Spatial transcriptomics for gene discovery identifies Slc13a5 as a modulator of bone mechanoadaptation

Meslier, Q. A.; Beeve, A. T.; Gupta, A.; Palomo, D.; Saleem, S.; Eck, S.; Lawson, L.; Shuster, J.; Brennan, M.; Dirckx, N.; Silva, M. J.; Scheller, E. L.

doi:10.64898/2026.03.11.711126

bioRxiv · 10.64898/2026.03.11.711126

Spatial transcriptomics for gene discovery identifies Slc13a5 as a modulator of bone mechanoadaptation

Meslier, Q. A.·Beeve, A. T.·Gupta, A.·Palomo, D.·Saleem, S.·Eck, S.·Lawson, L.·Shuster, J.·Brennan, M.·Dirckx, N.·Silva, M. J.·Scheller, E. L.

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Abstract

Bone is a dynamic tissue that continuously adapts its structure in response to mechanical loading, an essential process for maintaining skeletal health. However, this adaptive capacity declines with aging, contributing to increased fragility and fracture risk. Developing therapeutic strategies that preserve or restore bone mechanoadaptation in patients with increased bone fragility requires identifying key molecular regulators of this process. We applied spatial transcriptomics (GeoMx, NanoString) to characterize gene expression changes induced by mechanical loading in the murine tibia, focusing on periosteal and bone compartments in regions under tension and compression. Spatial data were validated and cross-compared with previously published bulk RNA-seq and laser-capture microdissection datasets, identifying a set of 12 genes consistently regulated by loading across independent platforms and laboratories. As part of a functional analysis, we selected Slc13a5, a citrate transporter implicated in bone mineralization and metabolism. Conditional deletion of Slc13a5 in osteolineage cells using Osteocalcin-Cre significantly increased the loading-induced mineralizing surface in tensile regions compared with Cre- Slc13a5fl/fl littermates. In addition, Slc13a5 cKO mice exhibited lower resorption around the neutral axis after loading compared to controls. Together, these findings identify Slc13a5 as a regulator of bone adaptation in regions experiencing low mechanical stimulation and suggest it as a potential therapeutic target for conditions characterized by impaired mechanoadaptive responses. This study highlights spatial transcriptomics as a powerful gene discovery framework for bone, enabling identification of novel targets to understand mechanisms and develop therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/711126v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@14fc0e9org.highwire.dtl.DTLVardef@1023a16org.highwire.dtl.DTLVardef@133aa0eorg.highwire.dtl.DTLVardef@e19c86_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Meslier, Q. A., Beeve, A. T., Gupta, A., Palomo, D., Saleem, S., Eck, S., Lawson, L., Shuster, J., Brennan, M., Dirckx, N., Silva, M. J., Scheller, E. L.. 2026-03-13. Spatial transcriptomics for gene discovery identifies Slc13a5 as a modulator of bone mechanoadaptation. https://doi.org/10.64898/2026.03.11.711126

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