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Introduction: In the last decade, cancer immunotherapy has delivered impressive results in clinical settings. However, its efficacy has not been consistent probably because of several environmental and genetic factors influencing the outcome. Many studies have indicated that intestinal microbiota could affect the outcome of immune checkpoint inhibitors-based immunotherapy, both in animal models and patients. In particular, the Bifidobacterium genus seems to have a role as a positive regulator of in vivo antitumor immunity by promoting proinflammatory signals in innate immune cells. According to the considerable evidence that demonstrated its crucial role in the carcinogenesis and, overall, in the response to immunotherapy, we decided to use a commercial probiotic and grow its principal strain, the Bifidobacterium longum BB-536, in order to test its capability to affect antitumoral immune responses. Methods: Prior to in vivo studies, we carried out a feasibility evaluation study to test in vitro, antitumoral effects of the isolated probiotic strain. Tumor cell viability was used as parameter to determine Bifidobacterium longum BB-536 anti-proliferative ability before or after heat inactivation. Results: Interestingly, we found that B. longum inhibits cell growth, both in mouse melanoma B16-OVA and colorectal CT26 cells, showing a more pronounced effect on the latter ones. Conclusion: This preliminary evaluation of live and heat-inactivated probiotic in tumor cell lines indicates a potential cell growth inhibitory effect of these bacterial strains and encourage further studies in mouse models.

In recent years, the development and the huge diffusion of Next Generation Sequencing (NGS)-based techniques has allowed the study of microbial communities at a previously unimaginable resolution level. Consequently, the knowledge of the role and functions of the human microbiota in various body sites has increased, identifying several fundamental roles for the microbiota in the development and maintenance of body homeostasis, also in relation to various ages of life. On the other hand, a number of microbiota qualitative and/or quantitative alterations have been associated with several diseases, and the trend is increasing. Since targeted interventions can modify the microbiota, the definition of its composition in physiological and pathological conditions acquires crucial importance for the development of new diagnostic tools and/or therapeutic approaches aimed at manipulating the microbiota. In this context, the definition of standardized protocols and common guidelines to study the microbiota, and therefore the role of Laboratory Medicine, appears to be fundamental for the diffusion of metagenomic analyses in diagnostic contexts and will acquire greater relevance in the near future.

Communication is becoming more important than ever for health care and health care professionals, as the recent COVID-19 pandemic has dramatically highlighted. The fast evolution of the mass and social media and the continuous development of new health-related platforms and applications are imposing new challenges that involve also laboratory medicine and that need to be carefully considered. In fact, these novel, fast and effective strategies of communication are inherently prone to the risk of publishing misleading, incorrect or fake information which can spread uncontrollably and diffuse all over the world in a very short time. However, social media are undoubtedly a great opportunity to communicate, in a responsible and credible way, health-related data and scientific updates and discoveries. As for the therapeutic alliance, it is now required to establish an "information alliance" between different healthcare professionals which, based on a trustworthy relationship, will allow the correct diffusion of health-related information and will contribute to citizens' education.

Over 15% of couples worldwide suffer from infertility and in 50% of cases a male factor is found. According to the World Health Organization, sperm analysis is the most appropriate test to assess male infertility. Since quite often, the conventional semen parameters are related to sperm DNA damage, the integration of this evaluation with sperm DNA fragmentation (SDF) could independently predict the sperm reproductive potential. Unfortunately, this analysis has not entered into routine clinical practice. The aim of this review is to discuss the importance of the SDF analysis and its clinical implication and to evaluate the extrinsic and intrinsic factors that affect the DNA fragmentation. In addition, principles and protocols of different methods used to evaluate and quantify the SDF are reviewed; advantages and disadvantages of different methods are reported.

This glossary has been conceived to help readers, who are less experienced with molecular biology, to approach this field of laboratory medicine, which is gaining increasing importance in the analytical and diagnostic processes. The glossary is organized into two separate sections: general terms of molecular biology and clinical molecular biology (molecular biology techniques, and molecular diagnostic testing). For some of the terms, a link to articles published in Biochimica Clinica, where these terms are employed is included. For each term the corresponding English version is reported; in addition, all the entries of the glossary are listed in the Appendix both in Italian and in English alphabetical order.

We review the clinical molecular biology approach for the prevention of cardiological diseases, essentially via risk assessment at personal level by DNA analysis. Intense physical activity, particularly during athletic performances, can result in syncope or even cardiac arrest, often followed by sudden cardiac death. An approach to the prevention of such tragic events is predictive medicine (presence of pathogenic mutations in cardiac genes), besides the conventional tools used in cardiology (mainly electro and echocardiogram under stress conditions). Accordingly, we list the major cardiac diseases and their related genes and derivative proteins which are instrumental for normal heart function. Alterations can occur in ion channel genes, in genes encoding desmosomial and junctional proteins, sarcomeric and Z-disc proteins, proteins for the cytoskeleton at the nuclear envelope, and in genes encoding mitochondrial proteins. Thus, we constructed two sets of gene panels: one set to discriminate among confounding heart diseases, and another set based on a cost-benefit criterion according to the most or less frequent genes bearing pathogenic variants that entail a higher or lower predisposing risk. This approach should be used to monitor pre-participation athletes and also amateurs who belong to families in which at least 1-2 subjects are affected by cardiac alterations. The risk should be identified with the aim to monitor subjects in order to prevent cardiac arrest and even sudden cardiac death.

This document represents the second part of a glossary on molecular biology. In particular, the main laboratory techniques for molecular biology are be described. Indeed, recent technological advances made available a number of technologies featured by higher accuracy and sensitivity that are becoming commonly used in routine molecular diagnostics. Aiming to support less experienced readers, the terms related to the main molecular biology techniques are listed herein. For each term the corresponding English version is reported (see also the complete list, both in Italian and in English alphabetical order, reported in the Appendix). In addition, for some of the terms, a link to articles published in Biochimica Clinica, where they have been used, is reported.

Breast cancer (BC) is still the most common tumor in women worldwide. Up to 20-25% of all BCs are of hereditary-familial nature and can be related to germline predisposing-mutations of which the most relevant are present in the high penetrance-genes BRCA1 and BRCA2. These mutations escalate the lifetime risk of BCs and also of other cancers. Thus, their early identification in tumor-prone family members is important to improve the clinical management of patients and their families. In addition, despite their high penetrance, only a small fraction of patients carry BRCA1 or BRCA2 mutations. This suggests that familial BCs may be related to germline mutations in other high-, moderate- and low-penetrance cancer genes. Consequently, the request for laboratory methods able to detect cancer-related pathogenic mutations in a short time and with high accuracy and sensitivity is raised. Recent technological advances in next generation sequencing (NGS) methods development are showing their potential also in this field. Indeed, NGS-based approaches are now currently used for BRCA genes analysis superseding conventional approaches. Moreover, the possibility to simultaneously sequence a panel of target genes is effective to further investigate patients with a personal and/or family history suggestive for an inherited BCs but with no mutations after BRCA molecular test. Implementation of this second-level molecular screening in routine diagnostic workflow will increase the diagnostic sensitivity and improve the management of both patients and their families. In addition, these methodologies could lead to the identification of other BC-related genes, thereby increasing knowledge about hereditary BCs molecular bases.

[Laboratory Medicine: specialists of tomorrow] Laboratory Medicine rides the wave of technological progress, the metamorphosis of information systems and data management. The Young Specialist is not a mere observer, but rather takes a leading role in this change, taking advantage of the opportunities offered by “omics” technologies, capturing new ideas and innovative stimuli that lead to a new concept of work and research oriented to health and prevention. Thanks to the support of international web platforms, training and exchange programs supported by the International Scientific Societies and Federations that favor professional and scientific growth, Young Scientists work in a global context. In this scenario, the SIBioC Young Scientists Study Group, with the auspices of SIBioC, EFLM and IFCC, organized a meeting on "Laboratory Medicine: Specialists of tomorrow" with the aim of discussing and highlighting some of the most important challenges, such as technological progress, training and internationalization of young people. Finally, the future of laboratory medicine looks at a multidisciplinary approach that leads to integrated diagnosis, identification of the frail patient, the use of the Point of Care Testing as an indispensable tool in crisis areas, making the dialogue between physician and laboratory specialist a fundamental step for the diagnosis and treatment with the final aim of a better outcome for the patient.

Pituitary adenomas (PAs), usually benign lesions, can sometimes present with “aggressive” features (rapid growth, local invasiveness, scarce response to conventional treatments). Despite the fact that a few genetic alterations have been associated to this clinical behavior, the role of epigenetic modifications, mainly methylation and miRNAs activity, is now opening new frontiers in this field. We evaluated the methylation profile of 21 PA (11 GH-omas, 10 nonfunctioning tumors—NFPAs) samples from TNS surgery and 5 normal pituitaries, collected at our neurosurgery between 2015 and 2017. DNA was extracted and sequenced, selecting 184,841 target regions. Moreover, methylation profiles were correlated with demographic, radiological, and clinicopathological features. NFPAs showed higher methylation levels vs. GH-omas, with 178 differentially methylated regions (DMRs) mainly consisting of noncoding and intronic sequences, and mostly localized in the open sea regions. We also found three hypermethylated genes (C7orf50, GNG7, and BAHCC1) involved in tumorigenesis processes and potentially influencing pituitary tumor pathophysiology. Among the clinicopathological features, only the maximum diameter resulted significantly higher in NFPAs. Our data provide further evidence of the complex epigenetic background of pituitary tumors. In line with the current literature, we confirmed a significant prevalence of hypermethylation in NFPAs vs. GH-omas, whose pathophysiological consequence is yet to be defined.

BackgroundBreast cancer (BC) is the most common malignancy in women, in whom it reaches 20% of the total neoplasia incidence. Most BCs are considered sporadic and a number of factors, including familiarity, age, hormonal cycles and diet, have been reported to be BC risk factors. Also the gut microbiota plays a role in breast cancer development. In fact, its imbalance has been associated to various human diseases including cancer although a consequential cause-effect phenomenon has never been proven.MethodsThe aim of this work was to characterize the breast tissue microbiome in 34 women affected by BC using an NGS-based method, and analyzing the tumoral and the adjacent non-tumoral tissue of each patient.ResultsThe healthy and tumor tissues differed in bacterial composition and richness: the number of Amplicon Sequence Variants (ASVs) was higher in healthy tissues than in tumor tissues (p = 0.001). Moreover, our analyses, able to investigate from phylum down to species taxa for each sample, revealed major differences in the two richest phyla, namely, Proteobacteria and Actinobacteria. Notably, the levels of Actinobacteria and Proteobacteria were, respectively, higher and lower in healthy with respect to tumor tissues.ConclusionsOur study provides information about the breast tissue microbial composition, as compared with very closely adjacent healthy tissue (paired samples within the same woman); the differences found are such to have possible diagnostic and therapeutic implications; further studies are necessary to clarify if the differences found in the breast tissue microbiome are simply an association or a concausative pathogenetic effect in BC. A comparison of different results on similar studies seems not to assess a universal microbiome signature, but single ones depending on the environmental cohorts’ locations.

Physical activity, combined with adequate nutrition, is considered a protective factor against cardiovascular disease, musculoskeletal disorders, and intestinal dysbiosis. Achieving optimal performance requires a significantly high energy expenditure, which must be correctly supplied to avoid the occurrence of diseases such as muscle injuries, oxidative stress, and heart pathologies, and a decrease in physical performance during competition. Moreover, in sports activities, the replenishment of water, vitamins, and minerals consumed during training is essential for safeguarding athletes’ health. In this scenario, vitamins play a pivotal role in numerous metabolic reactions and some muscle biochemical adaptation processes induced by sports activity. Vitamins are introduced to the diet because the human body is unable to produce these micronutrients. The aim of this review is to highlight the fundamental role of vitamin supplementation in physical activity. Above all, we focus on the roles of vitamins A, B6, D, E, and K in the prevention and treatment of cardiovascular disorders, muscle injuries, and regulation of the microbiome.

Background: Polyethylene glycol (PEG) is recommended as first-line treatment of pediatric functional constipation. However, the oral route of administration is often poorly feasible in children mostly due to poor palatability. Promelaxin microenemas exert a topical evacuative action and may offer a valuable option in pediatric FC.Aim: To assess whether Promelaxin microenemas would be non-inferior to PEG 4000 in young children with FC.Methods: This is a randomized, open-label, multi-centric, non-inferiority trial enrolling infants and young children aged 6–48 months, with FC according to Rome III criteria. After 1 week of run in, children were randomized to 2 weeks of Promelaxin or PEG, followed by a 6-week on-demand treatment period. Primary endpoint was response rate to randomized treatment, with “response” defined as at least 3 evacuations per week and an average increase of at least one evacuation per week as compared to baseline. Safety, stool consistency and the analysis of fecal microbiota were secondary endpoints.Results: Out of the 158 patients who entered the trial, 153 patients were treated (77 and 76, PEG and Promelaxin arm, respectively). In the primary analysis, the 95% confidence interval (CI) for the treatment's effect lay entirely above the non-inferiority margin in both Full Set (FAS) and Per Protocol (PP) analyses, providing evidence of the non-inferiority of Promelaxin vs. PEG 4000 [response rate difference: 16.5% (CI 1.55–31.49%) and 11.03% (CI −5.58 to 27.64%), FAS and PP analyses, respectively]. Mean compliance to the randomized treatment was >80% in both arms. Secondary endpoints did not significantly differ between the two arms, except for the average number of total days of on-demand treatment that was significantly lower in the Promelaxin arm [14.6 (12.7) vs. 9.8 (9.1), mean (SD); primary endpoint responders in PEG and Promelaxin arm, respectively; p = 0.027]. Microbiota evenness significantly increased in the PEG 4000 arm at V4 as compared to the Promelaxin arm (p < 0.05). In addition, at V5, patients treated with PEG showed a significantly decreased microbiota density as compared to patients treated with Promelaxin (p = 0.036).Conclusions: Promelaxin microenemas are non-inferior to oral PEG in children with FC.Clinical Trial Registration:www.ClinicalTrials.gov, identifier: NCT02751411.

Fifteen percent of male infertility is associated with urogenital infections, several pathogens are able to alter the testicular and accessory glands’ microenvironment, resulting in the impairment of biofunctional sperm parameters. The purpose of this study was to assess the influence of urogenital infections on the quality of 53 human semen samples through standard analysis, microbiological evaluation, and molecular characterization of sperm DNA damage. The results showed a significant correlation between infected status and semen volume, sperm concentration, and motility. Moreover, a high risk of fragmented sperm DNA was demonstrated in the altered semen samples. Urogenital infections are often asymptomatic and thus an in-depth evaluation of the seminal sample can allow for both the diagnosis and therapy of infections while providing more indicators for male infertility management.

Laboratory medicine, along with genetic investigations in sports medicine, is taking on an increasingly important role in monitoring athletes’ health conditions. Acute or intense exercise can result in metabolic imbalances, muscle injuries or reveal cardiovascular disorders. This study aimed to monitor the health status of a basketball player with an integrated approach, including biochemical and genetic investigations and advanced imaging techniques, to shed light on the causes of recurrent syncope he experienced during exercise. Biochemical analyses showed that the athlete had abnormal iron, ferritin and bilirubin levels. Coronary Computed Tomographic Angiography highlighted the presence of an intramyocardial bridge, suggesting this may be the cause of the observed syncopes. The athlete was excluded from competitive activity. In order to understand if this cardiac malformation could be caused by an inherited genetic condition, both array-CGH and whole exome sequencing were performed. Array-CGH showed two intronic deletions involving MACROD2 and COMMD10 genes, which could be related to a congenital heart defect; whole exome sequencing highlighted the genotype compatible with Gilbert syndrome. However, no clear pathogenic mutations related to the patient’s cardiological phenotype were detected, even after applying machine learning methods. This case report highlights the importance and the need to provide exhaustive personalized diagnostic work up for the athletes in order to cover the cause of their malaise and for safeguarding their health. This multidisciplinary approach can be useful to create ad personam training and treatments, thus avoiding the appearance of diseases and injuries which, if underestimated, can become irreversible disorders and sometimes can result in the death of the athlete.

The current diagnostic path of infertile couples is long lasting and often ineffective. Genetic tests, in particular, appear as a limiting step due to their jeopardized use on one side, and to the limited number of genes evaluated on the other. In this context, the development and diffusion, also in routine diagnostic settings, of next generation sequencing (NGS)-based methods for the analyses of several genes in multiple subjects at a time is improving the diagnostic sensitivity of molecular analyses. Thus, we developed One4Two&reg, a custom NGS panel to optimize the diagnostic journey of infertile couples. The panel validation was carried out in three steps analyzing a total of 83 subjects. Interestingly, all the previously identified variants were confirmed, assessing the analytic sensitivity of the method. Moreover, additional pathogenic variants have been identified underlying the diagnostic efficacy of the proposed method. One4Two&reg, allows the simultaneous analysis of infertility-related genes, disease-genes of common inherited diseases, and of polymorphisms related to therapy outcome. Thus, One4Two&reg, is able to improve the diagnostic journey of infertile couples by simplifying the whole process not only for patients, but also for laboratories and reproduction specialists moving toward an even more personalized medicine.

International audience; The molecular complexity of human breast cancer (BC) renders the clinical management of the disease challenging. Long non-coding RNAs (lncRNAs) are promising biomarkers for BC patient stratification, early detection, and disease monitoring. Here, we identified the involvement of the long intergenic non-coding RNA 01087 (LINC01087) in breast oncogenesis. LINC01087 appeared significantly downregulated in triple-negative BCs (TNBCs) and upregulated in the luminal BC subtypes in comparison to mammary samples from cancer-free women and matched normal cancer pairs. Interestingly, deregulation of LINC01087 allowed to accurately distinguish between luminal and TNBC specimens, independently of the clinicopathological parameters, and of the histological and TP53 or BRCA1/2 mutational status. Moreover, increased expression of LINC01087 predicted a better prognosis in luminal BCs, while TNBC tumors that harbored lower levels of LINC01087 were associated with reduced relapse-free survival. Furthermore, bioinformatics analyses were performed on TNBC and luminal BC samples and suggested that the putative tumor suppressor activity of LINC01087 may rely on interferences with pathways involved in cell survival, proliferation, adhesion, invasion, inflammation and drug sensitivity. Altogether, these data suggest that the assessment of LINC01087 deregulation could represent a novel, specific and promising biomarker not only for the diagnosis and prognosis of luminal BC subtypes and TNBCs, but also as a predictive biomarker of pharmacological interventions.

Background Syndromic dilated cardiomyopathy (DCM) includes a group of complex disorders with a very heterogeneous genetic etiology, leading to delay in definitive diagnosis. Conversely, an early genetic diagnosis is very important in determining the disease course, the prognosis, and may guide personalized treatments and family counseling. Methods We analyzed two brothers with a multisystemic disorder, including dilated cardiomyopathy, diabetes, bilateral neurosensorial hearing loss, and optic atrophy, using different genetic approaches, namely mitochondrial DNA sequencing, comparative genomic hybridization‐array (a‐CGH) and whole exome sequencing (WES). Results Sequencing of the wide mitochondrial genome revealed, in both brothers, the known homoplasmic variant rs2853826 in the subunit 3 of the NADH dehydrogenase gene (MT‐ND3), whose pathogenicity was conflicting. Comparative genomic hybridization‐array analysis revealed in both patients and their father two heterozygous deletions in Phosphodiesterase 4d‐Interacting Protein (PDE4DIP) and Protocadherin‐related 15 (PCDH15) genes, respectively. The use of WES detected a pathogenetic mutation in ALMS1, enabling the definitive diagnosis of Alström syndrome. Conclusion We demonstrated how the diagnosis of a complex heterogeneous disease may be difficult, due to several overlapping manifestations and the possible interaction of more genetic variants that could lead to a more severe and complex phenotype. This paper strongly evidences how genomics is revolutionizing the diagnosis of rare complex disease, representing one of the most essential steps to enable a definitive diagnosis and to establish the etiology for diseases, such as syndromic DCM., The diagnosis of a complex heterogeneous disease may be difficult, due to several overlapping manifestations and the possible interaction of more genetic variants. By using different genetic approaches we obtained a definitive diagnosis of Alström syndrome in two brothers with a multisystemic disorder.

The purpose of this paper is to present a clinical and laboratory study of a family, in which a 12-year-old boy was examined to assess his health status before starting competitive sports. A variety of clinical and instrumental tests were used to evaluate the status of the heart and its functions. Using Sanger sequencing (SS), we sequenced six related genes to verify suspected arrhythmogenic right ventricular cardiomyopathy (ARVC) hypothesized at the cardiac assessment and, subsequently, by a next-generation sequencing (NGS)-based multi-gene panel for more paramount genetic risk of sudden cardiac death (SCD) assessment. SS revealed two variants in the PKP2 gene, one was inherited from the father and the other from the mother. The analysis on a large panel of genes (n = 138), putatively associated with sudden cardiac death, revealed, in the proband, a third variant in a different gene (DES) that encodes the protein desmin. Our results indicate that: i) NGS revealed a mutational event in a gene not conventionally screened as a first-line test in the presence of clinical suspicion of the arrhythmic disease; ii) a plurality of variants in different genes in the same subject (the proband) may increase the risk of heart disease; iii) in silico analysis with various methodological software and bioinformatic prediction tools indicates that the cumulative effects of the three variants in the same subject constitute an additional risk factor. This case report indicates that more pathogenic variants or likely pathogenic variants can contribute to the clinical phenotype of an individual, thereby contributing to the diagnosis and prognosis of inherited heart diseases.

Coeliac disease (CD) is a multifactorial autoimmune disorder and gut dysbiosis contributes to its pathogenesis. We previously profiled by 16S rRNA sequencing duodenal and oropharyngeal microbiomes in active CD (a-CD), gluten-free diet (GFD) patients, and controls (CO) and found significantly higher levels of Neisseria spp., with pro-inflammatory activities, in a-CD patients than in the other two groups. In this study, we developed a fast and simple qPCR-based method to evaluate the abundance of the oral Neisseria spp. and the diagnostic performances of the test in CD diagnosis. The Neisseria spp. abundances detected by quantitative PCR (qPCR) were: CO = 0.14, GFD = 0.15, a-CD = 2.08, showing a similar trend to those previously measured by next generation sequencing (NGS). In particular, Neisseria spp. values obtained by both methods were significantly higher (p < 0.001) in a-CD than in the other two groups GFD and CO—the latter almost overlapping. We calculated by ROC curve analysis the threshold of 1.12 ng/μL of Neisseria spp. to discriminate between CO+GFD and a-CD patients with 100% and 96.7% of diagnostic sensitivity and specificity, respectively. In conclusion, our data, if confirmed in other cohorts, suggest the q-PCR evaluation of oral Neisseria spp. could be a fast and simple method to assess CD-associated dysbiosis for diagnostic purposes.

The gut microbiota may have an impact on obesity. To date, the majority of studies in obese patients reported microbiota composition in stool samples. The aim of this study was to investigate the duodenal mucosa dysbiosis in adult obese individuals from Campania, a region in Italy with a very high percentage of obese people, to highlight microbial taxa likely associated with obesity. Duodenum biopsies were taken during upper gastrointestinal endoscopy in 19 obese (OB) and 16 lean control subjects (CO) and microbiome studied by 16S rRNA gene sequencing. Duodenal microbiome in our groups consisted of six phyla: Proteobacteria, Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes and Acidobacteria. Proteobacteria (51.1% vs. 40.1%) and Firmicutes (33.6% vs. 44.9%) were significantly (p < 0.05) more and less abundant in OB compared with CO, respectively. Oribacterium asaccharolyticum, Atopobium parvulum and Fusobacterium nucleatum were reduced (p < 0.01) and Pseudomonadales were increased (p < 0.05) in OB compared with CO. Receiver operating characteristic curve analysis showed Atopobium and Oribacterium genera able to discriminate with accuracy (power = 75% and 78%, respectively) OB from CO. In conclusion, increased Proteobacteria and decreased Firmicutes (Lachnospiraceae) characterized the duodenal microbiome of obese subjects. These data direct to further studies to evaluate the functional role of the dysbiotic-obese-associated signature.

Misfolded and abnormal β-sheets forms of wild-type proteins, such as cellular prion protein (PrPC) and amyloid beta (Aβ), are believed to be the vectors of neurodegenerative diseases, prion and Alzheimer’s disease (AD), respectively. Increasing evidence highlights the “prion-like” seeding of protein aggregates as a mechanism for pathological spread in AD, tauopathy, as well as in other neurodegenerative diseases, such as Parkinson’s. Mutations in both PrPC and Aβ precursor protein (APP), have been associated with the pathogenesis of these fatal disorders with clear evidence for their pathogenic significance. In addition, a critical role for the gut microbiota is emerging; indeed, as a consequence of gut−brain axis alterations, the gut microbiota has been involved in the regulation of Aβ production in AD and, through the microglial inflammation, in the amyloid fibril formation, in prion diseases. Here, we aim to review the role of microbiome (“the other human genome”) alterations in AD and prion disease pathogenesis.

Humans’ health is the result of a complex and balanced interplay between genetic factors, environmental stimuli, lifestyle habits, and the microbiota composition. The knowledge about their single contributions, as well as the complex network linking each to the others, is pivotal to understand the mechanisms underlying the onset of many diseases and can provide key information for their prevention, diagnosis and therapy. This applies also to reproduction. Reproduction, involving almost 10% of our genetic code, is one of the most critical human’s functions and is a key element to assess the well-being of a population. The last decades revealed a progressive decline of reproductive outcomes worldwide. As a consequence, there is a growing interest in unveiling the role of the different factors involved in human reproduction and great efforts have been carried out to improve its outcomes. As for many other diseases, it is now clear that the interplay between the underlying genetics, our commensal microbiome, the lifestyle habits and the environment we live in can either exacerbate the outcome or mitigate the adverse effects. Here, we aim to analyze how each of these factors contribute to reproduction highlighting their individual contribution and providing supporting evidence of how to modify their impact and overall contribution to a healthy reproductive status.

Non-alcoholic-fatty liver disease (NAFLD) is spreading worldwide. Specific drugs for NAFLD are not yet available, even if some plant extracts show beneficial properties. We evaluated the effects of a combination, composed by Berberis Aristata, Elaeis Guineensis and Coffea Canephora, on the development of obesity, hepatic steatosis, insulin-resistance and on the modulation of hepatic microRNAs (miRNA) levels and microbiota composition in a mouse model of liver damage. C57BL/6 mice were fed with standard diet (SD, n = 8), high fat diet (HFD, n = 8) or HFD plus plant extracts (HFD+E, n = 8) for 24 weeks. Liver expression of miR-122 and miR-34a was evaluated by quantitativePCR. Microbiome analysis was performed on cecal content by 16S rRNA sequencing. HFD+E-mice showed lower body weight (p &lt, 0.01), amelioration of insulin-sensitivity (p = 0.021), total cholesterol (p = 0.014), low-density-lipoprotein-cholesterol (p &lt, 0.001), alanine-aminotransferase (p = 0.038) and hepatic steatosis compared to HFD-mice. While a decrease of hepatic miR-122 and increase of miR-34a were observed in HFD-mice compared to SD-mice, both these miRNAs had similar levels to SD-mice in HFD+E-mice. Moreover, a different microbial composition was found between SD- and HFD-mice, with a partial rescue of dysbiosis in HFD+E-mice. This combination of plant extracts had a beneficial effect on HFD-induced NAFLD by the modulation of miR-122, miR-34a and gut microbiome.

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Background Cow's milk allergy (CMA) is one of the most common food allergies in children. Epigenetic mechanisms have been suggested to play a role in CMA pathogenesis. We shown that DNA methylation of Th1/Th2 cytokine genes and FoxP3 affects CMA disease course. Preliminary evidence suggest that also the miRNome could be implicated in the pathogenesis of allergy. Main study outcome was to comparatively evaluate miRNome in children with CMA and in healthy controls. Methods Peripheral blood mononuclear cells were obtained from children aged 4-18 months: 10 CMA patients, 9 CMA patients who outgrew CMA, and 11 healthy controls. Small RNA libraries were sequenced using a next-generation sequencing-based approach. Functional assessment of IL-4 expression was also performed. Results Among the miRNAs differently expressed, 2 were up-regulated and 14 were down-regulated in children with active CMA compared to healthy controls. miR-193a-5p resulted the most down-regulated miRNA in children with active CMA compared to healthy controls. The predicted targets of miR-193a-5p resulted up-regulated in CMA patients compared to healthy controls. Peripheral blood CD4+ T cells transfected with a miR193a-5 inhibitor showed a significant up-regulation of IL-4 mRNA and its protein expression. Children who outgrew CMA showed miRNA-193a-5p level, and its related targets expression, similar to that observed in healthy controls. Conclusions Our results suggest that miR-193a-5p is a post-transcriptional regulator of IL-4 expression and could have a role in IgE-mediated CMA. This miRNA could be a novel diagnostic and therapeutic target for this common form of food allergy in childhood. This article is protected by copyright. All rights reserved.

Genetic modifications during development of paediatric groups 3 and 4 medulloblastoma are responsible for their highly metastatic properties and poor patient survival rates. PRUNE1 is highly expressed in metastatic medulloblastoma group 3, which is characterized by TGF-β signalling activation, c-MYC amplification, and OTX2 expression. We describe the process of activation of the PRUNE1 signalling pathway that includes its binding to NME1, TGF-β activation, OTX2 upregulation, SNAIL (SNAI1) upregulation, and PTEN inhibition. The newly identified small molecule pyrimido-pyrimidine derivative AA7.1 enhances PRUNE1 degradation, inhibits this activation network, and augments PTEN expression. Both AA7.1 and a competitive permeable peptide that impairs PRUNE1/NME1 complex formation, impair tumour growth and metastatic dissemination in orthotopic xenograft models with a metastatic medulloblastoma group 3 cell line (D425-Med cells). Using whole exome sequencing technology in metastatic medulloblastoma primary tumour cells, we also define 23 common 'non-synonymous homozygous' deleterious gene variants as part of the protein molecular network of relevance for metastatic processes. This PRUNE1/TGF-β/OTX2/PTEN axis, together with the medulloblastoma-driver mutations, is of relevance for future rational and targeted therapies for metastatic medulloblastoma group 3. Genetic modifications during development of paediatric groups 3 and 4 medulloblastoma are responsible for their highly metastatic properties and poor patient survival rates. PRUNE1 is highly expressed in metastatic medulloblastoma group 3, which is characterized by TGF-β signalling activation, c-MYC amplification, and OTX2 expression. We describe the process of activation of the PRUNE1 signalling pathway that includes its binding to NME1, TGF-β activation, OTX2 upregulation, SNAIL (SNAI1) upregulation, and PTEN inhibition. The newly identified small molecule pyrimido-pyrimidine derivative AA7.1 enhances PRUNE1 degradation, inhibits this activation network, and augments PTEN expression. Both AA7.1 and a competitive permeable peptide that impairs PRUNE1/NME1 complex formation, impair tumour growth and metastatic dissemination in orthotopic xenograft models with a metastatic medulloblastoma group 3 cell line (D425-Med cells). Using whole exome sequencing technology in metastatic medulloblastoma primary tumour cells, we also define 23 common 'non-synonymous homozygous' deleterious gene variants as part of the protein molecular network of relevance for metastatic processes. This PRUNE1/TGF-β/OTX2/PTEN axis, together with the medulloblastoma-driver mutations, is of relevance for future rational and targeted therapies for metastatic medulloblastoma group 3. 10.1093/brain/awy039-video1 awy039media1 5742053534001

The aim of this study was to verify the reliability of a next generation sequencing (NGS)-based method as a strategy to detect all possible BRCA mutations, including large genomic rearrangements. Genomic DNA was obtained from a peripheral blood sample provided by a patient from Southern Italy with early onset breast cancer and a family history of diverse cancers. BRCA molecular analysis was performed by NGS, and sequence data were analyzed using two software packages. Comparative genomic hybridization (CGH) array was used as confirmatory method. A novel large duplication, involving exons 4–26, of BRCA2 was directly detected in the patient by NGS workflow including quantitative analysis of copy number variants. The duplication observed was also found by CGH array, thus confirming its extent. Large genomic rearrangements can affect the BRCA1/2 genes, and thus contribute to germline predisposition to familial breast and ovarian cancers. The frequency of these mutations could be underestimated because of technical limitations of several routinely used molecular analysis, while their evaluation should be included also in these molecular testing. The NGS-based strategy described herein is an effective procedure to screen for all kinds of BRCA mutations.

Clinical findings and data obtained in animal models indicate that nutrient uptake and exposure to environmental agents during pregnancy may affect fetal/newborn gestational programming, thereby resulting in obesity and/or obesity-related disorders in offspring. Human amniotic mesenchymal stem cells (hA-MSCs) differentiate into adipocytes and are thus a suitable model to investigate adipocyte functions in obesity. The aim of this study was to elucidate the miRNome of hA-MSCs and its contribution to obesity in pregnancy. To this aim we used the following: (i) high-resolution small RNA sequencing to characterize the microRNA (miRNA) profiles of hA-MSCs of 13 obese (Ob-) and 7 control (Co-) pregnant women at delivery; (ii) multiple-method integrated bioinformatics to predict the metabolic pathways potentially miRNA deregulated in Ob-hA-MSCs; and (iii) microarray mRNA expression profiling to verify obese-associated mRNA alterations. In summary, 12 miRNAs were differentially expressed between Ob-hA-MSCs and Co-hA-MSCs, with a multiple-methods bioinformatic consensus on miR-138-5p and miR-222-3p, which were overexpressed in Ob-hA-MSCs versus Co-hA-MSCs. The top 20 significant pathways predicted to be deregulated through miR-138-5p and/or miR-222-3p/target interaction included fat cell differentiation and deposits, lipid/carbohydrate homeostasis, response to stress, metabolic syndrome, heart disease, and ischemia. In conclusion, our finding of miR-138-5p/miR-222-3p overexpression in Ob-hA-MSCs, together with the transcriptomic data, suggests that these miRNAs in obese pregnancy could derange metabolic pathways previously found impaired in tissues from obese adults or in obesity-associated disorders and concur to modify gestational programming as has been demonstrated in animal models. This raises the possibility of using diet-based strategies to normalize the perinatal miRNome in obesity.

Background: The development of technologies that detect monogenic diseases in embryonic and fetal samples are opening novel diagnostic possibilities for preimplantation genetic diagnosis (PGD) and prenatal diagnosis (PND) thereby changing laboratory practice. Molecular diagnostic laboratories use different workflows for PND depending on the disease, type of biological sample, the presence of one or more known mutations, and the availability of the proband. Paternity verification and contamination analysis are also performed. The aim of this study was to test the efficacy of a single workflow designed to optimize the molecular diagnosis of monogenic disease in families at-risk of transmitting a genetic alteration. Methods: We used this strategy, which we designated “SEeMORE strategy” (Single-tube Electrophoresis analysis-based genotyping to detect MOnogenic diseases Rapidly and Effectively from conception to birth). It consists of a multiplex PCR that simultaneously carries out linkage analysis, direct analysis, maternal contamination and parenthood testing. We analyzed samples from previously diagnosed families for PND (cystic fibrosis or Duchenne muscular dystrophy) without, however, knowing the results. Results: The results obtained with the SEeMORE strategy concurred with those obtained with traditional PND. In addition, this strategy has several advantages: (i) use of one or a few cells; (ii) reduction of the procedure to 1 day; and (iii) a reduction of at least 2–3-fold of the analytic cost. Conclusions: The SEeMORE strategy is effective for the molecular diagnosis of monogenic diseases, irrespective of the amount of starting material and of the disease mutation, and can be used for PND and PGD.

Hypertrophic cardiomyopathy is a relatively frequent disease with a prevalence of 0.2% worldwide and a remarkable genetic heterogeneity, with more than 30 causative genes reported to date. Current PCR-based strategies are inadequate for genomic investigations involving many candidate genes. Here, we report a next-generation sequencing procedure associated with DNA sequence capture that is able to sequence 202 cardiomyopathy-related genes simultaneously. We developed a complementary data analysis pipeline to select and prioritize genetic variants. The overall procedure can screen a large number of target genes simultaneously, thereby potentially revealing new disease-causing and modifier genes. By using this procedure, we analyzed hypertrophic cardiomyopathy patients in a shorter time and at a lower cost than with current procedures. The specificity of the next-generation sequencing-based procedure is at least as good as other techniques routinely used for mutation searching, and the sensitivity is much better. Analysis of the results showed some novel variants potentially involved in the pathogenesis of hypertrophic cardiomyopathy: a missense mutation in MYH7 and a nonsense variant in INS-IGF2 (patient 1), a splicing variant in MYBPC3 and an indel/frameshift variant in KCNQ1 (patient 2), and two concomitant variations in CACNA1C (patient 3). Sequencing of DNA from the three patients within a pool allowed detection of most variants identified in each individual patient, indicating that this approach is a feasible and cost-effective procedure.

Increasing evidence points to a role for dysfunctional glutamate N-methyl-D-aspartate receptor (NMDAR) neurotransmission in schizophrenia. D-aspartate is an atypical amino acid that activates NMDARs through binding to the glutamate site on GluN2 subunits. D-aspartate is present in high amounts in the embryonic brain of mammals and rapidly decreases after birth, due to the activity of the enzyme D-aspartate oxidase (DDO). The agonistic activity exerted by D-aspartate on NMDARs and its neurodevelopmental occurrence make this D-amino acid a potential mediator for some of the NMDAR-related alterations observed in schizophrenia. Consistently, substantial reductions of D-aspartate and NMDA were recently observed in the postmortem prefrontal cortex of schizophrenic patients. Here we show that DDO mRNA expression is increased in prefrontal samples of schizophrenic patients, thus suggesting a plausible molecular event responsible for the D-aspartate imbalance previously described. To investigate whether altered D-aspartate levels can modulate schizophrenia-relevant circuits and behaviors, we also measured the psychotomimetic effects produced by the NMDAR antagonist, phencyclidine, in Ddo knockout mice (Ddo(-)(/-)), an animal model characterized by tonically increased D-aspartate levels since perinatal life. We show that Ddo(-/-) mice display a significant reduction in motor hyperactivity and prepulse inhibition deficit induced by phencyclidine, compared with controls. Furthermore, we reveal that increased levels of D-aspartate in Ddo(-/-) animals can significantly inhibit functional circuits activated by phencyclidine, and affect the development of cortico-hippocampal connectivity networks potentially involved in schizophrenia. Collectively, the present results suggest that altered D-aspartate levels can influence neurodevelopmental brain processes relevant to schizophrenia.