Evidence map›Paper›PMID 29213088›Full record

ArticleScientific reports2017

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma.

Kevin Brennan, June Ho Shin, Joshua K Tay, Marcos Prunello, Andrew J Gentles, John B Sunwoo, Olivier Gevaert

Open access · goldAbstract read
In one paragraph

Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
64citing papers in PubMed, 1 pooled it
2.2field-weighted citation impact, top 11% 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

64 citing papers in PubMed, 1 synthesis or guideline pooled it, 87 citations in OpenAlex.

  1. Pooled it
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  15. How the chromatin landscape influences nuclear morphology.Frontiers in cell and developmental biology · 2025
    Review
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4 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

7 authors at 4 institutions in 3 countries.

Kevin BrennanDepartment of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA.
June Ho ShinDepartment of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA.
Joshua K TayDepartment of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA.
Marcos PrunelloDepartment of Statistics, College of Pharmaceutical and Biochemical Sciences, National University of Rosario, Rosario, Argentina.
Andrew J GentlesDepartment of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA.ORCID 0000-0002-0941-9858
John B SunwooDepartment of Otolaryngology - Head and Neck Surgery, Stanford University School of Medicine, Stanford, USA. sunwoo@stanford.edu.ORCID 0000-0002-8393-4196
Olivier GevaertDepartment of Medicine, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, USA. ogevaert@stanford.edu.ORCID 0000-0002-9965-5466
Stanford University · USStanford Medicine · USNational University Health System · SGNational University of Rosario · AR

Funding

Translational Oncology Research Program (Project-005)P30CA124435 · NCI · STANFORD UNIVERSITY · PI Melinda L. Telli · 2007 to 2026
$71.4M
Organoid-based Discovery of Oncogenic Drivers and Treatment Resistance MechanismsU01CA217851 · NCI · STANFORD UNIVERSITY · PI CURTIS, CHRISTINA N, JI, HANLEE P · 2017 to 2021
$4.7M
Identification of Cooperative Genetic Alterations in the Pathogenesis of Oral CancerU01DE025188 · NIDCR · STANFORD UNIVERSITY · PI GEVAERT, OLIVIER, KUO, CALVIN J · 2015 to 2018
$3.8M
Radiogenomics Framework for Non-Invasive Personalized MedicineR01EB020527 · NIBIB · STANFORD UNIVERSITY · PI GEVAERT, OLIVIER · 2015 to 2018
$2.3M
NCI NIH HHS P30 CA124435NCI NIH HHS U01 CA217851NIBIB NIH HHS R01 EB020527NIDCR NIH HHS U01 DE025188
6 · The paper itself

Abstract

Chromatin modifying enzymes are frequently mutated in cancer, resulting in widespread epigenetic deregulation. Recent reports indicate that inactivating mutations in the histone methyltransferase NSD1 define an intrinsic subtype of head and neck squamous cell carcinoma (HNSC) that features pronounced DNA hypomethylation. Here, we describe a similar hypomethylated subtype of lung squamous cell carcinoma (LUSC) that is enriched for both inactivating mutations and deletions in NSD1. The 'NSD1 subtypes' of HNSC and LUSC are highly correlated at the DNA methylation and gene expression levels, featuring ectopic expression of developmental transcription factors and genes that are also hypomethylated in Sotos syndrome, a congenital disorder caused by germline NSD1 mutations. Further, the NSD1 subtype of HNSC displays an 'immune cold' phenotype characterized by low infiltration of tumor-associated leukocytes, particularly macrophages and CD8

Indexed as

DNA MethylationAnimalsCarcinoma, Squamous CellCD8-Positive T-LymphocytesCell Line, TumorHead and Neck NeoplasmsHistone-Lysine N-MethyltransferaseHistone MethyltransferasesHumansImmunotherapyIntracellular Signaling Peptides and ProteinsLung NeoplasmsMacrophagesMiceMice, Inbred NODNuclear ProteinsHistone-Lysine N-MethyltransferaseHistone MethyltransferasesIntracellular Signaling Peptides and ProteinsNSD1 protein, humanNuclear ProteinsProgrammed Cell Death 1 ReceptorRNA, Small Interfering

Identifiers

PMID29213088
PMCPMC5719078
OpenAlexW2766463353

What OpenQuestion holds

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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 OpenQuestion graph.