@article {10799, title = {In vivo microbiome and associated immune markers: New insights into the pathogenesis of vaginal dysbiosis.}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 02 02}, pages = {2307}, abstract = {

The microbiota fulfils a key role in the training and function of the immune system, which contributes to the symbiosis between the host and complex microbial communities. In this study, we characterized the interplay between vaginal bacteria and local immune mediators during dysbiosis in selected women of reproductive age who were grouped according to Nugent{\textquoteright}s criteria. The abundance of Gardnerella vaginalis and Bifidobacterium breve was increased in the intermediate dysbiotic status, while the presence of a plethora of non-resident bacteria characterized the group with overt vaginosis. In response to these increases, the anti-inflammatory IL1ra and pro-inflammatory IL2 increased, while the embryo trophic factors FGFβ and GMCSF decreased compared to the healthy milieu. A specific pattern, including IL1α, IL1β, IL8, MIG, MIP1α and RANTES, distinguished the intermediate group from the vaginosis group, while IL5 and IL13, which are secreted by Th2 cells, were significantly associated with the perturbation of the commensals Lactobacilli, Gardnerella and Ureaplasma. Summarizing, we postulate that although the dysbiotic condition triggers a pro-inflammatory process, the presence of a steady state level of Th2 may influence clinical manifestations. These results raise clinically relevant questions regarding the use of vaginal immunological markers as efficacious tools to monitor microbial alterations.

}, keywords = {Adult, Biomarkers, Cytokines, Dysbiosis, Female, Humans, Microbiota, Th2 Cells, Vagina}, issn = {2045-2322}, doi = {10.1038/s41598-018-20649-x}, author = {Campisciano, Giuseppina and Zanotta, Nunzia and Licastro, Danilo and De Seta, Francesco and Comar, Manola} } @article {10542, title = {Identification of proteins with different abundance associated with cell migration and proliferation in leiomyoma interstitial fluid by proteomics.}, journal = {Oncol Lett}, volume = {13}, year = {2017}, month = {2017 May}, pages = {3912-3920}, abstract = {

Uterine leiomyoma is the most common female reproductive tract benign tumor. Little is known about protein composition and changes in the leiomyoma interstitial fluid (IF). The present study focused on changes in protein abundance in the IF of leiomyoma. Leiomyoma IFs and adjacent myometrial IFs were obtained and analyzed by two-dimensional electrophoresis (2-DE) coupled with mass spectrometry and western blotting for 2-DE data validation. A total of 25 unique proteins were observed to change significantly (P<0.05). Of these proteins with different abundance, 22 had not been previously identified in leiomyoma IF. analysis predicted that three of these proteins were secreted via classical mechanisms, while 22 were secreted via non-classical mechanisms. Ingenuity Pathway Analysis identified 17 proteins associated with cellular migration and proliferation. Among these, phosphoglycerate mutase 1 had not been previously associated with leiomyoma. The abundance of seven proteins was further validated by western blotting. A comparative proteomic approach identified a number of proteins associated with cellular migration and proliferation, with changes in abundance in IF likely to be involved in tumor development. Further studies will be required to investigate the role of these proteins in leiomyoma IF and their possible association with tumor development and growth.

}, issn = {1792-1074}, doi = {10.3892/ol.2017.5943}, author = {Ura, Blendi and Scrimin, Federica and Franchin, Cinzia and Arrigoni, Giorgio and Licastro, Danilo and Monasta, Lorenzo and Ricci, Giuseppe} } @article {3499, title = {Next generation sequencing in nonsyndromic intellectual disability: from a negative molecular karyotype to a possible causative mutation detection.}, journal = {Am J Med Genet A}, volume = {164A}, year = {2014}, month = {2014 Jan}, pages = {170-6}, abstract = {

The identification of causes underlying intellectual disability (ID) is one of the most demanding challenges for clinical Geneticists and Researchers. Despite molecular diagnostics improvements, the vast majority of patients still remain without genetic diagnosis. Here, we report the results obtained using Whole Exome and Target Sequencing on nine patients affected by isolated ID without pathological copy number variations, which were accurately selected from an initial cohort of 236 patients. Three patterns of inheritance were used to search for: (1) de novo, (2) X-linked, and (3) autosomal recessive variants. In three of the nine proband-parent trios analyzed, we identified and validated two de novo and one X-linked potentially causative mutations located in three ID-related genes. We proposed three genes as ID candidate, carrying one de novo and three X-linked mutations. Overall, this systematic proband-parent trio approach using next generation sequencing could explain a consistent percentage of patients with isolated ID, thus increasing our knowledge on the molecular bases of this disease and opening new perspectives for a better diagnosis, counseling, and treatment.

}, keywords = {Computational Biology, Exome, Female, Genes, Recessive, Genes, X-Linked, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, Humans, Intellectual Disability, Karyotype, Male, Mutation, Workflow}, issn = {1552-4833}, doi = {10.1002/ajmg.a.36274}, author = {Athanasakis, Emmanouil and Licastro, Danilo and Faletra, Flavio and Fabretto, Antonella and Dipresa, Savina and Vozzi, Diego and Morgan, Anna and d{\textquoteright}Adamo, Adamo P and Pecile, Vanna and Biarn{\'e}s, Xevi and Gasparini, Paolo} } @article {1967, title = {Molecular diagnosis of Usher syndrome: application of two different next generation sequencing-based procedures.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e43799}, abstract = {

Usher syndrome (USH) is a clinically and genetically heterogeneous disorder characterized by visual and hearing impairments. Clinically, it is subdivided into three subclasses with nine genes identified so far. In the present study, we investigated whether the currently available Next Generation Sequencing (NGS) technologies are already suitable for molecular diagnostics of USH. We analyzed a total of 12 patients, most of which were negative for previously described mutations in known USH genes upon primer extension-based microarray genotyping. We enriched the NGS template either by whole exome capture or by Long-PCR of the known USH genes. The main NGS sequencing platforms were used: SOLiD for whole exome sequencing, Illumina (Genome Analyzer II) and Roche 454 (GS FLX) for the Long-PCR sequencing. Long-PCR targeting was more efficient with up to 94\% of USH gene regions displaying an overall coverage higher than 25{\texttimes}, whereas whole exome sequencing yielded a similar coverage for only 50\% of those regions. Overall this integrated analysis led to the identification of 11 novel sequence variations in USH genes (2 homozygous and 9 heterozygous) out of 18 detected. However, at least two cases were not genetically solved. Our result highlights the current limitations in the diagnostic use of NGS for USH patients. The limit for whole exome sequencing is linked to the need of a strong coverage and to the correct interpretation of sequence variations with a non obvious, pathogenic role, whereas the targeted approach suffers from the high genetic heterogeneity of USH that may be also caused by the presence of additional causative genes yet to be identified.

}, keywords = {Child, Preschool, Exome, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Molecular Diagnostic Techniques, Pilot Projects, Sequence Analysis, DNA, Usher Syndromes}, issn = {1932-6203}, doi = {10.1371/journal.pone.0043799}, author = {Licastro, Danilo and Mutarelli, Margherita and Peluso, Ivana and Neveling, Kornelia and Wieskamp, Nienke and Rispoli, Rossella and Vozzi, Diego and Athanasakis, Emmanouil and D{\textquoteright}Eustacchio, Angela and Pizzo, Mariateresa and D{\textquoteright}Amico, Francesca and Ziviello, Carmela and Simonelli, Francesca and Fabretto, Antonella and Scheffer, Hans and Gasparini, Paolo and Banfi, Sandro and Nigro, Vincenzo} }