Cancer Reports. Volume 23, Issue 1 p194-212.e6, 3 April 2018 10.1016/j.celrep.2018.03.063
This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smoking and/or human papillomavirus (HPV). SCCs harbor 3q, 5p and other recurrent chromosomal copy number alterations (CNAs), DNA mutations, and/or aberrant methylation of genes and microRNAs, that are correlated with expression of multi-gene programs linked to squamous cell stemness, epithelial-to-mesenchymal differentiation, growth, genomic integrity, oxidative damage, death, and inflammation. Low-CNA SCCs tended to be HPV(+) and display hypermethylation with repression of TET1 demethylase and FANCF, previously linked to predisposition to SCC, or harbor mutations affecting CASP8, RAS-MAPK pathways, chromatin modifiers, and immunoregulatory molecules. We uncovered hypomethylation of the alternative promoter that drives expression of the DNp63 oncogene and embedded miR944. Co-expression of immune checkpoint, T-regulatory, and Myeloid suppressor cells signatures may explain reduced efficacy of immune therapy. These findings support new possibilities for molecular classification and therapeutic approaches.
Data in the GDC
- GDC Manifests
- Open-Access Data - Download Manifest (67 Files)
- Controlled-Access Data - Download Manifest (10 Files)
Data Files
- MAF Files
- TCGA-LUSC
- LUSC_public_filtered.maf
- LUSC_exome_calls.maf
- LUSC_controlled_filtered.maf
- TCGA-HNSC
- HNSC_public_filtered.maf
- HNSC_exome_calls.maf
- HNSC_controlled_filtered.maf
- TCGA-ESCA
- ESCA_public_filtered.maf
- ESCA_exome_calls.maf
- ESCA_controlled_filtered.maf
- TCGA-CESC
- CESC_public_filtered.maf
- CESC_exome_calls.maf
- CESC_controlled_filtered.maf
- TCGA-BLCA
- BLCA_public_filtered.maf
- BLCA_exome_calls.maf
- BLCA_controlled_filtered.maf
- Clinical Data Files
- Summary - Data_summary.xlsx
- LUSC - LUSC_clinical.tsv
- HNSC - HNSC_clinical.tsv
- ESCA - ESCA_clinical.tsv
- CESC - CESC_clinical.tsv
- BLCA - BLCA_clinical.tsv
- Methylation Data Files
- Methylation - Methylation.xlsx
- LUSC - LUSC_Methyl450.tsv
- LUSC - LUSC_Methy27.tsv
- HNSC - HNSC_Methyl.tsv
- ESCA - ESCA_Methyl.tsv
- CESC - CESC_Methyl.tsv
- BLCA - BLCA_Methyl.tsv
- miRNA Data Files
- miRNA - miRNA.xlsx
- LUSC - LUSC_miRNA.tsv
- HNSC - HNSC_miRNA.tsv
- ESCA - ESCA_miRNA.tsv
- CESC - CESC_miRNA.tsv
- BLCA - BLCA_miRNA.tsv
- RNASeq Data Files
- RNASeq - RNASeqV2.xlsx
- TCGA-LUSC
- LUSC_RNASeqV2_isoform_normal.tsv
- LUSC_RNASeqV2_geneExp_normal.tsv
- LUSC_RNASeqV2_final_isoform.tsv
- LUSC_RNASeqV2_final_geneExp.tsv
- TCGA-HNSC
- HNSC_RNASeqV2_isoform_normal.tsv
- HNSC_RNASeqV2_geneExp_normal.tsv
- HNSC_RNASeqV2_final_isoform.tsv
- HNSC_RNASeqV2_final_geneExp.tsv
- TCGA-ESCA
- ESCA_RNASeqV2_isoform_normal.tsv
- ESCA_RNASeqV2_geneExp_normal.tsv
- ESCA_RNASeqV2_final_isoform.tsv
- ESCA_RNASeqV2_final_geneExp.tsv
- TCGA-CESC
- CESC_RNASeqV2_isoform_normal.tsv
- CESC_RNASeqV2_geneExp_normal.tsv
- CESC_RNASeqV2_final_isoform.tsv
- CESC_RNASeqV2_final_geneExp.tsv
- TCGA-BLCA
- BLCA_RNASeqV2_isoform_normal.tsv
- BLCA_RNASeqV2_geneExp_normal.tsv
- BLCA_RNASeqV2_final_isoform.tsv
- BLCA_RNASeqV2_final_geneExp.tsv
- RPPA Data Files
- RPPA Standard AB List - RPPA_Standard_Ab_List_Updated.xlsx
- RPPA - RPPA.xlsx
- LUSC - LUSC_RPPA.tsv
- HNSC - HNSC_RPPA.tsv
- ESCA - ESCA_RPPA.tsv
- CESC - CESC_RPPA.tsv
- BLCA - BLCA_RPPA.tsv
- Copy Number Data Files
- GISTIC copy number bins by gene - all_thresholded.by_genes.txt.zip
- GISTIC copy number values by gene - all_data_by_genes.zip
- TCGA-LUSC
- LUSC_data_by_genes.txt
- LUSC_SNP6.seg
- TCGA-HNSC
- HNSC_data_by_genes.txt
- HNSC_SNP6.seg
- TCGA-ESCA
- ESCA_data_by_genes.txt
- ESCA_SNP6.seg
- TCGA-CESC
- CESC_data_by_genes.txt
- CESC_SNP6.seg
- TCGA-BLCA
- BLCA_data_by_genes.txt
- BLCA_SNP6.seg
- Supplementary Data Files
- Final freeze list of samples - Final_freeze.xlsx
- GISTIC regions - all_lesions.conf_99_03102017.txt
- HPV status of samples - HPV_status.docx
Additional Resources
- FireBrowse Portal (link is external)
- cBioPortal for Cancer Genomics (link is external) Memorial Sloan-Kettering Cancer Center
- Mutation Data
- PanCanAtlas Additional Files
Instructions for Data Download
Open Access Data
- Download the appropriate manifest file from the publication page
- Use the manifest file to download data using the GDC Data Transfer Tool (DTT) or the GDC API
- GDC DTT ( Download, User's Guide)
- GDC API ( User’s Guide)
Controlled Access Data
- Download the appropriate manifest file from the publication page
- Download a token from the GDC Data Portal
- GDC Data Portal ( Launch, User’s Guide)
- Use the manifest file and token to download data using the GDC DTT or the GDC API
- GDC DTT ( Download, User’s Guide)
- GDC API ( User’s Guide)
For assistance, please contact the GDC Help Desk: support@nci-gdc.datacommons.io.