Lysosomal Storage Diseases (LSDs) include roughly 70 inherited metabolic disorders, most of which are expressed in an autosomal recessive pattern. These conditions arise from mutations in genes encoding lysosomal enzymes, leading to intracellular buildup of substrates and subsequent lysosomal dysfunction. LSDs can be broadly classified based on the nature of the stored substrate, encompassing Sphingolipidoses, Mucopolysaccharidoses, Lysosomal Glycogen Storage Disease, Oligosaccharidoses, Mucolipidoses, and Lysosomal Proteinoses. Although individually rare, LSDs collectively affect approximately 1 in 5000 live births. They usually manifest in childhood, but adult-onset types are also detected. Clinical manifestations are heterogeneous and may involve the central nervous system, skeletal system, skin, heart, muscles, kidneys, and other organs. Several therapeutic strategies are available for LSDs, including Enzyme Replacement Therapy to restore deficient enzymes, Hematopoietic Stem Cell Transplantation to provide functional donor-derived cells, Substrate Reduction Therapy and pharmacological chaperones to modulate substrate turnover or enhance enzyme stability, alongside symptomatic and supportive treatments. Ongoing research is also exploring gene therapy-based strategies. Current diagnostic criteria remain insufficient for reliable presymptomatic diagnosis, highlighting the need for more sensitive and specific approaches. In this context, untargeted metabolomics is a powerful strategy to investigate pathogenic pathways, identify novel diagnostic and prognostic biomarkers, and uncover potential therapeutic targets. Accordingly, this review provides an overview of LSDs, focusing on untargeted metabolomics studies and their contribution to the discovery of novel biomarkers and previously unrecognised pathogenic mechanisms relevant to diagnostic and therapeutic innovation.

Biotinidase deficiency (BD) is an autosomal recessive inherited disorder in which the enzyme biotinidase (BTD) is totally or partially defective and the vitamin biotin is not recycled. More than 200 pathogenic variants in the BTD gene have been identified, causing complete or partial loss of enzyme activity and leading to profound or partial BD. Although the genotype–phenotype correlation is not fully defined, some genotypes are associated with profound forms and others with partial forms of BD. The patients with partial BD are mostly asymptomatic but symptoms may appear during stressful conditions such as infections. The patients with profound BD may present neurological problems, hearing loss, visual abnormalities, and organic aciduria, if not treated with biotin supplementation. BD is included in most newborn screening programs (NBS). Screening test relies on measurement of BTD enzyme activity in dried blood spot (DBS), followed by a plasma BTD assay and BTD molecular analysis as confirmatory test. We describe a male newborn with partial BD identified through the newborn screening program. Low BTD activity on DBS was detected; BTD molecular analysis showed the proband to be compound heterozygous for the c.1270G>C (p.Asp424His) mild known variant, and for the rare variant c.690C>G (p.Phe230Leu) previously identified by our group. In this study, we provide the biochemical and clinical characterization of a patient carrying the c.690C>G (p.Phe230Leu) variant, and our findings support a possible contribution of this variant to the partial BD phenotype.