Hu Wen, Foord Careen, Hsu Justine, Fan Li, Corley Michael J, Bhatia Tarun N, Xu Siwei, Belchikov Natan, He Yi, Pang Alina Ps, Lanjewar Samantha N, Jarroux Julien, Joglekar Anoushka, Milner Teresa A, Ndhlovu Lishomwa C, Zhang Jing, Butelman Eduardo, Sloan Steven A, Lee Virginia My, Gan Li, Tilgner Hagen U
Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
Center for Neurogenetics, Weill Cornell Medicine, New York, NY, USA.
bioRxiv. 2024 Feb 28:2024.02.24.581897. doi: 10.1101/2024.02.24.581897.
Multimodal measurements have become widespread in genomics, however measuring open chromatin accessibility and splicing simultaneously in frozen brain tissues remains unconquered. Hence, we devised Single-Cell-ISOform-RNA sequencing coupled with the Assay-for-Transposase-Accessible-Chromatin (ScISOr-ATAC). We utilized ScISOr-ATAC to assess whether chromatin and splicing alterations in the brain convergently affect the same cell types or divergently different ones. We applied ScISOr-ATAC to three major conditions: comparing (i) the Rhesus macaque () prefrontal cortex (PFC) and visual cortex (VIS), (ii) cross species divergence of Rhesus macaque versus human PFC, as well as (iii) dysregulation in Alzheimer's disease in human PFC. We found that among cortical-layer biased excitatory neuron subtypes, splicing is highly brain-region specific for L3-5/L6 IT_ neurons, moderately specific in L2-3 IT_ neurons and unspecific in L2-3 IT_ neurons. In contrast, at the chromatin level, L2-3 IT_ neurons show the highest brain-region specificity compared to other subtypes. Likewise, when comparing human and macaque PFC, strong evolutionary divergence on one molecular modality does not necessarily imply strong such divergence on another molecular level in the same cell type. Finally, in Alzheimer's disease, oligodendrocytes show convergently high dysregulation in both chromatin and splicing. However, chromatin and splicing dysregulation most strongly affect distinct oligodendrocyte subtypes. Overall, these results indicate that chromatin and splicing can show convergent or divergent results depending on the performed comparison, justifying the need for their concurrent measurement to investigate complex systems. Taken together, ScISOr-ATAC allows for the characterization of single-cell splicing and chromatin patterns and the comparison of sample groups in frozen brain samples.
多模态测量在基因组学中已广泛应用，然而，在冷冻脑组织中同时测量开放染色质可及性和剪接情况仍未实现。因此，我们设计了结合转座酶可及染色质分析的单细胞异构体RNA测序（ScISOr-ATAC）。我们利用ScISOr-ATAC评估大脑中的染色质和剪接改变是趋同影响相同细胞类型还是趋异影响不同细胞类型。我们将ScISOr-ATAC应用于三种主要情况：比较（i）恒河猴（）前额叶皮层（PFC）和视觉皮层（VIS），（ii）恒河猴与人类PFC的跨物种差异，以及（iii）人类PFC中阿尔茨海默病的失调情况。我们发现，在皮层层偏向性兴奋性神经元亚型中，剪接对L3-5/L6 IT_神经元具有高度脑区特异性，对L2-3 IT_神经元具有中等特异性，而对L2-3 IT_神经元则无特异性。相比之下，在染色质水平上，与其他亚型相比，L2-3 IT_神经元表现出最高的脑区特异性。同样，在比较人类和猕猴的PFC时，一种分子模式上的强烈进化差异并不一定意味着同一细胞类型在另一个分子水平上也有强烈差异。最后，在阿尔茨海默病中，少突胶质细胞在染色质和剪接方面均表现出趋同的高度失调。然而，染色质和剪接失调对不同的少突胶质细胞亚型影响最为强烈。总体而言，这些结果表明，根据所进行的比较，染色质和剪接可能显示趋同或趋异的结果，这证明了同时测量它们以研究复杂系统的必要性。综上所述，ScISOr-ATAC能够表征冷冻脑样本中的单细胞剪接和染色质模式，并对样本组进行比较。
