4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39803891", "kind": "science-record", "revision": 3, "content_hash": "sha256:a79e34a58a6ca1320b99d0aa88fb7ceeaeb701459eb498f0396a52ac3f87ce9c", "created_at": "2026-11-01T20:30:07Z", "updated_at": "2026-11-01T22:13:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "4D-DIA Proteomics Uncovers New Insights into Host Salivary Response Following SARS-CoV-2 Omicron Infection.", "doi": "10.1021/acs.jproteome.4c00630", "pmid": "39803891", "authors": ["Iasmim Lopes de Lima", "Thais Regiani Cataldi", "Carlos Brites", "Mônica Teresa Veneziano Labate", "Sara Nunes Vaz", "Felice Deminco", "Gustavo Santana da Cunha", "Carlos Alberto Labate", "Marcos Nogueira Eberlin"], "journal": "Journal of proteome research", "year": 2025, "abstract": "Since late 2021, Omicron variants have dominated the epidemiological scenario as the most successful severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sublineages, driving new and breakthrough infections globally over the past two years. In this study, we investigated for the first time the host salivary response of COVID-19 patients infected with Omicron variants (BA.1, BA.2, and BA.4/5) by using an untargeted four-dimensional data-independent acquisition (4D-DIA)-based proteomics approach. We identified 137 proteins whose abundance levels differed between the COVID-19 positive and negative groups. Salivary signatures were mainly enriched in ribosomal proteins, linked to mRNAviral translation, protein synthesis and processing, immune innate, and antiapoptotic signaling. The higher abundance of 14-3-3 proteins (YWHAG, YWHAQ, YWHAE, and SFN) in saliva, first reported here, may be associated with increased infectivity and improved viral replicative fitness. We also identified seven proteins (ACTN1, H2AC2, GSN, NDKA, CD109, GGH, and PCYOX) that yielded comprehension into Omicron infection and performed outstandingly in screening patients with COVID-19 in a hospital setting. This panel also presented an enhanced anti-COVID-19 and anti-inflammatory signature, providing insights into disease severity, supported by comparisons with other proteome data sets. The salivary signature provided valuable insights into the host's response to SARS-CoV-2 Omicron infection, shedding light on the pathophysiology of COVID-19, particularly in cases associated with mild disease. It also underscores the potential clinical applications of saliva for disease screening in hospital settings. Data are available via ProteomeXchange with the identifier PXD054133.", "claims": [{"id": "claim-method", "statement": "A two-sided Student’s t test was performed to identify differentially expressed proteins (DEPs) (log 2 Fold Change (FC) ≥ 1.2, FDR < 0.01) in the groups analyzed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39803891", "locator": "sections[8] \"Statistical Analysis, Feature Selection, and Model Classification\" paragraph 2", "quote": "A two-sided Student’s t test was performed to identify differentially expressed proteins (DEPs) (log 2 Fold Change (FC) ≥ 1.2, FDR < 0.01) in the groups analyzed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Availability StatementThe mass spectrometry proteomics data have been deposited to the PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) via the PRIDE partner repository with the data set identifier PXD054133.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39803891", "locator": "sections[22] \"notes\" paragraph 1", "quote": "Data Availability StatementThe mass spectrometry proteomics data have been deposited to the PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) via the PRIDE partner repository with the data set identifier PXD054133."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 137 salivary proteins with abundance levels differing between COVID-19-positive and COVID-19-negative groups.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39803891", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 137 proteins whose abundance levels differed between the COVID-19 positive and negative groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified 137 salivary proteins with abundance levels differing between COVID-19-positive and COVID-19-negative groups.", "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:39803891"], "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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