Abstract LB-168: Comprehensive genomic characterization of small cell lung cancer
Authors: George Julie , Lim Jing Shan , Peifer Martin , Sage Julien , Thomas Roman 
Published: August 2015

Small cell lung cancer (SCLC) is a highly aggressive, neuroendocrine tumor of the lung that accounts for 15-20% of all lung cancer malignancies. SCLC patients are usually diagnosed with an extensive stage of a tumor, which complicates further surgical resections. The current standard of care is a platinum-based chemotherapy and targeted therapies have not yet been identified for the treatment of SCLC patients.

We sought to comprehensively characterize the genomic alterations in SCLC to identify novel candidate targets for therapy. To this end, we performed whole genome sequencing on 110 tumor-normal pairs and transcriptome sequencing on 80 primary tumors.

Following the paradigm of classical Knudson tumor suppressors, TP53 and RB1 were detected with somatic, bi-allelic genomic alterations, thus emphasizing the loss of both tumor suppressors as an obligatory event in SCLC. Two cases did not carry genomic alterations in TP53 and RB1, but instead were found to undergo chromothripsis; genomic rearrangements between chromosome 3 and 11 led to the upregulation of Cyclin D1, thus revealing an alternative mechanism of Rb1 deregulation. Additionally, SCLC tumors were found to harbor complex genomic rearrangements of the RB1 and TP53 family members RBL1 (p107), RBL2 (p130) and TP73, the latter resulting in the oncogenic splice variant TP73Δex2/3.

SCLC tumors revealed focal amplifications of MYC transcription factors and FGFR1 in 10% and 6% of the cases analyzed, respectively. Additionally, low frequent alterations were detected in SCLC, such as focal amplifications of IRS2, a candidate oncogene involved in the IGF1R tyrosine kinase signaling pathway. A few SCLC cases were found to harbor mutations with possible immediate therapeutic implications; including mutations in BRAF, KIT and PIK3CA.

The integrative study for significantly mutated genes confirmed that the histone acetyl transferases CREBBP and EP300 were inactivated in 25% of the tumors(1). Additionally, SCLC tumors showed frequent alterations of centrosomal proteins and in 25% of the cases inactivating mutations of NOTCH family genes. The transcriptional profile of SCLC tumors confirmed a high expression of neuroendocrine markers and of the NOTCH pathway regulator Dlk1, pointing to the notion that NOTCH functions as a tumor suppressor in SCLC tumors. We sought to analyze the impact of Notch re-activation in a preclinical SCLC mouse model by introducing the Notch intracellular domain (NICD) in mice with conditional lung epithelial triple knock-out (TKO) of Trp53, Rb1 and Rbl2(2). NICD expression dramatically reduced the number of tumors arising in TKO mice and led to an extended survival. Additionally, Notch activation abrogated the expression of neuroendocrine markers.

In summary, this whole genome sequencing analysis provides a comprehensive understanding of the genomic nature of SCLC tumors endorsing universal bi-allelic loss of TP53 and RB1 as key events in the pathogenesis of SCLC. This study further emphasizes NOTCH as a tumor suppressor and regulator of neuroendocrine differentiation in SCLC tumors. Furthermore, this large-scale study uncovers several biological key processes and candidate therapeutic targets in this deadly form of cancer.

(1) Peifer, M. et al. Nat. Genet. 44, 1104-10 (2012).

(2) Schaffer, B. E. et al. Cancer Res. 70, 3877-83 (2010).

Citation Format: Julie George, Jing Shan Lim, Martin Peifer, Julien Sage, Roman Thomas. Comprehensive genomic characterization of small cell lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-168. doi:10.1158/1538-7445.AM2015-LB-168