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TP53 loss creates therapeutic vulnerability in colorectal cancer

2015-04-22 00:01:46

Nature; 22 April 2015; DOI: doi:10.1038/nature14418



Yunhua Liu, Xinna Zhang, Cecil Han, Guohui Wan, Xingxu Huang, Cristina Ivan, Dahai Jiang, Cristian Rodriguez-Aguayo, Gabriel Lopez-Berestein, Pulivarthi H. Rao, Dipen M. Maru, Andreas Pahl, Xiaoming He, Anil K. Sood, Lee M. Ellis, Jan Anderl, Xiongbin Lu



Abstract



TP53, a well-known tumour suppressor gene that encodes p53, is frequently inactivated by mutation or deletion in most human tumours. A tremendous effort has been made to restore p53 activity in cancer therapies. However, no effective p53-based therapy has been successfully translated into clinical cancer treatment owing to the complexity of p53 signalling. Here we demonstrate that genomic deletion of TP53 frequently encompasses essential neighbouring genes, rendering cancer cells with hemizygous TP53 deletion vulnerable to further suppression of such genes. POLR2A is identified as such a gene that is almost always co-deleted with TP53 in human cancers. It encodes the largest and catalytic subunit of the RNA polymerase II complex, which is specifically inhibited by α-amanitin. Our analysis of The Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE) databases reveals that POLR2A expression levels are tightly correlated with its gene copy numbers in human colorectal cancer. Suppression of POLR2A with α-amanitin or small interfering RNAs selectively inhibits the proliferation, survival and tumorigenic potential of colorectal cancer cells with hemizygous TP53 loss in a p53-independent manner. Previous clinical applications of α-amanitin have been limited owing to its liver toxicity. However, we found that α-amanitin-based antibody–drug conjugates are highly effective therapeutic agents with reduced toxicity. Here we show that low doses of α-amanitin-conjugated anti-epithelial cell adhesion molecule (EpCAM) antibody lead to complete tumour regression in mouse models of human colorectal cancer with hemizygous deletion of POLR2A. We anticipate that inhibiting POLR2A will be a new therapeutic approach for human cancers containing such common genomic alterations.



INTRODUCTION



Genomic deletion of a tumour suppressor gene often encompasses several neighbouring genes that may not contribute to cancer development, but are essential for cell proliferation and survival. This partial loss of essential genes has been postulated to render cancer cells highly vulnerable to further inhibition of those genes. Analysis of TCGA revealed that hemizygous deletion of the TP53 gene occurs frequently in human cancers. We identified POLR2A as an essential gene in the proximity of TP53. Concomitant deletion of POLR2A occurs in virtually all the human colorectal tumours containing hemizygous TP53 deletion.



Among the 12 subunits in the human RNA polymerase II complex, POLR2A encodes the largest subunit that is indispensable for the polymerase activity in messenger RNA synthesis. Inhibiting POLR2A with a specific inhibitor, α-amanitin, causes extensive cell death, and homozygous deletion of POLR2A is lethal in human cells. We found that 104 (53%) out of 195 colorectal cancer (CRC) cases bear hemizygous loss of the 17p13 region, resulting in concomitant deletion of TP53 and POLR2A. However, no homozygous deletion of POLR2A was observed, consistent with the notion that POLR2A is essential for cell survival. Analysis of TCGA and CCLE databases revealed that expression of POLR2A is tightly correlated with its gene copy number. This positive correlation was also validated in 20 pairs of matched normal and CRC tissue samples and human CRC tissue microarray. POLR2A loss (hemizygous loss) cell lines expressed POLR2A proteins at significantly lower levels than POLR2A neutral cell lines. Unlike POLR2A, p53 levels are determined by post-transcriptional and post-translational events. Despite a correlation between TP53 copy number and mRNA expression, p53 protein levels are not associated with its gene copy numbers in human CRC.



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