A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution

The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in the regulation of many vital functions. Notable among them are the parabrachial nucleus, the Kolliker Fuse, the Barrington nucleus, the locus coeruleus, and the laterodorsal, ventral, and dorsal tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled ~1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed many neuronal subtypes' unique marker genes. We also demonstrated that many neuronal subtypes found in mice were transcriptionally similar to those found in humans, enhancing this study's translational value. Finally, we developed a freely-accessible, GPU-powered interactive dashboard to provide access to this spatially-resolved transcriptional dataset.“脑桥背侧”（dorsal pons）又称“脑桥被盖背侧区”（dorsal pontine tegmentum，缩写dPnTg），是脑干的组成部分。该区域结构复杂、细胞排布致密，其内核团参与调控多种关键生理功能。其中较为关键的核团包括臂旁核（parabrachial nucleus）、科利克-富塞核（Kolliker Fuse）、巴林顿核（Barrington nucleus）、蓝斑（locus coeruleus），以及背外侧被盖核、腹侧被盖核与背侧被盖核。本研究采用单细胞核RNA测序（single-nucleus RNA-seq，snRNA-seq），基于神经元独特的转录组特征解析其亚型；随后借助多重误差稳健荧光原位杂交（multiplexed error robust fluorescence in situ hybridization，MERFISH）完成神经元亚型的空间定位。研究团队对dPnTg区域内约100万个细胞进行了采样，明确了120余种神经元亚型的空间分布特征。分析结果揭示了该区域此前未被预见的高转录组多样性，并精准定位了多种神经元亚型的特异性标记基因。本研究还证实，小鼠体内的多种神经元亚型与人类对应亚型在转录组层面具有高度相似性，提升了本研究的转化应用价值。最后，团队开发了一款免费开放、基于图形处理器（Graphics Processing Unit，GPU）的交互式可视化仪表盘，以供研究者获取这套空间分辨转录组数据集。