Centronuclear myopathies (CNM) are a clinically and genetically heterogeneous group of rare
congenital muscle disorders characterized by myober hypotrophy and progressive muscle weak-
ness. Three principal genetic subtypes are recognized: mutations in MTM1 cause X-linked
myotubular myopathy, the most severe form, presenting at birth with profound hypotonia and
respiratory failure and frequently fatal in infancy; mutations in BIN1 underlie autosomal re-
cessive CNM of intermediate severity with childhood onset; and mutations in DNM2 cause
autosomal dominant CNM, the mildest form, with later onset and a more favorable prognosis.
While therapies targeting DNM2 reduction or BIN1 modulation show promise in murine mod-
els, clinical transition is hindered by a lack of non-invasive biomarkers to track muscle recovery
without repetitive biopsies. This study identies a serum-based metabolic Rescue Index to mon-
itor disease progression and therapeutic response across these CNM subtypes. By integrating
dierential abundance metabolomics from skeletal muscle and serum with transcriptomic and
proteomic datasets from wild-type, disease-model, and rescued mice, we applied a reverse ma-
trix analysis to map systemic metabolite shifts back to upstream genetic drivers and enzymatic
complexes.
We identify a convergent biomarker pair with robust cross-model reproducibility: N,N,N-
trimethyl-alanylproline betaine (TMAP) and trans-4-hydroxyproline. TMAP, a byproduct of
MuRF1-mediated myosin degradation, was signicantly elevated in disease states (log2 FC ≈
0.83) and fully reversed upon rescue. Conversely, trans-4-hydroxyproline was markedly sup-
pressed in disease and rose signicantly during recovery (r = −0.85 correlation with muscle
mass), reecting P4H-mediated extracellular matrix remodeling. Proteomic proling enabled
identication of P4HB (PDI) overexpression as the chaperone-driven mechanism underlying this
anabolic surge. Our ndings demonstrate that the TMAP/4-hydroxyproline ratio provides a
robust, biopsy-free surrogate for muscle structural integrity and metabolic normalization. This
Rescue Index aligns with the common therapeutic signatures of DNM2 reduction and BIN1
overexpression, oering a scalable diagnostic tool for human clinical trials to track real-time
pharmacological ecacy.
Overall, this work establishes a metabolomics-driven framework for non-invasive monitoring
of therapeutic response in CNM, with the TMAP/4-hydroxyproline ratio serving as a cross-
genotype metabolic indicator of structural muscle recovery. The convergent dysregulation of
these metabolites across MTM1, BIN1, and DNM2 models positions this Rescue Index as a
translationally relevant endpoint for upcoming gene therapy and antisense oligonucleotide trials
in centronuclear myopathies.