland, Oregon (OR) 97239, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Boris I.","family":"Chobrutskiy","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Oregon Health and Science University Hospital, Portland, Oregon (OR) 97239, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"George","family":"Blanck","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida (FL) 33612, USA"},{"name":"Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida (FL) 33612, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"7892","reference":[{"key":"1","doi-asserted-by":"crossref","unstructured":"Domper Arnal MJ, Ferr\u00e1ndez Arenas \u00c1, Lanas Arbeloa \u00c1. Esophageal cancer: Risk factors, screening and endoscopic treatment in Western and Eastern countries. World J Gastroenterol. 2015; 21:7933\u201343. https:\/\/doi.org\/10.3748\/wjg.v21.i26.7933. PMID:26185366","DOI":"10.3748\/wjg.v21.i26.7933"},{"key":"2","doi-asserted-by":"crossref","unstructured":"Baba Y, Nomoto D, Okadome K, Ishimoto T, Iwatsuki M, Miyamoto Y, Yoshida N, Baba H. Tumor immune microenvironment and immune checkpoint inhibitors in esophageal squamous cell carcinoma. Cancer Sci. 2020; 111:3132\u201341. https:\/\/doi.org\/10.1111\/cas.14541. PMID:32579769","DOI":"10.1111\/cas.14541"},{"key":"3","doi-asserted-by":"crossref","unstructured":"Yagi T, Baba Y, Ishimoto T, Iwatsuki M, Miyamoto Y, Yoshida N, Watanabe M, Baba H. PD-L1 Expression, Tumor-infiltrating Lymphocytes, and Clinical Outcome in Patients With Surgically Resected Esophageal Cancer. Ann Surg. 2019; 269:471\u201378. https:\/\/doi.org\/10.1097\/SLA.0000000000002616. PMID:29206673","DOI":"10.1097\/SLA.0000000000002616"},{"key":"4","doi-asserted-by":"crossref","unstructured":"Zhang Y, Zhang Y, Zhang L. Expression of cancer-testis antigens in esophageal cancer and their progress in immunotherapy. J Cancer Res Clin Oncol. 2019; 145:281\u201391. https:\/\/doi.org\/10.1007\/s00432-019-02840-3. PMID:30656409","DOI":"10.1007\/s00432-019-02840-3"},{"key":"5","doi-asserted-by":"crossref","unstructured":"Bhat AA, Nisar S, Maacha S, Carneiro-Lobo TC, Akhtar S, Siveen KS, Wani NA, Rizwan A, Bagga P, Singh M, Reddy R, Uddin S, Grivel JC, et al. Cytokine-chemokine network driven metastasis in esophageal cancer; promising avenue for targeted therapy. Mol Cancer. 2021; 20:2. https:\/\/doi.org\/10.1186\/s12943-020-01294-3. PMID:33390169","DOI":"10.1186\/s12943-020-01294-3"},{"key":"6","doi-asserted-by":"crossref","unstructured":"Lin EW, Karakasheva TA, Hicks PD, Bass AJ, Rustgi AK. The tumor microenvironment in esophageal cancer. Oncogene. 2016; 35:5337\u201349. https:\/\/doi.org\/10.1038\/onc.2016.34. PMID:26923327","DOI":"10.1038\/onc.2016.34"},{"key":"7","doi-asserted-by":"crossref","unstructured":"Yeagley M, Chobrutskiy BI, Gozlan EC, Medikonda N, Patel DN, Falasiri S, Callahan BM, Huda T, Blanck G. Electrostatic Complementarity of T-Cell Receptor-Alpha CDR3 Domains and Mutant Amino Acids Is Associated with Better Survival Rates for Sarcomas. Pediatr Hematol Oncol. 2021; 38:251\u201364. https:\/\/doi.org\/10.1080\/08880018.2020.1843576. PMID:33616477","DOI":"10.1080\/08880018.2020.1843576"},{"key":"8","doi-asserted-by":"crossref","unstructured":"Hsiang M, Chobrutskiy BI, Diaz M, Huda TI, Creadore S, Zaman S, Cios KJ, Gozlan EC, Blanck G. Chemical complementarity between immune receptors and cancer mutants, independent of antigen presentation protein binding, is associated with increased survival rates. Transl Oncol. 2021; 14:101069. https:\/\/doi.org\/10.1016\/j.tranon.2021.101069. PMID:33780706","DOI":"10.1016\/j.tranon.2021.101069"},{"key":"9","doi-asserted-by":"crossref","unstructured":"Arturo JF, Chobrutskiy BI, Yeagley M, Patel DN, Falasiri S, Patel JS, Blanck G. Electrostatic complementarity of B-cell receptor CDR3s and TP53-mutant amino acids in breast cancer is associated with increased disease-free survival rates. Cell Mol Immunol. 2020; 17:776\u201378. https:\/\/doi.org\/10.1038\/s41423-019-0328-8. PMID:31729463","DOI":"10.1038\/s41423-019-0328-8"},{"key":"10","doi-asserted-by":"crossref","unstructured":"Chobrutskiy BI, Yeagley M, Diviney A, Zaman S, Gozlan EC, Tipping P, Koohestani DM, Roca AM, Blanck G. A scoring system for the electrostatic complementarities of T-cell receptors and cancer-mutant amino acids: multi-cancer analyses of associated survival rates. Immunology. 2020; 159:373\u201383. https:\/\/doi.org\/10.1111\/imm.13165. PMID:31821535","DOI":"10.1111\/imm.13165"},{"key":"11","doi-asserted-by":"crossref","unstructured":"Chobrutskiy BI, Yeagley M, Tipping P, Zaman S, Diviney A, Patel DN, Falasiri S, Uversky VN, Blanck G. Chemical complementarity between immune receptor CDR3s and IDH1 mutants correlates with increased survival for lower grade glioma. Oncogene. 2020; 39:1773\u201383. https:\/\/doi.org\/10.1038\/s41388-019-1101-2. PMID:31740784","DOI":"10.1038\/s41388-019-1101-2"},{"key":"12","doi-asserted-by":"crossref","unstructured":"Chobrutskiy BI, Zaman S, Diviney A, Mihyu MM, Blanck G. T-cell receptor-\u03b1 CDR3 domain chemical features correlate with survival rates in bladder cancer. J Cancer Res Clin Oncol. 2019; 145:615\u201323. https:\/\/doi.org\/10.1007\/s00432-018-2815-1. PMID:30539280","DOI":"10.1007\/s00432-018-2815-1"},{"key":"13","doi-asserted-by":"crossref","unstructured":"Chobrutskiy BI, Chobrutskiy A, Zaman S, Yeagley M, Huda TI, Blanck G. High-throughput, sliding-window algorithm for assessing chemical complementarity between immune receptor CDR3 domains and cancer mutant peptides: TRG-PIK3CA interactions and breast cancer. Mol Immunol. 2021; 135:247\u201353. https:\/\/doi.org\/10.1016\/j.molimm.2021.02.026. PMID:33933816","DOI":"10.1016\/j.molimm.2021.02.026"},{"key":"14","doi-asserted-by":"crossref","unstructured":"Almeida LG, Sakabe NJ, deOliveira AR, Silva MC, Mundstein AS, Cohen T, Chen YT, Chua R, Gurung S, Gnjatic S, Jungbluth AA, Caballero OL, Bairoch A, et al. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res. 2009; 37:D816\u201319. https:\/\/doi.org\/10.1093\/nar\/gkn673. PMID:18838390","DOI":"10.1093\/nar\/gkn673"},{"key":"15","doi-asserted-by":"crossref","unstructured":"Mauro JA, Yavorski JM, Blanck G. Stratifying melanoma and breast cancer TCGA datasets on the basis of the CNV of transcription factor binding sites common to proliferation- and apoptosis-effector genes. Gene. 2017; 614:37\u201348. https:\/\/doi.org\/10.1016\/j.gene.2017.02.026. PMID:28257835","DOI":"10.1016\/j.gene.2017.02.026"},{"key":"16","doi-asserted-by":"crossref","unstructured":"Ostrand-Rosenberg S. Immune surveillance: a balance between protumor and antitumor immunity. Curr Opin Genet Dev. 2008; 18:11\u201318. https:\/\/doi.org\/10.1016\/j.gde.2007.12.007. PMID:18308558","DOI":"10.1016\/j.gde.2007.12.007"},{"key":"17","doi-asserted-by":"crossref","unstructured":"Ikeda H, Old LJ, Schreiber RD. The roles of IFN gamma in protection against tumor development and cancer immunoediting. Cytokine Growth Factor Rev. 2002; 13:95\u2013109. https:\/\/doi.org\/10.1016\/s1359-6101(01)00038-7. PMID:11900986","DOI":"10.1016\/S1359-6101(01)00038-7"},{"key":"18","doi-asserted-by":"crossref","unstructured":"Martin TD, Patel RS, Cook DR, Choi MY, Patil A, Liang AC, Li MZ, Haigis KM, Elledge SJ. The adaptive immune system is a major driver of selection for tumor suppressor gene inactivation. Science. 2021; 373:1327\u201335. https:\/\/doi.org\/10.1126\/science.abg5784. PMID:34529489","DOI":"10.1126\/science.abg5784"},{"key":"19","doi-asserted-by":"crossref","unstructured":"Barker VR, Varkhedi M, Patel DN, Hsiang M, Chobrutskiy A, Chobrutskiy BI, Blanck G. TCR CDR3-antigen chemical complementarity associated with poor ovarian cancer outcomes: A vestigial immune response to early cancer antigens? Am J Reprod Immunol. 2023; 89:e13639. https:\/\/doi.org\/10.1111\/aji.13639. PMID:36317868","DOI":"10.1111\/aji.13639"},{"key":"20","doi-asserted-by":"crossref","unstructured":"Gill TR, Samy MD, Butler SN, Mauro JA, Sexton WJ, Blanck G. Detection of Productively Rearranged TcR-\u03b1 V-J Sequences in TCGA Exome Files: Implications for Tumor Immunoscoring and Recovery of Antitumor T-cells. Cancer Inform. 2016; 15:23\u201328. https:\/\/doi.org\/10.4137\/CIN.S35784. PMID:26966347","DOI":"10.4137\/CIN.S35784"},{"key":"21","doi-asserted-by":"crossref","unstructured":"Tong WL, Tu YN, Samy MD, Sexton WJ, Blanck G. Identification of immunoglobulin V(D)J recombinations in solid tumor specimen exome files: Evidence for high level B-cell infiltrates in breast cancer. Hum Vaccin Immunother. 2017; 13:501\u20136. https:\/\/doi.org\/10.1080\/21645515.2016.1246095. PMID:28085544","DOI":"10.1080\/21645515.2016.1246095"},{"key":"22","doi-asserted-by":"crossref","unstructured":"Chobrutskiy BI, Zaman S, Tong WL, Diviney A, Blanck G. Recovery of T-cell receptor V(D)J recombination reads from lower grade glioma exome files correlates with reduced survival and advanced cancer grade. J Neurooncol. 2018; 140:697\u2013704. https:\/\/doi.org\/10.1007\/s11060-018-03001-1. PMID:30382482","DOI":"10.1007\/s11060-018-03001-1"},{"key":"23","doi-asserted-by":"crossref","unstructured":"Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, et al. The Immune Landscape of Cancer. Immunity. 2018; 48:812\u201330.e14. https:\/\/doi.org\/10.1016\/j.immuni.2018.03.023. PMID:29628290","DOI":"10.1016\/j.immuni.2018.03.023"},{"key":"24","doi-asserted-by":"crossref","unstructured":"Li B, Li T, Wang B, Dou R, Zhang J, Liu JS, Liu XS. Ultrasensitive detection of TCR hypervariable-region sequences in solid-tissue RNA-seq data. Nat Genet. 2017; 49:482\u201383. https:\/\/doi.org\/10.1038\/ng.3820. PMID:28358132","DOI":"10.1038\/ng.3820"},{"key":"25","doi-asserted-by":"crossref","unstructured":"Patel DN, Yeagley M, Arturo JF, Falasiri S, Chobrutskiy BI, Gozlan EC, Blanck G. A comparison of immune receptor recombination databases sourced from tumour exome or RNAseq files: Verifications of immunological distinctions between primary and metastatic melanoma. Int J Immunogenet. 2021; 48:409\u201318. https:\/\/doi.org\/10.1111\/iji.12550. PMID:34298587","DOI":"10.1111\/iji.12550"},{"key":"26","doi-asserted-by":"crossref","unstructured":"Clark KR, Tong WL, Callahan BM, Yavorski JM, Tu YN, Blanck G. TRB-J1 usage, in combination with the HLA-A*01:01 allele, represents an apparent survival advantage for uterine corpus endometrial carcinoma: Comparisons with microscopic assessments of lymphocyte infiltrates. Int J Immunogenet. 2019; 46:31\u201337. https:\/\/doi.org\/10.1111\/iji.12409. PMID:30474304","DOI":"10.1111\/iji.12409"},{"key":"27","doi-asserted-by":"crossref","unstructured":"Brown SD, Raeburn LA, Holt RA. Profiling tissue-resident T cell repertoires by RNA sequencing. Genome Med. 2015; 7:125. https:\/\/doi.org\/10.1186\/s13073-015-0248-x. PMID:26620832","DOI":"10.1186\/s13073-015-0248-x"},{"key":"28","doi-asserted-by":"crossref","unstructured":"Eakins RA, Chobrutskiy A, Teer JK, Patel DN, Hsiang M, Huda TI, Zaman S, Sexton WJ, Coppola D, Falasiri S, Blanck G, Chobrutskiy BI. Chemical complementarity between tumor resident, T-cell receptor CDR3s and MAGEA3\/6 correlates with increased melanoma survival: Potential relevance to MAGE vaccine auto-reactivity. Mol Immunol. 2022; 150:58\u201366. https:\/\/doi.org\/10.1016\/j.molimm.2022.08.001. PMID:35987136","DOI":"10.1016\/j.molimm.2022.08.001"},{"key":"29","doi-asserted-by":"crossref","unstructured":"Pakasticali N, Chobrutskiy A, Patel DN, Hsiang M, Zaman S, Cios KJ, Blanck G, Chobrutskiy BI. Chemical Complementarity of Breast Cancer Resident, T-Cell Receptor CDR3 Domains and the Cancer Antigen, ARMC3, is Associated With Higher Levels of Survival and Granzyme Expression. Cancer Inform. 2023; 22:11769351231177269. https:\/\/doi.org\/10.1177\/11769351231177269. PMID:37313373","DOI":"10.1177\/11769351231177269"},{"key":"30","doi-asserted-by":"crossref","unstructured":"Patel AR, Patel DN, Tu YN, Yeagley M, Chobrutskiy A, Chobrutskiy BI, Blanck G. Chemical complementarity between immune receptor CDR3s and candidate cancer antigens correlating with reduced survival: evidence for outcome mitigation with corticosteroid treatments. J Biomol Struct Dyn. 2023; 41:4632\u201340. https:\/\/doi.org\/10.1080\/07391102.2022.2070546. PMID:35538689","DOI":"10.1080\/07391102.2022.2070546"},{"key":"31","doi-asserted-by":"crossref","unstructured":"Huda TI, Diaz MJ, Gozlan EC, Chobrutskiy A, Chobrutskiy BI, Blanck G. Immunogenomics Parameters for Patient Stratification in Alzheimer\u2019s Disease. J Alzheimers Dis. 2022; 88:619\u201329. https:\/\/doi.org\/10.3233\/JAD-220119. PMID:35662120","DOI":"10.3233\/JAD-220119"}],"container-title":["Oncoscience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.oncoscience.us\/lookup\/doi\/10.18632\/oncoscience.590","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,10]],"date-time":"2023-11-10T14:34:06Z","timestamp":1699626846000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.oncoscience.us\/lookup\/doi\/10.18632\/oncoscience.590"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,10]]},"references-count":31,"alternative-id":["590"],"URL":"https:\/\/doi.org\/10.18632\/oncoscience.590","relation":{},"ISSN":["2331-4737"],"issn-type":[{"value":"2331-4737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,11,10]]}}}