Haplotype analysis reveals that the recurrent BRCA1 deletion of exons 23 and 24 is a Greek founder mutation

A recurrent large genomic rearrangement (LGR) encompassing exons 23 and 24 of the BRCA1 gene has been identified in breast-ovarian cancer families of Greek origin. Its breakpoints have been determined as c.5406 + 664_*8273del11052 (RefSeq: NM_007294.3) and a diagnostic polymerase chain reaction (PCR) has been set up for rapid screening. In a series of 2,092 high-risk families completely screened for BRCA1 and BRCA2 germline mutations, we have found the deletion in 35 families (1.68%), representing 7.83% of the mutations identified in both genes and 10.3% of the total BRCA1 mutations. In order to characterize this deletion as a founder mutation, haplotype analysis was conducted in 60 carriers from 35 families, using three BRCA1 intragenic microsatellite markers and four markers surrounding the BRCA1 locus. Our results demonstrate a common shared core disease-associated haplotype of 2.89Mb. Our calculations estimate that the deletion has originated from a common ancestor 1450 years ago, which most probably inhabited the Asia Minor area. The particular (LGR) is the third mutation of such type that is proven to have a Greek founder effect in the Greek population, illustrating the necessity for LGRs testing in individuals of Greek descent.

[Greek students' attitudes towards mental disorders]

Attitudes and beliefs of the population regarding the mentally ill have been universally subject of many researches. Research of different groups' opinion for mental disorders has given remarkable findings that assist in the right design of psychiatric services. Objective of this thesis is to study the attitude of students towards mental illness. In particular, it intends to study the differences derived from the age, gender, place of birth, kind of studies, year of study, duration of stay at the place of studies and the existence of mental disorders in the student's family. Data were collected from 536 students randomly selected from Universities and Technological Institutions both in Athens and Thessaloniki. In general, the participants are being divided based on the subject of their studies in undergraduates of human sciences, exact sciences, social and health sciences. The short version of the scale "Community Attitudes Toward the Mentality III" (CAMI) was used, which consists of 26 questions sorted to four subscales (domination scale, humanism scale, social exclusion scale and the scale measuring the community beliefs regarding the care of mentally ill), along with a special questionnaire in order to collect social and demographic data. Students' attitudes towards mental illness are influenced by demographic factors, the department they are studying at and the year of study. Female gender (p=0.000), personal contact with mentally ill (p=0.012), studying in Universities (p=0.031) and especially social sciences (p=0.009) are associated with positive attitudes. On the contrary, less years of studying are associated with negative attitudes whereas older students appear to score less in the Domination Scale (p=0.000). It is significant that the place of birth (p=0,335) and the duration of stay at the place of studies (r=0.735) did not show any association with the variables studied in this research. However these results cannot be compared with older researches since there are not sufficient findings. Women tend to show more humanitarian attitude towards the mentally ill in comparison to men, emphasizing the role the community plays in their support reinforcing their reintegration in the community verifying the results of research conducted in Greece and other countries. Furthermore, students who have previously been in contact with mentally ill tend to have more favorable attitude and understanding towards them. The findings concerning the age and the years of studying highlight the imperative need of exploring thoroughly the knowledge regarding the attitudes towards mental illness.

Abstract P2-07-02: Tumor infiltrating lymphocytes density and coding mutations effects on the outcome of operable triple negative breast cancer patients

Background-Aim: Neoantigens are considered to trigger host immune responses against tumors, which may be reflected by tumor infiltrating lymphocytes (TILs) density within the tumor stroma. High TILs levels have been associated with favorable triple-negative breast cancer (TNBC) patient outcome. Herein we evaluated the presence of coding mutations and TILs density with regard to outcome in a cohort of TNBC patients treated with anthracycline-based adjuvant chemotherapy.

Patients and Methods: Paraffin TNBC tissues from 242 patients treated in the context of four prospective clinical trials were histologically reviewed and submitted to massively parallel semiconductor sequencing with a custom panel targeting 57 breast cancer (BC)-related genes. Mutations (mut) were evaluated in 210 informative samples as missense/nonsense amino acid changing variants, with minor allele frequency <1% in the case of single nucleotide polymorphisms. TILs density was morphologically evaluated as percent of the stromal area in 197 tumors; lymphocyte predominant (LP) BC tumors were called for TILs >50%. Disease-free survival (DFS) was used as the endpoint for the present analysis.

Results: 426 Mut were observed for 40 genes in 147 TNBC patients (70%). Among mutated genes, ranging from 1 in 97 tumors up to >10 in 8 tumors, the most frequently affected were TP53 (102 tumors, 69%) and PIK3CA (40 tumors, 27%). Intriguingly, mut rate (p=0.042) and number of mut genes (p=0.018) per tumor were inversely associated with TILs density. Nineteen tumors (10%) were LP-TNBC, carrying TP53 and PIK3CA mut as the only coding alterations in 10 and 3 cases, respectively. LP-TNBC patients did not experience any relapses during a follow-up period of 46-152 months (mean 66 months). For the 90% of non-LP-TNBC, the previously reported outcome benefit for 10% increments of TILs density was only demonstrated for tumors with 31-50% TILs. In non-LP-TNBC, upon adjustment for standard clinicopathological parameters, PIK3CA mut, TP53 mut and TILs density as a continuous variable, TP53 mut and nodal status independently conferred unfavorable DFS (HR=1.89, 95% CI 1.03-3.47, p=0.040 and HR=2.89, 95% CI 1.59-5.24, p=0.001, respectively). When continuous TILs density was added in the multivariate models in the entire cohort, 10% increments significantly predicted favorable DFS (HR=0.73, 95% CI 0.59-0.91, p=0.006), while high nodal status predicted unfavorable DFS (HR=2.75, 95% CI 1.51-4.99, p<0.0001).

Conclusions: In the present study, tumors with higher TILs density, including LP-TNBC, were not characterized by multiple mutations or mutated genes with the panel tested. In TNBC, increasing TILs density is a strong favorable and high nodal status a strong unfavorable prognosticator. Importantly, LP-TNBC may be regarded as a distinct subgroup with excellent prognosis concerning 10% of TNBC. In non-LP-TNBC, TP53 mut and nodal status were significant unfavorable prognosticators. These data may suggest that the level of morphologically assessed TILs density does not necessarily correspond to the tumoral mutational load and merit validation in larger cohorts.

Citation Format: Kotoula V, Fountzilas E, Chatzopoulos K, Alexopoulou Z, Timotheadou E, Xanthakis I, Gogas H, Skondra M, Christodoulou C, Papadopoulou K, Chrisafi S, Koutras A, Xepapadakis G, Venizelos V, Efstratiou I, Patsea H, Kalogeras KT, Lakis S, Fountzilas G. Tumor infiltrating lymphocytes density and coding mutations effects on the outcome of operable triple negative breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-07-02.

Abstract P4-14-05: Genomic parameters affecting the outcome of patients with advanced breast cancer treated with trastuzumab

Background-Aim: There is an unmet need for de-selecting HER2-positive patients with advanced breast cancer (ABC), since only some of those patients benefit from the addition of anti-HER2 agents to chemotherapy. The aim of this study was to investigate candidate biomarkers, including MYC and MET, in parallel with an extended array of biomarkers previously associated with trastuzumab (T) resistance.

Patients and Methods: Two hundred and twenty-nine ABC patients treated with T and chemotherapy over a period of 13 years were included in the study. Paraffin tumors were retrospectively centrally assessed with immunohistochemistry (IHC) for breast cancer subtypes; fluorescence in situ hybridization (FISH) for HER2, TOP2A and centromere (CEN) 17, MYC and CEN8, MET and CEN7; qPCR for MYC and MET copy number (CN); and, for PI3K activation (PIK3CA mutations, PTEN and phospho-mTOR IHC). Patterns of CEN CN aberrations corresponding to chromosome "polysomy" were also evaluated, with cut-offs based on normal tissue. Time to progression (TTP) and survival were evaluated from the initiation of T as first-line treatment.

Results: Median follow-up was 70 months. Of the 229 patients treated with T as HER2-positive, central analysis identified 90 cases being HER2-negative, as per current guidelines (39.3% of the total cohort). HER2-positive patients showed a trend for survival benefit over HER2-negative patients (median 50.7 vs. 38.1 months, respectively, p=0.118). HER2-positive tumors were subtyped as Luminal-HER2 (n=77) and HER2-enriched (n=53); 156 patients presented with ABC and 65 with disease initially diagnosed at stage IV (de novo ABC). MET and MYC CN gains (≥2.5 copies) were found in 40 (25%) and 15 (9%) cases with qPCR, while MET and MYC amplification with FISH was present in 4 (2.5%) and 31 (18%) cases, respectively. Concordance between FISH and qPCR was low for MYC (kappa value 0.46) and absent for MET. Polysomy was collectively observed in 70 cases, in 54 of them (32% of all tumors) concerning any 1 of the 3 examined chromosomes. This condition, called restricted polysomy, interacted with ABC presentation, conferring decreased survival to patients with ABC (HR=2.32, 95% CI 1.43-3.76, Wald's p=0.001) but not to those with de novo ABC (interaction p=0.077). MYC CN gain was the only marker significantly associated with increased risk for progression (HR=3.22, 95% CI 1.66-6.24, p<0.001) and death (HR=5.45, 95% CI 2.89-10.28, p<0.001) at univariate analysis. Adjustment of all tested markers with standard clinicopathological parameters revealed that along with poor patient performance status that was associated with poor prognosis, MYC CN gain was an independent adverse prognosticator for both TTP and survival (all p-values <0.001). The HER2-enriched subtype was independently associated with T benefit for TTP (p=0.001) and survival (p=0.051). The interaction between restricted polysomy and disease presentation was also independently significant for survival (p=0.041).

Conclusions: MYC CN gain is a strong unfavorable prognosticator in T-treated ABC patients. Distinguishing between HER2-positive subtypes seems important for identifing T benefit in ABC. Chromosomal polysomy may distinctly affect T benefit in patients with pre-treated and de novo ABC.

Citation Format: Gogas H, Kotoula V, Alexopoulou Z, Christodoulou C, Kostopoulos I, Bobos M, Raptou G, Charalambous E, Tsolaki E, Xanthakis I, Pentheroudakis G, Koutras A, Bafaloukos D, Papakostas P, Aravantinos G, Psyrri A, Petraki K, Kalogeras KT, Fountzilas G, Pectasides D. Genomic parameters affecting the outcome of patients with advanced breast cancer treated with trastuzumab. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P4-14-05.

Prediction of the time period of stroke based on ultrasound image analysis of initially asymptomatic carotid plaques

Non-invasive ultrasound imaging of carotid plaques can provide information on the characteristics of the arterial wall including the size, morphology and texture of the atherosclerotic plaques. Several studies were carried out that demonstrated the usefulness of these feature sets for differentiating between asymptomatic and symptomatic plaques and their corresponding cerebrovascular risk stratification. The aim of this study was to develop predictive modelling for estimating the time period of a stroke event by determining the risk for short term (less or equal to three years) or long term (more than three years) events. Data from 108 patients that had a stroke event have been used. The information collected included clinical and ultrasound imaging data. The prediction was performed at base line where patients were still asymptomatic. Several image texture analysis and clinical features were used in order to create a classification model. The different features were statistically analyzed and we conclude that image texture analysis features extracted using Spatial Gray Level Dependencies method had the best statistical significance. Several predictive models were derived based on Binary Logistic Regression (BLR) and Support Vector Machines (SVM) modelling. The best results were obtained with the SVM modelling models with an average correct classifications score of 77±7% for differentiating between stroke event occurrences within 3 years versus more than 3 years. Further work is needed in investigating additional multiscale texture analysis features as well as more modelling techniques on more subjects.

Efficient light emission from inorganic and organic semiconductor hybrid structures by energy-level tuning

The fundamental limits of inorganic semiconductors for light emitting applications, such as holographic displays, biomedical imaging and ultrafast data processing and communication, might be overcome by hybridization with their organic counterparts, which feature enhanced frequency response and colour range. Innovative hybrid inorganic/organic structures exploit efficient electrical injection and high excitation density of inorganic semiconductors and subsequent energy transfer to the organic semiconductor, provided that the radiative emission yield is high. An inherent obstacle to that end is the unfavourable energy level offset at hybrid inorganic/organic structures, which rather facilitates charge transfer that quenches light emission. Here, we introduce a technologically relevant method to optimize the hybrid structure's energy levels, here comprising ZnO and a tailored ladder-type oligophenylene. The ZnO work function is substantially lowered with an organometallic donor monolayer, aligning the frontier levels of the inorganic and organic semiconductors. This increases the hybrid structure's radiative emission yield sevenfold, validating the relevance of our approach.

Abstract P3-05-15: TP53 mutation and nestin protein expression patterns affect the outcome of patients with triple negative breast cancer (TNBC)

Background-aim: Nestin has recently been proposed as an ideal positive biomarker for calling basal-like breast cancer (BL). BL and TNBC overlap in 70-80% of cases and, although very heterogeneous at the genomic and phenotypic levels, most of these carry TP53 mutations. Herein, we investigated the effect of TP53 mutations and Nestin expression on the outcome of early high-risk TNBC patients who had received adjuvant chemotherapy (anthracyclines and/or taxanes). Methods: TP53 mutations were assessed in 190 FFPE TNBC DNA samples with massive parallel sequencing (entire coding region) in Ion Torrent PI chips. Variant calling and annotation (Ion Reporter 1.6) was followed by stringent read quality filtering (p<0.001). Deleterious and hot-spot mutations (Ingenuity & Oncomine databases) in 183 informative tumors were accepted for analysis. Nestin protein expression was examined by immunohistochemistry (IHC) in 283 centrally assessed TNBC on tissue microarrays; positivity was set at 1% of cells regardless of staining intensity. Further BL and TNBC related IHC markers were also examined. Results: Nestin was expressed in 134/283 tumors (47.3%), more frequently in BL-TNBC (CK5+ and/or EGFR+, Fisher's exact p<0.001) and in highly proliferative tumors (p<0.001), while it was positively associated with high tumor grade (p = 0.017) and with P-cadherin IHC (p = 0.001). TP53 mutations were observed in 141/183 tumors (77%), out of which 30 carried truncating TP53 mutations (21.3%) and 59 double damaging mutations (41.8%) usually at similar coverage; among these, truncating mutations occurred in 16 cases. TP53 mutations were more common in BL-TNBC (p = 0.029). Double mutations were positively associated with E- and P-cadherin protein expression (p = 0.016 and p = 0.020, respectively) Although TP53 mutations in general and the presence of double mutations were not associated with p53 IHC, tumors with truncating mutations were almost exclusively p53 IHC negative (p<0.001) in line with the detection capacity of the employed antibody. As single markers, neither Nestin nor TP53 mutations (any pattern) had significant effects on patient outcome. When combined, a DFS-related interaction between Nestin and double TP53 mutations was observed (Wald's p = 0.016). Nestin positive tumors with double TP53 mutations (n = 22) conferred median DFS of 45 mo. This interval was significantly shorter as compared to that of patients with Nestin positive tumors without double TP53 mutations (n = 62; median DFS 56 mo; HR 2.2; 95%CI 1-4.5; p = 0.045) and Nestin negative tumors with double TP53 mutations (n = 25) that were associated with the most favorable DFS (median: 66 mo; HR 4; 95%CI 1.3-12.4; p = 0.016). Nestin negative tumors without double TP53 mutations performed similarly to both positive tumors, although not statistically significant. Conclusions: The presence of double TP53 mutations in TNBC may reflect the genetic instability and heterogeneity characterizing these tumors. This feature in combination with the putative cancer stem cell and BL marker Nestin seems to aggravate the outcome of TNBC patients treated with standard adjuvant chemotherapy regimens. These novel findings might be worthy pursuing for validation in larger patient series.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P3-05-15.

Abstract P4-04-10: Clinically relevant tumor mutation profiles in patients with triple negative breast cancer (TNBC)

TNBC account for ∼15% of breast cancers and are most difficult to treat. However, TNBC patient outcome is very heterogeneous. In an effort to characterize the biological characteristics of TNBC, we examined 190 routinely diagnosed tumor tissues from early high-risk breast cancer patients treated with adjuvant chemotherapy (anthracyclines and/or taxanes). Highly multiplexed PCR primer pools were designed for 43 genes previously implicated in TNBC with Ion Ampliseq optimized for FFPE samples. Upon library construction and clonal amplification, amplicons were massively sequenced on Ion Proton PI chips and base-called (Torrent Suite 3.6). Variants were called and annotated (Ion Reporter 1.6), and accepted for analysis upon stringent read quality filtering at p<0.001. Informative results were obtained in 183 cases (96.3%). Deleterious and hot-spot mutations (Ingenuity and Oncomine databases) were observed in 39/43 genes, and were more frequent in TP53 (77%), CDH1 (29%), PIK3CA (16.4%), ARID1B (10.4%). TP53 was affected as a single gene in 55/183 (30%) of the cases. Most TNBC (103/183, 56.3%) were mutant in more than one genes; double deleterious/damaging TP53 mutations were observed in 59 (32.2%) tumors at relatively high incidence; and, 29 (15.8%) tumors had extremely variable mutation profiles with >4 mutations per sample, most of them at low incidence but still indicative of dynamic clonal expansion. CDH1 mutations seldom occurred alone (2% of all tumors) and were probably non-founders, while mutations in some genes, e.g., AKT1 (9/12) and ARID1B (13/19) preferentially occurred in CDH1mutant tumors (p<0.001). In comparison to the 12 patients with tumors free of mutations in any of the genes tested (no events up to 120 mo after treatment start), patients with tumors bearing any number of mutations (n = 171) had significantly shorter disease-free survival (DFS, median: 56 mo, log-rank p = 0.031). Mutations in single genes were not significantly associated with disease outcome. The 29 patients with tumors bearing >4 mutations had longer median DFS (91 mo) as compared to those with 1 mutation (n = 68, median DFS 46.5 mo) or with 4 mutations (n = 21, median DFS 39 mo) (HR: 0.4; 95%CI: 0.2-0.8; Wald's p = 0.010). In comparison to patients with TP53&CDH1 non-mutant tumors (n = 26, median DFS 62 mo), patients with TP53mutant/CDH1non-mutant tumors relapsed significantly earlier (n = 103, median DFS 48 mo, HR 3.9, 95%CI 1.2-12.9, Wald's p = 0.023) and tended to have shorter overall survival. CDH1mutant/TP53non-mutant and tumors mutated in both genes did not show such associations (interaction Wald's p = 0.044). No interactive effects on patient outcome were observed between mutation markers and treatment with taxanes, adjuvant radiotherapy, or with standard clinicopathologic parameters. In conclusion, TNBC may be assigned as a TP53 disease. However, the present data underline the need for a broad assessment of tumor mutational profiles, including non-founder mutations, since they may interfere with patient outcome upon standard treatments. The application of targeted parallel sequencing on routinely processed FFPE tissue samples seems feasible and may help in assessing clinically relevant genomic variant profiles of these highly intra- and inter-heterogeneous tumors.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-10.

Prognostic significance of RACGAP1 mRNA expression in high-risk early breast cancer: a study in primary tumors of breast cancer patients participating in a randomized Hellenic Cooperative Oncology Group trial

PURPOSE

RACGAP1 is a Rac GTPase-activating protein involved in cell growth regulation, cell transformation and metastasis. The aim of the present study was to explore the prognostic and/or predictive significance of RACGAP1 mRNA expression on disease-free survival (DFS) and overall survival (OS) in high-risk early breast cancer patients and compare it to that of Ki67 protein expression and to the Nottingham prognostic index (NPI).

METHODS

A total of 595 high-risk breast cancer patients were treated in a two-arm trial evaluating postoperative dose-dense sequential chemotherapy with epirubicin followed by CMF with or without paclitaxel. RNA was extracted from 314 formalin-fixed paraffin-embedded primary tumor tissue samples followed by one-step quantitative RT-PCR for assessing RACGAP1 mRNA expression.

RESULTS

High RACGAP1 mRNA expression (above the median) was associated with poor DFS (log-rank, p = 0.002) and OS (p < 0.001). High histological grade, as well as high Ki67 protein expression, was more frequent in the high-expression group of RACGAP1. Results of the Cox multivariate regression analysis revealed that high RACGAP1 mRNA expression independently predicted poor overall survival (Wald's p = 0.008). High Ki67 protein expression was also an adverse prognostic factor for death (p = 0.016), while high NPI score values were not.

CONCLUSIONS

High RACGAP1 mRNA expression, as assessed by qRT-PCR, was found to be of adverse prognostic significance in high-risk early breast cancer patients treated with dose-dense sequential chemotherapy. The utility of RACGAP1 mRNA expression in patient selection for treatment with aggressive chemotherapy regimens should be further explored and validated in larger cohorts.

A quantitative x-ray detection system for gold nanoparticle tumour biomarkers

X-ray fluorescence techniques have proven beneficial for identifying and quantifying trace elements in biological tissues. A novel approach is being developed that employs x-ray fluorescence with an aim to locate heavy nanoparticles, such as gold, which are embedded into tissues. Such nanoparticles can be functionalized to act as markers for tumour characteristics to map the disease state, with the future aim of imaging them to inform cancer therapy regimes. The uptake of functionalized nanoparticles by cancer cells will also enable detection of small clusters of infiltrating cancer cells which are currently missed by commonly used imaging modalities. The novel system, consisting of an energy-resolving silicon drift detector with high spectral resolution, shows potential in both quantification of and sensitivity to nanoparticle concentrations typically found in tumours. A series of synchrotron measurements are presented; a linear relationship between fluorescence intensity and gold nanoparticle (GNP) concentration was found down to 0.005 mgAu ml(-1), the detection limit of the system. Successful use of a bench-top source, suitable for possible future clinical use, is also demonstrated, and found not to degrade the detection limit or accuracy of the GNP concentration measurement. The achieved system sensitivity suggests possible future clinical usefulness in measuring tumour uptake in vivo, particularly in shallow tumour sites and small animals, in ex vivo tissue and in 3D in vitro research samples.

Suicide and seasonality

OBJECTIVE

  Seasonal variation of deaths by suicide offers an important pathway in the study of possible suicide determinants of suicide and consequently suicide prevention.

METHOD

  We conducted a review of the literature on suicide seasonality, assessing articles published between 1979 and 2009.

RESULTS

  The majority of the studies confirm a peak in spring, mainly for men, older individuals, and violent methods of suicide. A secondary peak during autumn is observed. There is no common seasonality pattern for suicide methods. However, there are also certain studies that did not confirm seasonal variation. Inconsistent results with reduced, unchanged, and even increased suicide seasonality have been reported. Aspects on the association between seasonality and suicides are discussed. Except sex, age, and method of suicide, other parameters were taken into account to find more specific characteristics of seasonality in suicides as well. The influence of clinical, bioclimatic, sociodemographic as well as biological factors seems to affect the seasonal variation.

CONCLUSION

  Studies from both the Northern and the Southern hemisphere report a seasonal pattern for suicides. These studies are not only an important source of epidemiological data for suicides but also represent a global effort to uncover hidden parameters of this self-destructive behaviour.

Pixellated Cd(Zn)Te high-energy X-ray instrument

We have developed a pixellated high energy X-ray detector instrument to be used in a variety of imaging applications. The instrument consists of either a Cadmium Zinc Telluride or Cadmium Telluride (Cd(Zn)Te) detector bump-bonded to a large area ASIC and packaged with a high performance data acquisition system. The 80 by 80 pixels each of 250 μm by 250 μm give better than 1 keV FWHM energy resolution at 59.5 keV and 1.5 keV FWHM at 141 keV, at the same time providing a high speed imaging performance. This system uses a relatively simple wire-bonded interconnection scheme but this is being upgraded to allow multiple modules to be used with very small dead space. The readout system and the novel interconnect technology is described and how the system is performing in several target applications.