In recent years, the development of new diagnostic technologies, such as tandem mass spectrometry (MS/MS) and next-generation sequencing (NGS), has caused a veritable revolution in the diagnosis of genetic diseases, reducing time, cost, and invasiveness associated with prior diagnostic techniques. While MS/MS laid the foundation for the development of numerous, usually institutionally based, neonatal screening programs, NGS has gained traction in newborn screening (NBS), primarily through pilot projects and private funding across different countries. As a result, the traditional Wilson and Jungner criteria have been supplemented by additional criteria, including considerations of equity and access, in response to emerging technologies. This review aims to provide an up-to-date overview of the global landscape of metabolic screening panels, highlight the major ongoing genomic screening projects, and outline the current models for integrating these two screening systems. Substantial differences exist across countries in the numbers and types of diseases included in national NBS programmes. In this context, Italy represents a prominent case, as its neonatal screening framework has seen significant expansion and development in recent years, reaching a particularly comprehensive metabolic screening panel. Nonetheless, a number of initiatives to incorporate genomic technologies into the NBS pathway are currently underway, primarily involving high-income countries. Nonetheless, unlike metabolomic-based NBS programs, no country has a government-mandated NGS program as first-tier testing for newborns. New evidence is emerging from ongoing models of integration of multi-omics approaches into NBS, including the use of AI and machine learning. Identifying the most appropriate system for this integration to reduce the false-positive and false-negative rates associated with both screening types, ensure more equitable access to screening, and facilitate faster access to treatment may represent a useful and foresightful way to conceptualize NBS in the future. This transitional phase should promote rigorous improvements before full-scale adoption.

Background: Autism Spectrum Disorders (ASD) are neurodevelopmental disorders characterized by repetitive behaviors and social interaction deficits. While the severity of ASD is classified into levels (1-3) by the DSM-5, reliable circulating biomarkers to differentiate these levels are lacking. This retrospective pilot study examines plasma amino acid levels in children with ASD to identify the potential biomarkers of disease severity. Methods: Plasma samples from 30 children diagnosed with ASD (24 males, 6 females, aged 3-12 years) were analyzed. Participants were stratified into two groups based on the Autism Diagnostic Observation Schedule Calibrated Severity Score (ADOS CSS): Group 1, presenting with mild symptoms (Level 1, n = 11), and Group 2, characterized by moderate-to-severe symptoms (Levels 2-3, n = 19). This was further confirmed by the identification of electroencephalogram (EEG) anomalies (21.1%) and magnetic resonance imaging (MRI) abnormalities (5.3%), which were detected exclusively in Group 2 and absent in Group 1. Amino acid levels were measured by ion-exchange chromatography. Statistical analyses (Mann-Whitney U test and chi-square test) were used to compare AA levels between groups. Results: Statistically significant differences were observed in the levels of phosphoethanolamine, aspartic acid, and glutamic acid between the two groups. These amino acids (AA) were significantly higher in the moderate-to-severe symptoms group (Levels 2-3) compared to the mild symptoms group (Level 1) (p < 0.05). All AA values remained within age-appropriate reference ranges. Conclusions: Plasma levels of phosphoethanolamine, aspartic acid, and glutamic acid may serve as potential biomarkers for ASD severity in children. Results from this exploratory analysis suggest that AA profiling could differentiate ASD severity and identify specific metabolic pathways, such as excitatory neurotransmission and phospholipid turnover. Further studies with larger cohorts are necessary to validate these findings and explore the role of AAs in ASD pathophysiology.

Metachromatic leukodystrophy (MLD) is a rare inherited disorder of lysosomal storage, caused by a deficiency in the arylsulfatase A (ARSA) enzyme, leading to toxic accumulation of sulfatides, which progressively impair motor and cognitive function. MLD is a candidate for inclusion in newborn screening (NBS) programs, due to the narrow pre-symptomatic window for effective therapeutic intervention. We set up a prospective pilot NBS program for MLD in Tuscany, based on a two-step approach. The first-tier test quantified four sulfatides; if levels exceeded the cut-off, we performed the second-tier test by measuring ARSA activity on the same neonatal dried blood spot (DBS). We performed the first-tier test on 42,262 newborns over two years and the second-tier test on residual neonatal DBS from 90 of them (0.21%). We recalled 10 newborns (0.02%) for an additional DBS, due to insufficient residual material for a second-tier test (n = 4) or to low ARSA activity (n = 6). We found normal ARSA activity in all new DBS and identified no new cases of MLD. Retrospective analysis of eight neonatal and fifteen non-neonatal DBS from patients with genetically confirmed MLD showed that the algorithm accurately identified MLD patients. This diagnostic algorithm proved feasible and accurate for early detection of MLD in prospective NBS.

This study presents the case of a child with multiple congenital anomalies, severe hypotonia, and profound bilateral sensorineural hearing loss. Functional bioenergetic assessments showed no significant mitochondrial respiratory defects, and riboflavin (Rf) status evaluation excluded a deficiency in Rf transporters as a cause of hearing loss. Clinical findings were consistent with Kilquist syndrome (KILQS), and genetic investigations confirmed the diagnosis by identifying a novel homozygous splice-site variant, c.[3101-1G>C];[3101-1G>C], in the SLC12A2 gene, which encodes the Na+-K+-2Cl- Cotransporter 1 (NKCC1) protein. The effect of this mutation was further investigated using exon-walking PCR and Sanger sequencing, which confirmed exon 23 skipping in the patient's mRNA, resulting in a truncated NKCC1 protein. In silico structural modeling suggested compromised dimerization stability, which was supported by immunoblotting analysis, revealing the absence of the dimeric form of NKCC1 in patient-derived peripheral blood mononuclear cells. This study provides critical insights into the molecular and structural consequences of NKCC1 disruption, contributing to the understanding of its role in KILQS pathogenesis. Further studies are needed to elucidate the precise molecular mechanisms and explore potential therapeutic interventions.

Background: The advent of tandem mass spectrometry (MS/MS) had an essential role in the expansion of newborn screening (NBS) for different inborn errors of metabolism (IEMs). Nowadays, almost 50 IEMs are screened in Italy. The use of second-tier tests (2-TTs) in NBS minimizes the false positive rate; nevertheless, the metabolic profile is influenced not only by the genome but also by environmental factors and clinical variables. We reviewed the MS/MS NBS data from over 37,000 newborns (of which 8% required 2-TTs) screened in the Italian Abruzzo region to evaluate the impact of neonatal and maternal variables on propionate-related primary biomarker levels. Methods: Expanded NBS and 2-TT analyses were performed using MS/MS and liquid chromatography–MS/MS methods. We set up layered cut-offs dividing all 37,000 newborns into categories. Statistical analysis was used to create alarm thresholds for NBS-positive samples. Statistically significant differences were found in both neonatal and maternal conditions based on the 2-TTs carried out. According to the stratified cut-offs, only 1.47% of the newborns would have required a 2-TT while still retaining the ability to recognize the true-positive case of methylmalonic acidemia with homocystinuria, which has been identified by NBS. To further support the clinical applicability, we performed an external evaluation considering nine positive cases from an extra-regional neonatal population, confirming the potential of our model. Interestingly, the setting of alarm thresholds and their application would allow for establishing the degree of priority/urgency for 2-TTs. Conclusions: Tailoring NBS by customized cut-offs may enhance the application of precision medicine, focusing on true-positive cases and also reducing analysis costs and times.

Cystic fibrosis (CF) is the most common severe autosomal recessive genetic disorder among Caucasians. The improvement of genetic techniques has allowed the identification of an increasing number of genetic variants, including large rearrangements such as duplications. We report the first case of a whole CFTR gene duplication in a healthy newborn, who had normal sweat test, also carrying R74W and V855I variants on the same allele. Familial segregation analysis and the observed frequencies of all the CFTR gene variants, revealed that R74W and V855I were probably both present in a cis arrangement on the allele also containing the duplication (i.e., in a double complex allele). Since R74W is a “variant of varying clinical consequence” its arrangement in trans with one pathogenic variant may not be sufficient to cause a classic CF disease phenotype. Moreover, its duplication could even be an advantage that could compensate for the effect of the alteration.

Multiple acyl-CoA dehydrogenase deficiency (MADD) is a rare inborn error of metabolism affecting fatty acid and amino acid oxidation with an incidence of 1 in 200,000 live births. MADD has three clinical phenotypes: severe neonatal-onset with or without congenital anomalies, and a milder late-onset form. Clinical diagnosis is supported by urinary organic acid and blood acylcarnitine analysis using tandem mass spectrometry in newborn screening programs. MADD is an autosomal recessive trait caused by biallelic mutations in the ETFA, ETFB, and ETFDH genes encoding the alpha and beta subunits of the electron transfer flavoprotein (ETF) and ETF-coenzyme Q oxidoreductase enzymes. Despite significant advancements in sequencing techniques, many patients remain undiagnosed, impacting their access to clinical care and genetic counseling. In this report, we achieved a definitive molecular diagnosis in a newborn by combining whole-genome sequencing (WGS) with RNA sequencing (RNA-seq). Whole-exome sequencing and next-generation gene panels fail to detect variants, possibly affecting splicing, in deep intronic regions. Here, we report a unique deep intronic mutation in intron 1 of the ETFDH gene, c.35-959A>G, in a patient with early-onset lethal MADD, resulting in pseudo-exon inclusion. The identified variant is the third mutation reported in this region, highlighting ETFDH intron 1 vulnerability. It cannot be excluded that these intronic sequence features may be more common in other genes than is currently believed. This study highlights the importance of incorporating RNA analysis into genome-wide testing to reveal the functional consequences of intronic mutations.

The purpose of the present study was to evaluate the concentrations of some bone turnover markers in preterm neonates with uncomplicated clinical course in the first month of life. Samples from 13 preterm neonates were collected at three different times: at birth (T0) from umbilical cord blood (UCB); and at 15 (T1) and 30 (T2) days of life from peripheral blood (PB). The concentrations of calcium (Ca), phosphate (P), total alkaline phosphatase (ALP), Collagen Type 1 Amino-terminal Propeptide (PINP), osteocalcin (OC), Collagen Type 1 Carboxyl-Terminal Telopeptide (CTX) and Leptin were assessed. A statistically significant difference for ALP concentration at birth versus T1 and T2 was found. An evident increase in the median concentrations of CTX, OC and PINP from T0 to T2 were observed. A significant difference was also found for Leptin concentration at T0 compared to T1. In preterm infants, in the absence of acute or chronic medical conditions and without risk factors for metabolic bone disease (MBD) of prematurity, there is a significant increase in bone turnover markers during the first month of life. The knowledge of the variations in these markers in the first weeks of life, integrated by the variations in the biochemical indicators of bone metabolism, could help in recognizing any conditions at risk of developing bone diseases.

Many inherited metabolic disorders (IMDs), including disorders of amino acid, fatty acid, and carbohydrate metabolism, are treated with a dietary reduction or exclusion of certain macronutrients, putting one at risk of a reduced intake of micronutrients. In this review, we aim to provide available evidence on the most common micronutrient deficits related to specific dietary approaches and on the management of their deficiency, in the meanwhile discussing the main critical points of each nutritional supplementation. The emerging concepts are that a great heterogeneity in clinical practice exists, as well as no univocal evidence on the most common micronutrient abnormalities. In phenylketonuria, for example, micronutrients are recommended to be supplemented through protein substitutes; however, not all formulas are equally supplemented and some of them are not added with micronutrients. Data on pyridoxine and riboflavin status in these patients are particularly scarce. In long-chain fatty acid oxidation disorders, no specific recommendations on micronutrient supplementation are available. Regarding carbohydrate metabolism disorders, the difficult-to-ascertain sugar content in supplementation formulas is still a matter of concern. A ketogenic diet may predispose one to both oligoelement deficits and their overload, and therefore deserves specific formulations. In conclusion, our overview points out the lack of unanimous approaches to micronutrient deficiencies, the need for specific formulations for IMDs, and the necessity of high-quality studies, particularly for some under-investigated deficits.

Classic galactosemia is an autosomal recessive inherited liver disorder of carbohydrate metabolism caused by deficient activity of galactose-1-phosphate uridylyltransferase (GALT). While a galactose-restricted diet is lifesaving, most patients still develop long-term complications. In this study, we report on a two-week-old female patient who is a compound heterozygote for a known pathogenic variant (p.K285N) and a novel missense variant (p.A303D) in the GALT gene. Segregation analysis showed that the patient inherited the p.K285N pathogenic variant from her father and the p.A303D variant from her mother. A bioinformatics analysis to predict the impact of the p.A303D missense variant on the structure and stability of the GALT protein revealed that it may be pathogenic. Based on this finding, we performed a literature review of all GALT missense variants identified in homozygous and compound heterozygous galactosemia patients carrying the p.K285N pathogenic variant to explore their molecular effects on the clinical phenotype of the disease. Our analysis revealed that these missense variants are responsible for a wide range of molecular defects. This study expands the clinical and mutational spectrum in classic galactosemia and reinforces the importance of understanding the molecular consequences of genetic variants to incorporate genetic analysis into clinical care.

Newborn screening (NBS) for inborn errors of metabolism is one of the most advanced tools for secondary prevention in medicine, as it allows early diagnosis and prompt treatment initiation. The expanded newborn screening was introduced in Italy between 2016 and 2017 (Law 167/2016; DM 13 October 2016; DPCM 12-1-2017). A total of 1,586,578 infants born in Italy were screened between January 2017 and December 2020. For this survey, we collected data from 15 Italian screening laboratories, focusing on the metabolic disorders identified by tandem mass spectrometry (MS/MS) based analysis between January 2019 and December 2020. Aminoacidemias were the most common inborn errors in Italy, and an equal percentage was observed in detecting organic acidemias and mitochondrial fatty acids beta-oxidation defects. Second-tier tests are widely used in most laboratories to reduce false positives. For example, second-tier tests for methylmalonic acid and homocysteine considerably improved the screening of CblC without increasing unnecessary recalls. Finally, the newborn screening allowed us to identify conditions that are mainly secondary to a maternal deficiency. We describe the goals reached since the introduction of the screening in Italy by exchanging knowledge and experiences among the laboratories.

Abstract Background Congenital hypothyroidism (CH) is the most frequent congenital endocrine disorder. The purpose of the present study was to evaluate the incidence and etiological classification of CH in Apulia in a three-year period according to the reorganization of the regional screening program in a single central laboratory, as well as to analyze the growth characteristics and the associated risk factors of the CH newborns diagnosed during the study period. Methods Data derived from the reorganization of the newborn screening program for CH in a single central laboratory that collects dried blood spot (DBS) from 27 Maternity Hospitals are analyzed over a three-year period. Birth weight and length, daily dose of L-T4 at specific key points (3, 6, 12 and 18 months, 2, 2.5 and 3 years) were also obtained from medical records of the CH newborns during the study period and calculated as standard deviation score (SDS). Results The screening program diagnosed 90 newborns with confirmed CH (incidence 1:990; recall rate: 3.6%). In detail, 75.6% newborns had an eutopic thyroid, and 24.4% had thyroid dysgenesis; 33 out of the 90 newborns (36.6%) had one or more risk factors. Among these, the multiple pregnancies are the most important because they tripled the risk of CH. At diagnosis, TSH levels were different between patients with dysgenesis and those with an eutopic thyroid (p = 0.005). Treatment was started at a mean of 18.5 ± 12.8 days of life. The mean starting dose of levothyroxine (L-T4) was 11.38 ± 2.46 μg/kg/day. Conclusions The results of these study show an increase of CH cases in newborns with an eutopic thyroid compared to the traditional classification. The centralization of the screening program allows a closer cooperation between laboratory and clinical centers and facilitates the implementation of appropriate diagnostic evaluations and timely initiation of treatment, with positive effects on the management of the condition.

In this report, we describe the case of an 11-year-old boy, who came to our attention for myalgia and muscle weakness, associated with inappetence and vomiting. Hypertransaminasemia was also noted, with ultrasound evidence of hepatomegaly. Biochemical investigations revealed acylcarnitine and organic acid profiles resembling those seen in MADD, that is, multiple acyl-CoA dehydrogenase deficiencies (OMIM #231680) a rare inherited disorder of fatty acids, amino acids, and choline metabolism. The patient carried a single pathogenetic variant in the ETFDH gene (c.524G>A, p.Arg175His) and no pathogenetic variant in the riboflavin (Rf) homeostasis related genes (SLC52A1, SLC52A2, SLC52A3, SLC25A32, FLAD1). Instead, compound heterozygosity was found in the ACAD8 gene (c.512C>G, p.Ser171Cys; c.822C>A, p.Asn274Lys), coding for isobutyryl-CoA dehydrogenase (IBD), whose pathogenic variants are associated to IBD deficiency (OMIM #611283), a rare autosomal recessive disorder of valine catabolism. The c.822C>A was never previously described in a patient. Subsequent further analyses of Rf homeostasis showed reduced levels of flavins in plasma and altered FAD-dependent enzymatic activities in erythrocytes, as well as a significant reduction in the level of the plasma membrane Rf transporter 2 in erythrocytes. The observed Rf/flavin scarcity in this patient, possibly associated with a decreased ETF:QO efficiency might be responsible for the observed MADD-like phenotype. The patient's clinical picture improved after supplementation of Rf, l-carnitine, Coenzyme Q10, and also 3OH-butyrate. This report demonstrates that, even in the absence of genetic defects in genes involved in Rf homeostasis, further targeted molecular analysis may reveal secondary and possibly treatable biochemical alterations in this pattern.

Background: non-autoimmune thyroid disorder is a common finding in celiac patients, more frequent than in the general population. An impairment of iodine absorption has been hypothesized, but it has never been investigated so far. We aimed to evaluate the iodine absorption in children and adolescents with newly diagnosed celiac disease. Methods: 36 consecutive celiac patients (age 7.4 years, range 2.4–14.5 years) before starting a gluten-free diet (GFD) were enrolled. We assayed the urinary iodine concentration (UIC) in a 24-h urine sample, at baseline (T0) after 3 (T1) and 12 months (T2) of GFD. Results: UIC at T0 was 64 μg/L (IQR 45–93.25 μg/L) with an iodine deficiency rate of 77.8%. UIC was not different according to histological damage, clinical presentation (typical vs atypical); we found no correlation with the thyroid function tests and auxological parameters. UIC was not statistically different at T1 (76 μg/L) and T2 (89 μg/L) vsT0. UIC at T2 was similar between patients with positive and negative anti-transglutaminase antibodies at T2. No patients presented overt hypothyroidism during the study. Conclusions: We found that iodine absorption in celiac children is impaired compared to the general population; it increases slightly, but not significantly, during the GFD. We should regularly reinforce the need for a proper iodine intake in celiac disease patients to reduce iodine deficiency risk.

Background Smith-Lemli-Opitz syndrome (SLOS) is a rare genetic neurodevelopmental disorder caused by the defect in the 7-dehydrocholesterol reductase. This defect leads to the deficiency of cholesterol biosynthesis with accumulation of 7-dehydrocholesterol. Inhibitory factor 1 (IF 1 ) is a well-known mitochondrial protein. Recently, it has been discovered in the human serum where it is reported to be involved in the HDL-cholesterol intake. Here we report the IF 1 presence in the serum of two paediatric SLOS dizygotic twins treated with dietary cholesterol supplementation. Case presentation The patients showed a typical phenotype. They started dietary supplementation with cholesterol when 2 months old. The cholesterol intake was periodically titrated on the basis of weight increase and the twin 1 required a larger supplementation than the twin 2 during the follow-up. When 6.4-year-old, they underwent IF 1 assay that was 7-fold increased in twin 2 compared to twin 1 (93.0 pg/ml vs 13.0 pg/ml, respectively). Conclusions We report, for the first time, the presence of circulating IF 1 in the serum of SLOS patients, showing different levels among them. Our findings confirm that IF 1 could be a novel research target in cholesterol-related disorders and also in SLOS, and could contribute to the general debate on IF 1 as a new modulator of cholesterol levels.

A bioptic specimen from the muscles of a patient suffering from severe myopathy was inspected for the presence of human porin 31HL. Western blotting suggested that the specimen was free of the most abundant eukaryotic porin 31HL (HVDAC1). The specimen was treated with detergent and the soluble protein fraction was passed through a dry hydroxyapatite column. The passthrough of this column was inspected for channel formation in artificial lipid-bilayer membranes. The channel observed under these conditions had a single-channel conductance of about 2.5 nS in 1 M KCl, was cation selective, and was found to be virtually voltage independent. Experiments with a control specimen from a healthy human being, without any indication for muscle myopathy, revealed the presence of the voltage-dependent porin 31HL in the sample. It is discussed whether the patient's bioptic specimen contained another human porin, which has not been studied to date in its natural environment.