Evidence map›Paper›PMID 29990500›Full record

ArticleCancer cell2018

Genomic and Transcriptomic Analysis Reveals Incremental Disruption of Key Signaling Pathways during Melanoma Evolution.

A Hunter Shain, Nancy M Joseph, Richard Yu, Jamal Benhamida, Shanshan Liu, Tarl Prow, Beth Ruben, Jeffrey North, Laura Pincus, Iwei Yeh and 2 more

Registry-linked trialOpen access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cancer cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05119829 (Melanoma), which is not on this map. Cited by 123 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
123citing papers in PubMed, 2 pooled it
9.5field-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.

NCT05119829 unknown statusnot on this map

Melanoma: Genomic Profiles, Molecular Markers and Therapeutic Implications

TypeobservationalSponsorHellenic Cooperative Oncology GroupRan1998 to 2023Enrolled80ConditionsMelanoma
3 · Its place in the literature

Who cites it

123 citing papers in PubMed, 2 syntheses or guidelines pooled it, 221 citations in OpenAlex.

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  18. MCSPNature cancer · 2025
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63 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

12 authors at 2 institutions in 2 countries.

A Hunter ShainUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA. Electronic address: alan.shain@ucsf.edu.
Nancy M JosephUniversity of California San Francisco, Department of Pathology, San Francisco, CA, USA.
Richard YuUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA.
Jamal BenhamidaUniversity of California San Francisco, Department of Pathology, San Francisco, CA, USA.
Shanshan LiuUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA.
Tarl ProwFuture Industries Institute, University of South Australia, Adelaide, SA, Australia.
Beth RubenUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA; Palo Alto Medical Foundation, Palo Alto, CA, USA.
Jeffrey NorthUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA.
Laura PincusUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA.
Iwei YehUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA.
Robert JudsonUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA.
Boris C BastianUniversity of California San Francisco, Department of Dermatology, San Francisco, CA, USA; University of California San Francisco, Helen Diller Comprehensive Cancer Center, San Francisco, CA, USA; University of California San Francisco, Department of Pathology, San Francisco, CA, USA. Electronic address: boris.bastian@ucsf.edu.
University of California, San Francisco · USUniversity of South Australia · AU

Funding

Molecular and immunologic evolution of melanomas from pre-neoplastic lesionsR35CA220481 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BASTIAN, BORIS C. · 2017 to 2023
$6.3M
Molecular Pathology of CancerT32CA177555 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BASTIAN, BORIS C., OAKES, SCOTT A. · 2013 to 2017
$1.1M
Defining the role of SWI/SNF chromatin remodeling complex mutations during melanoma progressionK22CA217997 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SHAIN, ALAN HUNTER · 2018 to 2021
$651k
NCI NIH HHS K22 CA217997NCI NIH HHS R35 CA220481NCI NIH HHS T32 CA177555
6 · The paper itself

Abstract

We elucidated genomic and transcriptomic changes that accompany the evolution of melanoma from pre-malignant lesions by sequencing DNA and RNA from primary melanomas and their adjacent precursors, as well as matched primary tumors and regional metastases. In total, we analyzed 230 histopathologically distinct areas of melanocytic neoplasia from 82 patients. Somatic alterations sequentially induced mitogen-activated protein kinase (MAPK) pathway activation, upregulation of telomerase, modulation of the chromatin landscape, G1/S checkpoint override, ramp-up of MAPK signaling, disruption of the p53 pathway, and activation of the PI3K pathway; no mutations were specifically associated with metastatic progression, as these pathways were perturbed during the evolution of primary melanomas. UV radiation-induced point mutations steadily increased until melanoma invasion, at which point copy-number alterations also became prevalent.

Indexed as

TranscriptomeBiomarkers, TumorCell MovementCell Transformation, NeoplasticChromatin Assembly and DisassemblyComputational BiologyDatabases, GeneticDisease ProgressionDNA Copy Number VariationsG1 Phase Cell Cycle CheckpointsGene DosageGene Expression ProfilingGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansMAP Kinase Signaling SystemBiomarkers, TumorDNA-seqdysplastic nevusgenomicmelanomametastasisnevusRNA-seqtranscriptomictumor evolutiontumor progression

Identifiers

PMID29990500
PMCPMC6319271
OpenAlexW2841467362

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

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.