In:
Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 109, No. 5 ( 2012-01-31)
Abstract:
Pancreatic cancer is the fourth most deadly cancer in the United States. The 5-y survival rate remains less than 5%, highlighting the inadequacy of current therapies. A better molecular understanding of the disease will aid in the development of novel diagnostic methods and clinical therapies. Using modern-day genetics, we redefine an old complex as a mutational mountain in pancreatic cancer. This is a transformative finding with significant implications in the future fight against this deadly disease. To gain additional insight into the mechanisms behind this tumor suppression, we profile SWI/SNF-associated gene expression changes. To do this, we use a method called RNAi to specifically block, or “knock down,” the production of specific SWI/SNF subunits in pancreatic cells. Given that we find inactivating alterations in multiple components of SWI/SNF, we sought to identify the gene expression changes shared by knockdown of the different subunits. From these studies, we conclude that SWI/SNF appears to oppose down-regulation (or reduced expression) of genes caused by a different protein complex known as polycomb repressive complex 2 (PRC2). This is consistent with the findings of previous studies that the SWI/SNF and PRC2 complexes are antagonistic. This result is notable because emerging evidence suggests that overactivation of PRC2 contributes to the development of cancer (as does inactivation of SWI/SNF). The recurrent structural alterations in SWI/SNF subunits imply that the complex plays a tumor-suppressive role in pancreatic cancer. We functionally validate such a role through “add back” experiments of SMARCA4, one of the SWI/SNF ATP-using subunits. In other words, we re-express SMARCA4 in SMARCA4-deficient pancreatic cancer cells, which leads to tumor-suppressive traits, including reduced cell growth, and to cellular senescence (irreversible growth arrest) in some cases. On the other hand, the overexpression of SMARCA4 in a SWI/SNF-intact cell line has no discernible growth effects. We report here recurrent genetic changes (including deletions, rearrangements, and mutations) in five different components of SWI/SNF in pancreatic cancer: ARID1A, ARID1B, PBRM1, SMARCA4, and SMARCA2. These structural alterations target specific biochemical subunits of the complex, including both those thought to contact DNA and those that use ATP for energy to reorganize chromatin. Each individual subunit is altered by the genetic changes in 3–10% of pancreatic cancers. Cumulatively, however, SWI/SNF subunits are altered in 34% of tumors ( Fig. P1 ), making it the fourth most commonly altered tumor suppressor in pancreatic cancer, following CDKN2A (90%), SMAD4 (55%), and TP53 (50%). Thus, borrowing a metaphor from the cancer geneticist Bert Vogelstein and his colleagues ( 5 ), we have identified mutational “hills” that collectively represent a mutational “mountain” in pancreatic cancer. The field of genomics, a subdiscipline of genetics, has transformed substantially since 1984, especially in the past decade, with the advent of novel technologies for analyzing DNA (including DNA microarrays and high-throughput DNA sequencing). Some of the techniques used in this study are array-based comparative genomic hybridization to enumerate DNA copy number changes (a common source of genetic change and mutation), expression profiling to quantify levels of mRNA (an intermediary in the reading of genes to produce proteins), and high-throughput sequencing of mRNAs to discover novel (and aberrant) transcripts (mRNA sequences derived from genes). Applying these modern genomic techniques to profile human pancreatic cancers, we discover genetic hits converging on the SWI/SNF complex. In 1984, two seminal studies independently identified five genes crucial for several functions in yeast. These genes were found using genetic screens, studies that link specific genes to certain traits ( 1 , 2 ). Although these genes performed very different functions, biochemical and genetic studies revealed that they all encoded subunits of the same complex, later named SWItch/Sucrose NonFermentable (SWI/SNF) ( 3 , 4 ). Subsequent studies revealed SWI/SNF to be a so-called “chromatin remodeler,” functioning to reorganize chromatin (the protein-DNA structure that packs DNA into the nucleus) so as to control the expression of genes, and that it is conserved in humans. Using modern DNA analysis technology, we now link aberrant SWI/SNF complexes to human pancreatic cancer.
Type of Medium:
Online Resource
ISSN:
0027-8424
,
1091-6490
DOI:
10.1073/pnas.1114817109
Language:
English
Publisher:
Proceedings of the National Academy of Sciences
Publication Date:
2012
detail.hit.zdb_id:
209104-5
detail.hit.zdb_id:
1461794-8
SSG:
11
SSG:
12
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