Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart. Spatial transcriptomics reveals expression of novel genes during the remodelling of the embryonic human heart

Congenital heart defects are very common, with around 2% of the population having a valve anomaly. During development of the heart, and specifically the heart valves, cells change from distinct undifferentiated populations of progenitors into specialized cells organized with precise spatial locations within complex tissue structures. Knowledge of both the spatial location and the transcriptional profile of the progenitors and differentiated cells is necessary to understand the differentiation process and the formation of the complex 3-dimensional architecture of the valves. Disruption to these processes leads to congenital valve defects and these are associated with significant morbidity (valve disease is the most common cause of cardiac surgery in the over-50s), particularly during aging. Here we utilized a spatial transcriptomic approach (Stahl et al, 2016; DeLaughter et al, 2016; Vickovic et al, 2019) to derive data about gene expression in the arterial valves of the human embryo, during the sculpting phases of their development. We identified a number of genes that have not been previously linked to valve development and are strongly expressed in the remodelling valve leaflets. Examination of the mouse model for one of these, RBP1, shows previously undescribed defects in the great arteries and valve anomalies in mutant animals, highlighting that these genes are good candidate genes for causing BAV. Thus, we have developed new methodologies for ST data analysis and show that they have the ability to identify previously unknown developmentally important genes. ST is thus an exciting tool for novel gene discovery in the developing human embryo. Overall design: Spatial transcriptomics of 2 embryonic human hearts. Consecutive tissue sections were taken from each sample CS19 (5 sections) and CS16 (4 sections) CS = Carnegie stage.

先天性心脏缺损（Congenital heart defects）极为常见，约2%的人群存在瓣膜异常。在心脏发育进程中，尤其是心脏瓣膜的发育阶段，细胞会从特征鲜明的未分化祖细胞群体，转化为在复杂组织结构中具备精准空间定位的特化细胞。要充分理解瓣膜的分化过程及其复杂三维结构的形成机制，必须同时掌握祖细胞与分化细胞的空间位置信息与转录组特征。上述发育过程的紊乱会引发先天性瓣膜缺损，此类病变可造成显著的发病负担——瓣膜疾病是50岁以上人群心脏手术的最常见病因，且该发病风险随衰老过程进一步加剧。本研究采用空间转录组学（Spatial Transcriptomics）方法（Stahl等，2016；DeLaughter等，2016；Vickovic等，2019），获取人类胚胎动脉瓣膜在发育塑形阶段的基因表达数据。我们鉴定出多个此前未被关联至瓣膜发育过程、且在正在重塑的瓣膜瓣叶中显著高表达的基因。我们对其中一个名为RBP1的基因的小鼠模型开展验证分析，发现突变小鼠存在此前未被报道的大动脉发育异常与瓣膜畸形，提示此类基因是引发BAV的潜在致病候选基因。据此，本研究开发了全新的空间转录组学数据分析方法，并证实其可用于识别此前未知的发育相关重要功能基因。由此可见，空间转录组学是开展人类胚胎发育过程中新型功能基因发现研究的极具潜力的技术工具。总体实验设计：对2例人类胚胎心脏开展空间转录组学测序。每份样本均采集连续组织切片：CS19（卡内基分期19）样本取5张切片，CS16（卡内基分期16）样本取4张切片，其中CS即卡内基分期（Carnegie stage）。