Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1

Authors

Agrawal N

Frederick MJ

Pickering CR

Bettegowda C

Chang K

Li RJ

Fakhry C

Xie TX

Zhang J

Wang J

Zhang N

El-Naggar AK

Jasser SA

Weinstein JN

Trevino L

Drummond JA

Muzny DM

Wu Y

Wood LD

Hruban RH

Westra WH

Koch WM

Califano JA

Gibbs RA

Sidransky D

Vogelstein B

Velculescu VE

Papadopoulos N

Wheeler DA

Kinzler KW

Myers JN

Doi

10.1126/science.1206923

PMID: 21798897 · DOI: 10.1126/science.1206923 · Journal: Science (2011)

TL;DR

This study performed whole-exome sequencing of 32 primary head and neck squamous cell carcinomas (HNSCC) and validated findings in up to 88 additional tumors. Beyond confirming known mutations in TP53, CDKN2A, PIK3CA, and HRAS, the authors discovered frequent inactivating mutations in NOTCH1 (15% of patients) and novel mutations in FBXW7, establishing NOTCH1 as a tumor suppressor rather than an oncogene in this cancer type.

Cohort & data

  • Discovery set: 32 primary HNSCC tumors with matched normals, whole-exome sequenced (HNSC; dataset hnsc_jhu).
  • Prevalence set: Up to 88 additional HNSCC tumors for targeted validation of 6 recurrently mutated genes.
  • Total analyzed: 120 tumors across both sets.
  • Platforms: Illumina GAIIx/HiSeq (17 tumors), SOLiD V3/V4 (15 tumors) for whole-exome sequencing; Affymetrix SNP6.0 copy number analysis on 42 tumor/normal pairs; Sanger sequencing for mutation validation.
  • Coverage: Average 77-fold (Illumina) and 44-fold (SOLiD); 92.6% and 90% of targeted bases at 10x or greater.

Key findings

  • 911 candidate somatic mutations identified in 725 genes across 32 tumors; 609 (67%) confirmed by orthogonal sequencing (PMID:21798897).
  • HPV-negative tumors had significantly more mutations than HPV-positive tumors (20.6 +/- 16.7 vs 4.8 +/- 3 per tumor; p < 0.05).
  • Tobacco-associated tumors had more mutations than non-tobacco tumors (21.6 +/- 17.8 vs 9.5 +/- 6.5; p < 0.05), but mutational spectrum was NOT enriched for G:C>T:A transversions (unlike lung cancer).
  • TP53 mutations found in 47% of patients; absent in all HPV-positive tumors but present in 78% of HPV-negative tumors.
  • NOTCH1 was the second most frequently mutated gene (15%), with 28 mutations in 21 patients; 11/28 (39%) were truncating (nonsense/indels), and 7 patients harbored biallelic mutations.
  • CDKN2A mutated in 9%, PIK3CA in 6%, FBXW7 in 5%, and HRAS in 4% of patients.
  • Only 18% of HPV-negative tumors had activating oncogene mutations, while 89% harbored inactivating tumor suppressor mutations.
  • Recurrent copy number gains at 11q (CCND1), 3q (PIK3CA), and 7p (EGFR); recurrent deletions at 9p21.3 (CDKN2A).

Genes & alterations

Gene Alteration type Frequency Notes
NOTCH1 Nonsense, indels, missense 15% (21/120 patients) Tumor suppressor role; mutations in EGF-like ligand binding domain (N-terminal), distinct from hematopoietic tumor hotspots
TP53 Nonsense, indels, splice-site, missense 47% (63/120) 25 inactivating; absent in HPV-positive tumors
CDKN2A Nonsense, indels, splice-site, missense; homozygous deletion 9% (11/120) Frequent 9p21.3 deletion
PIK3CA Missense (activating) 6% Also amplified at 3q
FBXW7 Indels, missense 5% (6/120) Hotspot mutations blocking NOTCH1 degradation; first report in HNSCC
HRAS Activating 4% Known oncogene in HNSCC
EGFR Amplification (7p) Recurrent Copy number gain
CCND1 Amplification (11q13) Recurrent Copy number gain

Clinical implications

  • NOTCH1 functions as a tumor suppressor in HNSCC, not an oncogene as in T-cell leukemias, indicating that therapeutic strategies targeting the Notch pathway must be context-dependent.
  • The predominance of tumor suppressor gene inactivation (89% of HPV-negative tumors) over oncogene activation (18%) suggests that molecularly-targeted therapies directed at activated oncogenes will have limited applicability in HNSCC.
  • HPV-positive and HPV-negative HNSCCs are molecularly distinct diseases, supporting differentiated clinical management.
  • The authors conclude that prevention, surveillance, and early detection are optimal strategies for reducing HNSCC mortality given the paucity of directly targetable mutations.

Limitations & open questions

  • Discovery cohort of 32 tumors is relatively small; mutational frequencies may shift in larger cohorts.
  • 16% of candidate mutations could not be validated due to high GC content or primer design challenges.
  • Functional validation of NOTCH1 tumor suppressor activity in HNSCC cell lines was not performed in this study.
  • The role of FBXW7 mutations specifically in modulating the Notch pathway (vs. other substrates like cyclin E and c-Myc) requires further investigation.
  • No treatment outcome or survival data correlated with mutational findings.

Citations from this paper used in the wiki

  • “Nearly 40% of the 28 mutations identified in NOTCH1 were predicted to truncate the gene product, suggesting that NOTCH1 may function as a tumor suppressor gene rather than an oncogene in this tumor type.” (Abstract)
  • “TP53 mutations were not identified in any of the HPV-associated tumors but were found in 78% of the HPV-negative tumors.” (p. 3)
  • “Only 18% of the 28 tumors not associated with HPV from the Discovery set had activating mutations in a bona fide oncogene. In contrast, 89% of these tumors harbored inactivating mutations in at least one bona fide tumor suppressor gene.” (p. 5)
  • “FBXW7 mutations have not been previously observed in HNSCC, though they are frequent in other tumor types.” (p. 3)

This page was processed by paper-compiler on 2026-05-06.