Characterizing the developing human brain transcriptome at single-base resolution

以单碱基分辨率表征发育中的人脑转录组

• 批准号: 9264591
• 负责人: Andrew Ellis Jaffe
• 金额: $ 27.39万
• 依托单位: LIEBER INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-05-01 至 2019-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9264591
• 关键词: Age; Aging; Alzheimer' s Disease; Autopsy; Big Data; Brain; Brain Diseases; Brain region; Cell Line; Clinical; Code; Computer software; Conserved Sequence; DNA Methylation; Data; Data Analyses; Data Set; Databases; Dependence; Development; Developmental Process; Dissection; Epigenetic Process; First Pregnancy Trimester; Gene Expression; Genes; Genetic Risk; Genetic Transcription; Genome; Genomic Segment; Genomics; Genotype; Goals; Human; Institutes; Life; Longevity; Major Depressive Disorder; Measurement; Medical Genetics; Mental disorders; Methods; Microarray Analysis; Mus; Parkinson Disease; Pattern; Pilot Projects; Play; Process; RNA; RNA analysis; Regulation; Research Personnel; Resolution; Resources; Risk; Role; Sampling; Schizophrenia; Scientist; Signal Transduction; Specificity; Technology; Testing; Transcript; Validation; aged; analytical tool; base; brain tissue; clinical risk; clinically relevant; clinically significant; design; differential expression; experimental study; fetal; frontal lobe; genome wide association study; genome-wide; genomic tools; improved; insight; interest; novel; public health relevance; risk variant; secondary analysis; tool; trait; transcriptome; transcriptome sequencing

 DESCRIPTION (provided by applicant): Human post-mortem brain tissue provides a valuable resource for identifying expression-based determinants of development and subsequent dysregulation in brain disorders (Kleinman 2011). RNA sequencing (RNA-seq) generates potentially unbiased characterization of the transcriptome, and has now been performed on over 1,000 non-psychiatric human brain samples across the lifespan within our lab (LIBD) and via the BrainSpan project (www.brainspan.org). We propose to combine and re-process these data together to make them more comparable, starting from raw sequencing reads. Our goal is further interrogate the clinical relevance of developmentally dynamic regions of gene expression across brain development. Our preliminary RNAseq data demonstrates extensive developmental regulation of previously unannotated intra- and inter-genic sequence conserved across multiple brain regions in both humans and mice. Base-level analysis of these combined RNA-seq data can greatly improve existing gene annotation databases like Ensembl and UCSC, which currently lack many fetal brain-specific transcripts that we have identified and characterized in our samples. We will perform base-level resolution analyses on both the entire dataset, from first trimester of fetal life through the aged (>85 years), and then secondary analyses exploring differential expression across different brain regions, to identify dynamic expressed sequence. Identified differentially expressed regions (DERs) will be interrogated for clinical significance through enrichment analysis with regard to predefined clinical gene sets, for examples significant loci from genome-wide association studies (GWAS) for brain disorders like schizophrenia, and also by directly associating genetic risk with expression levels within identified DERs. We will further provide the genomic tools to allow researchers with interests in other genes and loci to design their own validation experiments in cell lines and/or primary brain tissue for these clinically relevant loci. A more comprehensive characterization of the human brain transcriptome, leveraging "big data" across two complementary datasets, will be valuable for scientists studying a wide range of developmental processes and brain disorders.

 描述（由申请人提供）：人类死后脑组织为鉴定脑疾病中发育和随后失调的基于表达的决定因素提供了宝贵的资源（Kleinman 2011）。RNA测序（RNA-seq）可以对转录组进行潜在的无偏表征，现在已经在我们实验室（LIBD）和BrainSpan项目（www.brainspan.org）的整个生命周期内对1,000多个非精神病人类大脑样本进行了测序。我们建议从原始测序读数开始，将这些数据联合收割机并重新处理在一起，以使它们更具可比性。我们的目标是进一步询问大脑发育过程中基因表达的发育动态区域的临床相关性。 我们的初步RNAseq数据表明，在人类和小鼠的多个大脑区域中保守的先前未注释的基因内和基因间序列的广泛发育调节。对这些组合RNA-seq数据的碱基水平分析可以极大地改善现有的基因注释数据库，如Ensembl和UCSC，这些数据库目前缺乏我们在样本中鉴定和表征的许多胎儿脑特异性转录物。我们将对整个数据集进行基础水平分辨率分析，从胎儿生命的前三个月到老年人（>85岁），然后进行二次分析，探索不同脑区的差异表达，以确定动态表达序列。将通过关于预定义的临床基因集的富集分析来询问鉴定的差异表达区域（DER）的临床意义， 例如，从全基因组关联研究（GWAS）中获得的大脑疾病（如精神分裂症）的重要位点，以及将遗传风险与已鉴定的DER内的表达水平直接关联。我们将进一步提供基因组工具，以允许对其他基因和基因座感兴趣的研究人员在细胞系和/或原代脑组织中为这些临床相关基因座设计自己的验证实验。 利用两个互补数据集的“大数据”对人脑转录组进行更全面的表征，对于研究各种发育过程和大脑疾病的科学家来说将是有价值的。

项目成果

regionReport: Interactive reports for region-level and feature-level genomic analyses.

RegionReport：用于区域级和特征级基因组分析的交互式报告。

• DOI: 10.12688/f1000research.6379.2
• 发表时间: 2015
• 期刊: F1000Research
• 作者: Collado-Torres,Leonardo;Jaffe,AndrewE;Leek,JeffreyT
• 通讯作者: Leek,JeffreyT

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor.

• DOI: 10.12688/f1000research.12223.1
• 发表时间: 2017-01-01
• 期刊: F1000Research
• 作者: Collado-Torres, Leonardo;Nellore, Abhinav;Jaffe, Andrew E
• 通讯作者: Jaffe, Andrew E

Flexible expressed region analysis for RNA-seq with derfinder.

• DOI: 10.1093/nar/gkw852
• 发表时间: 2017-01-25
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Collado-Torres L;Nellore A;Frazee AC;Wilks C;Love MI;Langmead B;Irizarry RA;Leek JT;Jaffe AE
• 通讯作者: Jaffe AE