Gene-panel testing of breast and ovarian cancer patients identifies a recurrent RAD51C duplication.

Gene-panel sequencing allows comprehensive analysis of multiple genes simultaneously and is now routinely used in clinical mutation testing of high-risk breast and ovarian cancer patients. However, only BRCA1 and BRCA2 are often analyzed also for large genomic changes. Here, we have analyzed 10 clinically relevant susceptibility genes in 95 breast or ovarian cancer patients with gene-panel sequencing including also copy number variants (CNV) analysis for genomic changes. We identified 12 different pathogenic BRCA1, BRCA2, TP53, PTEN, CHEK2, or RAD51C mutations in 18 of 95 patients (19%). BRCA1/2 mutations were observed in 8 patients (8.4%) and CHEK2 protein-truncating mutations in 7 patients (7.4%). In addition, we identified a novel duplication encompassing most of the RAD51C gene. We further genotyped the duplication in breast or ovarian cancer families (n = 1149), in unselected breast (n = 1729) and ovarian cancer cohorts (n = 553), and in population controls (n = 1273). Seven additional duplication carries were observed among cases but none among controls. The duplication associated with ovarian cancer risk (3/590 of all ovarian cancer patients, 0.5%, P = .032 compared with controls) and was found to represent a large fraction of all identified RAD51C mutations in the Finnish population. Our data emphasizes the importance of comprehensive mutation analysis including CNV detection in all the relevant genes.

Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

BACKGROUND: Selection of systemic therapy for primary breast cancer is currently based on clinical biomarkers along with stage. Novel genomic tests are continuously being introduced as more precise tools for guidance of therapy, although they are often developed for specific patient subgroups. The Sweden Cancerome Analysis Network - Breast (SCAN-B) initiative aims to include all patients with breast cancer for tumour genomic analysis, and to deliver molecular subtype and mutational data back to the treating physician. METHODS: An infrastructure for collection of blood and fresh tumour tissue from all patients newly diagnosed with breast cancer was set up in 2010, initially including seven hospitals within the southern Sweden regional catchment area, which has 1.8 million inhabitants. Inclusion of patients was implemented into routine clinical care, with collection of tumour tissue at local pathology departments for transport to the central laboratory, where routines for rapid sample processing, RNA sequencing and biomarker reporting were developed. RESULTS: More than 10 000 patients from nine hospitals have currently consented to inclusion in SCAN-B with high (90 per cent) inclusion rates from both university and secondary hospitals. Tumour samples and successful RNA sequencing are being obtained from more than 70 per cent of patients, showing excellent representation compared with the national quality registry as a truly population-based cohort. Molecular biomarker reports can be delivered to multidisciplinary conferences within 1 week. CONCLUSION: Population-based collection of fresh tumour tissue is feasible given a decisive joint effort between academia and collaborative healthcare groups, and with governmental support. An infrastructure for genomic analysis and prompt data output paves the way for novel systemic therapy for patients from all hospitals, irrespective of size and location.

Defect-Induced Water Bilayer Growth on Anatase TiO2(101).

Preparing an anatase TiO2(101) surface with a high density of oxygen vacancies and associated reduced Ti species in the near-surface region results in drastic changes in the water adsorption chemistry compared to adsorption on a highly stoichiometric surface. Using synchrotron radiation excited photoelectron spectroscopy, we observe a change in the water growth mode, from layer-by-layer growth on the highly stoichiometric surface to bilayer growth on the reduced surface. Furthermore, we have been able to observe Ti3+ enrichment at the surface upon water adsorption. The Ti3+ enrichment occurs concomitant with effective water dissociation into hydroxyls with a very high thermal stability. The water bilayer on the reduced surface is thermally more stable than that on the stoichiometric surface, and it is more efficient in promoting further water dissociation upon heating. The results thus show how the presence of subsurface defects can alter the wetting mechanism of an oxide surface.

Targeted sequencing of BRCA1 and BRCA2 across a large unselected breast cancer cohort suggests that one-third of mutations are somatic.

BACKGROUND: A mutation found in the BRCA1 or BRCA2 gene of a breast tumor could be either germline or somatically acquired. The prevalence of somatic BRCA1/2 mutations and the ratio between somatic and germline BRCA1/2 mutations in unselected breast cancer patients are currently unclear. PATIENTS AND METHODS: Paired normal and tumor DNA was analyzed for BRCA1/2 mutations by massively parallel sequencing in an unselected cohort of 273 breast cancer patients from south Sweden. RESULTS: Deleterious germline mutations in BRCA1 (n = 10) or BRCA2 (n = 10) were detected in 20 patients (7%). Deleterious somatic mutations in BRCA1 (n = 4) or BRCA2 (n = 5) were detected in 9 patients (3%). Accordingly, about 1 in 9 breast carcinomas (11%) in our cohort harbor a BRCA1/2 mutation. For each gene, the tumor phenotypes were very similar regardless of the mutation being germline or somatically acquired, whereas the tumor phenotypes differed significantly between wild-type and mutated cases. For age at diagnosis, the patients with somatic BRCA1/2 mutations resembled the wild-type patients (median age at diagnosis, germline BRCA1: 41.5 years; germline BRCA2: 49.5 years; somatic BRCA1/2: 65 years; wild-type BRCA1/2: 62.5 years). CONCLUSIONS: In a population without strong germline founder mutations, the likelihood of a BRCA1/2 mutation found in a breast carcinoma being somatic was ∼1/3 and germline 2/3. This may have implications for treatment and genetic counseling.

Photochemistry of Carboxylate on TiO2(110) Studied with Synchrotron Radiation Photoelectron Spectroscopy.

We present a dedicated synchrotron radiation photoelectron spectroscopy (SR-PES) study of a photochemical reaction on the surface of rutile TiO2(110). The photoreaction kinetics of carboxylate species (trimethyl acetate, TMA) upon irradiation by UV and soft X-rays were monitored, and we show that it is possible to control the reaction rates from UV light and soft X-rays independently. We directly observe Ti4+ → Ti3+ conversion upon irradiation, attributed to electron trapping at Ti sites close to surface OH groups formed by deprotonation of the parent molecule, trimethylacetic acid (TMAA). TMA photolysis on two surface preparations with different oxygen vacancy densities shows that the vacancy-related charge quenches the amount of charge that can be trapped at hydroxyls upon irradiation. During the initial stages of reaction the correlation between the amount of photodepleted TMA and the amount of charge trapped in the Ti 3d band gap state is nearly 1:1. A first-order kinetics analysis reveals that the reaction rate decreases with decreasing TMA coverage. There is also a coverage-dependent difference in the electronic structure of TMA moieties, primarily involving the carboxyl anchor group. These changes are consistent with a decreased hole affinity of the adsorbed TMA and hence a decreased reaction rate. This discovery adds to the previously presented picture of a reactivity that is inversely proportional to the number of surface hydroxyls, suggesting that the balance between the amounts of TMA, OH, and trapped charge needs to be considered.

Decreased STAT3 in human idiopathic fetal growth restriction contributes to trophoblast dysfunction.

Abnormal trophoblast function is associated with fetal growth restriction (FGR). The JAK-STAT pathway is one of the principal signalling mechanisms by which cytokines and growth factors modulate cell proliferation, differentiation, cell migration and apoptosis. The expression of placental JAK-STAT genes in human idiopathic FGR is unknown. In this study, we propose the hypothesis that JAK-STAT pathway genes are differentially expressed in idiopathic FGR-affected pregnancies and contribute to abnormal feto-placental growth by modulating the expression of the amino acid transporter SNAT2, differentiation marker CGB/human chorionic gonadotrophin beta-subunit (ß-hCG) and apoptosis markers caspases 3 and 8, and TP53. Expression profiling of FGR-affected placentae revealed that mRNA levels of STAT3, STAT2 and STAT5B decreased by 69, 52 and 50%, respectively, compared with gestational-age-matched controls. Further validation by real-time PCR and immunoblotting confirmed significantly lower STAT3 mRNA and STAT3 protein (total and phosphorylated) levels in FGR placentae. STAT3 protein was localised to the syncytiotrophoblast (ST) in both FGR and control placentae. ST differentiation was modelled by in vitro differentiation of primary villous trophoblast cells from first-trimester and term placentae, and by treating choriocarcinoma-derived BeWo cells with forskolin in cell culture. Differentiation in these models was associated with increased STAT3 mRNA and protein levels. In BeWo cells treated with siRNA targeting STAT3, the mRNA and protein levels of CGB/ß-hCG, caspases 3 and 8, and TP53 were significantly increased, while that of SNAT2 was significantly decreased compared with the negative control siRNA. In conclusion, we report that decreased STAT3 expression in placentae may contribute to abnormal trophoblast function in idiopathic FGR-affected pregnancies.

Energy partition in magnetic reconnection in Earth's magnetotail.

The partition of energy flux in magnetic reconnection is examined experimentally using Cluster satellite observations of collisionless reconnection in Earth's magnetotail. In this plasma regime, the dominant component of the energy flux is ion enthalpy flux, with smaller contributions from the electron enthalpy and heat flux and the ion kinetic energy flux. However, the Poynting flux is not negligible, and in certain parts of the ion diffusion region the Poynting flux in fact dominates. Evidence for earthward-tailward asymmetry is ascribed to the presence of Earth's dipole fields.

In situ x-ray photoelectron spectroscopy of model catalysts: at the edge of the gap.

We present high-pressure x-ray photoelectron spectroscopy (HP-XPS) and first-principles kinetic Monte Carlo study addressing the nature of the active surface in CO oxidation over Pd(100). Simultaneously measuring the chemical composition at the surface and in the near-surface gas phase, we reveal both O-covered pristine Pd(100) and a surface oxide as stable, highly active phases in the near-ambient regime accessible to HP-XPS. Surprisingly, no adsorbed CO can be detected during high CO(2) production rates, which can be explained by a combination of a remarkably short residence time of the CO molecule on the surface and mass-transfer limitations in the present setup.

Heterogeneous reaction between Li and anatase TiO2 nanoparticles under ultra-high vacuum.

We demonstrate heterogeneous chemistry between Li and anatase TiO2 nanoparticles under UHV. The reduction of TiO2 upon formation of lithium oxide proceeds via two different schemes: one that reduces Ti(4+) to Ti(3+) and one that reduces Ti(4+) directly to Ti(2+). The second scheme sets in only after a critical degree of reduction (i.e. Li amount) has been reached (Li/Ti = 0.28) and is associated with restructuring of the film. Two films with different morphologies were compared and the results demonstrate that the reaction between Li and larger TiO2 structures (30-50 nm) is kinetically restricted while such effects were significantly less prominent for small particles (10 nm).

Active learning strategies for the deduplication of electronic patient data using classification trees.

INTRODUCTION: Supervised record linkage methods often require a clerical review to gain informative training data. Active learning means to actively prompt the user to label data with special characteristics in order to minimise the review costs. We conducted an empirical evaluation to investigate whether a simple active learning strategy using binary comparison patterns is sufficient or if string metrics together with a more sophisticated algorithm are necessary to achieve high accuracies with a small training set. MATERIAL AND METHODS: Based on medical registry data with different numbers of attributes, we used active learning to acquire training sets for classification trees, which were then used to classify the remaining data. Active learning for binary patterns means that every distinct comparison pattern represents a stratum from which one item is sampled. Active learning for patterns consisting of the Levenshtein string metric values uses an iterative process where the most informative and representative examples are added to the training set. In this context, we extended the active learning strategy by Sarawagi and Bhamidipaty (2002). RESULTS: On the original data set, active learning based on binary comparison patterns leads to the best results. When dropping four or six attributes, using string metrics leads to better results. In both cases, not more than 200 manually reviewed training examples are necessary. CONCLUSIONS: In record linkage applications where only forename, name and birthday are available as attributes, we suggest the sophisticated active learning strategy based on string metrics in order to achieve highly accurate results. We recommend the simple strategy if more attributes are available, as in our study. In both cases, active learning significantly reduces the amount of manual involvement in training data selection compared to usual record linkage settings.

High resolution photoemission and x-ray absorption spectroscopy of a lepidocrocite-like TiO2 nanosheet on Pt(110) (1 × 2).

The electronic structure of TiO(2) nanosheets on the Pt(110)-(1 × 2) surface has been investigated by using high resolution photoemission spectroscopy and x-ray absorption spectroscopy (XAS). The Ti 2p XAS spectra of the deposited TiO(2) films have been theoretically evaluated and, from the comparison with the experimental data, the assignment to a lepidocrocite-like structure is confirmed. Coexistence of TiO(2) islands with PtO(2) stripes for incomplete nanosheets is confirmed by high resolution photoemission data. The location of the valence and conduction band edges of the nanosheet has been experimentally determined allowing us to describe in details subtle electronic effects due to the interface with the substrate. The locations of the valence band maximum and the leading peak in the O 1s XAS spectrum indicate a band gap similar to anatase but with the Fermi level closer to mid-gap than found for bulk, n-type TiO(2).

The fabrication and characterization of PbTiO3 nanomesas realized on nanostructured SrRuO3/SrTiO3 templates.

We report the fabrication of PbTiO(3) nanomesas down to 30 nm lateral size and 4 nm high on nanostructured SrRuO(3)/SrTiO(3) templates by off-axis radio frequency magnetron sputtering. The templates were prepared using a top-down lithography approach based on scanning tunneling microscopy. The growth rate of the PbTiO(3) nanomesas was found to decrease with increasing growth temperature as well as with shrinking template size. Piezoresponse force microscopy measurements for the PbTiO(3) nanomesas showed a strong increase in response with decreasing lateral size. A decrease of the coercive voltage was also observed for the same lateral size range. This laterally size-dependent behavior is attributed to reduction of in-plane strain, when shrinking the nanomesa lateral dimensions.

Identification of novel candidate genes associated with cleft lip and palate using array comparative genomic hybridisation.

AIM AND METHOD: We analysed DNA samples isolated from individuals born with cleft lip and cleft palate to identify deletions and duplications of candidate gene loci using array comparative genomic hybridisation (array-CGH). RESULTS: Of 83 syndromic cases analysed we identified one subject with a previously unknown 2.7 Mb deletion at 22q11.21 coinciding with the DiGeorge syndrome region. Eighteen of the syndromic cases had clinical features of Van der Woude syndrome and deletions were identified in five of these, all of which encompassed the interferon regulatory factor 6 (IRF6) gene. In a series of 104 non-syndromic cases we found one subject with a 3.2 Mb deletion at chromosome 6q25.1-25.2 and another with a 2.2 Mb deletion at 10q26.11-26.13. Analyses of parental DNA demonstrated that the two deletion cases at 22q11.21 and 6q25.1-25.2 were de novo, while the deletion of 10q26.11-26.13 was inherited from the mother, who also has a cleft lip. These deletions appear likely to be causally associated with the phenotypes of the subjects. Estrogen receptor 1 (ESR1) and fibroblast growth factor receptor 2 (FGFR2) genes from the 6q25.1-25.2 and 10q26.11-26.13, respectively, were identified as likely causative genes using a gene prioritization software. CONCLUSION: We have shown that array-CGH analysis of DNA samples derived from cleft lip and palate subjects is an efficient and productive method for identifying candidate chromosomal loci and genes, complementing traditional genetic mapping strategies.

NLRP7 is increased in human idiopathic fetal growth restriction and plays a critical role in trophoblast differentiation.

Fetal growth restriction (FGR) the leading cause of perinatal mortality and morbidity is highly related to abnormal placental development, and placentas from FGR pregnancies are often characterized by increased inflammation. However, the mechanisms of FGR-associated inflammation are far from being understood. NLRP7, a member of a family of receptors involved in the innate immune responses, has been shown to be associated with gestational trophoblastic diseases. Here, we characterized the expression and the functional role of NLRP7 in the placenta and investigated its involvement in the pathogenesis of FGR. We used primary trophoblasts and placental explants that were collected during early pregnancy, and established trophoblast-derived cell lines, human placental villi, and serum samples from early pregnancy (n = 38) and from FGR (n = 40) and age-matched controls (n = 32). Our results show that NLRP7 (i) is predominantly expressed in the trophoblasts during the hypoxic period of placental development and its expression is upregulated by hypoxia and (ii) increases trophoblast proliferation ([3H]-thymidine) and controls the precocious differentiation of trophoblasts towards syncytium (syncytin 1 and 2 and ß-hCG production and xCELLigence analysis) and towards invasive extravillous trophoblast (2D and 3D cultures). We have also demonstrated that NLRP7 inflammasome activation in trophoblast cells increases IL-1ß, but not IL-18 secretion. In relation to the FGR, we demonstrated that major components of NLRP7 inflammasome machinery are increased and that IL-1ß but not IL-18 circulating levels are increased in FGR. Altogether, our results identified NLRP7 as a critical placental factor and provided evidence for its deregulation in FGR. NLRP7 inflammasome is abundantly expressed by trophoblast cells. It is regulated by a key parameter of placental development, hypoxia. It controls trophoblast proliferation, migration, and invasion and exhibits anti-apoptotic role. NLRP7 machinery is deregulated in FGR pregnancies. KEY MESSAGES: NLRP7 inflammasome is abundantly expressed by trophoblast cells. It is regulated by a key parameter of placental development, hypoxia. It controls trophoblast proliferation, migration, and invasion and exhibits anti-apoptotic role. NLRP7 machinery is deregulated in FGR pregnancies.

Decreased placental glypican expression is associated with human fetal growth restriction.

Placental mediated fetal growth restriction (FGR) is a leading cause of perinatal morbidity and mortality. Heparan sulphate proteoglycans (HSPG) are highly expressed in placentae and regulate haemostasis. We hypothesise that altered expression of HSPGs, glypicans (GPC) may contribute to the development of FGR and small-for-gestational-age (SGA). GPC expression was determined in first-trimester chorionic villous samples collected from women with later SGA pregnancies and in placentae from third-trimester FGR and gestation-matched uncomplicated pregnancies. The expression of both GPC1 and GPC3 were significantly reduced in first-trimester SGA as well as in the third-trimester FGR placentae compared to controls. This is the first study to report a relationship between altered placental GPC expression and subsequent development of SGA/FGR.

Genomic profiling of malignant melanoma using tiling-resolution arrayCGH.

Malignant melanoma is an aggressive, heterogeneous disease where new biomarkers for diagnosis and clinical outcome are needed. We searched for chromosomal aberrations that characterize its pathogenesis using 47 different melanoma cell lines and tiling-resolution bacterial artificial chromosome-arrays for comparative genomic hybridization. Major melanoma genes, including BRAF, NRAS, CDKN2A, TP53, CTNNB1, CDK4 and PTEN, were examined for mutations. Distinct copy number alterations were detected, including loss or gain of whole chromosomes but also minute amplifications and homozygous deletions. Most common overlapping regions with losses were mapped to 9p24.3-q13, 10 and 11q14.1-qter, whereas copy number gains were most frequent on chromosomes 1q, 7, 17q and 20q. Amplifications were delineated to oncogenes such as MITF (3p14), CCND1 (11q13), MDM2 (12q15), CCNE1 (19q12) and NOTCH2 (1p12). Frequent findings of homozygous deletions on 9p21 and 10q23 confirmed the importance of CDKN2A and PTEN. Pair-wise comparisons revealed distinct sets of alterations, for example, mutually exclusive mutations in BRAF and NRAS, mutual mutations in BRAF and PTEN, concomitant chromosome 7 gain and 10 loss and concomitant chromosome 15q22.2-q26.3 gain and 20 gain. Moreover, alterations of the various melanoma genes were associated with distinct chromosomal imbalances suggestive of specific genomic programs in melanoma development.

The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions.

Multiple genetic loci confer susceptibility to breast and ovarian cancers. We have previously developed a model (BOADICEA) under which susceptibility to breast cancer is explained by mutations in BRCA1 and BRCA2, as well as by the joint multiplicative effects of many genes (polygenic component). We have now updated BOADICEA using additional family data from two UK population-based studies of breast cancer and family data from BRCA1 and BRCA2 carriers identified by 22 population-based studies of breast or ovarian cancer. The combined data set includes 2785 families (301 BRCA1 positive and 236 BRCA2 positive). Incidences were smoothed using locally weighted regression techniques to avoid large variations between adjacent intervals. A birth cohort effect on the cancer risks was implemented, whereby each individual was assumed to develop cancer according to calendar period-specific incidences. The fitted model predicts that the average breast cancer risks in carriers increase in more recent birth cohorts. For example, the average cumulative breast cancer risk to age 70 years among BRCA1 carriers is 50% for women born in 1920-1929 and 58% among women born after 1950. The model was further extended to take into account the risks of male breast, prostate and pancreatic cancer, and to allow for the risk of multiple cancers. BOADICEA can be used to predict carrier probabilities and cancer risks to individuals with any family history, and has been implemented in a user-friendly Web-based program (http://www.srl.cam.ac.uk/genepi/boadicea/boadicea_home.html).

GAPDH, 18S rRNA and YWHAZ are suitable endogenous reference genes for relative gene expression studies in placental tissues from human idiopathic fetal growth restriction.

Comparative gene expression studies in the placenta may provide insights into molecular mechanisms of important genomic alterations in pregnancy disorders. Endogenous reference genes often referred to as housekeeping genes, are routinely used to normalise gene expression levels. For this reason, it is important that these genes be empirically evaluated for stability between placental samples including samples from complicated pregnancies. To address this issue, six candidate housekeeping genes including several commonly used ones (ACTB, GAPDH, 18S rRNA, TBP, SDHA and YWHAZ) were investigated for their expression stability in placentae obtained from pregnancies complicated by idiopathic FGR (n=25) and gestation-matched control pregnancies (n=25). Real-time PCR was performed using pre-validated gene expression assay kits. The geNorm program was used for gene stability measure (M) for the entire housekeeping genes in all control and FGR-affected placental samples. Results showed that GAPDH and 18S rRNA were most stable, with an average expression stability of M=0.441 and 0.443, respectively, followed by YWHAZ (M=0.472). SDHA, ACTB and TBP were the least stable housekeeping genes (M=0.495, 0.548 and 1.737, respectively). We recommend geometric averaging of two or more housekeeping genes to determine relative gene expression levels between FGR-affected and control placentae.

Novel homeobox genes are differentially expressed in placental microvascular endothelial cells compared with macrovascular cells.

Angiogenesis is fundamental to normal placental development and aberrant angiogenesis contributes substantially to placental pathologies. The complex process of angiogenesis is regulated by transcription factors leading to the formation of endothelial cells that line the microvasculature. Homeobox genes are important transcription factors that regulate vascular development in embryonic and adult tissues. We have recently shown that placental homeobox genes HLX, DLX3, DLX4, MSX2 and GAX are expressed in placental endothelial cells. Hence, the novel homeobox genes TLX1, TLX2, TGIF, HEX, PHOX1, MEIS2, HOXB7, and LIM6 were detected that have not been reported in endothelial cells previously. Importantly, these homeobox genes have not been previously reported in placental endothelial cells and, with the exception of HEX, PHOX1 and HOXB7, have not been described in any other endothelial cell type. Reverse transcriptase PCR was performed on cDNA from freshly isolated placental microvascular endothelial cells (PLEC), and the human placental microvascular endothelial cell line HPEC. cDNAs prepared from control term placentae, human microvascular endothelial cells (HMVEC) and human umbilical vein macrovascular endothelial cells (HUVEC) were used as controls. PCR analyses showed that all novel homeobox genes tested were expressed by all endothelial cells types. Furthermore, real-time PCR analyses revealed that homeobox genes TLX1, TLX2 and PHOX1 relative mRNA expression levels were significantly decreased in HUVEC compared with microvascular endothelial cells, while the relative mRNA expression levels of MEIS2 and TGIF were significantly increased in macrovascular cells compared with microvascular endothelial cells. Thus we have identified novel homeobox genes in microvascular endothelial cells and have shown that homeobox genes are differentially expressed between micro- and macrovascular endothelial cells.

Oxidation and Reduction of TiOx Thin Films on Pd(111) and Pd(100).

Thin films of TiOx on Pd(100) and Pd(111) have been investigated with respect to their properties after oxidation and reduction cycles. High-resolution photoemission spectroscopy (HRPES) and low energy electron diffraction (LEED) have been applied to characterize the thin film oxidation states and structure before and after oxidation and reduction under ultrahigh vacuum conditions. Fully oxidized TiO2 films were formed on both surfaces. These structures display Moiré patterns in LEED, in one dimension for Pd(100) and in two dimensions for Pd(111), and they have previously not been reported for TiO2/Pd. The oxidation process causes strong reduction in the interaction between the oxide thin film and the Pd substrate, most significantly for Pd(111). Reversible oxidation/reduction cycling of TiOx thin films on Pd(111) and Pd(100) was possible.