In Silico Approach in Designing a Novel Multi-Epitope Vaccine Candidate against Non-Small Cell Lung Cancer with Overexpressed G Protein-Coupled Receptor 56.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32856858", "kind": "science-record", "revision": 8, "content_hash": "sha256:e1258d38bd6c4bc70c94cb50209d93d262d36b69614cf12ba377e1fb09594b83", "created_at": "2026-11-01T15:41:09Z", "updated_at": "2026-11-01T22:02:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "In Silico Approach in Designing a Novel Multi-Epitope Vaccine Candidate against Non-Small Cell Lung Cancer with Overexpressed G Protein-Coupled Receptor 56.", "doi": "10.31557/APJCP.2020.21.8.2297", "pmid": "32856858", "authors": ["Leana Rich M Herrera"], "journal": "Asian Pacific journal of cancer prevention : APJCP", "year": 2020, "abstract": "BACKGROUND: Majority of cancer-related deaths worldwide is attributed to non-small cell lung cancer (NSCLC). G protein-coupled receptor 56 (GPR56) is overexpressed and associated in the progression of NSCLC. The aim of this study is to use immunoinformatics approach in designing a multi-epitope vaccine to target overexpressed GPR56 which can potentially activate antibody-mediated cell death mechanisms and inhibit pathways involved in the proliferation, migration and survival of NSCLC.\nMETHODS: Herein, the reported overexpression of GPR56 was further investigated by conducting a differential gene expression analysis of NSCLC samples from GEO DataSets (GSE29249). Results confirmed significant overexpression of GPR56 in NSCLC compared to adjacent normal samples. A multi-epitope vaccine (Fvax) was constructed in silico by adjoining B lymphocytes (BL) and helper T lymphocytes (HTL) epitopes from the extracellular sequence of GPR56. Population coverage (PC) of HTL epitopes was also estimated. To enhance its immunogenicity, sequences of flagellin domains were fused as adjuvant. Fvax was evaluated in silico for antigenicity, allergenicity, peptide toxicity, physicochemical properties and cross-reactivity. Its tertiary structure was predicted, refined, and validated followed by structural epitope prediction. Lastly, Fvax DNA was optimized and cloned in silico.\nRESULTS: This is the first work to design a potential vaccine against GPR56-overexpressing NSCLC. Fvax has 3 BL and 7 HTL immunogenic epitopes on GPR56. In silico evaluations suggest that Fvax is antigenic, non-toxic, non-allergenic, stable, and has accessible BL epitopes with high PC worldwide for HTL epitopes.\nCONCLUSION: Overall, results showed that Fvax is a potential vaccine against NSCLC. The approach of this study efficiently minimized the number of tests, cost and time required to select the best epitopes and to design a vaccine for the treatment of NSCLC.<br />.", "claims": [{"id": "claim-data-access", "statement": "As a confirmatory step, gene expression profile of ADGRG1 (encoding GRP56) from Gene Expression Omnibus (GEO) database (GSE29249) was analyzed with GEO2R. Tissue profiles from NSCLC samples (n=6) were compared to normal adjacent samples (n=6).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32856858", "locator": "sections[2] \"Materials and Methods\" paragraph 3", "quote": "As a confirmatory step, gene expression profile of ADGRG1 (encoding GRP56) from Gene Expression Omnibus (GEO) database (GSE29249) was analyzed with GEO2R. Tissue profiles from NSCLC samples (n=6) were compared to normal adjacent samples (n=6)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32856858"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE29249"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE29249"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32856858", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.31557/APJCP.2020.21.8.2297", "sha256": "sha256:73245ad11f460a164ec4e9d0193893672ac4adc0842c06d78e672f9fd6893e2b", "bytes": 33070, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.31557/APJCP.2020.21.8.2297", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7771954", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE29249", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29249", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29249", "version": null, "note": "As a confirmatory step, gene expression profile of ADGRG1 (encoding GRP56) from Gene Expression Omnibus (GEO) database (GSE29249) was analyzed with GEO2R. Tissue profiles from NSCLC samples (n=6) were compared to normal adjacent samples (n=6).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "As a confirmatory step, gene expression profile of ADGRG1 (encoding GRP56) from Gene Expression Omnibus (GEO) database (GSE29249) was analyzed with GEO2R. Tissue profiles from NSCLC samples (n=6) were compared to normal adjacent samples (n=6).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM723159", "GSM723160", "GSM723161", "GSM723162", "GSM723163", "GSM723164", "GSM723165", "GSM723166", "GSM723167", "GSM723168", "GSM723169", "GSM723170"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Genome-wide analysis of  gene expression in Non-small Cell Lung Cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32856858:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bde2aa8d532e0f2914fbcc065c382d173f0b47452e71b5a957e09f2f63242235", "bytes": 352, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[1]#T1", "version": null, "note": "Candidate BL Epitopes", "structure": {"pmcid": "PMC7771954", "section_index": 3, "section_title": "Results", "row_count": 4, "column_count": 4}, "table": {"label": "Table 1", "caption": "Candidate BL Epitopes", "rows": [["Epitope", "Start", "End", "Antigenicity score"], ["SDKASSLLCFQHQEESLAQG", "113", "132", "0.5978"], ["FTFSFHSPPHTAAHNASVDM", "157", "176", "0.5035"], ["VQNTKVANLTEPVVLTFQHQ", "317", "336", "0.7225"]], "row_count": 4, "column_count": 4, "numeric_cells": 9, "header_rows": 1, "locator": "section[3]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32856858:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6901214ea1f96980b6835283d51884360b26900ca55ef9635a01e72e84274939", "bytes": 1341, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[2]#T2", "version": null, "note": "Candidate HTL Epitopes", "structure": {"pmcid": "PMC7771954", "section_index": 3, "section_title": "Results", "row_count": 8, "column_count": 6}, "table": {"label": "Table 2", "caption": "Candidate HTL Epitopes", "rows": [["Epitope", "Start", "End", "Antigenicity Score", "IC50 (min-max)", "MHC II Allele"], ["PASQQLQSLESKLTS", "204", "218", "0.7646", "18 – 335", "HLA-DRB1*01:01, HLA-DRB1*04:01, HLA-DRB1*04:04, HLA-DRB1*04:05, HLA-DRB1*07:01, HLA-DRB1*09:01, HLA-DRB1*11:01, HLA-DRB1*15:01, HLA-DRB4*01:01, HLA-DRB5*01:01"], ["VFWVEDPTLSSPGHW", "347", "361", "0.5624", "128 – 400", "HLA-DRB1*01:01, HLA-DRB1*03:01, HLA-DRB1*04:01, HLA-DRB3*01:01"], ["LGIVVQNTKVANLTE", "313", "327", "0.5526", "194 – 412", "HLA-DRB1*01:01, HLA-DRB1*07:01, HLA-DRB1*08:02, HLA-DRB1*13:02"], ["SQFLKHPQKASRRPS", "187", "201", "0.5505", "113 – 454", "HLA-DRB1*01:01, HLA-DRB1*11:01, HLA-DRB1*12:01, HLA-DRB5*01:01"], ["YHFCLYWNRHAGRLH", "88", "102", "0.6198", "99 – 410", "HLA-DRB1*01:01, HLA-DRB1*04:01, HLA-DRB1*04:04, HLA-DRB1*07:01, HLA-DRB1*09:01, HLA-DRB1*11:01, HLA-DRB1*15:01, HLA-DRB5*01:01"], ["SFTFSFHSPPHTAAH", "156", "170", "0.6298", "99 – 433", "HLA-DRB1*01:01, HLA-DRB1*04:01, HLA-DRB1*04:04, HLA-DRB1*07:01, HLA-DRB1*09:01, HLA-DRB1*15:01"], ["EPVVLTFQHQLQPKN", "204", "218", "0.6536", "229 – 493", "HLA-DRB1*01:01, HLA-DRB1*04:01, HLA-DRB1*04:04, HLA-DRB1*04:05, HLA-DRB1*07:01, HLA-DRB1*11:01, HLA-DRB4*01:01, HLA-DRB5*01:01"]], "row_count": 8, "column_count": 6, "numeric_cells": 36, "header_rows": 1, "locator": "section[3]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:32856858:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a3058756c38f5b81ca620a6560ff9bf0e956efab76180ae629dd17870ff5a83d", "bytes": 687, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[3]#T3", "version": null, "note": "Linear BL Epitopes on Fvax", "structure": {"pmcid": "PMC7771954", "section_index": 3, "section_title": "Results", "row_count": 8, "column_count": 6}, "table": {"label": "Table 3", "caption": "Linear BL Epitopes on Fvax", "rows": [["No.", "Start", "End", "Epitopes", "Residues", "PI"], ["1", "453", "499", "EDSDYATEVSNMSRAQILQQAGTSVLAQANQVPQNVLSLLRHHHHHH", "47", "0.818"], ["2", "189", "273", "CFQHQEESLAQGGPGPGFTFSFHSPPHTAAHNASVDMGPGPGVQNTKVANLTEPVVLTFQHQGPGPGPASQQLQSLESKLTSGPG", "85", "0.79"], ["3", "1", "47", "VAQVINTNSLSLLTQNNLNKSQSALGTAIERLSSGLRINSAKDDAAG", "47", "0.739"], ["4", "90", "112", "QRVRELAVQSANSTNSQSDLDSI", "23", "0.701"], ["5", "300", "308", "VQNTKVANL", "9", "0.664"], ["6", "400", "415", "ATTTENPLQKIDAALA", "16", "0.65"], ["7", "174", "181", "NVEAAAKS", "8", "0.553"]], "row_count": 8, "column_count": 6, "numeric_cells": 35, "header_rows": 1, "locator": "section[3]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:32856858:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d930a1d682c2e02d8c415e07ef91de83e02e41cf4b57af47eb2004bb3944f26f", "bytes": 1933, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[3]/table-wrap[4]#T4", "version": null, "note": "Discontinuous Epitopes on Fvax", "structure": {"pmcid": "PMC7771954", "section_index": 3, "section_title": "Results", "row_count": 4, "column_count": 4}, "table": {"label": "Table 4", "caption": "Discontinuous Epitopes on Fvax", "rows": [["No.", "Discontinuous epitopes", "Residues", "PI"], ["8", "A:C189,A:F190,A:Q191,A:H192,A:Q193,A:E194,A:E195,A:S196,A:L197,A:A198,A:Q199,A:G200,A:G201,A:P202,A:G203,A:P204,A:G205,A:F206,A:T207,A:F208,A:S209,A:F210,A:H211,A:S212,A:P213,A:P214,A:H215,A:T216,A:A217,A:A218,A:H219,A:N220,A:A221,A:S222,A:V223,A:D224,A:M225,A:G226,A:P227,A:G228,A:P229,A:G230,A:V231,A:Q232,A:N233,A:T234,A:K235,A:V236,A:A237,A:N238,A:L239,A:T240,A:E241,A:P242,A:V243,A:V244,A:L245,A:T246,A:F247,A:Q248,A:H249,A:Q250,A:G251,A:P252,A:G253,A:P254,A:G255,A:P256,A:A257,A:S258,A:Q259,A:Q260,A:L261,A:Q262,A:S263,A:L264,A:E265,A:S266,A:K267,A:L268,A:T269,A:S270,A:G271,A:P272,A:G273", "85", "0.79"], ["9", "A:V1,A:A2,A:Q3,A:V4,A:I5,A:N6,A:T7,A:N8,A:S9,A:L10,A:S11,A:L12,A:L13,A:T14,A:Q15,A:N16,A:N17,A:L18,A:N19,A:K20,A:S21,A:Q22,A:S23,A:A24,A:L25,A:G26,A:T27,A:A28,A:I29,A:E30,A:R31,A:L32,A:S33,A:S34,A:G35,A:L36,A:R37,A:I38,A:N39,A:S40,A:A41,A:K42,A:D43,A:D44,A:A45,A:A46,A:G47,A:E453,A:D454,A:S455,A:D456,A:Y457,A:A458,A:T459,A:E460,A:V461,A:S462,A:N463,A:M464,A:S465,A:R466,A:A467,A:Q468,A:I469,A:L470,A:Q471,A:Q472,A:A473,A:G474,A:T475,A:S476,A:V477,A:L478,A:A479,A:Q480,A:A481,A:N482,A:Q483,A:V484,A:P485,A:Q486,A:N487,A:V488,A:L489,A:S490,A:L491,A:L492,A:R493,A:H494,A:H495,A:H496,A:H497,A:H498,A:H499", "94", "0.778"], ["10", "A:V92,A:R93,A:E94,A:L95,A:A96,A:V97,A:Q98,A:S99,A:A100,A:N101,A:S102,A:T103,A:N104,A:S105,A:Q106,A:S107,A:D108,A:L109,A:D110,A:S111,A:I112,A:E115,A:L168,A:G169,A:L173,A:N174,A:V175,A:E176,A:A177,A:A178,A:A179,A:K180,A:S181,A:V300,A:Q301,A:N302,A:T303,A:K304,A:V305,A:A306,A:N307,A:L308,A:G355,A:S356,A:F357,A:A399,A:A400,A:T401,A:T402,A:T403,A:E404,A:N405,A:P406,A:L407,A:Q408,A:K409,A:I410,A:D411,A:A412,A:A413,A:L414,A:A415,A:D418,A:T419,A:S422", "65", "0.626"]], "row_count": 4, "column_count": 4, "numeric_cells": 12, "header_rows": 1, "locator": "section[3]/table-wrap[4]#T4"}}], "gaps": ["asset:data:geo:GSE29249 not downloaded", "asset:data:geo:GSE29249 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "SVM"}}, {"id": "method-2", "family": "sequence_alignment", "specific": "blast", "label": "Sequence alignment / homology", "dsl_operations": ["sequence_align", "alignment_identity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["sequence_records"], "evidence": {"score": 0.8, "band": "high", "quote": "BLAST"}}, {"id": "method-3", "family": "epidemiological_modelling", "specific": "incidence_rate", "label": "Epidemiological rate modelling", "dsl_operations": ["incidence_rate_model", "offset_regression"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["event_counts_with_exposure_time"], "evidence": {"score": 0.8, "band": "high", "quote": "incidence rate"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: support_vector_machine."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE29249"], "resolved_accessions": ["GSE29249"], "statements": ["As a confirmatory step, gene expression profile of ADGRG1 (encoding GRP56) from Gene Expression Omnibus (GEO) database (GSE29249) was analyzed with GEO2R. Tissue profiles from NSCLC samples (n=6) were compared to normal adjacent samples (n=6)."], "basis": "The paper names GSE29249 in Gene Expression Omnibus (GEO) DataSets and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "assets": ["source:pmid:32856858", "data:geo:GSE29249", "asset:table:pmid:32856858:1", "asset:table:pmid:32856858:2", "asset:table:pmid:32856858:3", "asset:table:pmid:32856858:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE29249"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:08Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 3, "usage": {"prompt_tokens": 26521, "completion_tokens": 807, "cached_tokens": 656}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32856858", "type": "paper", "label": "pmid:32856858"}, {"id": "source:pmid:32856858", "type": "manuscript", "label": "PMID 32856858 full text"}, {"id": "data:geo:GSE29249", "type": "dataset", "label": "GEO GSE29249"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32856858", "type": "paper", "label": "pmid:32856858"}, {"id": "source:pmid:32856858", "type": "manuscript", "label": "PMID 32856858 full text"}, {"id": "data:geo:GSE29249", "type": "dataset", "label": "GEO GSE29249"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32856858", "type": "extraction", "used": ["source:pmid:32856858"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE29249", "type": "accession_resolution", "used": ["data:geo:GSE29249"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32856858", "parent_hash": "sha256:6daf345234d28eddf6ad7c111ff881d6f0e9fa07a177f0e7bd58719689c12e65", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE29249 licence not read", "asset:data:geo:GSE29249 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["train_classifier", "cross_validate", "roc_auc"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["SVM"], "order_basis": "analysis_only", "id": "assay:1"}]}