Table 3.

Advances in the Application of ST to Physiological Mechanisms of the Musculoskeletal System

Author	ST Technologies	Resource	Tissues/ Structures	Sample type	Key research achievements	References
Xiao et al.	Visium/RNAscope	mice	femurs	FFPE	Confirmed the feasibility of applying spatial barcode-based ST technologies to fully mineralized mature long bone tissue. Analyzed the cellular composition and interaction networks of the SSPCs’ microenvironment.	12
Zhang et al.	Visium/RNA-ISH	human	embryonic limb	FF	Constructed the first single-cell spatiotemporal transcriptome landscape of human embryonic limb development.	14
Mirzazadeh et al.	RRST	mice	growth plate	FF	Identified significantly-upregulated soluble factors in the SOC and SOC-adjacent areas of mice, including Ccl9, Basp1, and Apln in the SOC area and Msmp in the SOC-adjacent area which may influence spatially-proximate chondrocytes.	64
Piña et al.	Visium/RNAscope	mice	secondary palate	FFPE	Accurately pinpointed the onset of palatal ossification between E14.5 and E15.5, and identified the spatiotemporal localization of marker genes (Deup1, Lrrc23, Dynlrb2) during palatal fusion.	75
Gribaudo et al.	tomo-seq/RNAscope	organoid models	-	FF	Confirmed that human trunk self-organization organoid model can replicate multi-tissue concomitant morphogenesis of the spinal cord and vertebral column similar to in vivo conditions.	76
Chen et al.	Visium/ISS	mice	intervertebral disc	FF	Constructed the first spatial transcriptome atlas of the intervertebral disc.	77
Zhang et al.	stereo-seq	mice	shoulder region	not mentioned	Intricately described the complexity and spatial heterogeneity of fibrocartilage attachment site cells in the shoulder region of postnatal mice. Revealed the molecular dynamics during fibrocartilage differentiation.	78
Lui et al.	LCM/RNA-ISH	mice	tibial articular cartilage	FF/FFPE	Identified new signaling pathways with spatial regulation during the growth of mouse articular cartilage. Revealed similarities in gene spatial expression patterns from the superficial to the deep regions of joint cartilage and from hypertrophic to resting zones of growth plate cartilage.	79
Chau et al.	manual microdissection/RNA-ISH	rat	proximal tibial epiphyses	FF/FFPE	Revealed similarities in gene spatial expression patterns from the superficial to the deep regions of joint cartilage and from hypertrophic to resting zones of growth plate cartilage.	80
Bian et al.	Visium/FISH	mice	Hindlimbs	FFPE	Uncovered the critical role of the G protein-coupled receptor ADGRG6 in regulating chondrocyte proliferation and differentiation, as well as maintaining growth plate homeostasis by Indian Hedgehog signaling.	81
Tong et al.	LCM	mice	knee joints	FF	Provided critical insights into the molecular and spatial mechanisms driving SOC development. Indicated that mesenchymal progenitors in the periarticular region around epiphyseal cartilage play a critical role in initiating SOC development and forming subchondral bone.	82
Tower et al.	Visium	mice	calvaria	FF	Discovered that the presence of sensory innervation maintains the undifferentiated state of mesenchymal cells in cranial sutures to keep cranial sutures patent, while the absence of sensory innervation leads to dysregulation of BMP/TGF-β signaling, manifesting as premature closure of cranial sutures.	83
Baccin et al.	LCM	mice	femurs	FF	Established the first spatial atlas of the bone marrow microenvironment.	84
D’Ercole et al.	Visium/LCM	mice	tibialis anterior, associated extensor digitorum longus	FF	Examined the distinct morphofunctional regions in muscle and their reaction to reversible nerve injury, emphasizing the polyamine pathway as a possible contributor to muscle atrophy.	85
Karlsen et al.	Visium	human	myotendinous junction	FF	Analyzed the different myofibre domains in the human myotendinous junction at the single-nucleus spatial level.	86
Steffen et al.	Visium	rat	patellar tendons	FF	Presented the first spatial gene expression landscape of healthy tendon, and clarified the spatial expression patterns of tendon-associated genes.	87