👤 Fortunata Carbone

Cholestatic liver diseases are a heterogeneous group of conditions that can remain unexplained despite a comprehensive diagnostic assessment. Genetic disorders may underlie many of these unexplained adult-onset cholestasis cases. However, genetic testing in adults has been focused on genes linked to progressive familial intrahepatic cholestasis (PFIC). This study evaluated the diagnostic utility of whole exome sequencing (WES) by targeting a broader set of genes beyond PFIC genes. Adults with unexplained cholestatic liver disease from one tertiary center underwent WES. Pathogenic and rare damaging variants in candidate cholestatic and liver disease genes were prioritized, and genotype-phenotype correlations were conducted. Twenty-one patients with three distinct cholestatic phenotypes (recurrent lithiasis, intrahepatic cholestasis, and primary sclerosing cholangitis with unusual features) were included. WES yielded a genetic diagnosis of inherited cholestatic or liver disorder mimicking the cholestatic phenotype in 5 cases (23.8%). ABCB4 was the causative gene in 2 cases (40.0%), whereas genes outside the PFIC spectrum (ABCC2, PPOX, APOB) accounted for the other 3 (60.0%). This study highlights the value of WES in the diagnostic workup of adult-onset cholestatic liver disease and expands our understanding of its genetic landscape, paving the way for larger-scale studies. Show less

Food addiction (FA) has gained more scientific attention but needs deeper understanding. Data indicates that the central melanocortin (MC) system through the MC4 receptor (MC4R) and its polymorphisms play a crucial role in the regulation of eating behaviour and in the motivation for the rewarding properties of food potentially leading to obesity. This may also contribute to the emergence of altered reward-related behaviors such as FA. The study aims to evaluate the genetic contribution of rs17782313, rs12970134, rs10871777, rs6567160, rs17700144 MC4R polymorphisms to the development of FA and to assess the association between these MC4R variations and clinical features. Eating (EDE-Q, BES, NEQ, GQ) and general psychopathology (BDI-II, STAI-S, DERS) were evaluated in patients with obesity with and without FA. Y-FAS 2.0 was used to assess FA. A blood sample was collected from all patients for the genotyping of MC4R polymorphisms. All the polymorphisms were equally distributed between groups except for rs17782313. A direct association between rs17782313 with FA was evident. Patients with FA and with C allele showed higher risk of FA compared to group without FA. There was a significant effect of rs17782313 on psychopathological variables in patients with FA. Allele C carriers exhibited higher anxiety and depression than T carriers. The rs17782313 of the MC4R showed an association with FA. A significant direct influence of C allele on anxiety and depression emerged in the group with FA but not in patients without FA. Show less

Neurodegenerative and inflammatory processes influence the clinical course of multiple sclerosis (MS). The β-site amyloid precursor protein cleaving enzyme 1 (BACE1) has been associated with cognitive dysfunction, amyloid deposition and neuroinflammation in Alzheimer's disease. We explored in a group of 50 patients with relapsing-remitting MS the association between the cerebrospinal fluid (CSF) levels of BACE1, clinical characteristics at the time of diagnosis and prospective disability after three-years follow-up. In addition, we assessed the correlations between the CSF levels of BACE 1, amyloid β (Aβ) 1-40 and 1-42, phosphorylated tau (pTau), lactate, and a set of inflammatory and anti-inflammatory molecules. BACE1 CSF levels were correlated positively with depression as measured with Beck Depression Inventory-Second Edition scale, and negatively with visuospatial memory performance evaluated by the Brief Visuospatial Memory Test-Revised. In addition, BACE CSF levels were positively correlated with Bayesian Risk Estimate for MS at onset, and with Expanded Disability Status Scale score assessed three years after diagnosis. Furthermore, a positive correlation was found between BACE1, amyloid β 42/40 ratio (Spearman's r = 0.334, p = 0.018, n = 50), pTau (Spearman's r = 0.304, p = 0.032, n = 50) and lactate concentrations (Spearman's r = 0.361, p = 0.01, n = 50). Finally, an association emerged between BACE1 CSF levels and a group of pro and anti-inflammatory molecules, including interleukin (IL)-4, IL-17, IL-13, IL-9 and interferon-γ. BACE1 may have a role in different key mechanisms such as neurodegeneration, oxidative stress and inflammation, influencing mood, cognitive disorders and disability progression in MS. Show less

The application of Machine Learning (ML) to genetic individual-level data represents a foreseeable advancement for the field, which is still in its infancy. Here, we aimed to evaluate the feasibility and accuracy of an ML-based model for disease risk prediction applied to Primary Biliary Cholangitis (PBC). Genome-wide significant variants identified in subjects of European ancestry in the recently released second international meta-analysis of GWAS in PBC were used as input data. Quality-checked, individual genomic data from two Italian cohorts were used. The ML included the following steps: import of genotype and phenotype data, genetic variant selection, supervised classification of PBC by genotype, generation of "if-then" rules for disease prediction by logic learning machine (LLM), and model validation in a different cohort. The training cohort included 1345 individuals: 444 were PBC cases and 901 were healthy controls. After pre-processing, 41,899 variants entered the analysis. Several configurations of parameters related to feature selection were simulated. The best LLM model reached an Accuracy of 71.7%, a Matthews correlation coefficient of 0.29, a Youden's value of 0.21, a Sensitivity of 0.28, a Specificity of 0.93, a Positive Predictive Value of 0.66, and a Negative Predictive Value of 0.72. Thirty-eight rules were generated. The rule with the highest covering (19.14) included the following genes: RIN3, KANSL1, TIMMDC1, TNPO3. The validation cohort included 834 individuals: 255 cases and 579 controls. By applying the ruleset derived in the training cohort, the Area under the Curve of the model was 0.73. This study represents the first illustration of an ML model applied to common variants associated with PBC. Our approach is computationally feasible, leverages individual-level data to generate intelligible rules, and can be used for disease prediction in at-risk individuals. Show less

In cats, mutations in myosin binding protein C (encoded by the MYBPC3 gene) have been associated with hypertrophic cardiomyopathy (HCM). However, the molecular mechanisms linking these mutations to HCM remain unknown. Here, we establish Drosophila melanogaster as a model to understand this connection by generating flies harboring MYBPC3 missense mutations (A31P and R820W) associated with feline HCM. The A31P and R820W flies displayed cardiovascular defects in their heart rates and exercise endurance. We used RNA-seq to determine which processes are misregulated in the presence of mutant MYBPC3 alleles. Transcriptome analysis revealed significant downregulation of genes encoding small nucleolar RNA (snoRNAs) in exercised female flies harboring the mutant alleles compared to flies that harbor the wild-type allele. Other processes that were affected included the unfolded protein response and immune/defense responses. These data show that mutant MYBPC3 proteins have widespread effects on the transcriptome of co-regulated genes. Transcriptionally differentially expressed genes are also candidate genes for future evaluation as genetic modifiers of HCM as well as candidate genes for genotype by exercise environment interaction effects on the manifestation of HCM; in cats as well as humans. Show less

The ligand hepatocyte growth factor/scatter factor (HGF) and its receptor tyrosine kinase, c-Met, are highly expressed in most human malignant mesotheliomas (MMs) and may contribute to their increased growth and viability. Based upon our observation that RNA silencing of fos-related antigen 1 (Fra-1) inhibited c-met expression in rat mesotheliomas (1), we hypothesized that Fra-1 was a key player in HGF-induced proliferation in human MMs. In three of seven human MM lines evaluated, HGF increased Fra-1 levels and phosphorylation of both extracellular signal-regulated kinase 5 (ERK5) and AKT that were inhibited by the phosphatidylinositol 3-kinase (PI3K) inhibitor, LY290042. HGF-dependent phosphorylation and Fra-1 expression were decreased after knockdown of Fra-1, whereas overexpression of Fra-1 blocked the expression of mitogen/extracellular signal-regulated kinase kinases (MEK)5 at the mRNA and protein levels. Stable MM cell lines using a dnMEK5 showed that basal Fra-1 levels were increased in comparison to empty vector control lines. HGF also caused increased MM cell viability and proliferating cell nuclear antigen (PCNA) expression that were abolished by knockdown of MEK5 or Fra-1. Data suggest that HGF-induced effects in some MM cells are mediated via activation of a novel PI3K/ERK5/Fra-1 feedback pathway that might explain tumor-specific effects of c-Met inhibitors on MM and other tumors. Show less