Biallelic germline DDX41 variants in a patient with bone dysplasia, ichthyosis, and dysmorphic features.

DDX41 (DEAD­box helicase 41) is a member of the largest family of RNA helicases. The DEAD-box RNA helicases share a highly conserved core structure and regulate all aspects of RNA metabolism. The functional role of DDX41 in innate immunity is also highly conserved. DDX41 acts as a sensor of viral DNA and activates the STING-TBK1-IRF3-type I IFN signaling pathway. Germline heterozygous variants in DDX41 have been reported in familial myelodysplasia syndrome (MDS)/acute myeloid leukemia (AML) patients; most patients also acquired a somatic variant in the second DDX41 allele. Here, we report a patient who inherited compound heterozygous DDX41 variants and presented with bone dysplasia, ichthyosis, and dysmorphic features. Functional analyses of the patient-derived dermal fibroblasts revealed a reduced abundance of DDX41 and abrogated activation of the IFN genes through the STING-type I interferon pathway. Genome-wide transcriptome analyses in the patient's fibroblasts revealed significant gene dysregulation and changes in the RNA splicing events. The patient's fibroblasts also displayed upregulation of periostin mRNA expression. Using an RNA binding protein assay, we identified DDX41 as a novel regulator of periostin expression. Our results suggest that functional impairment of DDX41, along with dysregulated periostin expression, likely contributes to this patient's multisystem disorder.

Loss of the endoplasmic reticulum protein Tmem208 affects cell polarity, development, and viability.

Nascent proteins destined for the cell membrane and the secretory pathway are targeted to the endoplasmic reticulum (ER) either posttranslationally or cotranslationally. The signal-independent pathway, containing the protein TMEM208, is one of three pathways that facilitates the translocation of nascent proteins into the ER. The in vivo function of this protein is ill characterized in multicellular organisms. Here, we generated a CRISPR-induced null allele of the fruit fly ortholog CG8320/Tmem208 by replacing the gene with the Kozak-GAL4 sequence. We show that Tmem208 is broadly expressed in flies and that its loss causes lethality, although a few short-lived flies eclose. These animals exhibit wing and eye developmental defects consistent with impaired cell polarity and display mild ER stress. Tmem208 physically interacts with Frizzled (Fz), a planar cell polarity (PCP) receptor, and is required to maintain proper levels of Fz. Moreover, we identified a child with compound heterozygous variants in TMEM208 who presents with developmental delay, skeletal abnormalities, multiple hair whorls, cardiac, and neurological issues, symptoms that are associated with PCP defects in mice and humans. Additionally, fibroblasts of the proband display mild ER stress. Expression of the reference human TMEM208 in flies fully rescues the loss of Tmem208, and the two proband-specific variants fail to rescue, suggesting that they are loss-of-function alleles. In summary, our study uncovers a role of TMEM208 in development, shedding light on its significance in ER homeostasis and cell polarity.

Bi-allelic SNAPC4 variants dysregulate global alternative splicing and lead to neuroregression and progressive spastic paraparesis.

The vast majority of human genes encode multiple isoforms through alternative splicing, and the temporal and spatial regulation of those isoforms is critical for organismal development and function. The spliceosome, which regulates and executes splicing reactions, is primarily composed of small nuclear ribonucleoproteins (snRNPs) that consist of small nuclear RNAs (snRNAs) and protein subunits. snRNA gene transcription is initiated by the snRNA-activating protein complex (SNAPc). Here, we report ten individuals, from eight families, with bi-allelic, deleterious SNAPC4 variants. SNAPC4 encoded one of the five SNAPc subunits that is critical for DNA binding. Most affected individuals presented with delayed motor development and developmental regression after the first year of life, followed by progressive spasticity that led to gait alterations, paraparesis, and oromotor dysfunction. Most individuals had cerebral, cerebellar, or basal ganglia volume loss by brain MRI. In the available cells from affected individuals, SNAPC4 abundance was decreased compared to unaffected controls, suggesting that the bi-allelic variants affect SNAPC4 accumulation. The depletion of SNAPC4 levels in HeLa cell lines via genomic editing led to decreased snRNA expression and global dysregulation of alternative splicing. Analysis of available fibroblasts from affected individuals showed decreased snRNA expression and global dysregulation of alternative splicing compared to unaffected cells. Altogether, these data suggest that these bi-allelic SNAPC4 variants result in loss of function and underlie the neuroregression and progressive spasticity in these affected individuals.

Can tandem alternative splicing and evasion of premature termination codon surveillance contribute to attenuated Peutz-Jeghers syndrome?

Alternative use of short distance tandem sites such as NAGNn AG are a common mechanism of alternative splicing; however, single nucleotide variants are rarely reported as likely to generate or to disrupt tandem splice sites. We identify a pathogenic intron 5 STK11 variant (NM_000455.4:c.[735-6A>G];[=]) segregating with the mucocutaneous features but not the hamartomatous polyps of Peutz-Jeghers syndrome in two individuals. By RNAseq analysis of peripheral blood mRNA, this variant was shown to generate a novel and preferentially used tandem proximal splice acceptor (AAGTGAAG). The variant transcript (NM_000455.4:c.734_734 + 1insTGAAG), which encodes a frameshift (p.[Tyr246Glufs*43]) constituted 36%-43% of STK11 transcripts suggesting partial escape from nonsense mediated mRNA decay and translation of a truncated protein. A review of the ClinVar database identified other similar variants. We suggest that nucleotide changes creating or disrupting tandem alternative splice sites are a pertinent disease mechanism and require contextualization for clinical reporting. Additionally, we hypothesize that some pathogenic STK11 variants cause an attenuated phenotype.

Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis-a prospective multicentre translational study.

BACKGROUND: Acute pancreatitis (AP) is an inflammatory disorder that causes a considerable economic health burden. While the overall mortality is low, around 20% of patients have a complicated course of disease resulting in increased morbidity and mortality. There is an emerging body of evidence that the microbiome exerts a crucial impact on the pathophysiology and course of AP. For several decades multiple clinical and laboratory parameters have been evaluated, and complex scoring systems were developed to predict the clinical course of AP upon admission. However, the majority of scoring systems are determined after several days and achieve a sensitivity around 70% for early prediction of severe AP. Thus, continued efforts are required to investigate reliable biomarkers for the early prediction of severity in order to guide early clinical management of AP patients. METHODS: We designed a multi-center, prospective clinical-translational study to test whether the orointestinal microbiome may serve as novel early predictor of the course, severity and outcome of patients with AP. We will recruit 400 AP patients and obtain buccal and rectal swabs within 72 h of admission to the hospital. Following DNA extraction, microbiome analysis will be performed using 3rd generation sequencing Oxford Nanopore Technologies (ONT) for 16S rRNA and metagenomic sequencing. Alpha- and beta-diversity will be determined and correlated to the revised Atlanta classification and additional clinical outcome parameters such as the length of hospital stay, number and type of complications, number of interventions and 30-day mortality. DISCUSSION: If AP patients show a distinct orointestinal microbiome dependent on the severity and course of the disease, microbiome sequencing could rapidly be implemented in the early clinical management of AP patients in the future. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04777812.

Pan-cancer RNA-seq data stratifies tumours by some hallmarks of cancer.

Numerous genetic and epigenetic alterations cause functional changes in cell biology underlying cancer. These hallmark functional changes constitute potentially tissue-independent anticancer therapeutic targets. We hypothesized that RNA-Seq identifies gene expression changes that underly those hallmarks, and thereby defines relevant therapeutic targets. To test this hypothesis, we analysed the publicly available TCGA-TARGET-GTEx gene expression data set from the University of California Santa CruzToil recompute project using WGCNA to delineate co-correlated 'modules' from tumour gene expression profiles and functional enrichment of these modules to hierarchically cluster tumours. This stratified tumours according to T cell activation, NK-cell activation, complement cascade, ATM, Rb, angiogenic, MAPK, ECM receptor and histone modification signalling. These correspond to the cancer hallmarks of avoiding immune destruction, tumour-promoting inflammation, evading growth suppressors, inducing angiogenesis, sustained proliferative signalling, activating invasion and metastasis, and genome instability and mutation. This approach did not detect pathways corresponding to the cancer enabling replicative immortality, resisting cell death or deregulating cellular energetics hallmarks. We conclude that RNA-Seq stratifies tumours along some, but not all, hallmarks of cancer and, therefore, could be used in conjunction with other analyses collectively to inform precision therapy.

Loss of incretin effect contributes to postprandial hyperglycaemia in cystic fibrosis-related diabetes.

AIM: To investigate the incretin axis in people with cystic fibrosis. METHODS: Adults with cystic fibrosis-related diabetes, cystic fibrosis without diabetes, and controls (adults without cystic fibrosis and without diabetes) underwent an oral glucose tolerance test and then a closely matched isoglycaemic i.v. glucose infusion. On each occasion, glucose, insulin, C-peptide, total and active glucagon-like peptide-1 and gastric inhibitory polypeptide responses were recorded and incremental areas under curves were calculated for 60 and 240 min. RESULTS: Five adults with cystic fibrosis-related diabetes, six with cystic fibrosis without diabetes and six controls, matched for age and BMI, completed the study. Glucose during oral glucose tolerance test closely matched those during isoglycaemic i.v. glucose infusion. The calculated incretin effect was similar in the control group and the cystic fibrosis without diabetes group (28% and 29%, respectively), but was lost in the cystic fibrosis-related diabetes group (cystic fibrosis-related diabetes vs control group: -6% vs 28%; p=0.03). No hyposecretion of glucagon-like peptide-1 or gastric inhibitory polypeptide was observed; conversely, 60-min incremental area under the curve for total glucagon-like peptide-1 was significantly higher in the cystic fibrosis-related diabetes group than in the control group [1070.4 (254.7) vs 694.97 (308.1); p=0.03] CONCLUSIONS: The incretin effect was lost in cystic fibrosis-related diabetes despite adequate secretion of the incretin hormones. These data support the concept that reduced incretin hormone insulinotropic activity contributes significantly to postprandial hyperglycaemia in cystic fibrosis-related diabetes.

Gratings for synchrotron and FEL beamlines: a project for the manufacture of ultra-precise gratings at Helmholtz Zentrum Berlin.

Blazed gratings are of dedicated interest for the monochromatization of synchrotron radiation when a high photon flux is required, such as, for example, in resonant inelastic X-ray scattering experiments or when the use of laminar gratings is excluded due to too high flux densities and expected damage, for example at free-electron laser beamlines. Their availability became a bottleneck since the decommissioning of the grating manufacture facility at Carl Zeiss in Oberkochen. To resolve this situation a new technological laboratory was established at the Helmholtz Zentrum Berlin, including instrumentation from Carl Zeiss. Besides the upgraded ZEISS equipment, an advanced grating production line has been developed, including a new ultra-precise ruling machine, ion etching technology as well as laser interference lithography. While the old ZEISS ruling machine GTM-6 allows ruling for a grating length up to 170 mm, the new GTM-24 will have the capacity for 600 mm (24 inch) gratings with groove densities between 50 lines mm-1 and 1200 lines mm-1. A new ion etching machine with a scanning radiofrequency excited ion beam (HF) source allows gratings to be etched into substrates of up to 500 mm length. For a final at-wavelength characterization, a new reflectometer at a new Optics beamline at the BESSY-II storage ring is under operation. This paper reports on the status of the grating fabrication, the measured quality of fabricated items by ex situ and in situ metrology, and future development goals.

Reliability of TMS metrics in patients with chronic incomplete spinal cord injury.

STUDY DESIGN: Test-retest reliability analysis in individuals with chronic incomplete spinal cord injury (iSCI). OBJECTIVES: The purpose of this study was to examine the reliability of neurophysiological metrics acquired with transcranial magnetic stimulation (TMS) in individuals with chronic incomplete tetraplegia. SETTING: Cleveland Clinic Foundation, Cleveland, Ohio, USA. METHODS: TMS metrics of corticospinal excitability, output, inhibition and motor map distribution were collected in muscles with a higher MRC grade and muscles with a lower MRC grade on the more affected side of the body. Metrics denoting upper limb function were also collected. All metrics were collected at two sessions separated by a minimum of two weeks. Reliability between sessions was determined using Spearman's correlation coefficients and concordance correlation coefficients (CCCs). RESULTS: We found that TMS metrics that were acquired in higher MRC grade muscles were approximately two times more reliable than those collected in lower MRC grade muscles. TMS metrics of motor map output, however, demonstrated poor reliability regardless of muscle choice (P=0.34; CCC=0.51). Correlation analysis indicated that patients with more baseline impairment and/or those in a more chronic phase of iSCI demonstrated greater variability of metrics. CONCLUSION: In iSCI, reliability of TMS metrics varies depending on the muscle grade of the tested muscle. Variability is also influenced by factors such as baseline motor function and time post SCI. Future studies that use TMS metrics in longitudinal study designs to understand functional recovery should be cautious as choice of muscle and clinical characteristics can influence reliability.

Validation of mitosis counting by automated phosphohistone H3 (PHH3) digital image analysis in a breast carcinoma tissue microarray.

Mitosis counting in H&E stained sections is the most informative constituent of the Nottingham histological grade in breast carcinoma prognosis. Phosphohistone H3 (PHH3) immunohistochemistry (IHC) is a highly specific marker of mitoses, with practical application in identifying mitoses in poorly fixed or distorted tissue and is of prognostic significance in breast carcinoma. Our aim was to assess methods of PHH3 IHC mitosis counting in a tissue microarray (TMA) of 2 mm cores from 36 resected breast carcinomas. Mitoses in H&E and PHH3 stained slides were manually scored by pathologist consensus and expressed as counts/2 mm. PHH3 stained cores were also evaluated by automated digital image analysis (DIA). Results were compared using Spearman correlation. A strong and significant correlation was observed between manual PHH3 and manual H&E mitotic counts (correlation = 0.81; p < 0.0001) and between automated PHH3 DIA and manual H&E mitotic counts (correlation = 0.79; p < 0.0001). More mitoses were identified with PHH3 IHC than with H&E. Manual and DIA PHH3 counts were strongly and significantly correlated (correlation = 0.83; p < 0.0001) and of similar absolute values. PHH3 DIA is a valid alternative to manual counting with potential application in breast cancer reporting and prognostication.

Serological responses to Cryptosporidium antigens in inhabitants of Hungary using conventionally filtered surface water and riverbank filtered drinking water.

In this study the putative protective seroprevalence (PPS) of IgG antibodies to the 27-kDa and 15/17-kDa Cryptosporidium antigens in sera of healthy participants who were and were not exposed to Cryptosporidium oocysts via surface water-derived drinking water was compared. The participants completed a questionnaire regarding risk factors that have been shown to be associated with infection. The PPS was significantly greater (49-61%) in settlements where the drinking water originated from surface water, than in the control city where riverbank filtration was used (21% and 23%). Logistic regression analysis on the risk factors showed an association between bathing/swimming in outdoor pools and antibody responses to the 15/17-kDa antigen complex. Hence the elevated responses were most likely due to the use of contaminated water. Results indicate that waterborne Cryptosporidium infections occur more frequently than reported but may derive from multiple sources.

Handling of radioactive seed localisation breast specimens in the histopathology laboratory: the Western Australian experience.

Radio-guided occult lesion localisation using iodine-125 seeds (ROLLIS) is a novel method of localisation for impalpable in situ and invasive carcinomas that has been the subject of a recent pilot study and pilot study extension in Western Australia. Robust protocols for radiation safety, specimen labelling, specimen tracking, seed retrieval and seed disposal were developed at two Western Australian laboratories to minimise the risk of seed loss. The processes are safe and effective with no significant radiation exposure to pathologists and with acquisition of all seeds intact and undamaged. The success can be attributed to developing specific seed retrieval techniques, suited to local preferences at each institution, with input from surgeons, radiologists and medical physics personnel. These techniques are now routine and will continue in the randomised control phase of the ROLLIS study.

Enhancements in specimen preparation of Cu(In,Ga)(S,Se)2 thin films.

When producing slices from Cu(In,Ga)(S,Se)(2) thin films for solar cells by use of a focused ion beam (FIB), agglomerates form on the Cu(In,Ga)(S,Se)(2) surfaces, which deteriorate substantially the imaging and analysis in scanning electron microscopy. Similar problems are also experienced when depth-profiling Cu(In,Ga)(S,Se)(2) thin films by means of glow-discharge or secondary ion mass spectrometry. The present work shows that the agglomerates are composed of (mainly) Cu, and that their formation may be impeded considerably by either cooling of the sample or by use of reactive gases during the ion-beam sputtering. The introduction of XeF(2) during FIB slicing resulted in excellent images, in which the microstructures of most layers in the Cu(In,Ga)(S,Se)(2) thin film stack are visible, including the microstructure of the 20 nm thin MoSe(2) layer. Acquisition of high-quality two-dimensional and also three-dimensional electron backscatter diffraction data was possible. The present work gives a basis for enhanced SEM imaging and analysis not only in the case of Cu(In,Ga)(S,Se)(2) thin films but also when dealing with further material systems exhibiting similar formations of agglomerates.

[Ondansetron: a meta-analysis on its efficacy to prevent postoperative nausea and vomiting after craniotomy in adults and children]. / Méta-analyse : ondansétron en prophylaxie des nausées et vomissements postopératoires chez l'adulte et l'enfant après craniotomie.

OBJECTIVE: To justify the use of ondansetron as a preventive treatment for postoperative nausea and vomiting (PONV) of adults and children in neurosurgery. STUDY DESIGN: Meta-analysis. PATIENTS AND METHODS: Six published, randomized, double-blinded, placebo-controlled trials were selected to study the efficacy of ondansetron on PONV in adults undergoing craniotomy. Similarly, three studies were selected in children. The treated adults received 4 or 8 mg of ondansetron during the peroperative period. As for children, they were given a repeated dose of 0.15 mg/kg of ondansetron. The emetic episodes noted for 24 hours in children and until 48 hours in adults were analyzed. The results were presented as relative risks (RR) following a fixed model and a 95% confidence interval (CI). The test for heterogeneity was measured with the I(2) Altman DG test. RESULTS: At 24 hours, among the 308 adults tested, nausea and vomiting were significantly reduced by 22% and 57%, respectively; no significant reduction in vomiting was noted for the 149 children patients. At 48 hours, no significant modification was observed in adults. CONCLUSIONS: Peroperative intravenous dose of ondansetron 4 mg in neurosurgery in adults is required to prevent PONV during the first postoperative 24 hours. However, further studies are needed to determine best time and dose infusion to prolong clinical efficacy.

Highly ordered nanopatterns on Ge and Si surfaces by ion beam sputtering.

The bombardment of surfaces with low-energy ion beams leads to material erosion and can be accompanied by changes in the topography. Under certain conditions this surface erosion can result in well-ordered nanostructures. Here an overview of the pattern formation on Si and Ge surfaces under low-energy ion beam erosion at room temperature will be given. In particular, the formation of ripple and dot patterns, and the influence of different process parameters on their formation, ordering, shape and type will be discussed. Furthermore, the internal ion beam parameters inherent to broad beam ion sources are considered as an additional degree of freedom for controlling the pattern formation process. In this context: (i) formation of ripples at near-normal ion incidence, (ii) formation of dots at oblique ion incidence without sample rotation, (iii) transition between patterns, (iv) formation of ripples with different orientations and (v) long range ordered dot patterns will be presented and discussed.

Ion-induced nanopatterns on semiconductor surfaces investigated by grazing incidence x-ray scattering techniques.

In this review we cover and describe the application of grazing incidence x-ray scattering techniques to study and characterize nanopattern formation on semiconductor surfaces by ion beam erosion under various conditions. It is demonstrated that x-rays under grazing incidence are especially well suited to characterize (sub)surface structures on the nanoscale with high spatial and statistical accuracy. The corresponding theory and data evaluation is described in the distorted wave Born approximation. Both ex situ and in situ studies are presented, performed with the use of a specially designed sputtering chamber which allows us to follow the temporal evolution of the nanostructure formation. Corresponding results show a general stabilization of the ordering wavelength and the extension of the ordering as a function of the ion energy and fluence as predicted by theory. The in situ measurements are especially suited to study the early stages of pattern formation, which in some cases reveal a transition from dot to ripple formation. For the case of medium energy ions crystalline ripples are formed buried under a semi-amorphous thick layer with a ripple structure at the surface being conformal with the crystalline/amorphous interface. Here, the x-ray techniques are especially advantageous since they are non-destructive and bulk-sensitive by their very nature. In addition, the GI x-ray techniques described in this review are a unique tool to study the evolving strain, a topic which remains to be explored both experimentally and theoretically.

Large area smoothing of surfaces by ion bombardment: fundamentals and applications.

Ion beam erosion can be used as a process for achieving surface smoothing at microscopic length scales and for the preparation of ultrasmooth surfaces, as an alternative to nanostructuring of various surfaces via self-organization. This requires that in the evolution of the surface topography different relaxation mechanisms dominate over the roughening, and smoothing of initially rough surfaces can occur. This contribution focuses on the basic mechanisms as well as potential applications of surface smoothing using low energy ion beams. In the first part, the fundamentals for the smoothing of III/V semiconductors, Si and quartz glass surfaces using low energy ion beams (ion energy: ≤2000 eV) are reviewed using examples. The topography evolution of these surfaces with respect to different process parameters (ion energy, ion incidence angle, erosion time, sample rotation) has been investigated. On the basis of the time evolution of different roughness parameters, the relevant surface relaxation mechanisms responsible for surface smoothing are discussed. In this context, physical constraints as regards the effectiveness of surface smoothing by direct ion bombardment will also be addressed and furthermore ion beam assisted smoothing techniques are introduced. In the second application-orientated part, recent technological developments related to ion beam assisted smoothing of optically relevant surfaces are summarized. It will be demonstrated that smoothing by direct ion bombardment in combination with the use of sacrificial smoothing layers and the utilization of appropriate broad beam ion sources enables the polishing of various technologically important surfaces down to 0.1 nm root mean square roughness level, showing great promise for large area surface processing. Specific examples are given for ion beam smoothing of different optical surfaces, especially for substrates used for advanced optical applications (e.g., in x-ray optics and components for extreme ultraviolet lithography).