Spatial multi-modal atlas of bone tissue from human femur

The skeletal system plays a pivotal role in the human body, and bone-related diseases present an urgent public health challenge. Understanding the bone microenvironment is essential for elucidating the mechanisms underlying bone homeostasis and developing innovative therapeutic strategies for bone diseases such as osteoporosis and osteoarthritis. In this study, we applied spatial and single-cell transcriptomic assays on bone tissue from human femur to comprehensively characterize the multi-dimensional cellular landscape of the human bone marrow microenvironment. We identified one niche related to bone formation and characterized cell-cell communication within bone marrow. Notably, we performed comprehensive dependency analysis, uncovering critical cellular relationships and molecular dependencies within the bone ecosystem. By mapping spatial distributions of gene expression, cellular composition, and pathway activities, we constructed a high-resolution atlas of the human bone microenvironment. This atlas not only delineates the intricate cellular architecture but also illuminates key molecular processes and dependencies governing bone metabolism. Overall design: Human femoral head bone samples (~1 cm × 1 cm × 0.5 cm) were collected during hip replacement surgeries and immediately fixed in 10% formalin at 4°C for 48 hours. After rinsing with sterile PBS, the samples were decalcified in 14% EDTA for 3 weeks, followed by dehydration in increasing ethanol concentrations, clearing with xylene, and embedding in paraffin. Spatial transcriptomics was conducted using the Visium CytAssist Spatial Gene Expression for FFPE protocol. Tissue sections were deparaffinized, stained with H&E, and processed with the Visium CytAssist instrument to transfer analytes for downstream library construction and sequencing on an Illumina NovaSeq 6000 system.