Medical Genetics, Human Genetics, Molecular Genetics, Epigenomics, Molecular Biology
53
Scopus Publications
Scopus Publications
A variant of the autophagic receptor NDP52 counteracts phospho-TAU accumulation and emerges as a protective factor for Alzheimer’s disease Anna Mattioni, Claudia Carsetti, Krenare Bruqi, Valerio Caputo, Valentina Cianfanelli, et al. Cell Death and Disease, 2025 Selective elimination of early pathological TAU species may be a promising therapeutic strategy to reduce the accumulation of TAU, which contributes to neurodegeneration and is a hallmark of Alzheimer’s disease (AD). Pathological hyper-phosphorylated TAU can be degraded through selective autophagy, and NDP52/CALCOCO2 is one of the autophagy receptors involved in this process. In 2021, we discovered a variant of NDP52, called NDP52GE (rs550510), that is more efficient at promoting autophagy. We here anticipate that this variant could be a powerful factor that could eliminate pathological forms of TAU better than its WT form (NDP52WT). Indeed, we provide evidence that in in vitro systems and in a Drosophila melanogaster model of TAU-induced AD, the NDP52GE variant is much more effective than the NDP52WT in reducing the accumulation of pathological forms of TAU through the autophagic process and rescues typical neurodegenerative phenotypes induced by hTAU toxicity. Mechanistically, we showed that NDP52WT and NDP52GE bind pTAU with comparable efficiency, but that NDP52GE binds the autophagic machinery (LC3C and LC3B) more efficiently than NDP52WT does, which could explain its greater efficiency in removing pTAU. Finally, by performing a genetic analysis of a cohort of 435 AD patients, we defined the NDP52GE variant as a protective factor for AD. Overall, our work highlights the variant NDP52GE as a resilience factor in AD that shows a robust effectiveness in driving pathological TAU degradation.
The Diagnostic Value of Copy Number Variants in Genetic Cardiomyopathies and Channelopathies Valerio Caputo, Virginia Veronica Visconti, Enrica Marchionni, Valentina Ferradini, Clara Balsano, et al. Journal of Cardiovascular Development and Disease, 2025 Sudden cardiac death represents an unexpected death for which a strong underlying genetic background has been described. The primary causes are identified in cardiomyopathies and channelopathies, which are heart diseases of the muscle and electrical system, respectively, without coronary artery disease, hypertension, valvular disease, and congenital heart malformations. Genetic variants, especially single nucleotide variants and short insertions/deletions impacting essential myocardial functions, have shown that cardiomyopathies display high heritability. However, genetic heterogeneity, incomplete penetrance, and variable expression may complicate the interpretation of genetic findings, thus delaying the management of seriously at-risk patients. Moreover, recent studies show that the diagnostic yield related to genetic cardiomyopathies ranges from 28 to 40%, raising the need for further research. In this regard, investigating the occurrence of structural variants, especially copy number variants, may be crucial. Based on these considerations, this review aims to provide an overview of copy number variants identified in cardiomyopathies and discuss them, considering diagnostic yield. This review will ultimately address the necessity of incorporating copy number variants into routine genetic testing for cardiomyopathies and channelopathies, a process increasingly enabled by advances in next-generation sequencing technologies.
Towards Precision in Sarcopenia Assessment: The Challenges of Multimodal Data Analysis in the Era of AI Valerio Caputo, Ivan Letteri, Silvano Junior Santini, Gaia Sinatti, Clara Balsano International Journal of Molecular Sciences, 2025 Sarcopenia, a condition characterised by the progressive decline in skeletal muscle mass and function, presents significant challenges in geriatric healthcare. Despite advances in its management, complex etiopathogenesis and the heterogeneity of diagnostic criteria underlie the limited precision of existing assessment methods. Therefore, efforts are needed to improve the knowledge and pave the way for more effective management and a more precise diagnosis. To this purpose, emerging technologies such as artificial intelligence (AI) can facilitate the identification of novel and accurate biomarkers by modelling complex data resulting from high-throughput technologies, fostering the setting up of a more precise approach. Based on such considerations, this review explores AI’s transformative potential, illustrating studies that integrate AI, especially machine learning and deep learning, with heterogeneous data such as clinical, anthropometric and molecular data. Overall, the present review will highlight the relevance of large-scale, standardised studies to validate biomarker signatures using AI-driven approaches.
Automatic Generation of Learning Material for Residential Students in ED: Prompt Engineering and Evaluation Antonella Fontana, Gaia Sinatti, Sara Cicchinelli, Silvano Santini, Valerio Caputo, et al. 2024 21st International Conference on Information Technology Based Higher Education and Training Ithet 2024, 2024 Emergency Department (ED) physicians must manage all types of pathologies and quickly implement the appropriate diagnostic and therapeutic pathways. Flashcards can be a valuable support and consultation tool because they are simple and effective learning methods. Accordingly, we started a project that aims to develop an app that provides flashcards to help resident students in the ED learn the correct diagnostic and therapeutic guidelines. However, developing the appropriate flashcard content is long, complex, and expensive. This research discusses how we tackled this issue through automated content generation: we first report on the prompt engineering phase and then on the evaluation of the learning material. The prompt engineering phase returned some valuable lessons learned that can be useful to researchers involved in a similar process. The (intrinsic and extrinsic) evaluation showed that the automated material was of good quality, even if the lack of in-depth contextual knowledge by the Large Language Model (LLM) of the specific domain of ED was one of the significant problems, and minor revisions remained necessary. In conclusion, the research summarized in this paper provides additional evidence about the pros and cons of using LLMs for automated content generation in the specific context of medical education.
Prevalence of fungal colonization among patients with psoriasis in difficult-to-treat areas: impact of apremilast on mycotic burden and clinical outcomes Elena Campione, Terenzio Cosio, Enrico Salvatore Pistoia, Fabio Artosi, Ruslana Gaeta Shumack, et al. Frontiers in Immunology, 2024 IntroductionFungi, including Candida, may be a trigger or exacerbate psoriasis, especially in difficult to treat (DTT) areas, through the activation of IL-17/23 axis.MethodsIn this study, seventy patients with DDT psoriasis were enrolled to evaluate Candida species and/or other opportunistic fungi colonization rate at baseline (T0) and the impact of apremilast on fungal load, clinical outcome, serum cytokine levels and biochemical serum profile of patients after 16, 24 and 52 weeks of treatment.ResultsIn our population, 33 (47%) patients were colonized by Candida spp. at baseline. In 24 (34%) individuals Candida was detected in the oral cavity while in the remaining 9 (13%) individuals the fungus was isolated from stool samples. Twenty subjects were colonized by only the species C. albicans, whereas in the remaining 13 a combination of two or more species (C. albicans plus non-albicans strains) was found in the oral cavity. Moreover, 27 (39%) patients were affected by onychomycosis. At 52 weeks, apremilast treatment induced a full recovery from Candida colonization in 83% of patients colonized with a single species of Candida (C. albicans); while in those co-infected by two or more Candida spp. induced a significant reduction (colony counts >10 CFU/mL) in fungal load was observed in comparison to baseline. Among patients with onychomycosis, 78% (21/27) of them presented a complete clinical resolution of nail psoriasis and concomitant nail infections. Finally, improvements in clinical scores i.e., PASI, NAPSI, DLQI, itch VAS, PAIN VAS, scPGA and sPGA-G and biochemical serum profile, as well as a significant decrease in serum IL-17A, TGF-β 1 and IL-10 levels (from 8.51 to 4.16 pg/mL; from 66.10 to 48.70 ng/mL and from 20.05 to 14 pg/mL, respectively) were observed in all patients.ConclusionsFungi may play a role in the psoriasis pathogenesis. Apremilast has been shown to ameliorate psoriasis signs and symptoms and counteract fungal overgrowth, probably by dampening inflammation, triggered by the fungal infections themselves. Thus, apremilast may represent an effective therapeutic approach in the treatment of DTT psoriasis and modulate the fungal colonization.
The Role of Epigenetic Control of Mitochondrial (Dys)Function in MASLD Onset and Progression Valerio Caputo, Giovanni Tarantino, Silvano Junior Santini, Giovanna Fracassi, Clara Balsano Nutrients, 2023 Metabolic dysfunction-associated steatotic fatty liver disease (MASLD), a novel definition for NAFLD, represents one of the most common causes of liver disease, and its incidence is increasing worldwide. It is characterized by a complex etiopathogenesis in which mitochondrial dysfunction exerts a pivotal role together with alteration of lipid metabolism, inflammation, and oxidative stress. Nutrients and bioactive compounds can influence such mechanisms so that changes in diet and lifestyle are regarded as important treatment strategies. Notably, natural compounds can exert their influence through changes of the epigenetic landscape, overall resulting in rewiring of molecular networks involved in cell and tissue homeostasis. Considering such information, the present review aims at providing evidence of epigenetic modifications occurring at mitochondria in response to natural and bioactive compounds in the context of liver (dys)function. For this purpose, recent studies reporting effects of compounds on mitochondria in the context of NAFLD/MASLD, as well as research showing alteration of DNA methylation and non-coding RNAs-related circuits occurring at liver mitochondria, will be illustrated. Overall, the present review will highlight the importance of understanding the bioactive compounds-dependent epigenetic modulation of mitochondria for improving the knowledge of MASLD and identifying biomarkers to be employed for effective preventative strategies or treatment protocols.
Epigenetic profiling of the D4Z4 locus: Optimization of the protocol for studying DNA methylation at single CpG site level Domenica Megalizzi, Giulia Trastulli, Valerio Caputo, Luca Colantoni, Carlo Caltagirone, et al. Electrophoresis, 2023 The alteration of epigenetic modifications, including DNA methylation, can contribute to the etiopathogenesis and progression of many diseases. Among them, facioscapulohumeral dystrophy (FSHD) is a muscular disorder characterized by the loss of repressive epigenetic features affecting the D4Z4 locus (4q35). As a consequence, these alterations are responsible for DNA hypomethylation and a transcriptional‐active chromatin conformation change that, in turn, lead to the aberrant expression of DUX4 in muscle cells. In the present study, methylation levels of 29 CpG sites of the DR1 region (within each repeat unit of the D4Z4 macrosatellite) were assessed on 335 subjects by employing primers designed for enhancing the performance of the assay. First, the DR1 original primers were optimized by adding M13 oligonucleotide tails. Moreover, the DR1 reverse primer was replaced with a degenerate one. As a result, the protocol optimization allowed a better sequencing resolution and a more accurate evaluation of DR1 methylation levels. Moreover, the assessment of the repeatability of measurements proved the reliability and robustness of the assay. The optimized protocol emerges as an excellent method to detect methylation levels compatible with FSHD.
Whole exome sequencing highlights rare variants in CTCF, DNMT1, DNMT3A, EZH2 and SUV39H1 as associated with FSHD Claudia Strafella, Valerio Caputo, Sara Bortolani, Eleonora Torchia, Domenica Megalizzi, et al. Frontiers in Genetics, 2023 Introduction: Despite the progress made in the study of Facioscapulohumeral Dystrophy (FSHD), the wide heterogeneity of disease complicates its diagnosis and the genotype-phenotype correlation among patients and within families. In this context, the present work employed Whole Exome Sequencing (WES) to investigate known and unknown genetic contributors that may be involved in FSHD and may represent potential disease modifiers, even in presence of a D4Z4 Reduced Allele (DRA).Methods: A cohort of 126 patients with clinical signs of FSHD were included in the study, which were characterized by D4Z4 sizing, methylation analysis and WES. Specific protocols were employed for D4Z4 sizing and methylation analysis, whereas the Illumina® Next-Seq 550 system was utilized for WES. The study included both patients with a DRA compatible with FSHD diagnosis and patients with longer D4Z4 alleles. In case of patients harboring relevant variants from WES, the molecular analysis was extended to the family members.Results: The WES data analysis highlighted 20 relevant variants, among which 14 were located in known genetic modifiers (SMCHD1, DNMT3B and LRIF1) and 6 in candidate genes (CTCF, DNMT1, DNMT3A, EZH2 and SUV39H1). Most of them were found together with a permissive short (4–7 RU) or borderline/long DRA (8–20 RU), supporting the possibility that different genes can contribute to disease heterogeneity in presence of a FSHD permissive background. The segregation and methylation analysis among family members, together with clinical findings, provided a more comprehensive picture of patients.Discussion: Our results support FSHD pathomechanism being complex with a multigenic contribution by several known (SMCHD1, DNMT3B, LRIF1) and possibly other candidate genes (CTCF, DNMT1, DNMT3A, EZH2, SUV39H1) to disease penetrance and expressivity. Our results further emphasize the importance of extending the analysis of molecular findings within the proband’s family, with the purpose of providing a broader framework for understanding single cases and allowing finer genotype-phenotype correlations in FSHD-affected families.
D4Z4 Methylation Levels Combined with a Machine Learning Pipeline Highlight Single CpG Sites as Discriminating Biomarkers for FSHD Patients Valerio Caputo, Domenica Megalizzi, Carlo Fabrizio, Andrea Termine, Luca Colantoni, et al. Cells, 2022 The study describes a protocol for methylation analysis integrated with Machine Learning (ML) algorithms developed to classify Facio-Scapulo-Humeral Dystrophy (FSHD) subjects. The DNA methylation levels of two D4Z4 regions (DR1 and DUX4-PAS) were assessed by an in-house protocol based on bisulfite sequencing and capillary electrophoresis, followed by statistical and ML analyses. The study involved two independent cohorts, namely a training group of 133 patients with clinical signs of FSHD and 150 healthy controls (CTRL) and a testing set of 27 FSHD patients and 25 CTRL. As expected, FSHD patients showed significantly reduced methylation levels compared to CTRL. We utilized single CpG sites to develop a ML pipeline able to discriminate FSHD subjects. The model identified four CpGs sites as the most relevant for the discrimination of FSHD subjects and showed high metrics values (accuracy: 0.94, sensitivity: 0.93, specificity: 0.96). Two additional models were developed to differentiate patients with lower D4Z4 size and patients who might carry pathogenic variants in FSHD genes, respectively. Overall, the present model enables an accurate classification of FSHD patients, providing additional evidence for DNA methylation as a powerful disease biomarker that could be employed for prioritizing subjects to be tested for FSHD.
