Evidence map›Paper›PMID 35508466›Full record

ReviewNature communications2022

Integrative proteogenomic characterization of hepatocellular carcinoma across etiologies and stages.

Charlotte K Y Ng, Eva Dazert, Tuyana Boldanova, Mairene Coto-Llerena, Sandro Nuciforo, Caner Ercan, Aleksei Suslov, Marie-Anne Meier, Thomas Bock, Alexander Schmidt and 9 more

Open access · goldAbstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
96citing papers in PubMed, 2 pooled it
20.1field-weighted citation impact, top 1% of its field
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

96 citing papers in PubMed, 2 syntheses or guidelines pooled it, 145 citations in OpenAlex.

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36 more citing papers are in PubMed but not listed here.

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

19 authors at 3 institutions in 2 countries.

Charlotte K Y NgDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0002-6100-0026
Eva Dazert *Biozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0002-7292-2261
Tuyana Boldanova *Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Mairene Coto-LlerenaDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0001-7596-1250
Sandro NuciforoDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0002-1863-1869
Caner ErcanInstitute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0002-5611-2699
Aleksei SuslovDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Marie-Anne MeierDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Thomas BockBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0002-9314-5318
Alexander SchmidtBiozentrum, University of Basel, Basel, Switzerland.ORCID 0000-0002-3149-2381
Sylvia KettererDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Xueya WangDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Stefan WielandDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0002-4444-977X
Matthias S MatterInstitute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0002-2005-5266
Marco ColombiBiozentrum, University of Basel, Basel, Switzerland.
Salvatore PiscuoglioDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland.ORCID 0000-0003-2686-2939
Luigi M TerraccianoInstitute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland.
Michael N HallBiozentrum, University of Basel, Basel, Switzerland.
Markus H HeimDepartment of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland. markus.heim@unibas.ch.ORCID 0000-0002-7523-4894
University of Basel · CHHumanitas University · ITUniversity of Bern · CH

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Proteogenomic analyses of hepatocellular carcinomas (HCC) have focused on early-stage, HBV-associated HCCs. Here we present an integrated proteogenomic analysis of HCCs across clinical stages and etiologies. Pathways related to cell cycle, transcriptional and translational control, signaling transduction, and metabolism are dysregulated and differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. We describe candidate copy number-driven driver genes involved in epithelial-to-mesenchymal transition, the Wnt-β-catenin, AKT/mTOR and Notch pathways, cell cycle and DNA damage regulation. The targetable aurora kinase A and CDKs are upregulated. CTNNB1 and TP53 mutations are associated with altered protein phosphorylation related to actin filament organization and lipid metabolism, respectively. Integrative proteogenomic clusters show that HCC constitutes heterogeneous subgroups with distinct regulation of biological processes, metabolic reprogramming and kinase activation. Our study provides a comprehensive overview of the proteomic and phophoproteomic landscapes of HCCs, revealing the major pathways altered in the (phospho)proteome.

Indexed as

Carcinoma, HepatocellularLiver NeoplasmsProteogenomicsbeta CateninHumansMutationProteomicsbeta Catenin

Identifiers

PMID35508466
PMCPMC9068765
OpenAlexW4225410183

What Socratic holds

Textmetadata
LicenceCC BY
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.