Identification of early biomarkers of transcriptomics in alveolar macrophage for the prognosis of intubated ARDS patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36056346", "kind": "science-record", "revision": 4, "content_hash": "sha256:f245b1d51c734c00f6f0f54bf51d220a458cf8691c0a17573a55cda6662d30b4", "created_at": "2026-11-01T18:15:14Z", "updated_at": "2026-11-01T22:07:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of early biomarkers of transcriptomics in alveolar macrophage for the prognosis of intubated ARDS patients.", "doi": "10.1186/s12890-022-02130-8", "pmid": "36056346", "authors": ["Songchang Shi", "Shuo Wei", "Xiaobin Pan", "Lihui Zhang", "Shujuan Zhang", "Xincai Wang", "Songjing Shi", "Wei Lin"], "journal": "BMC pulmonary medicine", "year": 2022, "abstract": "BACKGROUND: Currently, the rate of morbidity and mortality in acute respiratory distress syndrome (ARDS) remains high. One of the potential reasons for the poor and ineffective therapies is the lack of early and credible indicator of risk prediction that would help specific treatment of severely affected ARDS patients. Nevertheless, assessment of the clinical outcomes with transcriptomics of ARDS by alveolar macrophage has not been performed.\nMETHODS: The expression data GSE116560 was obtained from the Gene Expression Omnibus databases (GEO) in NCBI. This dataset consists of 68 BAL samples from 35 subjects that were collected within 48 h of ARDS. Differentially expressed genes (DEGs) of different outcomes were analyzed using R software. The top 10 DEGs that were up- or down-regulated were analyzed using receiver operating characteristic (ROC) analysis. Kaplan-Meier survival analysis within two categories according to cut-off and the value of prediction of the clinical outcomes via DEGs was verified. GO enrichment, KEGG pathway analysis, and protein-protein interaction were also used for functional annotation of key genes.\nRESULTS: 24,526 genes were obtained, including 235 up-regulated and 292 down-regulated DEGs. The gene ADORA3 was chosen as the most obvious value to predict the outcome according to the ROC and survival analysis. For functional annotation, ADORA3 was significantly augmented in sphingolipid signaling pathway, cGMP-PKG signaling pathway, and neuroactive ligand-receptor interaction. Four genes (ADORA3, GNB1, NTS, and RHO), with 4 nodes and 6 edges, had the highest score in these clusters in the protein-protein interaction network.\nCONCLUSIONS: Our results show that the prognostic prediction of early biomarkers of transcriptomics as identified in alveolar macrophage in ARDS can be extended for mechanically ventilated critically ill patients. In the long term, generalizing the concept of biomarkers of transcriptomics in alveolar macrophage could add to improving precision-based strategies in the ICU patients and may also lead to identifying improved strategy for critically ill patients.", "claims": [{"id": "claim-method", "statement": "Key genes related to prognosis were subsequently screened out based on the results of cox regression of survival analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36056346", "locator": "sections[6] \"Survival analysis of top 10 DEGs\" paragraph 2", "quote": "Key genes related to prognosis were subsequently screened out based on the results of cox regression of survival analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the current study are publicly available in the [Gene Expression Omnibus databased] repository/database, [https://www.ncbi.nlm.nih.gov/geo/; GSE116560].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36056346", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed during the current study are publicly available in the [Gene Expression Omnibus databased] repository/database, [https://www.ncbi.nlm.nih.gov/geo/; GSE116560]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ADORA3 was selected as the most appropriate gene for predicting clinical outcome based on survival analysis.", "kind": "quantitative", "target": {"value": 0.059, "unit": "p-value", "tolerance": null, "source": "This was chosen as the most appropriate value to predict the outcome according to the survival analysis (Fig. 4B), p = 0.059 (< 0.10)."}, "evidence": [{"asset": "source:pmid:36056346", "locator": "sections[11] \"Identification the key genes via survival analysis\" paragraph 2", "quote": "This was chosen as the most appropriate value to predict the outcome according to the survival analysis (Fig. 4B), p = 0.059 (< 0.10)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ADORA3 was selected as the most appropriate gene for predicting clinical outcome based on survival analysis.", "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:36056346"], "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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