by ecancer reporter Clare Sansom

About 12-15% of all cases of primary lung cancer are categorised as small cell lung cancer (SCLC).

This form of the disease occurs often in heavy smokers, and almost never in non-smokers; the tumour cells are small, contain little cytoplasm and express neuroendocrine markers.

Although initial chemotherapy is often successful, the disease generally returns quickly and the prognosis is poor, with fewer than 15% of patients surviving for 3 years after diagnosis.

Sequencing the exomes – that is, the coding regions of the genomes – of small cell lung tumours has revealed only a few frequently mutated genes; this suggests that complex gene rearrangements that cannot be picked up from exome sequencing alone may contribute significantly to the development of these tumours.

A large, international group of researchers led by Roman Thomas from the University of Cologne, Cologne, Germany have profiled a large sample of these tumours using whole genome sequencing.

Complete genome sequences were obtained from a total of 110 small cell lung tumours and their matched normal DNA.

Further analyses included transcriptome sequencing of 71 of the original samples plus 10 others, and Affymetrix SNP analysis of 103 of the original samples plus 39 others.

Whole genome or exome sequences were also obtained from eight samples from mouse models of this tumour.

The overall mutation rate was found to be high in these tumours at an average of 8.62 non-synonymous mutations per million base pairs.

There was a high proportion of C:G>A:T transversions, which is known to be a characteristic of tumours induced by smoking.

An analysis of the genetic heterogeneity of the tumours showed that cells in these tumours were much less diverse than those in the commonest type of lung cancer, lung adenocarcinoma, and that their genetic heterogeneity did not correlate with clinical stage.

The tumour suppressor genes TP53 and RB1 were found to be mutated in almost all the SCLC tumours, confirming previous findings in both human tumours and mouse models.

Other genes mutated in a significant proportion of all tumours included KIAA1211, COL22A1, RGS7 and FPR1: the last named two of these are involved in G-protein coupled receptor signalling.

Clustered mutations and recurrent inactivations were observed in two histone acetyltransferase genes, CREBBP and EP300; in genes that function in the centrosome; in the TP53 homologue TP73; and in NOTCH family genes.

Finally, frequent mutations and translocations were observed in several tumour suppressor genes that have already been implicated in murine SCLC, PTEN, RBL1 and RBL2, and in genes that have been successfully targeted by drugs in other tumour types such as BRAF

Mutations in CREBBP, EP300, TP73, RBL1, RBL2 and genes in the NOTCH family were found to be mutually exclusive, suggesting that they may play a similar role in tumour development.

Interestingly, all but two of the 110 SCLC samples had inactivating mutations in both RB1 and TP53.

The other two samples showed signs of chromothripsis, a ‘catastrophic’ event in which many chromosomal rearrangements occur in a localised region of the genome.

In both these cases, chromothripsis led to an over-expression of cyclin D1, which is a negative regulator of RB1: this provides an alternative mechanism for RB1 inactivation and further suggests that loss of both RB1 and TP53 expression is an obligatory step in the development of SCLC.

Genomic rearrangements were found to cluster in several points on the genome, including the TP73 locus on chromosome 1.

Some of these rearrangements led to the loss of either exon 2 or exons 2 and 3 of this gene; these shortened variants of TP73 have been observed in other tumour types and their protein products are known to be oncogenic.

All tumours shared a pattern of high expression of neuroendocrine marker genes, and in most cases this was associated with low expression of genes in the Notch signalling pathway.

It has previously been proposed that activation of the Notch pathway can restrict the growth of tumours that express neuroendocrine markers.

The researchers tested this hypothesis in a tumourigenic mouse model in which the genes Trp53, Rb1 and Rbl2 had been knocked out, and found that Notch activation significantly reduced the number of tumours the mice developed and increased their survival.

In summary, this first comprehensive genomic study of SCLC tumours has revealed a number of genes and pathways that might be effective targets for drug development against this aggressive tumour type.

Reference

George. J., Lim, J.S., Jang, S.J. and 97 others (2015). Comprehensive genomic profiles of small cell lung cancer. Nature, published online ahead of print 13 July 2015.