Evidence map›Paper›PMID 38310443›Full record

ArticleJournal of proteome research2024

Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients.

Samuele Sala, Philipp Nitschke, Reika Masuda, Nicola Gray, Nathan G Lawler, James M Wood, Joshua N Buckler, Georgy Berezhnoy, Jose Bolaños, Berin A Boughton and 18 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of proteome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
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

28 authors.

Samuele SalaThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.
Philipp NitschkeThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0002-5814-7529
Reika MasudaThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.
Nicola GrayThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0002-0094-5245
Nathan G LawlerThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0001-9649-425X
James M WoodFerrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand.ORCID 0000-0002-5965-1006
Joshua N BucklerFerrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand.ORCID 0000-0002-4397-9947
Georgy BerezhnoyDepartment of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany.
Jose BolañosChemistry Department, Universidad del Valle, Cali 76001, Colombia.
Berin A BoughtonThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0001-6342-9814
Caterina LonatiCenter for Preclinical Research, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy.
Titus RösslerDepartment of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany.
Yogesh SinghInstitute of Medical Genetics and Applied Genomics, University Hospital Tübingen, 72074 Tübingen, Germany.
Ian D WilsonDivision of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.ORCID 0000-0002-8558-7394
Samantha LodgeThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0001-9193-0462
Aude-Claire MorillonThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.
Ruey Leng LooThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0001-5307-5709
Drew HallThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.
Luke WhileyThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0002-9088-4799
Gary B EvansFerrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand.
Tyler L GroveDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.ORCID 0000-0002-4763-0646
Steven C AlmoDepartment of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.
Lawrence D HarrisFerrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand.ORCID 0000-0002-4214-1018
Elaine HolmesThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0002-0556-8389
Uta MerleDepartment of Internal Medicine IV, University Hospital Heidelberg, 69120 Heidelberg, Germany.
Christoph TrautweinDepartment of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany.ORCID 0000-0003-4672-6395
Jeremy K NicholsonThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0002-8123-8349
Julien WistThe Australian National Phenome Centre and Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia.ORCID 0000-0002-3416-2572

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We present compelling evidence for the existence of an extended innate viperin-dependent pathway, which provides crucial evidence for an adaptive response to viral agents, such as SARS-CoV-2. We show the in vivo biosynthesis of a family of novel endogenous cytosine metabolites with potential antiviral activities. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif, indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally enabled the characterization and quantification of the most abundant serum metabolites, showing the potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine- and uracil-based) analogue structures, eight of which were previously unknown in humans

Indexed as

COVID-19Antiviral AgentsCytosineHumansImmunity, InnateMetabolic Networks and PathwaysMolecular StructureSARS-CoV-2Antiviral AgentsCytosineantiviralsbiomarkersCOVID-19deoxydidehydronucleosidesextended viperin pathwayNMR spectroscopynucleosidespolypharmacyRSAD2SARS-CoV-2urineviperin

Identifiers

PMID38310443
PMCPMC10913068

What Socratic holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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 Socratic graph.