Description of clusters in Differential Altas.

Osteoblasts, the key cells responsible for bone formation and the maintenance of skeletal integrity, originate from a diverse array of progenitor cells. However, the mechanisms underlying osteoblast differentiation from these multiple osteoprogenitors remain poorly understood. To address this knowledge gap, we developed a comprehensive framework to investigate osteoblast differentiation at multiple scales, encompassing cells, genes, and gene modules. We constructed a reference atlas focused on differentiation, which incorporates various osteoprogenitors and provides a seven-level cellular taxonomy. To reconstruct the differentiation process, we developed a model that identifies the transcription factors and pathways involved in differentiation from different osteoprogenitors. Acknowledging that covariates such as age and tissue type can influence differentiation, we created an algorithm to detect differentially expressed genes throughout the differentiation process. Additionally, we implemented methods to identify conserved pseudotemporal gene modules across multiple samples. Overall, our framework systematically addresses the heterogeneity observed during osteoblast differentiation from diverse sources, offering novel insights into the complexities of bone formation and serving as a valuable resource for understanding osteogenesis.

成骨细胞（Osteoblasts）是负责骨形成与维持骨骼完整性的关键细胞，其起源于多种不同的祖细胞。然而，从这些多种骨祖细胞（osteoprogenitors）分化为成骨细胞的潜在分子机制仍未得到充分阐明。为填补这一研究空白，我们构建了一套多尺度研究成骨细胞分化的综合性分析框架，研究范畴涵盖细胞、基因及基因模块（gene modules）三个层面。我们构建了聚焦于分化过程的参考图谱（reference atlas），该图谱纳入了多种骨祖细胞，并提供了七级细胞分类系统。为重构成骨细胞的分化进程，我们开发了一款模型，可识别不同骨祖细胞在分化过程中所涉及的转录因子（transcription factors）与信号通路（pathways）。考虑到年龄、组织类型等协变量（covariates）会对分化过程产生影响，我们研发了一款算法，用于检测整个分化进程中的差异表达基因（differentially expressed genes）。此外，我们还开发了可在多个样本间识别保守伪时间基因模块（pseudotemporal gene modules）的分析方法。总体而言，我们的研究框架系统性地解决了不同来源骨祖细胞在成骨细胞分化过程中所观察到的异质性问题，为阐明骨形成的复杂机制提供了全新视角，同时也为理解成骨过程（osteogenesis）提供了极具价值的研究资源。