Kang Zhixin, Zhu Tongtong, Zou Dong, Liu Mengyao, Zhang Yifan, Wang Lu, Zhang Zhang, Liu Feng
State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
Genomics Proteomics Bioinformatics. 2025 May 30;23(2). doi: 10.1093/gpbjnl/qzaf026.
Advancements in high-throughput omics technologies have facilitated a systematic exploration of crucial hematopoietic organs across diverse species. A thorough understanding of hematopoiesis in vivo and facilitation of generating functional hematopoietic stem and progenitor cells (HSPCs) in vitro necessitate a comprehensive hematopoietic cross-stage developmental landscape across species. To address this need, we developed HemAtlas, a platform designed for the systematic mapping of hematopoiesis both in vivo and in vitro. HemAtlas features detailed analyses of multi-omics datasets from humans, mice, zebrafish, and HSPC in vitro culture systems. Utilizing literature curation and data normalization, HemAtlas integrates various functional modules, allowing interactive exploration and visualization of any collected omics data based on user-specific interests. Moreover, by applying a systematic and uniform integration method, we constructed organ-wide hematopoietic references for each species with manually curated cell annotations, enabling a comprehensive decoding of cross-stage developmental hematopoiesis at the organ level. Of particular significance are three distinctive functions - single-cell cross-stage, cross-species, and cross-model analyses - that HemAtlas employs to elucidate the hematopoietic development in zebrafish, mice, and humans, and to offer guidance on the generation of HSPCs in vitro. Simultaneously, HemAtlas incorporates a comprehensive map of HSPC cross-stage development to reveal HSPC stage-specific properties. Taken together, HemAtlas serves as a crucial resource to advance our understanding of hematopoiesis and is available at https://ngdc.cncb.ac.cn/hematlas/.
高通量组学技术的进步推动了对不同物种关键造血器官的系统探索。要全面了解体内造血过程并促进体外生成功能性造血干细胞和祖细胞（HSPC），就需要全面了解跨物种的造血跨阶段发育图谱。为满足这一需求，我们开发了HemAtlas平台，该平台旨在对体内和体外的造血过程进行系统映射。HemAtlas的特点是对来自人类、小鼠、斑马鱼和HSPC体外培养系统的多组学数据集进行详细分析。通过文献整理和数据归一化，HemAtlas整合了各种功能模块，允许根据用户特定兴趣对任何收集到的组学数据进行交互式探索和可视化。此外，通过应用系统统一的整合方法，我们为每个物种构建了全器官造血参考，并进行了人工策划的细胞注释，从而能够在器官水平上全面解码跨阶段发育造血过程。特别重要的是HemAtlas采用的三个独特功能——单细胞跨阶段、跨物种和跨模型分析，用于阐明斑马鱼、小鼠和人类的造血发育，并为体外生成HSPC提供指导。同时，HemAtlas纳入了HSPC跨阶段发育的综合图谱，以揭示HSPC阶段特异性特性。总之，HemAtlas是推动我们对造血过程理解的重要资源，可在https://ngdc.cncb.ac.cn/hematlas/获取。
