Oral Squamous Cell Carcinoma — MD Anderson (Pickering 2013)

Overview

Multi-platform integrated genomic study of 40 oral squamous cell carcinomas (OSCC) from patients treated at MD Anderson Cancer Center, by Pickering et al. (Cancer Discovery 2013). Expression and methylation data deposited in GEO under accession GSE41117. PMID:23619168

Composition

• 40 OSCC patients at MD Anderson Cancer Center; fresh-frozen surgically-resected tumors with matched non-malignant adjacent tissue; >60% tumor nuclei content required. PMID:23619168
• Cancer type: oral squamous cell carcinoma (OCSC), a subset of head and neck squamous cell carcinoma (HNSC). PMID:23619168
• Copy-number profiling available for 38/40 tumors; exome sequencing on all 40; methylation and expression on all 40. PMID:23619168

Assays / panels (linked)

• affymetrix-snp6 — SNP arrays on 38 tumors; ASCAT for allele-specific copy number; gistic v2.0.12 for significance. PMID:23619168
• whole-exome-seq — Nimblegen capture with SOLiD or Illumina sequencing. PMID:23619168
• 450k-methylation-array — Illumina HumanMethylation450 arrays. PMID:23619168
• Affymetrix Human Exon 1.0ST mRNA arrays and Agilent Human microRNA microarrays rel12.0. PMID:23619168
• sanger-sequencing — validation of NOTCH1 and CASP8 alterations in 44 HNSCC cell lines. PMID:23619168

Papers using this cohort

• PMID:23619168 — Pickering et al., “Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers,” Cancer Discov 2013.

Notable findings derived from this cohort

• Notch pathway altered in 66% (23/35) of tumors; NOTCH1 mutated in 9% of primary tumors and functions as tumor suppressor — activated NOTCH1 (ICN1) caused G1 arrest, p21 induction, senescence, and suppressed xenograft growth. PMID:23619168
• CASP8 mutations in 10% (4/40) define a molecular subtype with fewer copy-number alterations and frequent co-occurrence of HRAS mutations (3/4 CASP8-mutant tumors had HRAS mutation; p=0.0016); validated in TCGA HNSCC. PMID:23619168
• FAT1 inactivation (mutation or deletion) in 46% of tumors; TP53 mutations in 60%, with splice-site mutations markedly enriched (13% vs. 2% baseline across tumor types). PMID:23619168
• Cell-cycle pathway altered in 94% of tumors via CCND1 amplification and/or CDKN2A loss; mitogenic signaling altered in 63%. PMID:23619168
• 80% (28/35) of tumors harbored at least one targetable alteration, 54% had ≥2; top targets include SRC-family kinases (29%), PI3K signaling (34%), and TNK2 (17%). PMID:23619168
• A CIMP-like methylation subgroup identified with higher methylation frequency and fewer CNAs, associated with non-tobacco use. PMID:23619168

Sources

• GEO: GSE41117 (expression and methylation)
• DOI: 10.1158/2159-8290.CD-12-0537

This page was processed by crosslinker on 2026-05-09.