Male with an apparently normal phenotype carrying a BRCA1 exon 20 duplication in trans to a BRCA1 frameshift variant

BACKGROUND

Reports of dual carriers of pathogenic BRCA1 variants in trans are extremely rare, and so far, most individuals have been associated with a Fanconi Anemia-like phenotype.

METHODS

We identified two families with a BRCA1 in-frame exon 20 duplication (Ex20dup). In one male individual, the variant was in trans with the BRCA1 frameshift variant c.2475delC p.(Asp825Glufs*21). We performed splicing analysis and used a transcription activation domain (TAD) assay to assess the functional impact of Ex20dup. We collected pedigrees and mapped the breakpoints of the duplication by long- and short-read genome sequencing. In addition, we performed a mitomycin C (MMC) assay from the dual carrier using cultured lymphoblastoid cells.

RESULTS

Genome sequencing and RNA analysis revealed the BRCA1 exon 20 duplication to be in tandem. The duplication was expressed without skipping any one of the two exon 20 copies, resulting in a lack of wild-type transcripts from this allele. TAD assay indicated that the Ex20dup variant has a functional level similar to the well-known moderate penetrant pathogenic BRCA1 variant c.5096G > A p.(Arg1699Gln). MMC assay of the dual carrier indicated a slightly impaired chromosomal repair ability.

CONCLUSIONS

This is the first reported case where two BRCA1 variants with demonstrated functional impact are identified in trans in a male patient with an apparently normal clinical phenotype and no BRCA1-associated cancer. The results pinpoint a minimum necessary BRCA1 protein activity to avoid a Fanconi Anemia-like phenotype in compound heterozygous status and yet still predispose carriers to hormone-related cancers. These findings urge caution when counseling families regarding potential Fanconi Anemia risk. Furthermore, prudence should be taken when classifying individual variants as benign based on co-occurrence in trans with well-established pathogenic variants.

Variants in the WDR44 WD40-repeat domain cause a spectrum of ciliopathy by impairing ciliogenesis initiation

WDR44 prevents ciliogenesis initiation by regulating RAB11-dependent vesicle trafficking. Here, we describe male patients with missense and nonsense variants within the WD40 repeats (WDR) of WDR44, an X-linked gene product, who display ciliopathy-related developmental phenotypes that we can model in zebrafish. The patient phenotypic spectrum includes developmental delay/intellectual disability, hypotonia, distinct craniofacial features and variable presence of brain, renal, cardiac and musculoskeletal abnormalities. We demonstrate that WDR44 variants associated with more severe disease impair ciliogenesis initiation and ciliary signaling. Because WDR44 negatively regulates ciliogenesis, it was surprising that pathogenic missense variants showed reduced abundance, which we link to misfolding of WDR autonomous repeats and degradation by the proteasome. We discover that disease severity correlates with increased RAB11 binding, which we propose drives ciliogenesis initiation dysregulation. Finally, we discover interdomain interactions between the WDR and NH2-terminal region that contains the RAB11 binding domain (RBD) and show patient variants disrupt this association. This study provides new insights into WDR44 WDR structure and characterizes a new syndrome that could result from impaired ciliogenesis.

Non-BRCA1/BRCA2 high-risk familial breast cancers are not associated with a high prevalence of BRCAness

BACKGROUND

Familial breast cancer is in most cases unexplained due to the lack of identifiable pathogenic variants in the BRCA1 and BRCA2 genes. The somatic mutational landscape and in particular the extent of BRCA-like tumour features (BRCAness) in these familial breast cancers where germline BRCA1 or BRCA2 mutations have not been identified is to a large extent unknown.

METHODS

We performed whole-genome sequencing on matched tumour and normal samples from high-risk non-BRCA1/BRCA2 breast cancer families to understand the germline and somatic mutational landscape and mutational signatures. We measured BRCAness using HRDetect. As a comparator, we also analysed samples from BRCA1 and BRCA2 germline mutation carriers.

RESULTS

We noted for non-BRCA1/BRCA2 tumours, only a small proportion displayed high HRDetect scores and were characterized by concomitant promoter hypermethylation or in one case a RAD51D splice variant previously reported as having unknown significance to potentially explain their BRCAness. Another small proportion showed no features of BRCAness but had mutationally active tumours. The remaining tumours lacked features of BRCAness and were mutationally quiescent.

CONCLUSIONS

A limited fraction of high-risk familial non-BRCA1/BRCA2 breast cancer patients is expected to benefit from treatment strategies against homologue repair deficient cancer cells.

CERT1 mutations perturb human development by disrupting sphingolipid homeostasis

Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are associated with intellectual disability, but the pathogenic mechanism remains obscure. Here, we characterize 31 individuals with de novo missense variants in CERT1. Several variants fall into a previously uncharacterized dimeric helical domain that enables CERT homeostatic inactivation, without which sphingolipid production goes unchecked. The clinical severity reflects the degree to which CERT autoregulation is disrupted, and inhibiting CERT pharmacologically corrects morphological and motor abnormalities in a Drosophila model of the disease, which we call ceramide transporter (CerTra) syndrome. These findings uncover a central role for CERT autoregulation in the control of sphingolipid biosynthetic flux, provide unexpected insight into the structural organization of CERT, and suggest a possible therapeutic approach for patients with CerTra syndrome.

Mutations affecting the N-terminal domains of SHANK3 point to different pathomechanisms in neurodevelopmental disorders

Shank proteins are major scaffolds of the postsynaptic density of excitatory synapses. Mutations in SHANK genes are associated with autism and intellectual disability. The effects of missense mutations on Shank3 function, and therefore the pathomechanisms are unclear. Several missense mutations in SHANK3 affect the N-terminal region, consisting of the Shank/ProSAP N-terminal (SPN) domain and a set of Ankyrin (Ank) repeats. Here we identify a novel SHANK3 missense mutation (p.L270M) in the Ankyrin repeats in patients with an ADHD-like phenotype. We functionally analysed this and a series of other mutations, using biochemical and biophysical techniques. We observe two major effects: (1) a loss of binding to δ-catenin (e.g. in the p.L270M variant), and (2) interference with the intramolecular interaction between N-terminal SPN domain and the Ank repeats. This also interferes with binding to the α-subunit of the calcium-/calmodulin dependent kinase II (αCaMKII), and appears to be associated with a more severe neurodevelopmental pathology.

Differential lncRNA expression profiling of cognitive function in middle and old aged monozygotic twins using generalized association analysis

Cognitive impairment is the most prominent symptom in neurodegenerative disorders affecting quality of life and mortality. However, despite years of research, the molecular mechanism underlying the regulation of cognitive function and its impairment is poorly understood. This study aims to elucidate the role of long non-coding RNAs (lncRNAs) expression and lncRNA-mRNA interaction networks, by analyzing lncRNA expression in whole blood samples of 400 middle and old aged monozygotic twins in association with cognitive function using both linear models and a generalized correlation coefficient (GCC) to capture the diverse patterns of correlation. We detected 13 probes (p < 1e-03) displaying nonlinear and 7 probes (p < 1e-03) showing linear correlations. After combining the results, we identified 20 lncRNA probes with p < 1e-03. The top lncRNA probes were annotated to genes, along with the non-coding MALAT1, that play roles in neurodegenerative diseases. The top lncRNAs were linked to functional clusters including peptidyl-glycine modification, vascular smooth muscle cells, mitotic spindle organization and protein tyrosine phosphatase. In addition, mapping of the top significant lncRNAs to the lncRNA-mRNA interaction network detected significantly enriched biological pathways involving neuroactive ligand-receptor interaction, proteasome and chemokines. We show that GCC served as a complementary approach in detecting lncRNAs missed by the conventional linear models. A combination of GCC and linear models identified lncRNAs of diverse patterns of association enriched for GO biological and molecular functions meaningful in cognitive performance and cognitive decline. The novel lncRNA regulatory network further contributed to detect significant pathways implicated in cognition.

Epileptic encephalopathy caused by ARV1 deficiency: Refinement of the genotype-phenotype spectrum and functional impact on GPI-anchored proteins

Early infantile epileptic encephalopathy 38 (EIEE38, MIM #617020) is caused by biallelic variants in ARV1, encoding a transmembrane protein of the endoplasmic reticulum with a pivotal role in glycosylphosphatidylinositol (GPI) biosynthesis. We ascertained seven new patients from six unrelated families harboring biallelic variants in ARV1, including five novel variants. Affected individuals showed psychomotor delay, hypotonia, early onset refractory seizures followed by regression and specific neuroimaging features. Flow cytometric analysis on patient fibroblasts showed a decrease in GPI-anchored proteins on the cell surface, supporting a lower residual activity of the mutant ARV1 as compared to the wildtype. A rescue assay through the transduction of lentivirus expressing wild type ARV1 cDNA effectively rescued these alterations. This study expands the clinical and molecular spectrum of the ARV1-related encephalopathy, confirming the essential role of ARV1 in GPI biosynthesis and brain function.

Global Gene Expression Profiling and Transcription Factor Network Analysis of Cognitive Aging in Monozygotic Twins

Cognitive aging is one of the major problems worldwide, especially as people get older. This study aimed to perform global gene expression profiling of cognitive function to identify associated genes and pathways and a novel transcriptional regulatory network analysis to identify important regulons. We performed single transcript analysis on 400 monozygotic twins using an assumption-free generalized correlation coefficient (GCC), linear mixed-effect model (LME) and kinship model and identified six probes (one significant at the standard FDR < 0.05 while the other results were suggestive with 0.18 ≤ FDR ≤ 0.28). We combined the GCC and linear model results to cover diverse patterns of relationships, and meaningful and novel genes like APOBEC3G, H6PD, SLC45A1, GRIN3B, and PDE4D were detected. Our exploratory study showed the downregulation of all these genes with increasing cognitive function or vice versa except the SLC45A1 gene, which was upregulated with increasing cognitive function. Linear models found only H6PD and SLC45A1, the other genes were captured by GCC. Significant functional pathways (FDR < 3.95e-10) such as focal adhesion, ribosome, cysteine and methionine metabolism, Huntington's disease, eukaryotic translation elongation, nervous system development, influenza infection, metabolism of RNA, and cell cycle were identified. A total of five regulons (FDR< 1.3e-4) were enriched in a transcriptional regulatory analysis in which CTCF and REST were activated and SP3, SRF, and XBP1 were repressed regulons. The genome-wide transcription analysis using both assumption-free GCC and linear models identified important genes and biological pathways implicated in cognitive performance, cognitive aging, and neurological diseases. Also, the regulatory network analysis revealed significant activated and repressed regulons on cognitive function.

Histone H3.3 beyond cancer: Germline mutations in Histone 3 Family 3A and 3B cause a previously unidentified neurodegenerative disorder in 46 patients

Although somatic mutations in Histone 3.3 (H3.3) are well-studied drivers of oncogenesis, the role of germline mutations remains unreported. We analyze 46 patients bearing de novo germline mutations in histone 3 family 3A (H3F3A) or H3F3B with progressive neurologic dysfunction and congenital anomalies without malignancies. Molecular modeling of all 37 variants demonstrated clear disruptions in interactions with DNA, other histones, and histone chaperone proteins. Patient histone posttranslational modifications (PTMs) analysis revealed notably aberrant local PTM patterns distinct from the somatic lysine mutations that cause global PTM dysregulation. RNA sequencing on patient cells demonstrated up-regulated gene expression related to mitosis and cell division, and cellular assays confirmed an increased proliferative capacity. A zebrafish model showed craniofacial anomalies and a defect in Foxd3-derived glia. These data suggest that the mechanism of germline mutations are distinct from cancer-associated somatic histone mutations but may converge on control of cell proliferation.

Chromosomal translocation disrupting the SMAD4 gene resulting in the combined phenotype of Juvenile polyposis syndrome and Hereditary Hemorrhagic Telangiectasia

Background

Patients with germline variants in SMAD4 can present symptoms of both juvenile polyposis syndrome (JPS) and Hereditary Hemorrhagic Telangiectasia (HHT): JP‐HHT syndrome. Next‐Generation Sequencing (NGS) techniques disclose causative sequence variants in around 90% of HHT patients fulfilling the Curaçao criteria. Here we report a translocation event involving SMAD4 resulting in JP‐HHT.

Methods

A patient fulfilling the Curaçao criteria was analyzed for variants in ENG, ACVRL1, and SMAD4 using standard techniques. Whole‐genome sequencing (WGS) using both short‐read NGS technology and long‐read Oxford Nanopore technology was performed to define the structural variant and exact breakpoints.

Results

No pathogenic variant was detected in ENG, ACVRL1, or SMAD4 in DNA extracted from blood. Due to abortus habitualis, the proband´s daughter was submitted for chromosomal analysis, and a cytogenetically balanced chromosomal reciprocal translocation t(1;18)(p36.1;q21.1) was detected in the daughter and the patient. The balanced translocation segregated with both gastrointestinal cancer and HHT in the family. WGS provided the exact breakpoints of the reciprocal translocation proving disruption of the SMAD4 gene.

Discussion

A disease‐causing reciprocal translocation between chromosome 1 and 18 with a breakpoint in the SMAD4 locus co‐segregated with JP‐HHT in an extended family. This observation warrants further analysis for chromosomal rearrangements in individuals with clinical HHT or JP‐HHT of unknown cause.

Differential long noncoding RNA profiling of BMI in twins

Aim: Many efforts have been deployed to identify genetic variants associated with BMI. Alternatively, we explore epigenetic contribution to BMI variation by focusing on long noncoding RNAs (lncRNAs) which represents a key layer of epigenetic control. Materials & methods: We analyzed lncRNA expression in whole blood of 229 monozygotic twin pairs in association with BMI using generalized estimating equations. Results & conclusion: Six lncRNA probes were identified as significant (false discovery rate <0.05), with BMI showing causal effects on the expression of the significant lncRNAs. Functional annotation of differential profiles identified Gene ontology biological processes including kidney development, regulations of lipid biosynthetic process, circadian rhythm, notch signaling, etc. Whole blood lncRNAs are significantly expressed in response to BMI variation.

Choline transporter-like 1 deficiency causes a new type of childhood-onset neurodegeneration

Cerebral choline metabolism is crucial for normal brain function, and its homoeostasis depends on carrier-mediated transport. Here, we report on four individuals from three families with neurodegenerative disease and homozygous frameshift mutations (Asp517Metfs*19, Ser126Metfs*8, and Lys90Metfs*18) in the SLC44A1 gene encoding choline transporter-like protein 1. Clinical features included progressive ataxia, tremor, cognitive decline, dysphagia, optic atrophy, dysarthria, as well as urinary and bowel incontinence. Brain MRI demonstrated cerebellar atrophy and leukoencephalopathy. Moreover, low signal intensity in globus pallidus with hyperintensive streaking and low signal intensity in substantia nigra were seen in two individuals. The Asp517Metfs*19 and Ser126Metfs*8 fibroblasts were structurally and functionally indistinguishable. The most prominent ultrastructural changes of the mutant fibroblasts were reduced presence of free ribosomes, the appearance of elongated endoplasmic reticulum and strikingly increased number of mitochondria and small vesicles. When chronically treated with choline, those characteristics disappeared and mutant ultrastructure resembled healthy control cells. Functional analysis revealed diminished choline transport yet the membrane phosphatidylcholine content remained unchanged. As part of the mechanism to preserve choline and phosphatidylcholine, choline transporter deficiency was implicated in impaired membrane homeostasis of other phospholipids. Choline treatments could restore the membrane lipids, repair cellular organelles and protect mutant cells from acute iron overload. In conclusion, we describe a novel childhood-onset neurometabolic disease caused by choline transporter deficiency with autosomal recessive inheritance.

Bi-allelic Loss-of-Function Variants in NUP188 Cause a Recognizable Syndrome Characterized by Neurologic, Ocular, and Cardiac Abnormalities

Nucleoporins (NUPs) are an essential component of the nuclear-pore complex, which regulates nucleocytoplasmic transport of macromolecules. Pathogenic variants in NUP genes have been linked to several inherited human diseases, including a number with progressive neurological degeneration. We present six affected individuals with bi-allelic truncating variants in NUP188 and strikingly similar phenotypes and clinical courses, representing a recognizable genetic syndrome; the individuals are from four unrelated families. Key clinical features include congenital cataracts, hypotonia, prenatal-onset ventriculomegaly, white-matter abnormalities, hypoplastic corpus callosum, congenital heart defects, and central hypoventilation. Characteristic dysmorphic features include small palpebral fissures, a wide nasal bridge and nose, micrognathia, and digital anomalies. All affected individuals died as a result of respiratory failure, and five of them died within the first year of life. Nuclear import of proteins was decreased in affected individuals' fibroblasts, supporting a possible disease mechanism. CRISPR-mediated knockout of NUP188 in Drosophila revealed motor deficits and seizure susceptibility, partially recapitulating the neurological phenotype seen in affected individuals. Removal of NUP188 also resulted in aberrant dendrite tiling, suggesting a potential role of NUP188 in dendritic development. Two of the NUP188 pathogenic variants are enriched in the Ashkenazi Jewish population in gnomAD, a finding we confirmed with a separate targeted population screen of an international sampling of 3,225 healthy Ashkenazi Jewish individuals. Taken together, our results implicate bi-allelic loss-of-function NUP188 variants in a recessive syndrome characterized by a distinct neurologic, ophthalmologic, and facial phenotype.

A Genome-Wide Integrative Association Study of DNA Methylation and Gene Expression Data and Later Life Cognitive Functioning in Monozygotic Twins

Monozygotic twins are genetically identical but rarely phenotypically identical. Epigenetic and transcriptional variation could influence this phenotypic discordance. Investigation of intra-pair differences in molecular markers and a given phenotype in monozygotic twins controls most of the genetic contribution, enabling studies of the molecular features of the phenotype. This study aimed to identify genes associated with cognition in later life using integrated enrichment analyses of the results of blood-derived intra-pair epigenome-wide and transcriptome-wide association analyses of cognition in 452 middle-aged and old-aged monozygotic twins (56–80 years). Integrated analyses were performed with an unsupervised approach using KeyPathwayMiner, and a supervised approach using the KEGG and Reactome databases. The supervised approach identified several enriched gene sets, including “neuroactive ligand receptor interaction” (p-value = 1.62^∗10-2), “Neurotrophin signaling” (p-value = 2.52^∗10-3), “Alzheimer’s disease” (p-value = 1.20^∗10-2), and “long-term depression” (p-value = 1.62^∗10-2). The unsupervised approach resulted in a 238 gene network, including the Alzheimer’s disease gene APP (Amyloid Beta Precursor Protein) as an exception node, and several novel candidate genes. The strength of the unsupervised method is that it can reveal previously uncharacterized sub-pathways and detect interplay between biological processes, which remain undetected by the current supervised methods. In conclusion, this study identified several previously reported cognition genes and pathways and, additionally, puts forward novel candidates for further verification and validation.

Global expression profiling of cognitive level and decline in middle-aged monozygotic twins

Only few studies have investigated the genomewide transcriptome of normative cognitive aging. We therefore aimed at investigating blood gene expression patterns associated with cognitive aging using a population-based sample of 235 middle-aged monozygotic twin pairs with longitudinal data on cognitive function. This unique setup enabled examination of gene expression differences associated with individual and intrapair differences in cognitive level and change while controlling for underlying genetic variation and shared early environment. Overall, increased expression of several gene sets was found to strongly correlate with a lower cognitive level and cognitive decline. The most significantly correlated gene sets were related to protein metabolism, translation, RNA metabolism, infectious disease, and the immune system, which are all processes previously linked to transcription signatures of pathological and normal brain aging, and aging in blood. The results of our study thus suggest that gene expression patterns of cognitive level and decline in our sample mirror those seen in cognitively impaired individuals, which could point toward a more generic response to cognitive aging and aging in general.

The Optimal Sequencing Depth of Tumor Biopsies for Identifying Clonal Cell Populations

The tumor content of a biopsy and the average depth of coverage are two essential aspects when performing DNA sequencing using next-generation sequencing technologies. The heterogeneous nature of cancer necessitates the identification of distinct clonal cell populations to better understand and treat cancer. Deep sequencing enables researchers to identify these populations, but no consensus on an optimal depth exists for identifying clonal populations. Data from eight deep-sequenced oral squamous cell carcinoma biopsies obtained from three stage IV patients, with various degrees of tumor content, were used to randomly down sample the depth before being subjected to cluster analysis. An increase in coverage resulted in an increase in resolution for clusters of mutations, enabling the identification of distinct clonal cell populations and clonal events. From a depth of 800×, limited gain in resolution can be achieved; and from a depth of 1200×, the resolution stabilizes. Overall, researchers should aim for an average depth of 1000× to 1200× when performing deep sequencing. The tumor content will, however, dictate the resolution and fidelity of the analysis, as an increase in tumor complexity increases the need for higher tumor content.

[Genomic medicine and artificial intelligence]

In this review, we discuss the management of genomic medicine, which is based on very large data sets with up to billions of data points when analysing the whole genome. By using artificial intelligence (AI) it is possible to find patterns in such data sets and thereby identify subgroups of patients differing clinically, or to extract informative data points and construct models, which will predict disease risk, prognosis or treatment response most often in a process including training and testing (machine learning). Future clinical decision making will increasingly be based on patterns and models obtained by AI analysis of many parameters.

Association of miR-548c-5p, miR-7-5p, miR-210-3p, miR-128-3p with recurrence in systemically untreated breast cancer

Current prognostic markers allocate the majority of lymph node (LN) negative and estrogen receptor (ER) positive breast cancer patients into the high-risk group. Accordingly, most patients receive systemic treatments although approximately 40% of these patients may have been cured by surgery and radiotherapy alone. Two studies identified seven prognostic microRNAs in systemically untreated, LN negative and ER positive breast cancer patients which may allow more precise patient classification. However, six of the seven microRNAs were analyzed in both studies but only found to be prognostic in one study. To validate their prognostic potential, we analyzed microRNA expression in an independent cohort (n = 110) using a pair-matched study design minimizing dependence of classical markers. The expression of hsa-miR-548c-5p was significantly associated with abridged disease-free survival (hazard ratio [HR]:1.96, p = 0.027). Contradicting published results, high hsa-miR-516-3p expression was associated with favorable outcome (HR:0.29, p = 0.0068). The association is probably time-dependent indicating later relapse. Additionally, re-analysis of previously published expression data of two matching cohorts (n = 100, n = 255) supports an association of hsa-miR-128-3p with shortened disease-free survival (HR:2.48, p = 0.0033) and an upregulation of miR-7-5p (p = 0.0038; p = 0.039) and miR-210-3p (p = 0.031) in primary tumors of patients who experienced metastases. Further analysis may verify the prognostic potential of these microRNAs.

De Novo Variants in GRIA4 Lead to Intellectual Disability with or without Seizures and Gait Abnormalities

Using trio whole-exome sequencing, we have identified de novo heterozygous pathogenic variants in GRIA4 in five unrelated individuals with intellectual disability and other symptoms. GRIA4 encodes an AMPA receptor subunit known as GluR4, which is found on excitatory glutamatergic synapses and is important for learning and memory. Four of the variants are located in the highly conserved SYTANLAAF motif in the transmembrane protein M3, and the fifth is in an extra-cellular domain. Molecular modeling of the altered protein showed that three of the variants in the SYTANLAAF motif orient toward the center of the pore region and most likely lead to disturbance of the gating mechanism. The fourth variant in the SYTANLAAF motif most likely results in reduced permeability. The variant in the extracellular domain potentially interferes with the binding between the monomers. On the basis of clinical information and genetic results, and the fact that other subunits of the AMPA receptor have already been associated with neurodevelopmental disorders, we suggest that pathogenic de novo variants in GRIA4 lead to intellectual disability with or without seizures, gait abnormalities, problems of social behavior, and other variable features.

The subclonal structure and genomic evolution of oral squamous cell carcinoma revealed by ultra-deep sequencing

Recent studies suggest that head and neck squamous cell carcinomas are very heterogeneous between patients; however the subclonal structure remains unexplored mainly due to studies using only a single biopsy per patient. To deconvolute the clonal structure and describe the genomic cancer evolution, we applied whole-exome sequencing combined with ultra-deep targeted sequencing on oral squamous cell carcinomas (OSCC). From each patient, a set of biopsies was sampled from distinct geographical sites in primary tumor and lymph node metastasis.

We demonstrate that the included OSCCs show a high degree of inter-patient heterogeneity but a low degree of intra-tumor heterogeneity. However, some OSCC cancers contain complex subclonal architectures comprising distinct subclones only found in geographically distinct regions of the primary tumors. In several cases we find mutations in the primary tumor that are not present in the lymph node metastasis. We conclude that metastatic potential in our population is acquired early in tumor evolution as evident by the ongoing parallel evolution in several primary tumors.

Neonatal High Bone Mass With First Mutation of the NF-κB Complex: Heterozygous De Novo Missense (p.Asp512Ser) RELA (Rela/p65)

Heritable disorders that feature high bone mass (HBM) are rare. The etiology is typically a mutation(s) within a gene that regulates the differentiation and function of osteoblasts (OBs) or osteoclasts (OCs). Nevertheless, the molecular basis is unknown for approximately one-fifth of such entities. NF-κB signaling is a key regulator of bone remodeling and acts by enhancing OC survival while impairing OB maturation and function. The NF-κB transcription complex comprises five subunits. In mice, deletion of the p50 and p52 subunits together causes osteopetrosis (OPT). In humans, however, mutations within the genes that encode the NF-κB complex, including the Rela/p65 subunit, have not been reported. We describe a neonate who died suddenly and unexpectedly and was found at postmortem to have HBM documented radiographically and by skeletal histopathology. Serum was not available for study. Radiographic changes resembled malignant OPT, but histopathological investigation showed morphologically normal OCs and evidence of intact bone resorption excluding OPT. Furthermore, mutation analysis was negative for eight genes associated with OPT or HBM. Instead, accelerated bone formation appeared to account for the HBM. Subsequently, trio-based whole exome sequencing revealed a heterozygous de novo missense mutation (c.1534_1535delinsAG, p.Asp512Ser) in exon 11 of RELA encoding Rela/p65. The mutation was then verified using bidirectional Sanger sequencing. Lipopolysaccharide stimulation of patient fibroblasts elicited impaired NF-κB responses compared with healthy control fibroblasts. Five unrelated patients with unexplained HBM did not show a RELA defect. Ours is apparently the first report of a mutation within the NF-κB complex in humans. The missense change is associated with neonatal osteosclerosis from in utero increased OB function rather than failed OC action. These findings demonstrate the importance of the Rela/p65 subunit within the NF-κB pathway for human skeletal homeostasis and represent a new genetic cause of HBM.

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.

Long non-coding RNA expression profiles predict metastasis in lymph node-negative breast cancer independently of traditional prognostic markers

Introduction

Patients with clinically and pathologically similar breast tumors often have very different outcomes and treatment responses. Current prognostic markers allocate the majority of breast cancer patients to the high-risk group, yielding high sensitivities in expense of specificities below 20%, leading to considerable overtreatment, especially in lymph node-negative patients. Seventy percent would be cured by surgery and radiotherapy alone in this group. Thus, precise and early indicators of metastasis are highly desirable to reduce overtreatment. Previous prognostic RNA-profiling studies have only focused on the protein-coding part of the genome, however the human genome contains thousands of long non-coding RNAs (lncRNAs) and this unexplored field possesses large potential for identification of novel prognostic markers.

Methods

We evaluated lncRNA microarray data from 164 primary breast tumors from adjuvant naïve patients with a mean follow-up of 18 years. Eighty two patients who developed detectable distant metastasis were compared to 82 patients where no metastases were diagnosed. For validation, we determined the prognostic value of the lncRNA profiles by comparing the ability of the profiles to predict metastasis in two additional, previously-published, cohorts.

Results

We showed that lncRNA profiles could distinguish metastatic patients from non-metastatic patients with sensitivities above 90% and specificities of 64-65%. Furthermore; classifications were independent of traditional prognostic markers and time to metastasis.

Conclusions

To our knowledge, this is the first study investigating the prognostic potential of lncRNA profiles. Our study suggest that lncRNA profiles provide additional prognostic information and may contribute to the identification of early breast cancer patients eligible for adjuvant therapy, as well as early breast cancer patients that could avoid unnecessary systemic adjuvant therapy. This study emphasizes the potential role of lncRNAs in breast cancer prognosis.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-015-0557-4) contains supplementary material, which is available to authorized users.

Hereditary breast cancer: clinical, pathological and molecular characteristics

Pathogenic mutations in BRCA1 or BRCA2 are only detected in 25% of families with a strong history of breast cancer, though hereditary factors are expected to be involved in the remaining families with no recognized mutation. Molecular characterization is expected to provide new insight into the tumor biology to guide the search of new high-risk alleles and provide better classification of the growing number of BRCA1/2 variants of unknown significance (VUS). In this review, we provide an overview of hereditary breast cancer, its genetic background, and clinical implications, before focusing on the pathologically and molecular features associated with the disease. Recent transcriptome and genome profiling studies of tumor series from BRCA1/2 mutation carriers as well as familial non-BRCA1/2 will be discussed. Special attention is paid to its association with molecular breast cancer subtypes as well as the latest advances in predicting BRCA1/2 involvement (BRCAness) using molecular signatures, for improved diagnostics and selection of patients sensitive to targeted therapeutics.

Use of next generation sequencing in head and neck squamous cell carcinomas: a review

Head and neck squamous cell carcinoma (HNSCC) can primarily be attributed to alcohol consumption, tobacco use and infection with human papilloma virus. The heterogeneous nature of HNSCC has exposed a lack of tools for clinicians to provide more accurate prognosis. There is a need for biomarkers that can characterise the diversity of the cancer, and perhaps in the future, some of these biomarkers can point to targets for use in targeted and personalised medicine. The introduction of next generation sequencing (NGS) has allowed researches to sequence thousands of genes at a time through fast and relatively inexpensive whole exome and genome sequencing. The challenge with these enormous amounts of data is to extract relevant clinical information. In this review, we systematically evaluate all the published literature on the use of NGS of genomic DNA in HNSCC.

Microarray-based RNA profiling of breast cancer: batch effect removal improves cross-platform consistency

Microarray is a powerful technique used extensively for gene expression analysis. Different technologies are available, but lack of standardization makes it challenging to compare and integrate data. Furthermore, batch-related biases within datasets are common but often not tackled. We have analyzed the same 234 breast cancers on two different microarray platforms. One dataset contained known batch-effects associated with the fabrication procedure used. The aim was to assess the significance of correcting for systematic batch-effects when integrating data from different platforms. We here demonstrate the importance of detecting batch-effects and how tools, such as ComBat, can be used to successfully overcome such systematic variations in order to unmask essential biological signals. Batch adjustment was found to be particularly valuable in the detection of more delicate differences in gene expression. Furthermore, our results show that prober adjustment is essential for integration of gene expression data obtained from multiple sources. We show that high-variance genes are highly reproducibly expressed across platforms making them particularly well suited as biomarkers and for building gene signatures, exemplified by prediction of estrogen-receptor status and molecular subtypes. In conclusion, the study emphasizes the importance of utilizing proper batch adjustment methods when integrating data across different batches and platforms.

RNA profiling reveals familial aggregation of molecular subtypes in non-BRCA1/2 breast cancer families

BACKGROUND

In more than 70% of families with a strong history of breast and ovarian cancers, pathogenic mutation in BRCA1 or BRCA2 cannot be identified, even though hereditary factors are expected to be involved. It has been proposed that tumors with similar molecular phenotypes also share similar underlying pathophysiological mechanisms. In the current study, the aim was to investigate if global RNA profiling can be used to identify functional subgroups within breast tumors from families tested negative for BRCA1/2 germline mutations and how these subgroupings relate to different breast cancer patients within the same family.

METHODS

In the current study we analyzed a collection of 70 frozen breast tumor biopsies from a total of 58 families by global RNA profiling and promoter methylation analysis.

RESULTS

We show that distinct functional subgroupings, similar to the intrinsic molecular breast cancer subtypes, exist among non-BRCA1/2 breast cancers. The distribution of subtypes was markedly different from the distribution found among BRCA1/2 mutation carriers. From 11 breast cancer families, breast tumor biopsies from more than one affected family member were included in the study. Notably, in 8 of these families we found that patients from the same family shared the same tumor subtype, showing a tendency of familial aggregation of tumor subtypes (p-value = 1.7e-3). Using our previously developed BRCA1/2-signatures, we identified 7 non-BRCA1/2 tumors with a BRCA1-like molecular phenotype and provide evidence for epigenetic inactivation of BRCA1 in three of the tumors. In addition, 7 BRCA2-like tumors were found.

CONCLUSIONS

Our finding indicates involvement of hereditary factors in non-BRCA1/2 breast cancer families in which family members may carry genetic susceptibility not just to breast cancer but to a particular subtype of breast cancer. This is the first study to provide a biological link between breast cancers from family members of high-risk non-BRCA1/2 families in a systematic manner, suggesting that future genetic analysis may benefit from subgrouping families into molecularly homogeneous subtypes in order to search for new high penetrance susceptibility genes.

Long non-coding RNA HOTAIR is an independent prognostic marker of metastasis in estrogen receptor-positive primary breast cancer

Expression of HOX transcript antisense intergenic RNA (HOTAIR)--a long non-coding RNA--has been examined in a variety of human cancers, and overexpression of HOTAIR is correlated with poor survival among breast, colon, and liver cancer patients. In this retrospective study, we examine HOTAIR expression in 164 primary breast tumors, from patients who do not receive adjuvant treatment, in a design that is paired with respect to the traditional prognostic markers. We show that HOTAIR expression differs between patients with or without a metastatic endpoint, respectively. Survival analysis shows that high HOTAIR expression in primary tumors is significantly associated with worse prognosis independent of prognostic markers (P = 0.012, hazard ratio (HR) 1.747). This association is even stronger when looking only at estrogen receptor (ER)-positive tumor samples (P = 0.0086, HR 1.985). In ER-negative tumor samples, we are not able to detect a prognostic value of HOTAIR expression, probably due to the limited sample size. These results are successfully validated in an independent dataset with similar associations (P = 0.018, HR 1.825). In conclusion, our findings suggest that HOTAIR expression may serve as an independent biomarker for the prediction of the risk of metastasis in ER-positive breast cancer patients.

Classifications within molecular subtypes enables identification of BRCA1/BRCA2 mutation carriers by RNA tumor profiling

Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority of BRCA1 tumors were basal-like while BRCA2 tumors were mainly luminal B. Using RNA profiles, we were able to distinguish BRCA1 tumors from sporadic tumors among basal-like tumors with 83% accuracy and BRCA2 from sporadic tumors among luminal B tumors with 89% accuracy. Furthermore, subtype-specific BRCA1/2 gene signatures were successfully validated in two independent data sets with high accuracies. Although additional validation studies are required, indication of BRCA1/2 involvement (“BRCAness”) by RNA profiling could potentially be valuable as a tool for distinguishing pathogenic mutations from benign variants, for identification of undetected mutation carriers, and for selecting patients sensitive to new therapeutics such as PARP inhibitors.

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.

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.

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 </=1 microM. AF2-induced stimulation of cAMP was unaffected by removal of the dorsal or ventral nerve cord, even though this form of denervation abolished the excitatory phase of the tension response. The effects of 0.1 and 1 microM AF2 on cAMP were also unaffected by 10 microM SDPNFLRF-NH(2) (PF1, an inhibitory FaRP) and 10 microM PF1022A (an inhibitory cyclodepsipeptide), even though each of these peptides abolished the excitatory phase of the tension response induced by AF2. Within an alanine-scan series of AF2 analogues, only KHAYLRF-NH(2) stimulated cAMP production with equipotency to AF2; the effects of this peptide on muscle tension also mimicked AF2. Another excitatory FaRP present in nematodes, KNEFIRF-NH(2) (AF1), also stimulated cAMP production, but was 100-fold less potent than AF2. The stimulatory effects of AF1 on tension and cAMP levels were blocked by an alanine-substituted analogue of this peptide (Ala(6)-AF1, KNEFIAF-NH(2)), while the stimulatory effects of AF2 on tension and cAMP were not affected by this analogue. AF2 and AF1 increase A. suum somatic muscle cAMP by targeting different receptors. Increases in cAMP stimulated by AF2 can be decoupled from the excitatory response caused by this peptide, and it is not possible to establish a causal linkage between the contractile response elicited by this peptide and its effects on cAMP accumulation.

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.

Prevention by means of fluoride of enamel erosion as caused by soft drinks and orange juice

Fluoride has been suggested to prevent erosion of the teeth, either after a topical treatment of the teeth or by addition of fluoride to the acidic drink. The main aim of the present study was to describe the dissolution of calcium fluoride in some soft drinks and orange juice and compare it with the amounts of calcium fluoride left on the enamel surfaces after a topical treatment. A further aim was to describe the dissolution of enamel in soft drinks and juice saturated for 3 days with solid calcium fluoride. Solid calcium fluoride was suspended in each of 10 soft drinks and orange juices and gently agitated for 72 h, after which the drinks were analyzed for calcium, phosphate and fluoride and pH was determined. To examine the erosion-preventive effect of the calcium fluoride-rich drink, intact teeth were exposed to the drinks with or without calcium fluoride. It was found that from 6 to 45 mg of calcium fluoride was dissolved per liter of drink. The more acidic the drink, the more calcium fluoride was dissolved, presumably due to HF formation. The teeth exposed to the soft drinks all showed erosion-like lesions. Very little effect of the 4-6 ppm ionic fluoride dissolved in the soft drinks was observed. In orange juice, however, the dissolved calcium fluoride established a saturation with respect to fluorapatite and consequently, the erosion-like lesion was replaced by a caries-like lesion. In conclusion, the acidic soft drinks are capable of dissolving considerable amounts of calcium fluoride and the erosion-preventive effect of even high fluoride concentrations is limited.

The influence of saliva on the formation of calcium fluoride-like material on human dental enamel

After a topical fluoride application two resulting features can be observed and measured: the formation of calcium fluoride and a decrease in caries incidence. For the formation of solid calcium fluoride the source of calcium may be either the enamel itself or remaining saliva or--in plaque--plaque fluid and calculus. The aim of the present study was to examine whether saliva through its calcium content has any influence on the amount of calcium fluoride formed by a topical fluoride treatment of enamel. The roots and the fissure systems of 64 freshly extracted intact third molars were covered with nail varnish and allocated to eight groups of 8. Half of the groups were put in fresh paraffin-stimulated saliva for 5 min after which surplus of saliva was shaken off whilst the other groups remained in distilled water. The teeth were given a 2-min topical treatment with either distilled water (control), neutral 0.2% NaF, neutral 2% NaF or 2% NaF acidified with 0.1 mol/l H3PO4. After the topical treatment the teeth were rinsed in running tap water for 5 min, dried and revarnished before determination of calcium fluoride. It was found that the amount of calcium fluoride formed depended on the concentration of fluoride (the higher the fluoride concentration, the higher was the amount of calcium fluoride), the acidity of the solution (presumably due to the increase in available calcium through enamel dissolution) and the presence of saliva (presumably due to its calcium content and its mucinous nature). As there was always more calcium fluoride formed in the presence of saliva, thorough drying of the teeth prior to topical treatments may be superfluous.

Enamel erosion by some soft drinks and orange juices relative to their pH, buffering effect and contents of calcium phosphate

The capability of a soft drink or a juice to erode dental enamel depends not only on the pH of the drink, but also on its buffering effect. As the latter is the ability of the drink to resist a change of pH it may add to the effects of the actual pH. The aim of the present study was to compare the pH and the buffering effect of various soft drinks with their erosive effects and the solubility of apatite. In 18 soft drinks, mineral waters and juices available on the Danish market, pH and the concentrations of calcium, phosphate and fluoride were determined. The buffering effect was determined by titration with NaOH. Human teeth (n = 54) covered with nail varnish except for 3x4-mm windows were exposed to 1.5 liters of the drink for either 7 days or 24 h under constant agitation. The depth of the erosions was assessed in longitudinal sections. The depth was found to vary greatly from 3 mm eroded by the most acidic drinks and fresh orange juice to only slightly affected surfaces by most of the mineral waters. The dissolution of enamel increased logarithmically inversely with the pH of the drink and parallel with the solubility of enamel apatite. Orange juice, pH 4.0, supplemented with 40 mmol/l calcium and 30 mmol/l phosphate did not erode the enamel as the calcium and phosphate saturated the drink with respect to apatite. Generally, the lower the pH the more NaOH was necessary to bring the pH to neutrality. In particular the buffering effect of the juice was high. For all drinks, no effect of their low fluoride concentrations was observed.

Occurrence of Piloderma fallax in young, rotation-age, and old-growth stands of Douglas-fir (Pseudotsuga menziesii) in the Cascade Range of Oregon, U.S.A

Yellow mycelia and cords of Piloderma fallax (Lib.) Stalp. were more frequently observed in old-growth stands than in younger managed stands of Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). Piloderma fallax frequency and percent cover data were collected from 900 plots in three replicate stands in each of three forest age classes over 2 years in both spring and fall. Piloderma fallax is strongly associated with stand age; it occurred in 57% of plots in old-growth, 6% of rotation-age, and 1% of young stands. Presence of Piloderma fallax was related to the percent cover of coarse woody debris (CWD) in decay class 5. Piloderma fallax was approximately 2.5 times more likely to occur in a plot with CWD decay class 5 present than in plots without. The probability that it would occur in a plot increased by approximately 20% for every 10% increase in percent cover of CWD decay class 5. However, the percent cover of Piloderma fallax was not strongly related to the percent cover of CWD in decay class 5. Frequency of occurrence did not differ among sampling times. Occurrence of Piloderma fallax may indicate suitable substrate for ectomycorrhizal fungi associated with CWD and may be important in forest management for the maintenance of biodiversity and old-growth components in young managed stands.Key words: Piloderma fallax, coarse woody debris, Pseudotsuga menziesii, forest management, ectomycorrhizal fungi, biodiversity.

A laboratory study evaluating the release of hydroxyl ions from various calcium hydroxide products in narrow root canal-like tubes

AIM

The aim of the present study was to describe pH changes in a variety of buffering solutions within a narrow test tube containing either a gutta-percha point with incorporate calcium hydroxide, a commercial calcium hydroxide paste (Calcicur) or a freshly mixed paste of calcium hydroxide in distilled water.

METHODOLOGY

The test material was placed centrally in a test tube of 2 mm inner diameter. Saline (1%) was placed at one end, whilst the buffering solutions were introduced at the other. The pH of the buffering solutions was monitored using electrodes placed at each end of the test tube.

RESULTS

It was found that the pH 4.01 buffer strongly resisted pH changes at levels below 6.0, whilst saliva and bovine serum was buffered less and more evenly in the whole range up to pH 11.5. The calcium hydroxide containing gutta-percha points caused the pH to increase quickly in the sodium chloride solution to levels above 11.5. However, in bovine serum, in saliva and in the pH 4.01 buffer the pH remained below 8.5, 8.0 and 6.0, respectively, 1 mm from the point. In contrast, the release of hydroxyl ions from the two calcium hydroxide pastes brought pH above pH 11.5 irrespective of the buffering of the solutions 5 mm from the paste.

CONCLUSION

It is concluded that Calcicur and the calcium hydroxide-water mixture contained substantially more available calcium hydroxide than did the calcium hydroxide containing gutta-percha points, with the result that the release of hydroxyl ions from the points was limited in comparison to that from the pastes.

Pharmacology of FMRFamide-related peptides in helminths

Nervous systems of helminths are highly peptidergic. Species in the phylum Nematoda (roundworms) possess at least 50 FMRFamide-related peptides (FaRPs), with more yet to be identified. To date, few non-FaRP neuropeptides have been identified in these organisms, though evidence suggests that other families are present. FaRPergic systems have important functions in nematode neuromuscular control. In contrast, species in the phylum Platyhelminthes (flatworms) apparently utilize fewer FaRPs than do nematodes; those species examined possess one or two FaRPs. Other neuropeptides, such as neuropeptide F (NPF), play key roles in flatworm physiology. Although progress has been made in the characterization of FaRP pharmacology in helminths, much remains to be learned. Most studies on nematodes have been done with Ascaris suum because of its large size. However, thanks to the Caenorhabditis elegans genome project, we know most about the FaRP complement of this free-living animal. That essentially all C. elegans FaRPs are active on at least one A. suum neuromuscular system argues for conservation of ligand-receptor recognition features among the Nematoda. Structure-activity studies on nematode FaRPs have revealed that structure-activity relationship (SAR) "rules" differ considerably among the FaRPs. Second messenger studies, along with experiments on ionic dependence and anatomical requirements for activity, reveal that FaRPs act through many different mechanisms. Platyhelminth FaRPs are myoexcitatory, and no evidence exists of multiple FaRP receptors in flatworms. Interestingly, there are examples of cross-phylum activity, with some nematode FaRPs being active on flatworm muscle. The extent to which other invertebrate FaRPs show cross-phylum activity remains to be determined. How FaRPergic nerves contribute to the control of behavior in helminths, and are integrated with non-neuropeptidergic systems, also remains to be elucidated.

Plaque pH and associated parameters in relation to caries

Intensified plaque acidogenicity in caries-prone subjects was reported many years ago, but emerging evidence has suggested that the relationship may not be as strong as once thought. We have now determined a range of acidogenicity variables in subjects having both caries prevalence and incidence data, and have included plaque mineral data in the analysis. pH measurements were made in 20 randomly selected subjects from a high-caries group (mean DMFS = 8. 95) and 20 from a caries-free group of Beijing children aged 12 years participating in a caries prediction study. Subgroups with a 12-month DMFS increment >/=2 or = 0 were also formed from the two groups, respectively. Measurements were made with an iridium oxide electrode inserted between teeth 13/14, 23/24, 34/35 and 44/45, before and every 5 min for 30 min after rinsing with 10% sucrose, and the 4 resulting 'Stephan curves' averaged using a plaque pH analysis program. Supragingival plaque was collected from buccal and lingual smooth surfaces of posterior and upper anterior teeth and its acid extract analysed for Ca, P and F. Caries-free subjects (based on past experience) had a significantly higher maximum plaque pH and pH value after 30 min (reflecting a faster return to resting pH), a lower minimum enamel dissolution capacity of plaque and recorded less time below pH 7.0 than did high-caries subjects. No other differences were significant, including those of the principal acidogenic parameters 'minimum pH attained after a sugar rinse', 'curve area below the critical pH of 5.5' and 'time below the critical pH'. Selection of the caries groups on the basis of both experience and incidence did not reveal significant differences in more parameters. Upper arch plaque was significantly more acidogenic than lower arch plaque, and there was a consistently strong association between upper and lower arch values in individuals. Ca, P and F in the subjects' plaque had little or no influence on the principal acidogenic parameters. Our failure to find a relationship between caries prevalence or activity and these principal acidogenicity parameters may be related to differences between fissure and smooth surface plaque, temporal variations in acidogenicity and/or to use of F toothpaste during the 1-year observation period. These results support the view that factors such as the frequency of acidogenic episodes may be more important in caries progression than the degree of acidogenicity during any one episode.

Individual variations of pH, buffer capacity, and concentrations of calcium and phosphate in unstimulated whole saliva

In order to evaluate the risk of development of dental caries and/or of formation of dental calculus, salivary variables have often been used, but not with particular success. A reason for the apparent lack of association could be that the individual temporal variation of a characteristic was so substantial relative to the overall variation that it is not possible to characterize an individual by a single salivary measurement. The aim here was to examine the individual variation of pH, buffer capacity, and concentrations of calcium and phosphate and to compare it with the overall variation of the characteristics in order to shed light on the above problem. Eight weekly samples of up to 4 ml of unstimulated whole saliva were collected from 11 dental students before tooth brushing on their arrival at 8 a.m. in the dental school. Calcium was determined by atomic absorption spectroscopy, phosphate colorimetrically, and pH electrometrically. The buffer capacity was assessed by titration of the saliva sample from the pH initially observed to pH 3. It was found that within each individual the concentration of calcium and of phosphate, pH, the hydroxyapatite ion product and the buffer capacity varied considerably over the 7 weeks. The individual range frequently covered more than a third of the total range. Further, within each of the variables, single individuals could be found whose samples covered 60% or more of the overall range, whilst others covered less than 10% of the range. It was therefore concluded that, although collected at the same time of the day, pH, buffer capacity and concentrations of calcium and phosphate in unstimulated whole saliva in the single individual vary so much that characterization of individuals and of their saliva based on a single salivary analysis is unreliable and hazardous.

Dissolution of powdered human enamel suspended in acid solutions at a high solid/solution ratio under a 5% CO2 atmosphere at 20 degrees C

The aim was to examine the nature of enamel dissolution in aqueous suspensions with a high solid/solution ratio and in a CO2-rich atmosphere. Before experimentation, a water-saturated mixture of 95% N2-5% CO2 was passed through the acid solutions for 24 hr. Samples of 2 g of powdered enamel were suspended in 7 ml of either 5 or 10 mmol/l HClO4, with or without 2 parts/10(6) fluoride and kept gently agitated for 24 hr in the above atmosphere. The same enamel samples were repeatedly exposed to fresh acid for 26 runs. All experiments were duplicated. The aqueous phase was analysed after 20 min and 24 hr for calcium, phosphate, fluoride, chloride, sodium and magnesium. It was found that after 20 min the fluoride was invariably taken up in the enamel and the solution was supersaturated with respect to hydroxyapatite with pH ranging 6.7-5.6. During the following 24 hr pH increased further, the supersaturation remained unchanged and the concentrations of calcium and phosphate in solution decreased. In contrast, sodium, magnesium and chloride were released from enamel during the entire period. In the later runs, the supersaturation with respect to hydroxyapatite was only modest and the decrease of calcium and phosphate concentrations limited, as were the release of sodium, magnesium and chloride. It is concluded that despite a CO2-rich atmosphere, calcium, phosphate and carbonate were released from enamel and quickly established a supersaturation with respect to hydroxyapatite with a secondary reprecipitation of mineral. It indicates that within the dental caries lesion in vivo, lesion fluid cannot exist undersaturated with respect to enamel apatite.