Inorganic pyrophosphate disrupts amorphous hydrated bone mineral interfaces in hypophosphatasia

Bone mineral molecular architecture is tightly regulated by the kinetics of calcium phosphate phase transformations. In the rare skeletal disease hypophosphatasia (HPP), caused by inactivating mutations in the ALPL gene encoding tissue-nonspecific alkaline phosphatase (TNSALP), accumulation of inorganic pyrophosphate (PPi) alters these phase dynamics. Using solid-state nuclear magnetic resonance spectroscopy and high-resolution electron microscopy, in patient samples we show that bone mineral from compound heterozygous HPP patients exhibits a loss of hydrated amorphous interfacial phases and instead contains highly crystalline hydroxyapatite (HAP), correlating with abnormally high bone mineral density and brittle atypical femoral fractures. Synthetic and cellular models demonstrate that elevated PPi impedes normal phase transitions from amorphous calcium phosphate precursors, bypassing intermediate states and driving ordered HAP nucleation. These findings link disrupted mineral phase kinetics to pathological bone mineral molecular structure, emphasising the critical importance of the hydrated amorphous shell around bone mineral for its material properties and redefining HPP as a molecular mineralization disorder. Our findings also illustrate how biochemical cues regulate non-equilibrium crystallization pathways in biomineralization.