A pan-cancer atlas of cancer hallmark-associated candidate driver lncRNAs.
A pan-cancer atlas of cancer hallmark-associated candidate driver lncRNAs.
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DOI：
10.1002/1878-0261.12381
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发表时间：
2018-11
影响因子：
6.6
通讯作者：
Li X
中科院分区：
文献类型：
--
作者：
Deng Y;Luo S;Zhang X;Zou C;Yuan H;Liao G;Xu L;Deng C;Lan Y;Zhao T;Gao X;Xiao Y;Li X
大量的癌症基因组测序工作已经发现了许多有助于肿瘤发生的重要驱动基因。然而，人们对癌症中长链非编码RNA（lncRNA）的遗传改变知之甚少。因此，需要系统地调查驱动lncRNA。通过对11种癌症类型的5918种肿瘤的综合分析，我们发现lncRNA发生了显着的基因组改变，其中许多与已知的癌症基因相互排斥。使用互斥的功能冗余假设，我们开发了一个计算框架来识别与不同癌症标志相关的驱动lncRNA。将其应用于泛癌症数据，我们确定了378个候选驱动lncRNA，其基因组特征与已知的癌症驱动基因高度相似（例如高度保守和早期复制）。我们进一步验证了参与肺腺癌和乳腺癌中“组织侵袭和转移”的候选驱动lncRNA，并强调了它们在改善临床结果中的潜在作用。总之，我们已经生成了癌症候选驱动lncRNA的全面景观，可以作为未来功能探索的起点，以及生物标志物和基于lncRNA的靶向治疗的鉴定。
Substantial cancer genome sequencing efforts have discovered many important driver genes contributing to tumorigenesis. However, very little is known about the genetic alterations of long non‐coding RNAs (lncRNAs) in cancer. Thus, there is a need for systematic surveys of driver lncRNAs. Through integrative analysis of 5918 tumors across 11 cancer types, we revealed that lncRNAs have undergone dramatic genomic alterations, many of which are mutually exclusive with well‐known cancer genes. Using the hypothesis of functional redundancy of mutual exclusivity, we developed a computational framework to identify driver lncRNAs associated with different cancer hallmarks. Applying it to pan‐cancer data, we identified 378 candidate driver lncRNAs whose genomic features highly resemble the known cancer driver genes (e.g. high conservation and early replication). We further validated the candidate driver lncRNAs involved in ‘Tissue Invasion and Metastasis’ in lung adenocarcinoma and breast cancer, and also highlighted their potential roles in improving clinical outcomes. In summary, we have generated a comprehensive landscape of cancer candidate driver lncRNAs that could act as a starting point for future functional explorations, as well as the identification of biomarkers and lncRNA‐based target therapy.
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影响因子：
7.3
作者：
Gao J;Aksoy BA;Dogrusoz U;Dresdner G;Gross B;Sumer SO;Sun Y;Jacobsen A;Sinha R;Larsson E;Cerami E;Sander C;Schultz N
通讯作者：
Schultz N
DOI：
10.1038/nrc1299
发表时间：
2004-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
通讯作者：
--
影响因子：
50.3
作者：
Dolma S;Selvadurai HJ;Lan X;Lee L;Kushida M;Voisin V;Whetstone H;So M;Aviv T;Park N;Zhu X;Xu C;Head R;Rowland KJ;Bernstein M;Clarke ID;Bader G;Harrington L;Brumell JH;Tyers M;Dirks PB
通讯作者：
Dirks PB
影响因子：
8
作者：
Benaud, CM;Dickson, RB
通讯作者：
Dickson, RB
影响因子：
16.6
作者：
Alvarez S;Díaz M;Flach J;Rodriguez-Acebes S;López-Contreras AJ;Martínez D;Cañamero M;Fernández-Capetillo O;Isern J;Passegué E;Méndez J
通讯作者：
Méndez J