Statistical and network analyses reveal mechanisms for the enhancement of macrophage immunity by manganese in Mycobacterium tuberculosis infection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38155943", "kind": "science-record", "revision": 4, "content_hash": "sha256:620d860c000e0fca1d76a0a8a055faad1f09ad898a59673f7b546837ff8453d5", "created_at": "2026-11-01T19:20:05Z", "updated_at": "2026-11-01T22:53:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Statistical and network analyses reveal mechanisms for the enhancement of macrophage immunity by manganese in Mycobacterium tuberculosis infection.", "doi": "10.1016/j.bbrep.2023.101602", "pmid": "38155943", "authors": ["Lidong Shan", "Zihai Wang", "Lingshan Wu", "Kaiqiang Qian", "Guisen Peng", "MeiLi Wei", "Bikui Tang", "Xi Jun"], "journal": "Biochemistry and biophysics reports", "year": 2024, "abstract": "Tuberculosis is a significant infectious disease that poses a serious risk to human health. Our previous research has indicated that manganese ions reduce the bacterial load of Mycobacterium tuberculosis in macrophages, but the exact immune defense mechanism remains unknown. Several critical proteins and pathways involved in the host's immune response during this process are still unidentified. Our research aims to identify these proteins and pathways and provide a rationale for the use of manganese ions in the adjuvant treatment of tuberculosis. We downloaded GSE211666 data from the GEO database and selected the RM (Post-infection manganese ion treatment group) and Ra (single-infection group) groups for comparison and analysis to identify differential genes. These differential genes were then enriched and analyzed using STRING, Cytoscape, and NDEx tools to identify the two most relevant pathways of the \"Host Response Signature Network.\" After conducting an in-depth analysis of these two pathways, we found that manganese ions mainly mediate (1) the interferon -gamma (IFN-γ) and its receptor IFNGR and the downstream JAK-STAT pathway and (2) the NFκB pathway to enhance macrophage response to interferon, autophagy, polarization, and cytokine release. Using qPCR experiments, we verified the increased expression of CXCL10, MHCII, IFNγ, CSF2, and IL12, all of which are cytokines that play a key role in resistance to Mycobacterium tuberculosis infection, suggesting that macrophages enter a state of pro-inflammatory and activation after the addition of manganese ions, which enhances their immunosuppressive effect against Mycobacterium tuberculosis. We conclude that our study provides evidence of manganese ion's ability to treat tuberculosis adjuvantly.", "claims": [{"id": "claim-method", "statement": "DESeq2 processes each gene using a negative binomial distribution to simulate the counts and fit the normalized count data. A Wald test was used to determine whether there was a significant difference between the two sample groups regarding dispersion and fold change using DESeq2.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38155943", "locator": "sections[12] \"RNA data acquisition and data processing\" paragraph 2", "quote": "DESeq2 processes each gene using a negative binomial distribution to simulate the counts and fit the normalized count data. A Wald test was used to determine whether there was a significant difference between the two sample groups regarding dispersion and fold change using DESeq2."}], "state": "complete"}, {"id": "claim-data-access", "statement": "No data was used for the research described in the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38155943", "locator": "sections[24] \"Data availability\" paragraph 2", "quote": "No data was used for the research described in the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "DESeq2 analysis identified 1137 differentially expressed host genes in manganese-ion-treated, Mycobacterium tuberculosis-infected macrophages compared with the infected control group.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38155943", "locator": "sections[3] \"Identification of differential genes (DEHGs)\" paragraph 4", "quote": "Eventually 1137 DEHGs were characterized with settings of |log2FC| > 1.5 and p-values <0.05."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "DESeq2 analysis identified 1137 differentially expressed host genes in manganese-ion-treated, Mycobacterium tuberculosis-infected macrophages compared with the infected control group.", "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:38155943"], "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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