多聚甲醛(PFA)固定是保留组织结构以进行解剖和病理观察的首选方法。同时,PFA与生物分子的胺基反应形成化学交联,将RNA保存在组织内。这对于在解剖和病理观察后表征分子基础的RNA测序具有很大的前景。然而,由于在延长的PFA固定的组织中RNA和其他生物分子之间形成交联的加合物,RNA是不可接近的。它也很难进行逆转录和PCR,导致低测序灵敏度和再现性降低。这里,我们开发了一种在PFA固定的组织中进行RNA测序的方法,这是易于使用,成本效益高,并允许有效的样品复用。我们使用交联逆转来回收RNA和使用随机引物的文库构建,而没有人工片段化。通过我们的方法,回收的RNA的产量和质量显着提高,与匹配的新鲜样品相比,测序质量指标和检测到的基因没有显示任何重大差异。此外,我们将我们的方法应用于小鼠大脑不同区域的基因表达分析,并确定了具有不同功能含义的独特基因表达谱。我们还发现,在5×FAD小鼠大脑的内侧隔膜(MS)/Broca(VDB)的垂直对角线带内,参与阿尔茨海默病(AD)发病机理的基因明显失调。因此,我们的方法可以提高PFA固定样品的高通量RNA测序的性能,并允许通过原位环境分离的小组织区域的纵向研究。
Paraformaldehyde (PFA) fixation is the preferred method for preserving tissue architecture for anatomical and pathological observations. Meanwhile, PFA reacts with the amine groups of biomolecules to form chemical cross-linking, which preserves
RNA within the tissue. This has great prospects for
RNA sequencing to characterize the molecular underpinnings after anatomical and pathological observations. However,
RNA is inaccessible due to cross-linked adducts forming between
RNA and other biomolecules in prolonged PFA-fixed tissue. It is also difficult to perform reverse transcription and PCR, resulting in low sequencing sensitivity and reduced reproducibility. Here, we developed a method to perform RNA sequencing in PFA-fixed tissue, which is easy to use, cost-effective, and allows efficient sample multiplexing. We employ cross-link reversal to recover RNA and library construction using random primers without artificial fragmentation. The yield and quality of recovered
RNA significantly increased through our method, and sequencing quality metrics and detected genes did not show any major differences compared with matched fresh samples. Moreover, we applied our method for gene expression analysis in different regions of the mouse brain and identified unique gene expression profiles with varied functional implications. We also find significant dysregulation of genes involved in Alzheimer\'s disease (AD) pathogenesis within the medial septum (MS)/vertical diagonal band of Broca (VDB) of the 5×FAD mouse brain. Our method can thus increase the performance of high-throughput
RNA sequencing with PFA-fixed samples and allows longitudinal studies of small tissue regions isolated by their in situ context.