Identification of MMP9 as a novel key gene in mantle cell lymphoma based on bioinformatic analysis and design of cyclic peptides as MMP9 inhibitors based on molecular docking.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30226602", "kind": "science-record", "revision": 7, "content_hash": "sha256:c1aaf35121774269b0f386859a8b922c849283654dee2b1b19b54eb750b0df05", "created_at": "2026-11-01T15:40:37Z", "updated_at": "2026-11-01T22:00:02Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of MMP9 as a novel key gene in mantle cell lymphoma based on bioinformatic analysis and design of cyclic peptides as MMP9 inhibitors based on molecular docking.", "doi": "10.3892/or.2018.6682", "pmid": "30226602", "authors": ["Wei Yan", "Shawn Xiang Li", "Minjie Wei", "Hua Gao"], "journal": "Oncology reports", "year": 2018, "abstract": "Mantle cell lymphoma (MCL) is an aggressive disease. MCL is associated with poor patient prognosis and limited survival. To identify key genes and explore targeting cyclic peptide inhibitors for the treatment of MCL, we downloaded two gene expression profiles (GSE32018 and GSE9327) from the Gene Expression Omnibus (GEO) database. We screened 84 differentially expressed genes (DEGs). Pathway analysis showed that DEMs were mainly enriched in the 'Pathway in cancer', 'PI3K‑Akt signaling pathway', 'Cytokine‑cytokine receptor interaction', 'Rap1 signaling pathway', 'NF‑κB signaling pathway' and 'Leukocyte trans‑endothelial migration'. We subsequently constructed a protein‑protein interaction (PPI) network of DEGs. In addition, matrix metalloproteinase 9 (MMP9) with a high degree in the PPI network was identified as a hub gene in MCL. Meanwhile in the Molecular Complex Detection (MCODE) analysis, MMP9 was located in the important cluster. Thus, MMP9 can be used as a therapeutic target for MCL and we designed cyclic peptides as MMP9 inhibitors. MMP9 protein structure was gathered from the Protein Data Bank (PDB), with a PDB ID: 1L6J. MMP9 and cyclic peptides were docked using Molecular Operating Environment (MOE) software after structural optimization. It was revealed that cyclic peptide 2 bound deeply in the binding pocket of MMP9 and had interaction with the active‑site Zn2+ ion in the catalytic domain. Cyclic peptides 1, 2, 4‑6 also displayed potential interaction with active residues of MMP9; thus, these cyclic peptides can serve as potential drug candidates to block MMP9 activity and future studies are warranted to confirm their efficacy.", "claims": [{"id": "claim-method", "statement": "The false-positive results for the microarray were then corrected by adjusted P-value (adj. P-value) using Benjamini-Hochberg method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30226602", "locator": "sections[5] \"Data processing\" paragraph 2", "quote": "The false-positive results for the microarray were then corrected by adjusted P-value (adj. P-value) using Benjamini-Hochberg method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets (GSE32018 and GSE9327) (11,12) analyzed during the current study are available in Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/pubmed.\nCrystallographic data for MMP9 analyzed during the current study are available in Protein Data Bank (PDB) www.rcsb.org. The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. The regulatory network and related transcription factors of MMP9 analyzed during the current study are available in Gene-RADAR www.gcbi.com.cn.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30226602", "locator": "sections[24] \"Availability of data and materials\" paragraphs 1-3", "quote": "The datasets (GSE32018 and GSE9327) (11,12) analyzed during the current study are available in Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/pubmed.\nCrystallographic data for MMP9 analyzed during the current study are available in Protein Data Bank (PDB) www.rcsb.org. The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. The regulatory network and related transcription factors of MMP9 analyzed during the current study are available in Gene-RADAR www.gcbi.com.cn."}], "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:30226602"], "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:GSE32018"], "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:GSE32018"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30226602", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/or.2018.6682", "sha256": "sha256:c63da691f24d48ce64e6648267f09b0c6edd59829eaaeefc666d20e590335d10", "bytes": 35536, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/or.2018.6682", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6151885", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32018", "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=GSE32018", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32018", "version": null, "note": "The datasets (GSE32018 and GSE9327) (11,12) analyzed during the current study are available in Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/pubmed.\nCrystallographic data for MMP9 analyzed during the current study are available in Protein Data Bank (PDB) www.rcsb.org. The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. The regulatory network and related transcription factors of MMP9 analyzed during the current study are available in Gene-RADAR www.gcbi.com.cn.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE32018 and GSE9327) (11,12) analyzed during the current study are available in Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/pubmed.\nCrystallographic data for MMP9 analyzed during the current study are available in Protein Data Bank (PDB) www.rcsb.org. The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. 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The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. The regulatory network and related transcription factors of MMP9 analyzed during the current study are available in Gene-RADAR www.gcbi.com.cn.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (GSE32018 and GSE9327) (11,12) analyzed during the current study are available in Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/pubmed.\nCrystallographic data for MMP9 analyzed during the current study are available in Protein Data Bank (PDB) www.rcsb.org. The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. 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(CAMs)", "5", "LAMA4, ITGA6, COL6A3, ITGB1, SPP1"], ["Jak-STAT signaling pathway", "5", "LAMA4, ITGA6, HLA-DMB, BIRC3, ITGB1"], ["Calcium signaling pathway", "5", "GNAQ, GRIN2D, PLCG2, PDGFRA, GNAS"], ["Epstein-Barr virus infection", "5", "PLCG2, VIM, HLA-A, ENTPD1, TRAF5"], ["Inflammatory bowel disease (IBD)", "4", "MAF, STAT4, RORA, HLA-DMB"], ["Melanoma", "4", "CCND1, FGF7, PDGFRA, CDH1"], ["Salivary secretion", "4", "GNAQ, LYZ, GUCY1A3, GNAS"], ["Gap junction", "4", "GNAQ, PDGFRA, GUCY1A3, GNAS"], ["Rheumatoid arthritis", "4", "TNFSF11, HLA-DMB, CXCL12, LTB"], ["Circadian entrainment", "4", "GNAQ, GRIN2D, GUCY1A3, GNAS"], ["Inflammatory mediator regulation of TRP channels", "4", "GNAQ, PLCG2, PRKCH, GNAS"], ["Bladder cancer", "3", "CCND1, MMP9, CDH1"]], "row_count": 25, "column_count": 3, "numeric_cells": 29, "header_rows": 1, "locator": "section[15]/table-wrap[1]#tI-or-40-05-2515"}}, {"id": "asset:table:pmid:30226602:3", "role": "table", "format": "jats-table", "media_type": 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"8.1607", "Zn500, His190, Glu402", "Leu187, Ala189, His401, His405, His411, Pro421, Met422"], ["3", "Cys-TFKEMVPDL-Cys", "−82.7207", "4.0789", "Zn500", "Gly186, Leu187, Leu188, Ala191, His401, Glu402, His405, His411, Pro421, Met422, Tyr423"], ["4", "Cys-TFKELVPDL-Cys", "−68.4973", "3.3641", "Zn500", "Gly186, Leu187, Leu188, His401, Glu402, His405, Asp410, His411, Pro421, Met422, Tyr423"], ["5", "Cys-TFKRGVPDL-Cys", "−71.9705", "1.6998", "Zn500, Ala191, Leu409, Asp410", "Leu187, Phe192, Pro193, His401, His405, Leu409, Asp410, His411, Pro421"], ["6", "Cys-TPKCWVPDL-Cys", "−68.3860", "1.7706", "Zn500, Ala191", "Leu187, Ala189, His190, Phe192, His401, Glu402, His405, Asp410, His411, Pro421"]], "row_count": 8, "column_count": 6, "numeric_cells": 34, "header_rows": 1, "locator": "section[18]/table-wrap[1]#tII-or-40-05-2515"}}], "gaps": ["asset:data:geo:GSE32018 not downloaded", "asset:data:geo:GSE32018 licence not read", "asset:data:geo:GSE9327 not downloaded", "asset:data:geo:GSE9327 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-3", "family": null, "specific": null, "label": "Benjamini-Hochberg method", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The false-positive results for the microarray were then corrected by adjusted P-value (adj. P-value) using Benjamini-Hochberg method."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE32018", "GSE9327"], "resolved_accessions": ["GSE32018", "GSE9327"], "statements": ["The datasets (GSE32018 and GSE9327) (11,12) analyzed during the current study are available in Gene Expression Omnibus (GEO) www.ncbi.nlm.nih.gov/pubmed.\nCrystallographic data for MMP9 analyzed during the current study are available in Protein Data Bank (PDB) www.rcsb.org. The expression level of MMP9 analyzed during the current study is available in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the current study are available in the Human Protein Atlas database www.proteinatlas.org. The regulatory network and related transcription factors of MMP9 analyzed during the current study are available in Gene-RADAR www.gcbi.com.cn."], "basis": "The paper names GSE32018, GSE9327 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:30226602", "data:geo:GSE32018", "asset:table:pmid:30226602:1", "asset:table:pmid:30226602:2", "asset:table:pmid:30226602:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32018"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:12:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28659, "completion_tokens": 1405, "cached_tokens": 9736}}, "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:30226602", "type": "paper", "label": "pmid:30226602"}, {"id": "source:pmid:30226602", "type": "manuscript", "label": "PMID 30226602 full text"}, {"id": "data:geo:GSE32018", "type": "dataset", "label": "GEO GSE32018"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30226602", "type": "paper", "label": "pmid:30226602"}, {"id": "source:pmid:30226602", "type": "manuscript", "label": "PMID 30226602 full text"}, {"id": "data:geo:GSE32018", "type": "dataset", "label": "GEO GSE32018"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30226602", "type": "extraction", "used": ["source:pmid:30226602"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32018", "type": "accession_resolution", "used": ["data:geo:GSE32018"], "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:30226602", "parent_hash": "sha256:4b6f09f5fa73531204971a6ce1a67f529a72d2a4d2ea3cf83efeaa2f9458d661", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE32018 licence not read", "asset:data:geo:GSE32018 not downloaded", "asset:data:geo:GSE9327 licence not read", "asset:data:geo:GSE9327 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["alyzes original submitter-supplied processed microarray data using the GEO query and limma R package", "ph nodes. The false-positive results for the microarray were then corrected by adjusted P-value (adj"], "order_basis": "paper_text_order:2109", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["lable in Oncomine www.oncomine.com (18). The immunohistochemistry staining results of MMP9 analyzed during the"], "order_basis": "paper_text_order:2977", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["limma"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}