Integrative genomic and functional profiling of the pancreatic cancer genome.
Integrative genomic and functional profiling of the pancreatic cancer genome.
复制标题
胰腺癌基因组的综合基因组和功能分析。
DOI：
10.1186/1471-2164-14-624
复制
发表时间：
2013-09-16
期刊：
影响因子：
4.4
通讯作者：
Pollack JR
中科院分区：
文献类型：
--
作者：
Shain AH;Salari K;Giacomini CP;Pollack JR
胰腺癌是一种致命的疾病，五年生存率不到5%。对潜在生物学的更好理解可能会提出新的治疗靶点。最近对胰腺癌基因组的调查发现了许多新的改变，但候选癌症基因的系统功能表征却落后了。为了应对这一挑战，我们设计了一种高度平行的基于RNA干扰的功能性筛选，以同时评估许多基因组学提名的候选胰腺癌基因。对于从反复改变的基因组位点中选择的185个候选胰腺癌基因，我们在10个不同的细胞系中进行了细胞生长/活力的合并shRNA文库筛选。通过富集或耗尽shRNA发夹，通过与条形码微阵列杂交来评估敲减相关的细胞生长效应。基于鉴定靶向相同基因的不同shRNA并在细胞系中显示一致的表型，使用一种新的分析方法（COr相关的靶向效应表型; COPOTE）来辨别可能的靶向敲减。敲除数据与基因组结构和基因表达谱相结合，并使用单个shRNA和/或独立的SiRNA验证选定的发现。合并的shRNA文库设计提供了可重复的数据。总的来说，COPOTE分析确定了52个可能的靶基因敲除。已知癌基因（KRAS、MYC、SMURF 1和CCNE 1）和肿瘤抑制基因（CDKN 2A）的敲除显示出对细胞生长的预期对比效应。此外，筛选证实了PLEKHG 2和MED 29作为19 q13扩增子驱动因子的假定作用。最值得注意的是，该分析还揭示了核孔蛋白NUP 153（表面上通过调节TGFβ信号传导）和Kruppel样转录因子KLF 5在胰腺癌中的新的可能致癌功能。通过整合物理和功能基因组数据，我们能够同时评估许多候选胰腺癌基因。我们的发现揭示了胰腺癌生物学的新方面，可能具有治疗意义。更广泛地说，我们的研究为癌症基因组研究中出现的候选基因的有效表征提供了一种通用策略。
Pancreatic cancer is a deadly disease with a five-year survival of less than 5%. A better understanding of the underlying biology may suggest novel therapeutic targets. Recent surveys of the pancreatic cancer genome have uncovered numerous new alterations; yet systematic functional characterization of candidate cancer genes has lagged behind. To address this challenge, here we have devised a highly-parallel RNA interference-based functional screen to evaluate many genomically-nominated candidate pancreatic cancer genes simultaneously. For 185 candidate pancreatic cancer genes, selected from recurrently altered genomic loci, we performed a pooled shRNA library screen of cell growth/viability across 10 different cell lines. Knockdown-associated effects on cell growth were assessed by enrichment or depletion of shRNA hairpins, by hybridization to barcode microarrays. A novel analytical approach (COrrelated Phenotypes for On-Target Effects; COPOTE) was used to discern probable on-target knockdown, based on identifying different shRNAs targeting the same gene and displaying concordant phenotypes across cell lines. Knockdown data were integrated with genomic architecture and gene-expression profiles, and selected findings validated using individual shRNAs and/or independent siRNAs. The pooled shRNA library design delivered reproducible data. In all, COPOTE analysis identified 52 probable on-target gene-knockdowns. Knockdown of known oncogenes (KRAS, MYC, SMURF1 and CCNE1) and a tumor suppressor (CDKN2A) showed the expected contrasting effects on cell growth. In addition, the screen corroborated purported roles of PLEKHG2 and MED29 as 19q13 amplicon drivers. Most notably, the analysis also revealed novel possible oncogenic functions of nucleoporin NUP153 (ostensibly by modulating TGFβ signaling) and Kruppel-like transcription factor KLF5 in pancreatic cancer. By integrating physical and functional genomic data, we were able to simultaneously evaluate many candidate pancreatic cancer genes. Our findings uncover new facets of pancreatic cancer biology, with possible therapeutic implications. More broadly, our study provides a general strategy for the efficient characterization of candidate genes emerging from cancer genome studies.
登录
查看更多内容
影响因子：
254.7
作者：
Jemal, Ahmedin;Siegel, Rebecca;Thun, Michael J.
通讯作者：
Thun, Michael J.
影响因子：
3.5
作者：
Moore, PS;Sipos, B;Scarpa, A
通讯作者：
Scarpa, A
影响因子：
56.9
作者：
Jain, M;Arvanitis, C;Felsher, DW
通讯作者：
Felsher, DW
影响因子：
8
作者：
Nandan, MO;Yoon, HS;Yang, VW
通讯作者：
Yang, VW
影响因子：
11.2
作者：
Kuuselo, Riina;Savinainen, Kimmo;Kallioniemi, Anne
通讯作者：
Kallioniemi, Anne