Unsupervised neural networks as a support tool for pathology diagnosis in MALDI-MSI experiments:A case study on thyroid biopsies

Artificial intelligence is getting a foothold in medicine for disease screening and diagnosis. While typical machine learning methods require large labeled datasets for training and validation, their application is limited in clinical fields since ground truth information can hardly be obtained on a sizeable cohort of patients. Unsupervised neural networks - such as Self-Organizing Maps (SOMs) - represent an alternative approach to identifying hidden patterns in biomedical data. Here we investigate the feasibility of SOMs for the identification of malignant and non-malignant regions in liquid biopsies of thyroid nodules, on a patient-specific basis. MALDI-ToF (Matrix Assisted Laser Desorption Ionization -Time of Flight) mass spectrometry-imaging (MSI) was used to measure the spectral profile of bioptic samples. SOMs were then applied for the analysis of MALDI-MSI data of individual patients' samples, also testing various pre-processing and agglomerative clustering methods to investigate their impact on SOMs' discrimination efficacy. The final clustering was compared against the sample's probability to be malignant, hyperplastic or related to Hashimoto thyroiditis as quantified by multinomial regression with LASSO. Our results show that SOMs are effective in separating the areas of a sample containing benign cells from those containing malignant cells. Moreover, they allow to overlap the different areas of cytological glass slides with the corresponding proteomic profile image, and inspect the specific weight of every cellular component in bioptic samples. We envision that this approach could represent an effective means to assist pathologists in diagnostic tasks, avoiding the need to manually annotate cytological images and the effort in creating labeled datasets

Case Report: Rare Homozygous RNASEH1 Mutations Associated With Adult-Onset Mitochondrial Encephalomyopathy and Multiple Mitochondrial DNA Deletions

Mitochondrial DNA (mtDNA) maintenance disorders embrace a broad range of clinical syndromes distinguished by the evidence of mtDNA depletion and/or deletions in affected tissues. Among the nuclear genes associated with mtDNA maintenance disorders, RNASEH1 mutations produce a homogeneous phenotype, with progressive external ophthalmoplegia (PEO), ptosis, limb weakness, cerebellar ataxia, and dysphagia. The encoded enzyme, ribonuclease H1, is involved in mtDNA replication, whose impairment leads to an increase in replication intermediates resulting from mtDNA replication slowdown. Here, we describe two unrelated Italian probands (Patient 1 and Patient 2) affected by chronic PEO, ptosis, and muscle weakness. Cerebellar features and severe dysphagia requiring enteral feeding were observed in one patient. In both cases, muscle biopsy revealed diffuse mitochondrial abnormalities and multiple mtDNA deletions. A targeted next-generation sequencing analysis revealed the homozygous RNASEH1 mutations c.129-3C>G and c.424G>A in patients 1 and 2, respectively. The c.129-3C>G substitution has never been described as disease-related and resulted in the loss of exon 2 in Patient 1 muscle RNASEH1 transcript. Overall, we recommend implementing the use of high-throughput sequencing approaches in the clinical setting to reach genetic diagnosis in case of suspected presentations with impaired mtDNA homeostasis

Stormorken syndrome caused by a p.R304W STIM1 mutation: The first Italian patient and a review of the literature

Stormorken syndrome is a rare autosomal dominant disease that is characterized by a complex phenotype that includes tubular aggregate myopathy (TAM), bleeding diathesis, hyposplenism, mild hypocalcemia and additional features, such as miosis and a mild intellectual disability (dyslexia). Stormorken syndrome is caused by autosomal dominant mutations in the STIM1 gene, which encodes an endoplasmic reticulum Ca2+ sensor. Here, we describe the clinical and molecular aspects of a 21-year-old Italian female with Stormorken syndrome. The STIM1 gene sequence identified a c.910C T transition in a STIM1 allele (p.R304W). The p.R304W mutation is a common mutation that is responsible for Stormorken syndrome and is hypothesized to cause a gain of function action associated with a rise in Ca2+ levels. A review of published STIM1 mutations (n = 50) and reported Stormorken patients (n = 11) indicated a genotype-phenotype correlation with mutations in a coiled coil cytoplasmic domain associated with complete Stormorken syndrome, and other pathological variants outside this region were more often linked to an incomplete phenotype. Our study describes the first Italian patient with Stormorken syndrome, contributes to the genotype/phenotype correlation and highlights the possibility of directly investigating the p.R304W mutation in the presence of a typical phenotype

Case report: A novel ACTA1 variant in a patient with nemaline rods and increased glycogen deposition

BackgroundCongenital myopathies are a group of heterogeneous inherited disorders, mainly characterized by early-onset hypotonia and muscle weakness. The spectrum of clinical phenotype can be highly variable, going from very mild to severe presentations. The course also varies broadly resulting in a fatal outcome in the most severe cases but can either be benign or lead to an amelioration even in severe presentations. Muscle biopsy analysis is crucial for the identification of pathognomonic morphological features, such as core areas, nemaline bodies or rods, nuclear centralizations and congenital type 1 fibers disproportion. However, multiple abnormalities in the same muscle can be observed, making more complex the myopathological scenario.Case presentationHere, we describe an Italian newborn presenting with severe hypotonia, respiratory insufficiency, inability to suck and swallow, requiring mechanical ventilation and gastrostomy feeding. Muscle biopsy analyzed by light microscopy showed the presence of vacuoles filled with glycogen, suggesting a metabolic myopathy, but also fuchsinophilic inclusions. Ultrastructural studies confirmed the presence of normally structured glycogen, and the presence of minirods, directing the diagnostic hypothesis toward a nemaline myopathy. An expanded Next Generation Sequencing analysis targeting congenital myopathies genes revealed the presence of a novel heterozygous c.965 T > A p. (Leu322Gln) variant in the ACTA1 gene, which encodes the skeletal muscle alpha-actin.ConclusionOur case expands the repertoire of molecular and pathological features observed in actinopathies. We highlight the value of ultrastructural examination to investigate the abnormalities detected at the histological level. We also emphasized the use of expanded gene panels in the molecular analysis of neuromuscular patients, especially for those ones presenting multiple bioptic alterations

Nuove tecniche nella chirurgia delle paratiroidi

La patologia delle paratiroidi ha assunto un rilievo sempre maggiore per le innovazioni in ambito diagnostico e chirurgico che ne hanno consentito una più precisa individuazione nosografica e terapeutica. L’utilizzo della scintigrafia con Sesta-MIBI consente una attendibile localizzazione dell’adenoma; l’introduzione del monitoraggio intraoperatorio del paratormone intatto ha reso possibile l’esplorazione unilaterale del collo con una mini-incisione. L’affermarsi della tecnologia video ha portato l’innovazione della paratiroidectomia endoscopica, realizzata per la prima volta nel 1996 e successivamente eseguita senza l’ausilio della CO2. La scintigrafia SPECT consente di ottenere una visione tridimensionale dell’adenoma ed è lo studio più preciso di localizzazione disponibile, consentendo di avviare il paziente ad accessi mini-invasivi. Presupposto fondamentale per l’utilizzo delle tecniche mini-invasive è la determinazione intraoperatoria del PTH, effettuabile con diverse tecniche. La nostra esperienza si basa su 135 pazienti sottoposti a paratiroidectomia negli ultimi 8 anni con 5 casi di iperparatiroidismo persistente sottoposti a successivo reintervento, una degenza postoperatoria media di 2 giorni e 6 complicanze (una emorragia e 5 casi di ipoparatiroidismo transitorio). L’utilizzo delle nuove tecnologie in chirurgia paratiroidea consente di ottenere risultati ottimali, un migliore risultato estetico ed una più rapida ripresa postoperatoria, con una bassa incidenza di ripresa di malattia e di complicanze