Evidence map›Paper›PMID 42015392›Full record

ArticleJournal of medical virology2026

Multiorgan Molecular Landscape of Severe COVID-19 Revealed by Consensus Gene Signatures and RAB8B Targeting.

Jonathan Peña Avila, Peter Park, Youvika Singh, Paulo P Amaral, Ícaro Castro, Felipe Ten-Caten, Viviane Schuch, André N A Gonçalves, Jeevan Giddaluru, Mauro César Cafundó Morais and 22 more

Abstract read
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In one paragraph

Article in Journal of medical virology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

32 authors.

Jonathan Peña AvilaDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Peter ParkDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Youvika SinghDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Paulo P AmaralInstituto de Ensino e Pesquisa, Insper, São Paulo, Brazil.
Ícaro CastroInterunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, São Paulo, Brazil.
Felipe Ten-CatenDepartment of Infectious and Parasitic Diseases, University of São Paulo Medical School, University of São Paulo, São Paulo, Brazil.
Viviane SchuchDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
André N A GonçalvesDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Jeevan GiddaluruDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Mauro César Cafundó MoraisDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.ORCID https://orcid.org/0000-0003-4248-750X
Rodrigo L T OgavaDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Thiago LubianaDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Gabriel Amoroso de CastroDepartment of Pharmaceutical Sciences, State University of Campinas, Campinas, Brazil.
Rodrigo AquinoDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.ORCID https://orcid.org/0000-0002-8889-3178
Luiz DurãoDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Júlia Raspante MartinsDepartment of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
Leandro JimenezDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
André G Costa-MartinsDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Patrícia Gonzalez-DiasDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Thiago Dominguez Crespo HirataDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Thomaz Lüscher DiasDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Débora Guerra PeixeInterunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics, University of São Paulo, São Paulo, São Paulo, Brazil.
Adriana SimizoHospital Israelita Albert Einstein, São Paulo, São Paulo, Brazil.
Juan Carlo Santos E SilvaDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Amanda Pereira VasconcelosDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.
Marcelo Berçot RodriguesDepartment of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, Brazil.
Bianca G CastelucciDepartment of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, Brazil.
João Victor Virgillio-da-SilvaDepartment of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, Brazil.
Larissa MenezesDepartment of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, Brazil.
Pedro M Moraes-VieiraDepartment of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas, Campinas, Brazil.ORCID https://orcid.org/0000-0002-8263-786X
Otavio Cabral-MarquesDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.ORCID https://orcid.org/0000-0002-3183-6236
Helder I NakayaDepartment of Clinical and Toxicological Analyses, University of São Paulo, São Paulo, São Paulo, Brazil.ORCID https://orcid.org/0000-0001-5297-9108

Funding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES) 88887.653301/2021-00National Council for Scientific and Technological Development (CNPq) Brazil 309482/2022-4São Paulo State Research Foundation (FAPESP) 2018/14933-2São Paulo State Research Foundation (FAPESP) 2018-18886-9São Paulo State Research Foundation (FAPESP) 2019/26284-1São Paulo State Research Foundation (FAPESP) 2019/27139-5São Paulo State Research Foundation (FAPESP) 2019/27146-1São Paulo State Research Foundation (FAPESP) 2020/12017-9São Paulo State Research Foundation (FAPESP) 2020/16030-0São Paulo State Research Foundation (FAPESP) 2022/04864-9São Paulo State Research Foundation (FAPESP) 2023/09291-0
6 · The paper itself

Abstract

Severe COVID-19 involves hyperinflammation and multiorgan pathology, but consistent gene signatures remain elusive. We aimed to identify consensus transcriptomic signatures and molecular mechanisms in severe COVID-19. We performed an integrative analysis of 39 studies spanning 11 tissue types, 1551 bulk RNA-seq samples, and over 2 million single cells. A vote-counting strategy combined with a systems-biology approach was applied to detect consensus differentially expressed genes (DEGs). Pathways related to interferon/TNF-α signaling, hypoxia response, and platelet activation were consistently enriched across data sets. Among consensus DEGs-such as IFITM3, BCL2A1, CAMK2D, and CCR1-RAB8B was prioritized for functional validation based on its recurrence in ~45% of tissues and its known role in vesicle trafficking, a process intimately linked to viral life cycles. Molecular dynamics simulations and in vitro assays in SARS-CoV-2-infected CaCo-2 cells demonstrated that RAB8B modulates VAMP-3 clustering and intracellular trafficking. Silencing of Rab8b-1 and Rab8b-2 reduced viral infection by 30% (p = 0.0302) and 76% (p < 0.001), respectively. This study defines robust consensus signatures and positions RAB8B as a critical host factor and potential therapeutic target in severe COVID-19. Further exploration of RAB8B inhibitors is warranted to explore therapeutic utility. An interactive database at https://covidatlas.sysbio.tools/.

Indexed as

COVID-19rab GTP-Binding ProteinsTranscriptomeCaco-2 CellsConsensus SequenceGene Expression ProfilingHumansMolecular Dynamics SimulationSARS-CoV-2rab GTP-Binding Proteinsbulk RNA‐seqgene expressionRAB8BSARS‐CoV‐2scRNA‐seqsevere COVID‐19

Identifiers

PMID42015392
PMCPMC13100344

What OpenQuestion holds

Textmetadata
LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.