Schizophrenia Research Institute, Sydney, Australia.
PLoS One. 2012;7(4):e36351. doi: 10.1371/journal.pone.0036351. Epub 2012 Apr 27.
While hybridization based analysis of the cortical transcriptome has provided important insight into the neuropathology of schizophrenia, it represents a restricted view of disease-associated gene activity based on predetermined probes. By contrast, sequencing technology can provide un-biased analysis of transcription at nucleotide resolution. Here we use this approach to investigate schizophrenia-associated cortical gene expression.
METHODOLOGY/PRINCIPAL FINDINGS: The data was generated from 76 bp reads of RNA-Seq, aligned to the reference genome and assembled into transcripts for quantification of exons, splice variants and alternative promoters in postmortem superior temporal gyrus (STG/BA22) from 9 male subjects with schizophrenia and 9 matched non-psychiatric controls. Differentially expressed genes were then subjected to further sequence and functional group analysis. The output, amounting to more than 38 Gb of sequence, revealed significant alteration of gene expression including many previously shown to be associated with schizophrenia. Gene ontology enrichment analysis followed by functional map construction identified three functional clusters highly relevant to schizophrenia including neurotransmission related functions, synaptic vesicle trafficking, and neural development. Significantly, more than 2000 genes displayed schizophrenia-associated alternative promoter usage and more than 1000 genes showed differential splicing (FDR<0.05). Both types of transcriptional isoforms were exemplified by reads aligned to the neurodevelopmentally significant doublecortin-like kinase 1 (DCLK1) gene.
This study provided the first deep and un-biased analysis of schizophrenia-associated transcriptional diversity within the STG, and revealed variants with important implications for the complex pathophysiology of schizophrenia.
虽然基于杂交的皮质转录组分析为精神分裂症的神经病理学提供了重要的见解，但它代表了基于预定探针的疾病相关基因活性的有限观点。相比之下，测序技术可以提供核苷酸分辨率转录的无偏分析。在这里，我们使用这种方法来研究与精神分裂症相关的皮质基因表达。
方法/主要发现：该数据是从 RNA-Seq 的 76 个碱基对读取中生成的，与参考基因组对齐，并组装成转录本，以定量死后颞上回（STG/BA22）中的外显子、剪接变体和替代启动子，来自 9 名男性精神分裂症患者和 9 名匹配的非精神病对照。然后对差异表达的基因进行进一步的序列和功能群分析。输出量超过 380 亿个碱基对，显示出明显的基因表达改变，包括许多先前与精神分裂症相关的基因。随后进行了基因本体富集分析，接着构建了功能图谱，确定了三个与精神分裂症高度相关的功能簇，包括神经递质相关功能、突触小泡转运和神经发育。重要的是，超过 2000 个基因显示出与精神分裂症相关的替代启动子使用，超过 1000 个基因显示出差异剪接（FDR<0.05）。这两种转录异构体都以对齐到神经发育意义重大的双皮质素样激酶 1（DCLK1）基因的读取为例。
本研究首次对 STG 中与精神分裂症相关的转录多样性进行了深入和无偏的分析，并揭示了对精神分裂症复杂病理生理学具有重要意义的变体。
