Integrated exome and transcriptome analysis prioritizes MAP4K4 de novo frameshift variants in autism spectrum disorder as a novel disease-gene association.

The application of next-generation sequencing (NGS) to clinical practice is still hampered by the ability to interpret the clinical relevance of novel variants and the difficulty of evaluating their effect in specific tissues. Here, we applied integrated genomic approaches for interrogating blood samples of two unrelated individuals with neurodevelopmental disorders and identified a novel neuro-pathogenic role for the Mitogen-Activated Protein Kinase 4 gene (MAP4K4). In particular, we identified two novel frameshift variants in coding exons expressed in the blood and neuronal isoforms. Both variants were predicted to generate non-sense-mediated decay. By transcriptome analysis, we simultaneously demonstrated the deleterious effect of the identified variants on the splicing activity and stability of MAP4K4 mRNA. Therefore, we propose MAP4K4 as a novel causative gene for non-syndromic and syndromic neurodevelopmental disorders. Altogether, we prove the efficacy of an integrated approach of exome and transcriptome sequencing in the resolution of undiagnosed cases by leveraging the analysis of variants in genes expressed in peripheral blood.

Evaluation of tumor-infiltrating lymphocytes and association with prognosis in BRCA-mutated breast cancer.

BACKGROUND: Patients with a BRCA1 or BRCA2 mutation (BRCA-mutated breast cancer) are frequently diagnosed with low differentiated and highly proliferating breast cancer characterized by high amounts of tumor-infiltrating lymphocytes (Tils). Stromal Tils (sTils) are highly prognostic in sporadic triple-negative and HER2 positive breast cancer however, their prognostic importance in BRCA-mutated breast cancers is unknown. MATERIAL AND METHODS: Formalin-fixed paraffin-embedded primary tumor tissue from 411 patients with a germline BRCA1 or BRCA2 mutation and diagnosed with early breast cancer was included. The percentage of sTils was quantified on full HE sections according to guidelines proposed by the Immuno-Oncology Biomarker in Breast Cancer Working Group. Distribution of sTils and associates with patient and tumor characteristics were assessed according to categorical sTils groups defined as low (<10%), intermediate (10-59%) and high (≥60%). Prognostic associations of sTils were evaluated as a continuous variable in univariate and multivariate models. Only follow-up time beyond date of BRCA mutation test was included. RESULTS: A large proportion had high sTils (27% in the full cohort, 36% in BRCA1-mutated, and 44% in ER negative breast cancers). Higher sTils were associated with BRCA1, ER negative breast cancer, high histological grade and medullary histology. In combined analysis for BRCA1 and BRCA2-mutated breast cancers, increasing sTils in 10% intervals were significantly associated with OS (HR 0.92, 95% CI 0.84-1.00, p = .05). For each 10% increment of sTils in BRCA1 breast cancers, a 10% reduction of mortality (adjusted HR 0.90 95% CI 0.81-0.99, p = .03) and a 13% reduction in risk of DFS-event (HR 0.87 95% CI 0.76-1.00, p = .05) was observed even after adjustment for ER status. No significant association with survival was of observed in the BRCA2 subgroup. Test for interaction of sTils and BRCA status was not statistically significant (p = .3). CONCLUSIONS: Breast cancer patients with a germline BRCA mutation had higher sTils than previously reported in sporadic breast cancers, and sTils were associated with favorable survival among BRCA carriers.

Clinical and molecular characterization of BRCA-associated breast cancer: results from the DBCG.

BACKGROUND: In breast cancer (BC) patients a cancer predisposing BRCA1/2 mutation is associated with adverse tumor characteristics, risk assessment and treatment allocation. We aimed to estimate overall- (OS) and disease-free survival (DFS) according to tumor characteristics and treatment among women who within two years of definitive surgery for primary BC were shown to carry a mutation in BRCA1/2 . MATERIAL AND METHODS: From the clinical database of the Danish Breast Cancer Group we included 141 BRCA1 and 96 BRCA2 BC patients. Estrogen receptor and HER2 status were centrally reviewed on paraffin-embedded tumor tissue. Information on risk reducing surgery was obtained from the Danish Pathology and Patient Registries and included as time-dependent variables in Cox proportional hazard models. RESULTS: Ten-year OS and DFS for BRCA1 BC patients were 78% (95% CI 69-85) and 74% (95% CI 64-81). Ten-year OS and DFS for BRCA2 BC were 88% (95% CI 78-94) and 84% (95% CI 74-91). BRCA1 BC patients as compared to BRCA2 BC patients had a higher risk of BC relapse or non-breast cancer within ten years of follow-up, independent of ER status (adjusted HR 2.78 95% CI 1.28-6.05, p = .01), but BRCA mutation was not associated with OS (adjusted HR 1.98, 95% CI 0.87-4.52, p = .10). In multivariate analysis, including both BRCA1 and BRCA2 carriers, no chemotherapy was associated with a higher risk of death (adjusted OS HR 3.58, 95% CI 1.29-9.97, p = .01) and risk reducing contralateral mastectomy (RRCM) was associated with a significantly reduced risk of death (adjusted OS HR 0.42, 95% CI =0.21-0.84, p = .01). CONCLUSION: Difference in OS between BRCA1 and BRCA2 BC patients could be ascribed to tumor-biology. BRCA1 BC patients may have a shorter ten-year DFS than BRCA2 BC patients. Chemotherapy and risk reducing contralateral mastectomy reduce mortality for both BRCA1 and BRCA2 BC patients.

Acute hypoxia induces upregulation of microRNA-210 expression in glioblastoma spheroids.

AIM: Tumor hypoxia and presence of tumor stem cells are related to therapeutic resistance and tumorigenicity in glioblastomas. The aim of the present study was therefore to identify microRNAs deregulated in acute hypoxia and to identify possible associated changes in stem cell markers. MATERIALS & METHODS: Glioblastoma spheroid cultures were grown in either 2 or 21% oxygen. Subsequently, miRNA profiling was performed and expression of ten stem cell markers was examined. RESULTS: MiRNA-210 was significantly upregulated in hypoxia in patient-derived spheroids. The stem cell markers displayed a complex regulatory pattern. CONCLUSION: MiRNA-210 appears to be upregulated in hypoxia in immature glioblastoma cells. This miRNA may represent a therapeutic target although it is not clear from the results whether this miRNA may be related to specific cancer stem cell functions.

Erosion of the teeth: prevalence and distribution in a group of Danish school children.

AIM: This was to describe the prevalence of eroded tooth surfaces among 15-17 years old school children in a Danish city and to assess the reliability of diagnosis of erosions performed by 9 clinical examiners. METHODS: During a calendar year (2000) a total of 558 children in 4 public schools in Aarhus were examined by 7 examiners and 2 coordinators using the following criteria: intact; erosion confined to enamel; erosion exposing less than half of the dentine, and erosion involving more dentine than half the surface. RESULTS: It was found that 14.0% (95% CL: 11.3%; 17.1%) of the children had more than 3 surfaces eroded. In the maxilla lingual surfaces were more affected than the facial surfaces. No lesions exposing more than half of the dentine were observed. Despite a careful calibration, including a thorough discussion of the criteria and the experience gained during the study, a substantial inter examiner difference in diagnosis was found. CONCLUSION: The most frequently eroded sites were the lingual surfaces of maxillary incisors; the identification of eroded areas is often difficult and subject to a low inter examiner reliability.

Effects of KHEYLRFamide and KNEFIRFamide on cyclic adenosine monophosphate levels in Ascaris suum somatic muscle.

KHEYLRF-NH(2) (AF2) is a FMRFamide-related peptide (FaRP) present in parasitic and free-living nematodes. At concentrations as low as 10 pM, AF2 induces a biphasic tension response, consisting of a transient relaxation followed by profound excitation, in neuromuscular strips prepared from Ascaris suum. In the present study, the effects of AF2 on cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP) and inositol-1,4,5-triphosphate (IP(3)) levels were measured following muscle tension recordings from 2 cm neuromuscular strips prepared from adult A. suum. AF2 induced a concentration- and time-dependent increase in cAMP, beginning at 1 nM; cAMP levels increased by 84-fold following 1 h exposure to 1 microM AF2. cGMP and IP(3) levels were unaffected by AF2 at concentrations

Saturation of human saliva with respect to calcium salts.

It may be assumed that free ionic concentrations of calcium and phosphate in resting saliva tend to equilibrate with those in plaque fluid, and that salivary data can therefore be used to illustrate chemical conditions in both saliva and plaque. In the present study, salivary data collected from the literature or obtained in our laboratory were used to calculate degrees of super- and undersaturation with respect to apatites, brushite, beta-tricalcium phosphate, octacalcium phosphate, calcium carbonate and calcium fluoride in the pH range from 3 to 9. Concentrations of calcium, phosphate, fluoride, carbonate, and background ion strength of resting parotid saliva, resting submandibular saliva, and resting and stimulated whole saliva were entered into a computer program, and curves illustrating saturation in the pH range 3-9 constructed. It was found that oral fluids are supersaturated with respect to apatites above pH 5.3 and with respect to octacalcium phosphate and beta-tricalcium phosphate above pH 6. Parotid saliva was undersaturated with respect to brushite whilst submandibular saliva was supersaturated with respect to that salt in the pH range 6-8. Stimulated whole saliva with 25 mmol/l carbonate became supersaturated with respect to calcium carbonate only above pH 7.3, which may explain the absence of this salt in the human oral cavity. To maintain the saturation of oral fluids with respect to calcium fluoride, i.e. to ensure its survival in the mouth required 6 ppm fluoride in the aqueous phase. Therefore, this salt, the outcome of topical fluoride therapy, will inevitably dissolve in the oral fluids.

Defluoridation of drinking water by boiling with brushite and calcite.

Existing methods for defluoridating drinking water involve expensive high technology or are slow, inefficient and/or unhygienic. A new method is now suggested, encompassing brushite and calcite suspension followed by boiling. Our aim was to examine the efficiency of the method and the chemical reactions involved. Brushite, 0.3-0.5 g, and an equal weight of calcite were suspended in 1 litre water containing 5-20 ppm fluoride. The suspensions were boiled in an electric kettle, left to cool and the calcium salts to sediment. Solution ion concentrations were determined and sediments were examined by X-ray diffraction. In distilled water initially containing 5, 10 and 20 ppm fluoride the concentration was reduced to 0.06, 0.4 and 5.9 ppm, respectively. Using Aarhus tap water which contained 2.6 mmol/l calcium the final concentrations were 1.2, 2.5 and 7.7 ppm, respectively, and runs without calcite gave results similar to those with calcite. Without boiling the fluoride concentration remained unaltered, as did the brushite and calcite salts, despite occasional agitation by hand. All solutions were supersaturated with respect to fluorapatite and hydroxyapatite and close to saturation with respect to brushite. Boiling produced well-crystallised apatite and traces of calcite, while boiling of brushite alone left a poorly crystallised apatite. We conclude that boiling a brushite/calcite suspension rapidly converts the two salts to apatite which incorporates fluoride if present in solution, and that this process may be exploited to defluoridate drinking water.

Fluoride is unable to reduce dental erosion from soft drinks.

The main aim of the present study was to compare the erosive capabilities of some fruit-flavoured drinks, fresh or saturated with CaF2, with their content of acids and with previous results from some carbonated soft drinks. The other aim was to measure and compare the rates of dissolution of CaF2 in some carbonated and non-carbonated drinks and water. Seven commercially available fruit-flavoured drinks were diluted for drinking. Two human molars, each with two approximately 4 x 4 mm windows, were exposed continuously to 500 ml of each drink with or without prior equilibration with CaF2 under gentle agitation for 48 h. The depths of the erosions were then measured on microradiographs made from sections. Dissolution rate of CaF2 was measured by suspending 0.5 g of the salt in 0.5 litre of the drinks for 2, 10 and 60 min followed by solution analysis. The pH of the drinks was 2.83-3.51. The amount of NaOH required to bring pH to 5.5 ranged from 12-42 mmol/l, which is more than the amount necessary for most carbonated soft drinks. Equilibration with CaF2 gave total fluoride concentrations of 3-8 ppm. The depths of the lesions induced by the drinks without added fluoride were 450-625 microm whilst those developed by the drinks equilibrated with CaF2 were 350-625 microm. The dissolution of CaF2 was faster in the carbonated drinks and in distilled water than in the non-carbonated drinks. In conclusion, non-carbonated fruit-flavoured drinks contain considerable amounts of acids which, in vitro, induce erosions in teeth similar to those induced by carbonated soft drinks. Saturation with CaF2 reduced the in vitro development of erosions by 28% induced by drinks with pH above 3; in drinks with pH below 3, erosions were not affected by pH, despite total fluoride concentrations of up to 20 ppm.

Type A allatostatins from Drosophila melanogaster and Diplotera puncata activate two Drosophila allatostatin receptors, DAR-1 and DAR-2, expressed in CHO cells.

The type-A allatostatins A (AST-A) are a group of insect peptides with a common C-terminal motif Y/FXFGL-NH(2). The existence of at least four putative type A Drosophila melanogaster ASTs (called type A drostatins or DST-As) has been predicted from the sequence of a recently cloned DST-A preprohormone [C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 273, 126-1131]. SRPYSFGL-NH(2), (DST-3A), the only DST isolated from Drosophila so far, activated the first cloned DST-A GPCR (DAR-1) [N. Birgül et al. (1999) EMBO J. 18, 5892-5900]. A newly cloned orphan Dm GPCR, which shares 47% overall and 60% transmembrane region sequence identity with DAR-1, was classified as a second putative Dm DST-A receptor (DAR-2) [C. Lenz et al. (2000) Biochem. Biophys. Res. Commun. 273, 571-577]. Although activation of DAR-2 by DSTs has been postulated, no experimental evidence for that has been presented to date. In this study, we expressed both DAR-1 and DAR-2 in CHO cells and used a GTPgammaS and a Ca(2+) mobilization assay for pharmacological evaluation of the receptors. Synthetically prepared DST-As, as well as selected Diplotera punctata (cockroach) ASTs, activated DAR-1 and DAR-2 in both functional assays indicating ligand redundancy and cross species activity. Cell pretreatment with pertussis toxin led to some differences in the nature and magnitude of signaling pathways at the DAR-1 and DAR-2 receptors, suggesting possible differential coupling to cellular effector system(s) and distinct biological functions of each receptor in vivo.