Targeted DNA methylation by homology-directed repair in mammalian cells. Transcription reshapes methylation on the repaired gene.

We report that homology-directed repair of a DNA double-strand break within a single copy Green Fluorescent Protein (GFP) gene in HeLa cells alters the methylation pattern at the site of recombination. DNA methyl transferase (DNMT)1, DNMT3a and two proteins that regulate methylation, Np95 and GADD45A, are recruited to the site of repair and are responsible for selective methylation of the promoter-distal segment of the repaired DNA. The initial methylation pattern of the locus is modified in a transcription-dependent fashion during the 15\u201320 days following repair, at which time no further changes in the methylation pattern occur. The variation in DNA modification generates stable clones with wide ranges of GFP expression. Collectively, our data indicate that somatic DNA methylation follows homologous repair and is subjected to remodeling by local transcription in a discrete time window during and after the damage. We propose that DNA methylation of repaired genes represents a DNA damage code and is source of variation of gene expression

A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome

Functional outcomes and clinical strength assessment after infraspinatus-sparing surgical approach to scapular fracture: Does it really make a difference?

Background: Surgical treatment of scapular fractures with posterior approach is frequently associated with postoperative infraspinatus hypotrophy and weakness. The aim of this retrospective study is to compare infraspinatus strength and functional outcomes in patients treated with the classic Judet versus modified Judet approach for scapular fracture. Patients and methods: 20 cases with scapular neck and body fracture treated with posterior approach for lateral border plate fixation were reviewed. In 11 of 20 cases, we used the modified Judet approach (MJ group), and in 9 cases we used the classic Judet approach (CJ group). All fractures were classified according to the AO classification system. At follow-up examinations, patients had X-ray assessment with acromiohumeral distance (AHD) measurement, clinical evaluation, active range of motion (ROM) examination, Constant Shoulder Score, and Disability of the Arm, Shoulder and Hand (DASH) Score. Infraspinatus strength assessment was measured using a dynamometer during infraspinatus strength test (IST) and infraspinatus scapular retraction test (ISRT). Results: Demographic data did not significantly differ between the CJ group and MJ group, except for mean follow-up, which was 4.15\ua0years in the CJ group and 2.33 in the MJ group (p\ua0<\ua00.001). All X-ray examinations showed fracture healing. AHD was significantly decreased in the CJ group (p\ua0=\ua00.006). We did not find significant differences in active ROM between the MJ and CJ groups in the injured arm (p\ua0<\ua00.05). The Constant Score was 75.83 (\ub114.03) in the CJ group and 82.75 (\ub110.72) in the MJ group (p\ua0=\ua00.31); DASH Score was 10.16 in the CJ group and 6.25 in the MJ group (p\ua0=\ua00.49). IST showed mean strength of 8.38\ua0kg (\ub11.75) in the MJ group and 4.61\ua0kg (\ub11.98) in the CJ group (p\ua0=\ua00.002), ISRT test was 8.7 (\ub11.64) in the MJ group and 4.95 (\ub12.1) in the CJ group (p\ua0=\ua00.002). Infraspinatus hypotrophy was detected during inspection in six patients (five in the CJ group and one in the MJ group); it was related to infraspinatus strength weakness in IST and ISRT (p\ua0<\ua00.001). Conclusions: Infraspinatus-sparing surgical approach for scapular fracture avoids infraspinatus hypotrophy and external-rotation strength weakness. We suggest use of the modified Judet approach for scapular fracture and to restrict the classic Judet approach to only when the surgeon believes that the fracture is not easily reducible with a narrower exposure. Level of evidence: Level\ua0IV

Role of prothrombotic polymorphisms in successful or unsuccessful aging

The study of the genetic profile of centenarians aims to identify the genes and allelic variants which may influence a greater life expectancy and that can be considered as predisposing factors associated to the aging diseases, such as Alzheimer. Centenarians, that represent a cohort of selected survivors, show an hypercoagulability state characterised by striking signs of high coagulation enzyme activity, as directly assessed by the tested higher plasma level of some important factors involved in the haemostasis balance. Anyway, these individuals seem to have a reduced susceptibility to dementia, as well as to cardiovascular events. In this study we analyze the frequencies of Leiden Factor V polymorphism (G1691A), and G20210A of prothrombin (FII) in three cohorts of subjects: patients with Alzheimer\u2019s disease (unsuccessful aging), nonagenarians (successful aging) and young healthy controls, to assess whether allelic variants associated to the modification of haemostatic system function, may play a role in the protection or susceptibility to Alzheimer disease, as well as to reach a successful aging. No significant differences were observed in the frequencies of the three groups studied. These results indicate that the presence or absence of the gene variants examined did not influence the achievement of advanced age and are not risk factors for Alzheimer\u2019s disease. The state of hypercoagulability and the possession of these risk alleles appear to be compatible with the achievement of longevity and are not implied as risk factors in Alzheimer disease development

Delphi survey on conventional conservative treatment of functional posterior shoulder instability

Background: Posterior shoulder instability is caused by structural or functional defects. While the former are mostly treated surgically, physiotherapy is considered the treatment of choice in functional shoulder instability. However, it often has limited success unless very specific and intensive training programs are applied by trained experts. Currently, there is no consensus on the treatment of functional posterior shoulder instability. Objective: To improve treatment of this pathology, a&nbsp;standardized treatment recommendation is required to serve as a&nbsp;guideline for physiotherapy. The aim of this study was to establish expert consensus for treatment recommendations for functional posterior shoulder instability. Design: The Delphi survey technique was employed. Methods: A&nbsp;standardized training program for treatment of functional posterior shoulder instability was developed by a&nbsp;local expert committee. Two rounds of an online Delphi survey were then conducted. The panel of the Delphi survey comprised nine leading scientific experts in the field of functional shoulder instability who treat patients with shoulder-related problems conservatively and operatively. Results: The response rate was 100% and there were no dropouts. The final program consists of three groups of exercises with increasing difficulty. The exercises are mostly easy to perform and focus on the scapula-retracting muscles and the muscles responsible for external rotation of the shoulder. The treatment program should be executed under the supervision of a&nbsp;therapist at the beginning and later may be performed by the patients themselves. Conclusion: Consensus on a&nbsp;new exercise guideline dedicated to the treatment of functional posterior shoulder instability was achieved. This guideline should not only help to treat this challenging pathology but also provide a&nbsp;starting point for further scientific research and ongoing improvement

Detection of specific antibodies against toscana virus among blood donors in northeastern Italy and correlation with sand fly abundance in 2014

Toscana virus (TOSV) is a Phlebovirus transmitted by phlebotomine sand flies and is an important etiological agent of summer meningitis in the Mediterranean basin. Since TOSV infection is often asymptomatic, we evaluated the seroprevalence in blood donors (BDs) in the Bologna and Ferrara provinces (Northeastern Italy)\u2014the areas with the highest and lowest numbers of TOSV neuroinvasive cases in the region, respectively. A total of 1208 serum samples from BDs were collected in April\u2013June 2014 and evaluated for the presence of specific TOSV-IgG by ELISA. The IgG-reactive samples were confirmed by indirect immunofluorescence assay (IIF) and by microneutralization test (MN). Serum samples were defined as positive for anti-TOSV IgG when reactive by ELISA and by at least one second-level test; TOSV seroprevalence was 6.8% in the Bologna province, while no circulation of TOSV was detected in the Ferrara province. Sand fly abundance in 2014 was also estimated by a geographic information system using a generalized linear model applied to a series of explanatory variables. TOSV seroprevalence rate was strongly associated with the sand fly abundance index in each municipality, pointing out the strong association between sand fly abundance and human exposure to TOSV

Genetic Characterization of Cancer of Unknown Primary Using Liquid Biopsy Approaches

Cancers of unknown primary (CUPs) comprise a heterogeneous group of rare metastatic tumors whose primary site cannot be identified after extensive clinical\u2013pathological investigations. CUP patients are generally treated with empirical chemotherapy and have dismal prognosis. As recently reported, CUP genome presents potentially druggable alterations for which targeted therapies could be proposed. The paucity of tumor tissue, as well as the difficult DNA testing and the lack of dedicated panels for target gene sequencing are further relevant limitations. Here, we propose that circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) could be used to identify actionable mutations in CUP patients. Blood was longitudinally collected from two CUP patients. CTCs were isolated with CELLSEARCH\uae and DEPArrayTM NxT and Parsortix systems, immunophenotypically characterized and used for single-cell genomic characterization with Ampli1TM kits. Circulating cell-free DNA (ccfDNA), purified from plasma at different time points, was tested for tumor mutations with a CUP-dedicated, 92-gene custom panel using SureSelect Target Enrichment technology. In parallel, FFPE tumor tissue was analyzed with three different assays: FoundationOne CDx assay, DEPArray LibPrep and OncoSeek Panel, and the SureSelect custom panel. These approaches identified the same mutations, when the gene was covered by the panel, with the exception of an insertion in APC gene. which was detected by OncoSeek and SureSelect panels but not FoundationOne. FGFR2 and CCNE1 gene amplifications were detected in single CTCs, tumor tissue, and ccfDNAs in one patient. A somatic variant in ARID1A gene (p.R1276 17) was detected in the tumor tissue and ccfDNAs. The alterations were validated by Droplet Digital PCR in all ccfDNA samples collected during tumor evolution. CTCs from a second patient presented a pattern of recurrent amplifications in ASPM and SEPT9 genes and loss of FANCC. The 92-gene custom panel identified 16 non-synonymous somatic alterations in ccfDNA, including a deletion (I1485Rfs 1719) and a somatic mutation (p. A1487V) in ARID1A gene and a point mutation in FGFR2 gene (p.G384R). Our results support the feasibility of non-invasive liquid biopsy testing in CUP cases, either using ctDNA or CTCs, to identify CUP genetic alterations with broad NGS panels covering the most frequently mutated genes