Integrated Analysis of Single-Cell RNA-Seq and Bulk RNA-Seq Unravels the Molecular Feature of Tumor-Associated Macrophage of Acute Myeloid Leukemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38205232", "kind": "science-record", "revision": 2, "content_hash": "sha256:bfed561b03fb84afb952d01f4f254c6820ddea8ca2ef6fd496eb9a9257a7b6e9", "created_at": "2026-11-01T19:20:07Z", "updated_at": "2026-11-01T21:32:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Analysis of Single-Cell RNA-Seq and Bulk RNA-Seq Unravels the Molecular Feature of Tumor-Associated Macrophage of Acute Myeloid Leukemia.", "doi": "10.1155/2024/5539065", "pmid": "38205232", "authors": ["Xin Gao"], "journal": "Genetics research", "year": 2024, "abstract": "Background: The association between acute myeloid leukemia (AML) and macrophage remains to be deeply explored.\nMethods: Gene expression profiles and clinical variable characteristics of AML patients were collected from TCGA, GEO, and TARGET databases. Consensus clustering was employed to construct the macrophage-related clusters. The macrophage-related index (MRI) was constructed using the LASSO and multivariate Cox analysis. The GSE71014 and TARGET datasets were utilized as external validation sets. Single-cell sequencing data for AML (GSE116256) was adopted to analyze modeled gene expression levels in cells.\nResults: Two macrophage-related clusters with different prognostic and immune infiltration characteristics were constructed in AML. Cluster B had a poorer prognosis, more cancer-promoting pathway enrichment, and an immunosuppressive microenvironment. Relied on the MRI, patients of different groups showed different levels of immune infiltration, different mutations, and prognoses. LGALS1 and BCL2A1 may play roles in promoting cancer in AML, while ELANE may have a significant effect on suppressing cancer.\nConclusion: Macrophage-related genes (MRGs) had significant impacts on the occurrence and progression of AML. MRI may better evaluate the prognosis and immune features of AML patients.", "claims": [{"id": "claim-method", "statement": "First, the prognostic MRGs were screened by univariate Cox regression analysis. We employed the consensus clustering algorithm to further evaluate the potential mechanism of action of MRGs in AML.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38205232", "locator": "sections[5] \"2.3. Construction of the Macrophage-Related Clusters\" paragraph 2", "quote": "First, the prognostic MRGs were screened by univariate Cox regression analysis. We employed the consensus clustering algorithm to further evaluate the potential mechanism of action of MRGs in AML."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are openly available in TCGA, GEO, TISCH2, and TARGET datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38205232", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The data that support the findings of this study are openly available in TCGA, GEO, TISCH2, and TARGET datasets."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A three-gene macrophage-related index comprising LGALS1, BCL2A1, and ELANE was constructed using LASSO and multivariate Cox analysis, with high MRI associated with poor prognosis in AML and validated in GSE71014 and TARGET.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38205232", "locator": "sections[11] \"3.3. Establishment and Validation of the Macrophage-Related Index\" paragraph 2", "quote": "After the Lasso regression analysis of 32 prognostic MRGs, we screened out 5 prognostic genes (Figures 4(a) and 4(b)). Then, we further used multivariate Cox regression analysis to select three MRGs to construct the model (Figure 4(c)) (MRI = 0.2478668 ∗ LGALS1Exp + 0.12453683 ∗ BCL2A1Exp + (−0.09398426) ∗ ELANEExp). The KM curve and survival status distribution suggested that high MRI was associated with poor prognosis (Figures 4(d) and 4(e))."}, {"asset": "source:pmid:38205232", "locator": "sections[11] \"3.3. Establishment and Validation of the Macrophage-Related Index\" paragraph 2", "quote": "ROC curves of MRI in 1, 2, and 3 years were 0.789, 0.809, and 0.749 (Figure 4(f))."}, {"asset": "source:pmid:38205232", "locator": "sections[11] \"3.3. Establishment and Validation of the Macrophage-Related Index\" paragraph 2", "quote": "GSE71014 and TARGET datasets were adopted as external validation datasets to verify the stability of MRI."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A three-gene macrophage-related index comprising LGALS1, BCL2A1, and ELANE was constructed using LASSO and multivariate Cox analysis, with high MRI associated with poor prognosis in AML and validated in GSE71014 and TARGET.", "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:38205232"], "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:GSE116256"], "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:GSE116256"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38205232", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2024/5539065", "sha256": 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