Key candidate genes and pathways in T lymphoblastic leukemia/lymphoma identified by bioinformatics and serological analyses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38464517", "kind": "science-record", "revision": 4, "content_hash": "sha256:8a361e72d6bad1dcabd432aa9fdbde7e81f53b0b785ae0c460b4322ba199fed0", "created_at": "2026-11-01T19:20:24Z", "updated_at": "2026-11-01T22:11:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Key candidate genes and pathways in T lymphoblastic leukemia/lymphoma identified by bioinformatics and serological analyses.", "doi": "10.3389/fimmu.2024.1341255", "pmid": "38464517", "authors": ["Yansong Ren", "Haoyue Liang", "Yali Huang", "Yuyang Miao", "Ruihua Li", "Junlian Qiang", "Lihong Wu", "Jinfeng Qi", "Ying Li", "Yonghui Xia", "Lunhui Huang", "Shoulei Wang", "Xiaodong Kong", "Yuan Zhou", "Qiang Zhang", "Guoqing Zhu"], "journal": "Frontiers in immunology", "year": 2024, "abstract": "T-cell acute lymphoblastic leukemia (T-ALL)/T-cell lymphoblastic lymphoma (T-LBL) is an uncommon but highly aggressive hematological malignancy. It has high recurrence and mortality rates and is challenging to treat. This study conducted bioinformatics analyses, compared genetic expression profiles of healthy controls with patients having T-ALL/T-LBL, and verified the results through serological indicators. Data were acquired from the GSE48558 dataset from Gene Expression Omnibus (GEO). T-ALL patients and normal T cells-related differentially expressed genes (DEGs) were investigated using the online analysis tool GEO2R in GEO, identifying 78 upregulated and 130 downregulated genes. Gene Ontology (GO) and protein-protein interaction (PPI) network analyses of the top 10 DEGs showed enrichment in pathways linked to abnormal mitotic cell cycles, chromosomal instability, dysfunction of inflammatory mediators, and functional defects in T-cells, natural killer (NK) cells, and immune checkpoints. The DEGs were then validated by examining blood indices in samples obtained from patients, comparing the T-ALL/T-LBL group with the control group. Significant differences were observed in the levels of various blood components between T-ALL and T-LBL patients. These components include neutrophils, lymphocyte percentage, hemoglobin (HGB), total protein, globulin, erythropoietin (EPO) levels, thrombin time (TT), D-dimer (DD), and C-reactive protein (CRP). Additionally, there were significant differences in peripheral blood leukocyte count, absolute lymphocyte count, creatinine, cholesterol, low-density lipoprotein, folate, and thrombin times. The genes and pathways associated with T-LBL/T-ALL were identified, and peripheral blood HGB, EPO, TT, DD, and CRP were key molecular markers. This will assist the diagnosis of T-ALL/T-LBL, with applications for differential diagnosis, treatment, and prognosis.", "claims": [{"id": "claim-method", "statement": "Orthogonal partial least squares discriminant analysis (OPLS-DA) was performed using SIMCA 14.1 to compare indicator levels between the control, T-LBL, and T-ALL groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38464517", "locator": "sections[5] \"OPLS-DA multivariate statistical method to establish identification model\" paragraph 2", "quote": "Orthogonal partial least squares discriminant analysis (OPLS-DA) was performed using SIMCA 14.1 to compare indicator levels between the control, T-LBL, and T-ALL groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38464517", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The genes and pathways associated with T-LBL/T-ALL were identified, and peripheral blood HGB, EPO, TT, DD, and CRP were key molecular markers.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38464517", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The genes and pathways associated with T-LBL/T-ALL were identified, and peripheral blood HGB, EPO, TT, DD, and CRP were key molecular markers."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The genes and pathways associated with T-LBL/T-ALL were identified, and peripheral blood HGB, EPO, TT, DD, and CRP were key molecular markers.", "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:38464517"], "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. 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