With more than 380 scientific citations, Oncomine has become an industry standard for cancer researchers. This series showcases recent scientific publications that use Oncomine in various and novel ways to further cancer research.

27 JULY 2010
Three independent studies demonstrate association of 3q26 – 3q28 genes with squamous cell carcinomas.

Although the 3q26 - 3q28 chromosomal region contains many candidate oncogenes (e.g., TP63, PIK3CA, and DCUN1D1) the precise target of recurrent amplifications in this region had, until recently, been undetermined. Three recent studies^1,2,3 have now identified SOX2, a transcription factor involved in maintaining self-renewal of undifferentiated embryonic stem cells, as the likely driver.

First, using lung, esophageal, and cervical squamous cell tumor samples, Bass¹ and Hussenet² both narrowed the common region of recurrent amplification to a few genes surrounding SOX2.

Figure 1: UCSC Genome Browser view of 3q26 surrounding SOX2

Applying a 3q26 chromosomal region filter on the Bass Lung⁴ squamous cell lung cancer copy number analysis in Oncomine, reveals clear amplifications of SOX2 and genomic neighbors in about 20% of patients.

Figure 2: Amplification of the 3q26 region is observed in about 20% of Lung SCC, consistent with published data. Red stripes indicate patients with amplifications in this region. SOX2 (3q26.32) and immediate genomic neighbors are indicated by arrows.

Both studies then correlated SCC mRNA expression levels with genes in this chromosomal interval. Using Oncomine, Hussenet et al. found eight of nine SOX2 genomic neighbors to be significantly up-regulated in primary SCC tumors. For example, in the Bild Lung dataset⁵, SOX2 is over-expressed in about 90 percent of the squamous cell lung tumors as compared to non-small cell lung tumors, and is among the most strongly over-expressed genes identified. Other identified genes include the squamous markers TP63 and KRT6A, as well as other cytokeratins.

Figure 3: Expression of 3q26 genes in Squamous Cell Lung Carcinoma. Note that of all genes in 3q26, SOX2 shows the most significant differential expression when comparing Lung Squamous Cell Carcinoma to Lung Adenocarcinoma.

Also, a third recent study characterizing NSCLC pathogenesis from Yuan et al. also used Oncomine to find high expression of SOX2 in lung SCC relative to lung adenocarcinoma³. For example, study authors used the Bhattacharjee Lung dataset⁶ - without filters limiting results to 3q26 - to show high expression of SOX2 and neighbors, as well as the squamous cell markers TP63 and keratin.

Figure 4: Ranked expression of all genes in Squamous Cell Lung Carcinoma. SOX2 is highly expressed in SCC without taking chromosomal position into account. High expression of SCC markers is also observed (arrows).

In lung adenocarcinoma another transcription factor, NKX2-1, has been shown to be amplified and over-expressed^7,8,9. The associations of SOX2 expression with SCC and NKX2-1 with adenocarcinoma are readily observed in Oncomine across multiple independent studies supporting the complementary roles of these two genes in distinct cancer lineage development

Figure 5: Confirmation of published expression patterns for NKX2-1 and SOX2. NKX2-1 is up in adenocarcinoma, while SOX2 is over-expressed in squamous cell carcinoma.

NOTE: Similar to what is observed for SOX2 in Figure 2, viewing genes in 14q13 (which contains NKX2-1) in the Weir Lung adenocarcinoma DNA copy number dataset reveals high amplification of NKX2-1 and immediate genomic neighbors in subsets of patients, supporting published reports (data not shown).

SOX2 is involved in the induction of pluripotent stem cells suggesting that it may regulate a transcriptional program in the development of SCC^10,11,12 — perhaps reprogramming mature cells to become pluripotent stem cells. To test this hypothesis, Hussenet² et al. used Oncomine to first identify lung SCC signatures, and then to search for associations in the Molecular Signatures Database¹³. Bass¹ et al. took a slightly different approach, querying lung SCC expression data with embryonic stem cell signatures¹⁴, while Yuan³ et al. used an embryonic OCT4/SOX2/NANOG signature to query the Bhattacharjee and Bild datasets in Oncomine. All found an overlap with embryonic stem cell-like signatures, i.e. expression of core embryonic stem cell transcription targets in squamous cell tumors. Yuan³ et al. additionally were able to separate lung squamous and lung adenocarcinoma tumors based on the OCT4/SOX2/NANOG signature.

Using a signature for SCC derived from a cancer vs. normal meta-analysis in Oncomine, concepts analysis reveals an association with embryonic stem cells.

Figure 6: Embryonic stem-like signatures and expression of targets of core ES transcription factors in tumors with higher SOX2 expression. Concepts analysis also associates lung SCC "signature" with ESCs.

In contrast to the embryonic stem cell-like association, 3q26 interval genes and SOX2 also paradoxically correlate with markers of squamous differentiation in lung SCCs. The squamous markers — TP63 and Keratins — are highly correlated with SOX2 expression (Oncomine meta-analysis shows this), suggesting that SOX2 promotes squamous identity rather than de-differentiation to a pluripotent state. In fact, Bass¹ et al. ectopically expressed SOX2 in a lung adenocarcinoma cell line and found induction of both TP63 and KRT6A, supporting a role in squamous identity rather than de-differentiation consistent with a role as a lineage survival oncogene.

SPECULATION: It may be that SOX2 is a crucial control gene for cell fate choices balancing cells between self-renewal and differentiation. Additional factors might then tip developmental decisions by promoting either de-differentiation or tumor progression.

Figure 7: Concept association of 3q26 chromosomal interval genes. This region strongly associates with lung cancer, as well as other cancer types of squamous cell origin (cervical and head and neck cancer).

Figure 8: Top lung associations with 3q26 genes are all with Squamous Cell Carcinoma.

Summary: Using Copy Number Variation analysis, two recent studies^1,2 have identified SOX2 as the potential driver gene in cancers of squamous cell origin. Both of these studies, as well as a third recent publication³, all additionally found SOX2 expression associated with lung SCC and not with lung adenocarcinoma.

Using copy number data available in Oncomine, it is clear that SOX2 and genomic neighbors are amplified in lung SCC. Additionally, multiple independent studies exhibit high expression of SOX2 in nearly 90% of lung SCCs supporting a potential oncogenic role for this gene.

These analyses, as well as Oncomine Concepts analysis, correlate SOX2 with markers of squamous differentiation. Concepts analysis using a 3q26 filter strongly associate genes in this interval with squamous cell tumors, further demonstrating a role in determining squamous identity.

Paradoxically, stem cell-like phenotypes are also associated with SOX2 expression in lung SCC, perhaps implicating SOX2 as a crucial control gene for cell fate choices balancing cells between self-renewal and differentiation.

These studies strongly associate both amplification and expression of SOX2 with squamous cell tumors suggesting that SOX2 over-expression is a triggering event.

Leveraging the wealth of primary tumor data in Oncomine, the authors supported their hypotheses (as we have here) elevating SOX2 as an oncogene involved in squamous cell carcinogenesis.

¹SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.
Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, et al.
Nat Genet. 2009 Nov;41(11):1238-42.

²SOX2 is an oncogene activated by recurrent 3q26.3 amplifications in human lung squamous cell carcinomas.
Hussenet T, Dali S, Exinger J, Monga B, Jost B, Dembelé D, Martinet N, Thibault C, Huelsken J, Brambilla E, du Manoir S.
PLoS One. 2010 Jan 29;5(1):e8960.

³Sex determining region Y-Box 2 (SOX2) is a potential cell-lineage gene highly expressed in the pathogenesis of squamous cell carcinomas of the lung.
Yuan P, Kadara H, Behrens C, Tang X, Woods D, Solis LM, Huang J, Spinola M, Dong W, Yin G, Fujimoto J, Kim E, Xie Y, Girard L, Moran C, Hong WK, Minna JD, Wistuba II.
PLoS One. 2010 Feb 9;5(2):e9112.

⁴SOX2 is an amplified lineage-survival oncogene in lung and esophageal squamous cell carcinomas.
Bass AJ, Watanabe H, Mermel CH, Yu S, Perner S, Verhaak RG, Kim SY, Wardwell L, Tamayo P, Gat-Viks I, Ramos AH, Woo MS, Weir BA, Getz G, Beroukhim R, O'Kelly M, Dutt A, Rozenblatt-Rosen O, Dziunycz P, Komisarof J, Chirieac LR, Lafargue CJ, Scheble V, Wilbertz T, Ma C, Rao S, Nakagawa H, Stairs DB, Lin L, Giordano TJ, Wagner P, Minna JD, Gazdar AF, Zhu CQ, Brose MS, Cecconello I, Jr UR, Marie SK, Dahl O, Shivdasani RA, Tsao MS, Rubin MA, Wong KK, Regev A, Hahn WC, Beer DG, Rustgi AK, Meyerson M.
Nat Genet. 2009 Nov;41(11):1238-42..

⁵Oncogenic pathway signatures in human cancers as a guide to targeted therapies.
Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR.
Nature. 2006 Jan 19;439(7074):353-7.

⁶Classification of human lung carcinomas by mRNA expression profiling reveals distinct adenocarcinoma subclasses.
Bhattacharjee A, Richards WG, Staunton J, Li C, Monti S, Vasa P, Ladd C, Beheshti J, Bueno R, Gillette M, Loda M, Weber G, Mark EJ, Lander ES, Wong W, Johnson BE, Golub TR, Sugarbaker DJ, Meyerson M.
Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13790-5.

⁷Oncogenic cooperation coamplification of developmental transcription factor genes in lung cancer.
Kendall, J. et al.
Proc. Natl. Acad. Sci. USA. 104, 16663–16668 (2007).

⁸Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer.
Kwei, K.A. et al.
Oncogene. 27, 3635–3640 (2008).

⁹Lineage-specific dependency of lung adenocarcinomas on the lung development regulator TTF-1.
Tanaka, H. et al.
Cancer Res. 67, 6007–6011 (2007).

¹⁰Core transcriptional regulatory circuitry in human embryonic stem cells.
Boyer LA, Lee TI, Cole MF, Johnstone SE, Levine SS, et al.
Cell. 122: 947–956 (2005).

¹¹Dissecting selfrenewal in stem cells with RNA interference.
Ivanova N, Dobrin R, Lu R, Kotenko I, Levorse J, et al.
Nature. 442: 533–538. (2006).

¹²SOX2 functions in adult neural stem cells.
Episkopou V.
Trends Neurosci. 28: 219–221. (2005).

¹³Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.
PNAS. 2005 Oct 25;102(43):15545-50.

¹⁴An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors.
Ben-Porath, I. et al.
Nat. Genet. 40, 499–507 (2008).

Oncomine 4.3 | Data (June 2010)