The Spatiotemporal Landscape of the Human Brain Epitranscriptome

人脑表观转录组的时空景观

• 批准号: 10378056
• 负责人: Christopher Edward Mason
• 金额: $ 64.94万
• 依托单位: WEILL MEDICAL COLL OF CORNELL UNIV
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-07-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10378056
• 关键词: ASD patient; Address; Adenosine; Adult; Affect; Alleles; Alternative Splicing; Atlases; Autopsy; Bioinformatics; Biological Assay; Brain; Brain Diseases; Brain region; CRISPR/Cas technology; Cells; Cerebellar Cortex; Chemicals; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Copy Number Polymorphism; Cytosine; DNA Methylation; DNA Modification Process; Data; Data Set; Development; Disease susceptibility; Environment; Epigenetic Process; Event; Female; Future; Gene Expression; Gene Expression Profile; Gene Expression Profiling; Genes; Genetic; Genetic Transcription; Genotype-Tissue Expression Project; Goals; High-Throughput Nucleotide Sequencing; Human; Human Activities; Institutes; Knock-out; Link; Maps; Mediating; Mental disorders; Modeling; Modification; Molecular; Neuroglia; Neurologic; Neurons; Patients; Prefrontal Cortex; Proteins; Quantitative Trait Loci; RNA; RNA Editing; RNA Splicing; RNA methylation; Reader; Regulation; Resources; Sampling; Site; Somatosensory Cortex; System; Temporal Lobe; Testing; Time; Tissue Banks; Tissues; Transcript; Translations; Untranslated RNA; Variant; Visualization; area striata; autism spectrum disorder; autistic; base; bisulfite sequencing; clinically relevant; data resource; epigenetic regulation; epigenome; epitranscriptome; follow-up; genome sequencing; induced pluripotent stem cell; inter-individual variation; male; methylome; nervous system disorder; neurodevelopment; neuropsychiatric disorder; postnatal; postnatal development; repository; response; risk variant; spatiotemporal; transcriptome; translational medicine; whole genome; work-study

ABSTRACT The human Brainspan data was created to identify all transcripts involved in neural development and to help understand of how specific risk genes affect human brain development. In addition, these data will have important clinical relevance for translational medicine; these data can help discern which risk alleles associated with psychiatric and neurological disorders influence transcription and alternative splicing across different regions and developmental stages. Also, most Brainspan samples were processing for whole-genome sequencing (WGS) and/or DNA methylation analysis, which enables direct comparisons of single basepair changes, copy number variation, and RNA editing events in the developing human brain. As such, Brainspan data holds biologically and clinically important data on the genetic and molecular mechanisms underlying the development and increased disease susceptibility of the human brain. To expand upon this resource, we aim to create a matched profile of the human brains RNA modification landscape (epitranscriptome), for both methyl-6-adenosine (m6A) and 5-methyl-cytosine (5mC). We will profile the developmental trajectory of the RNA modifications and their activity in non-coding regions and impact on splicing, RNA editing, AU-rich regulation of transcripts, and association with DNA methylation changes (epigenetics). Finally, we will also test the impact of these modifications from patient-derived iPS cells that will be grown and assayed over five time points. This will be accomplished over five years, and across 1,075 samples, across the Mason and Sestan labs, with collaborators at the Broad institute available to help with assays and access to GTEx data from adult brains with m6A profiles. We will achieve these goals across three main aims. (1) Create a neuro-developmental map for epitranscriptome sites and levels, with an emphasis on m6A and m5C, for 35 brains from four time periods, and five regions of the brain, chosen based on their large differences seen in the BrainSpan data and prior implication in neurological development. (2) Detail the inter-individual variation in epitranscriptome levels and their epigenetic regulation using m6A variation with the changes in expression levels, and then link epigenetic changes to altered gene expression and m6A regulation. (3) We will delineate the epitranscriptome changes in autism brains and manifestation in patient-derived iPS cells, including an examination of epitranscriptome variation across 30 banked Autistic brain samples and testing of the impact on disruption of the readers and writers of RNA regulation (on induced pluripotent stem cells). These will represent the first-ever epitranscriptome maps from primary tissue of Autism brains and help guide future studies that examine the dysregulation of Autism gene expression networks and epitranscriptome states.

抽象的 创建人类脑跨度数据是为了识别参与神经发育的所有转录本并 帮助了解特定风险基因如何影响人类大脑发育。此外，这些数据还会有 与转化医学具有重要的临床相关性；这些数据可以帮助识别哪些风险等位基因相关 精神和神经系统疾病影响转录和不同剪接 地区和发展阶段。此外，大多数 Brainspan 样本都经过全基因组处理 测序 (WGS) 和/或 DNA 甲基化分析，可直接比较单个碱基对 发育中的人类大脑中的变化、拷贝数变异和 RNA 编辑事件。因此，脑力 数据包含有关遗传和分子机制的生物学和临床重要数据 人类大脑的发育和疾病易感性增加。 为了扩展这一资源，我们的目标是创建人脑 RNA 的匹配图谱 甲基-6-腺苷 (m6A) 和 5-甲基-胞嘧啶 (5mC) 的修饰景观（外转录组）。 我们将描绘 RNA 修饰的发展轨迹及其在非编码区域的活性 以及对剪接、RNA 编辑、转录本富含 AU 调节以及与 DNA 甲基化关联的影响 变化（表观遗传学）。最后，我们还将测试来自患者的 iPS 细胞的这些修饰的影响 将在五个时间点进行生长和分析。这将在五年内完成 Mason 和 Sestan 实验室的 1,075 个样本，Broad 研究所的合作者可以提供帮助 进行分析并访问具有 m6A 配置文件的成人大脑的 GTEx 数据。 我们将通过三个主要目标来实现这些目标。 (1) 创建神经发育图 表观转录组位点和水平，重点是 m6A 和 m5C，来自四个时间段的 35 个大脑，以及 大脑的五个区域，根据 BrainSpan 数据和之前数据中的巨大差异进行选择 对神经发育的影响。 (2) 详细说明表观转录组水平的个体间差异和 他们利用m6A变异与表达水平的变化进行表观遗传调控，然后将表观遗传联系起来 改变基因表达和 m6A 调节。 (3) 我们将描述表观转录组的变化 自闭症大脑和患者来源的 iPS 细胞的表现，包括表观转录组检查 30 个储存的自闭症患者大脑样本的变化以及对读者干扰的影响测试 RNA 调控（诱导多能干细胞）的作者。这些将代表有史以来第一个 来自自闭症大脑原代组织的表观转录组图谱有助于指导未来的研究 自闭症基因表达网络和表观转录组状态的失调。

项目成果

Spatial omics technologies at multimodal and single cell/subcellular level.

• DOI: 10.1186/s13059-022-02824-6
• 发表时间: 2022-12-13
• 期刊: Genome biology
• 影响因子: 12.3

Circulating miRNA Spaceflight Signature Reveals Targets for Countermeasure Development.

• DOI: 10.1016/j.celrep.2020.108448
• 发表时间: 2020-12-08
• 期刊: Cell reports
• 影响因子: 8.8
• 作者: Malkani S;Chin CR;Cekanaviciute E;Mortreux M;Okinula H;Tarbier M;Schreurs AS;Shirazi-Fard Y;Tahimic CGT;Rodriguez DN;Sexton BS;Butler D;Verma A;Bezdan D;Durmaz C;MacKay M;Melnick A;Meydan C;Li S;Garrett-Bakelman F;Fromm B;Afshinnekoo E;Langhorst BW;Dimalanta ET;Cheng-Campbell M;Blaber E;Schisler JC;Vanderburg C;Friedländer MR;McDonald JT;Costes SV;Rutkove S;Grabham P;Mason CE;Beheshti A
• 通讯作者: Beheshti A

Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.

• DOI: 10.1186/s40793-023-00467-z
• 发表时间: 2023-03-30
• 期刊: Environmental microbiome
• 影响因子: 7.9

Haplotype diversity and sequence heterogeneity of human telomeres.

• DOI: 10.1101/gr.274639.120
• 发表时间: 2021-07
• 期刊: Genome research
• 影响因子: 7
• 作者: Grigorev K;Foox J;Bezdan D;Butler D;Luxton JJ;Reed J;McKenna MJ;Taylor L;George KA;Meydan C;Bailey SM;Mason CE
• 通讯作者: Mason CE

Fundamental Biological Features of Spaceflight: Advancing the Field to Enable Deep-Space Exploration.

• DOI: 10.1016/j.cell.2020.10.050
• 发表时间: 2020-11-25
• 期刊: Cell
• 影响因子: 64.5
• 作者: Afshinnekoo E;Scott RT;MacKay MJ;Pariset E;Cekanaviciute E;Barker R;Gilroy S;Hassane D;Smith SM;Zwart SR;Nelman-Gonzalez M;Crucian BE;Ponomarev SA;Orlov OI;Shiba D;Muratani M;Yamamoto M;Richards SE;Vaishampayan PA;Meydan C;Foox J;Myrrhe J;Istasse E;Singh N;Venkateswaran K;Keune JA;Ray HE;Basner M;Miller J;Vitaterna MH;Taylor DM;Wallace D;Rubins K;Bailey SM;Grabham P;Costes SV;Mason CE;Beheshti A
• 通讯作者: Beheshti A