RNA sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery
RNA sequencing-based transcriptomic profiles of embryonic lens development for cataract gene discovery
复制标题
DOI：
10.1007/s00439-018-1958-0
复制
发表时间：
2018-12-01
期刊：
影响因子：
5.3
通讯作者：
Lachke, Salil A.
中科院分区：
文献类型：
--
作者：
Anand, Deepti;Kakrana, Atul;Lachke, Salil A.
孤立性或综合征性先天性白内障是异质性发育缺陷，使得相关基因的鉴定具有挑战性。过去，小鼠透镜表达微阵列已成功应用于生物信息学工具（例如，iSyTE），以促进人类白内障相关基因的发现。为了为遗传学家开发新的资源，我们报告了小鼠透镜在关键胚胎阶段（E）10.5（透镜陷窝）、E12.5（初级纤维细胞分化）、E14.5和E16.5（次级纤维细胞分化）的高通量RNA测序（RNA-seq）谱。当透镜从内陷基板发育成透明组织时，这些阶段捕获重要事件。以前，在计算机全胚胎体（WB）消减为基础的晶状体富集表达已有效地优先考虑白内障相关基因。为了应用类似的方法，我们生成了新的小鼠WB RNA-seq数据集，并表明透镜RNA-seq数据集的计算机WB减法成功地鉴定了基于透镜富集表达的关键基因。在>= 2次/百万表达时，>= 1.5 log（2）倍富集（p < 0.05）截止值，E10.5透镜表现出1401个富集基因E12.5透镜中有1937个富集基因E14.5透镜表现出2514个富集基因（31%透镜表达基因），而E16.5透镜表现出2745个富集基因（34%透镜表达基因）。生物学途径分析鉴定了与透镜发育、转录调节和信号传导途径以及其他功能组相关的基因。此外，这些新的RNA-seq数据证实了已建立的白内障相关基因的高表达，并确定了透镜中新的潜在调节因子。最后，我们开发了新的透镜阶段特异性UCSC基因组Brower注释轨迹，并通过iSyTE（https：//research.bioinformatics.udel.edu/iSyTE/）公开访问这些轨迹，以便于用户友好地可视化透镜基因表达/富集，从而对来自白内障病例的高通量数据的基因进行优先排序。
Isolated or syndromic congenital cataracts areheterogeneous developmental defects, making the identification of the associated genes challenging. In the past, mouse lens expression microarrays have been successfully applied in bioinformatics tools (e.g., iSyTE) to facilitate human cataract-associated gene discovery. To develop a new resource for geneticists, we report high-throughput RNA sequencing (RNA-seq) profiles of mouse lens at key embryonic stages (E)10.5 (lens pit), E12.5 (primary fiber cell differentiation), E14.5 and E16.5 (secondary fiber cell differentiation). These stages capture important events as the lens develops from an invaginating placode into a transparent tissue. Previously, in silico whole-embryo body (WB)-subtraction-based lens-enriched expression has been effective in prioritizing cataract-linked genes. To apply an analogous approach, we generated new mouse WB RNA-seq datasets and show that in silico WB subtraction of lens RNA-seq datasets successfully identifies key genes based on lens-enriched expression. At >= 2 counts-per-million expression, >= 1.5 log(2) fold-enrichment (p < 0.05) cutoff, E10.5 lens exhibits 1401 enriched genes (17% lens-expressed genes), E12.5 lens exhibits 1937 enriched genes (22% lens-expressed genes), E14.5 lens exhibits 2514 enriched genes (31% lens-expressed genes), and E16.5 lens exhibits 2745 enriched genes (34% lens-expressed genes). Biological pathway analysis identified genes associated with lens development, transcription regulation and signaling pathways, among other functional groups. Furthermore, these new RNA-seq data confirmed high expression of established cataract-linked genes and identified new potential regulators in the lens. Finally, we developed new lens stage-specific UCSC Genome Brower annotation tracks and made these publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/) for user-friendly visualization of lens gene expression/enrichment to prioritize genes from high-throughput data from cataract cases.