A comprehensive transcriptional portrait of human cancer cell lines

Klijn, Christiaan; Durinck, Steffen; Stawiski, Eric; Haverty, Peter M.; Jiang, Zhaoshi; Liu, Hanbin; Degenhardt, Jeremiah D.; Mayba, Oleg; Gnad, Florian; Liu, Jinfeng; Pau, Grégoire; Reeder, Jens; Cao, Yi; Mukhyala, Kiran; Selvaraj, S.; Yu, Mamie; Zynda, Gregory J; Brauer, Matthew J.; Wu, Thomas D.; Gentleman, Robert; Manning, Gerard; Yauch, Robert L.; Bourgon, Richard; Stokoe, David; Modrušan, Zora; Neve, Richard M.; Sauvage, Frédéric J. de; Settleman, Jeffrey; Seshagiri, Somasekar; Zhang, Zemin

doi:10.1038/nbt.3080

Cited by 583 publications

(720 citation statements)

References 49 publications

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“…Daoy Cell Sequencing-Daoy cell RNA extraction, quality control, library preparation, and sequencing were done as described previously (38) on an Illumina HiSeq2500, generating 30 million single end 50 base pair reads.…”

Section: Methodsmentioning

confidence: 99%

The Orphan G Protein-coupled Receptor Gpr175 (Tpra40) Enhances Hedgehog Signaling by Modulating cAMP Levels

Singh¹,

Wen²,

Scales³

2015

Journal of Biological Chemistry

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Background: It is unclear whether Smoothened protein is the only G protein-coupled receptor (GPCR) that stimulates vertebrate Hedgehog (Hh) signaling. Results: Knockdown of Gpr175, a Hh-dependent ciliary GPCR, reduces Hh signaling in multiple cell lines. Conclusion: Gpr175 positively modulates Hh signaling by decreasing cAMP and Gli3 repressor levels via G␣ i1 . Significance: Regulation of Hh signaling by GPCRs is more complicated than thought.

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Section: Methodsmentioning

confidence: 99%

The Orphan G Protein-coupled Receptor Gpr175 (Tpra40) Enhances Hedgehog Signaling by Modulating cAMP Levels

Singh¹,

Wen²,

Scales³

2015

Journal of Biological Chemistry

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“…However, there was co-expression of the epithelial markers (E-cadherin, Ep-CAM, cytokeratins) which gives rise to a state of epithelialmesenchymal plasticity (EMP). [9,32] This is a dynamic state where cells gain and maintain both epithelial and mesenchymal cell types. [32,33] When the HPV-16 positive cell lines are compared to each other at a protein level, UD-SCC2 has a more mesenchymal nature to it than 93-VU-147T due to lower expression of E-cadherin and no EpCAM expression and the presence of Vimentin which is frequently used as a marker of EMT.…”

Section: Discussionmentioning

confidence: 99%

“…[9] Knowledge of the molecular alterations that exist within established HNSCC cell lines provides insight into the tumour phenotypes they represent. One crucial factor in the clinical manifestation of HNSCC that relates to the progressive attainment of molecular aberrations is the pre-existence of HPV infection, evidence of which can be readily demonstrated in some, but not all, HNSCC derived cell lines.…”

Section: Introductionmentioning

confidence: 99%

Epithelial-mesenchymal axis in head and neck cancer cell lines

Kulasinghe

Perry

Boyle

et al. 2015

JST

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Objectives: Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous tumour type which necessitates multiple in vitro models to attain an appreciation of its multiple subtypes. The phenomenon of epithelial-mesenchymal transition (EMT) is important to the development of a metastatic cancer cell phenotype being relevant to the ability of cancer cells to intravasate into vasculature and to invade tissues. The role of EMT in human papilloma virus (HPV) positive HNSCC is not well understood. This paper aims to characterize seven HNSCC cell lines (FaDu, SCC-25, SCC-15, CAL27, RPMI2650) including two new HPV-16 positive HNSCC cell lines (UD-SCC2, 93-VU-147T) for their epithelial and mesenchymal properties. Materials and methods:A panel of HNSCC cell lines from multiple head and neck anatomical sites were profiled for basal expression of epithelial and mesenchymal characteristics at mRNA, protein and functional levels (proliferative, migratory and invasive properties). Furthermore, 3D spheroid forming capabilities were investigated. Results:We found that the HPV-16 positive cell line, in particular UD-SCC2 demonstrated a more invasive and mesenchymal phenotype at the molecular and functional levels suggesting HPV infection may mediate some of these cellular properties. Moreover, HPV-negative cell lines were not strictly epithelial presenting with a dynamic range of expression.Conclusions: This study presents the molecular and phenotypic diversity of HNSCC cell lines. It highlights the need for more studies in this field and a scoring system where HNSCC cell lines are ranked according to their respective epithelial and mesenchymal nature. This data will be useful to anyone modelling HNSCC behaviour, providing a molecular context which will enable them to decipher cell phenotypes and to develop therapies which block EMT progression.

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“…Gene symbols from the annotation file were used for integration of RNA sequencing (RNA-seq) and DNA methylation data. RNA-seq (E-MTAB-2706) and Infinium 450K methylation array (GSE36216) data for the same panel of NSCLC cell lines were used to validate the correlations between gene expression and methylation (20). Spearman r < À0.3 was used to show inverse correlations between expression and methylation levels in NSCLC cell lines or TCGA tumor samples.…”

Section: Dna Methylation Array Datamentioning

confidence: 99%