Exon identity influences splicing induced by exonic variants and in silico prediction efficacy

BackgroundMinigenes and in silico prediction tools are commonly used to assess the impact on splicing of CFTR variants. Exon skipping is often neglected though it could impact the efficacy of targeted therapies. The aim of the study was to identify exon skipping associated with CFTR variants and to evaluate in silico predictions of seven freely available software.MethodsCFTR basal exon skipping was evaluated on endogenous mRNA extracted from non-CF nasal cells and on two CFTR minigene banks. In silico tools and minigene systems were used to evaluate the impact of CFTR exonic variants on exon skipping.ResultsData showed that out of 65 CFTR variants tested, 26 enhanced exon skipping and that in silico prediction efficacy was of 50%-66%. Some in silico tools presented predictions with a bias towards the occurrence of splicing events while others presented a bias towards the absence of splicing events (non-detection including true negatives and false negatives). Classification of exons depending on their basal exon skipping level increased prediction rates up to 80%.ConclusionThis study indicates that taking basal exon skipping into account could orientate the choice of the in silico tools to improve prediction rates. It also highlights the need to validate effects using in vitro assays or mRNA studies in patients. Eventually, it shows that variant-guided therapy should also target exon skipping associated with variants.     

Distinct immunopathological mechanisms of EBV-positive and EBV-negative posttransplant lymphoproliferative disorders

EBV-positive and EBV-negative posttransplant lymphoproliferative disorders (PTLDs) arise in different immunovirological contexts and might have distinct pathophysiologies. To examine this hypothesis, we conducted a multicentric prospective study with 56 EBV-positive and 39 EBV-negative PTLD patients of the K-VIROGREF cohort, recruited at PTLD diagnosis and before treatment (2013–2019), and compared them to PTLD-free Transplant Controls (TC, n = 21). We measured absolute lymphocyte counts (n = 108), analyzed NK- and T cell phenotypes (n = 49 and 94), and performed EBV-specific functional assays (n = 16 and 42) by multiparameter flow cytometry and ELISpot-IFNγ assays (n = 50). EBV-negative PTLD patients, NK cells overexpressed Tim-3; the 2-year progression-free survival (PFS) was poorer in patients with a CD4 lymphopenia (CD4⁺<300 cells/mm³, p <  .001). EBV-positive PTLD patients presented a profound NK-cell lymphopenia (median = 60 cells/mm³) and a high proportion of NK cells expressing PD-1 (vs. TC, p = .029) and apoptosis markers (vs. TC, p < .001). EBV-specific T cells of EBV-positive PTLD patients circulated in low proportions, showed immune exhaustion (p = .013 vs. TC) and poorly recognized the N-terminal portion of EBNA-3A viral protein. Altogether, this broad comparison of EBV-positive and EBV-negative PTLDs highlight distinct patterns of immunopathological mechanisms between these two diseases and provide new clues for immunotherapeutic strategies and PTLD prognosis.     

Differential-effects of transforming growth-factor-Beta-1 on protein-levels of p21 waf and cdk-2 and on cdk-2 kinase-activity in human rd and ccl64 mink lung-cells

Currently, the cyclin-dependent kinase inhibitor p21 WAF-1 is considered to be a crucial downstream effector in the p53-specific pathway of negative growth control in mammalian cells. Wild-type p53, but not mutant forms of this protein, transactivate the WAF-1 gene. We show a correlation between growth-inhibition and induction of WAF-1 protein expression following transforming growth factor-beta 1 (TGF-beta 1) treatment of two human tumour cell lines devoid of wild-type p53 protein and in SV40-transformed WI38 fibroblasts. Inversely, TGF-beta 1 treatment of normal WI38 fibroblasts stimulates their growth and represses WAF-1 protein synthesis. As the mink lung epithelial CCL64 cell line is frequently used in TGF-B studies we included it in this study: TGF-beta 1 growth-inhibition is accompanied by induction of WAF-1 synthesis concomitantly with a reduction of cdk2 synthesis and of its histone kinase activity. However in the human tumour line RD, TGF-beta 1 did not affect cdk-2 protein levels but did reduce its histone kinase activity.     

Beta-amyloid precursor protein is detectable on monocytes and is increased in Alzheimer's disease

Using the anti-beta-amyloid precursor protein (betaAPP) monoclonal antibodies 4G8, 6E10 and 22C11 and flow cytometry, we report that human circulating peripheral blood monocytes display surface immunoreactivity for betaAPP. In contrast, circulating lymphocytes do not possess cell surface betaAPP immunoreactivity, despite similar levels of betaAPP expression. Immunoblotting analysis showed that monocytes, but not lymphocytes, possess an 82 kDa C-terminal betaAPP fragment consistent with a processed transmembrane species. Monocyte surface betaAPP was upregulated approximately threefold by activation with lipopolysaccharide and interferon-gamma, activation did not produce detectable betaAPP on the cell surface of lymphocytes. Surface betaAPP immunoreactivity was reduced in a normal aged population compared to normal young controls (Young = 81.07 +/- 13.67 mean fluorescence units, Aged = 36.74 +/- 3.81, p < 0.01), but was significantly increased in AD subjects compared to age-matched healthy controls (AD = 60.31 +/- 7.42, p < 0.05). Our data suggest that a proportion of peripheral A beta may be derived from monocyte/macrophages, and that defects in brain cell processing of betaAPP in AD may be shared by this readily accessible peripheral cell.     

Sinus mucoceles and surgery in iatrogenic diseases

The increasing number of mucocele cases treated by the authors during the past ten years coincide with the expansion of functional endoscopic sinus surgery (FESS). The aim of this study is to evaluate the iatrogenic characteristics of this surgery by analysing the locations, time of development and the potential pathogenic factors of sinus mucoceles. Forty-two sinus mucoceles were operated in our department. These mucoceles were most frequently found in the anterior ethmoido-frontal system. Eleven patients had a history of endonasal ethmoidectomy mainly due to nasal polyposis. The time of mucocele formation after initial FESS (< 22 months) seems to be shorter than after exonasal sinus surgery or trauma (< 10 years). Endoscopic and CT-scan revealed different types of sinus obstruction findings: nasofrontal duct occlusion due to a fibrosis and osteogenic scar tissue process, or anterior ethmoid synechia in the case of ethmoido-frontal sinus mucocele, uncinate process fragment or scar tissue duct occlusion as far as maxillary sinus mucocele were concerned. We conclude that there seems to be a correlation between the expansion of FESS and the increasing number of mucocele cases. However, in this context it has to taken into consideration, that our department treats a considerable number of sinus pathology. Anterior ethmoid seems to be a favourable area for sinus mucocele formation. In order to prevent mucocele, it is essential to carry out FESS with great precaution. If endonasal surgery is performed, particularly in the anterior ethmoid, a close endoscopic follow-up, completed by radiological examinations, where necessary, must be ensured.     

Monitoring universal precautions: a new assessment tool.

OBJECTIVES: Two pilot studies were conducted to produce efficacy data on an observational tool designed to assess the use of Universal Precautions (UP) in patient care settings. The instrument addresses barrier precautions, hand-washing, handling of sharps, and avoidance of unprotected mouth to mouth resuscitation. DESIGN: The Universal Precautions Assessment Tool was submitted to a panel of 3 experts to establish consensual validity. It was pilot tested by 2 simultaneous observers to establish interrater reliability. SETTING: Pilot Study I was conducted in 3 different units within a 100-bed U.S. Army hospital. Pilot Study II was conducted in the emergency department of a large university-based hospital. PARTICIPANTS: Subjects observed were registered nurses providing acute patient care. RESULTS: Two simultaneous raters calculated UP compliance rates of 76.4% and 78.6%, respectively, for 9 nurses in Pilot Study I, and 62% and 65%, respectively, for 5 nurses in Pilot Study II. The intraclass correlation coefficient for the raters' scores in Pilot Study I was 0.992 with a 95% confidence interval (0.979, 0.997). Consensual validity was established. CONCLUSIONS: The instrument has acceptable interrater reliability under the conditions used. Limitations to use include the possibility of a Hawthorne effect and the fact that assessing proper implementation of UP occasionally relies on a "judgment call" by the observer. With test conditions adjusted to minimize these limitations and with proper consideration of sample size, the tool can be used by researchers and by monitors of hospital quality control to measure UP compliance of caregivers individually or collectively.     

The N170 occipito-temporal component is delayed and enhanced to inverted faces but not to inverted objects: an electrophysiological account of face-specific processes in the human brain

Behavioral studies have shown that picture-plane inversion impacts face and object recognition differently, thereby suggesting face-specific processing mechanisms in the human brain. Here we used event-related potentials to investigate the time course of this behavioral inversion effect in both faces and novel objects. ERPs were recorded for 14 subjects presented with upright and inverted visual categories, including human faces and novel objects (Greebles). A N170 was obtained for all categories of stimuli, including Greebles. However, only inverted faces delayed and enhanced N170 (bilaterally). These observations indicate that the N170 is not specific to faces, as has been previously claimed. In addition, the amplitude difference between faces and objects does not reflect face-specific mechanisms since it can be smaller than between non-face object categories. There do exist some early differences in the time-course of categorization for faces and non-faces across inversion. This may be attributed either to stimulus category per se (e.g. face-specific mechanisms) or to differences in the level of expertise between these categories.