Homologous recombination DNA repair gene alterations identify a subset of pancreatic cancers potentially responding to platinum based therapy

Il sequenziamento massivo dell’intero genoma di un gran numero di cancri del pancreas da parte del consorzio internazionale per il genoma del cancro (ICGC) ha identificato una media di 26 mutazioni per singolo tumore. Le mutazioni di KRAS sono l’impronta di questi tumori, seguite dalla inattivazione di TP53, SMAD4 e CDKN2A. Accanto a queste alterazioni sono state riscontrate mutazioni in diversi geni che insistono in 10 pathways molecolari, una delle quali è la pathway-BRCA coinvolta nella riparazione del DNA via ricombinazione omologa. Lo scopo di questa tesi è di utilizzare i dati dell’ICGC focalizzandosi su tale pathway, in quanto i geni che a questa partecipano sono coinvolti nella predisposizione ereditaria ai tumori e sono bersaglio di terapie specifiche quali i sali del platino e gli inibitori della poli-ADP-riboso polimerasi. Lo studio qui presentato ha visto la produzione di 100 xenotrapianti in topo immunodeficiente di cancri del pancreas da pazienti (PDX), per avere a disposizione un modello in vivo da utilizzare sia per la caratterizzazione molecolare che per la sperimentazione terapeutica. I 100 PDX e i rispettivi 100 tumori primitivi sono stati oggetto di analisi mutazionale dei geni più comunemente alterati nel cancro del pancreas e dei geni della pathway-BRCA. KRAS era mutato nel 96% dei casi; TP53 nel 66%, SMAD4 nel 16%, e CDKN2A nel 13%. Mutazioni pathogeniche dei geni della pathway-BRCA sono state rilevate nel 13% dei casi: ATM (1%), BARD1 (1%), BRCA1 (1%), BRCA2 (8%), REV3L (1%), e STK11 (1%). Tali mutazioni erano mutualmente esclusive. Con l’eccezione di due mutazioni in STK11 e REV3L, tutte le mutazioni erano germinali. Un ulteriore 13% di casi presentava varianti di significato sconosciuto in diversi geni di questa pathway. La concordanza fra i tumori primitivi e gli xenotrapianti è stata riscontrata nel 94% dei casi.L’esistenza di un sottogruppo significativo (13%) di cancri del pancreas con mutazioni germinali identifica pazienti che possono beneficiare di terapie mirate, e famiglie che possono rientrare in programmi di screening. Inoltre, questo studio ha identificato una serie di varianti di significato patogenico sconosciuto, che possono essere valutate per la potenziale risposta a terapia utilizzando i modelli PDX sviluppati. I PDX, infatti, rappresentano un modello prezioso che rispecchia fedelmente gli assetti genetici della malattia primitiva.Background: The International Cancer Genome Consortium (ICGC) whole genome sequencing effort identified an average of 26 mutations per pancreatic ductal adenocarcinoma (PDAC). KRAS mutations are the hallmark, followed by TP53, SMAD4 and CDKN2A inactivation. A dominating tail of decreasingly mutated genes follows, but individual pathogenic gene alterations aggregate into ten core molecular pathways, one of which is the homologous recombination (HR) DNA repair genes pathway. Aim: Within this framework, the aim of this thesis is to avail of ICGC data and focus on the HR DNA damage repair pathway, as genes in this pathway are involved in cancer predisposition and are targets of specific therapies such as platinum salts and innovative PARP inhibitors. The study also envisaged the creation of patient PDAC xenografts (PDX) as a model for primary cancers in molecular stratification and drug validation. Materials and methods: 100 PDAC and matched PDXs were analysed using targeted next generation sequencing to investigate variants in the genes commonly altered in PDAC and in the homologous recombination (HR) pathway genes.Results: KRAS was mutated in 96% of cases; TP53 in (66%), SMAD4 in 16%, and CDKN2A in 13%. Pathogenic HR mutations were found in 13% of cases: ATM (1%), BARD1 (1%), BRCA1 (1%), BRCA2 (8%), REV3L (1%), and STK11 (1%). These mutations were mutually exclusive. All but those in STK11 and REV3L were germ-line. An additional 13% of cases had variants of unknown significance (VUS) in genes of this pathway. Concordance between PDAC and PDX was found in 94% of cases.Conclusion: The finding of a significant PDAC subgroup (13%) with germ-line HR gene mutations identifies a group of patients that could profit from existing and novel target therapies as well as screening programs for family members. This study also identifies VUS that may be tested for potential response to therapy availing of the in vivo PDX avatars developed herein. PDX in fact, represent a valuable model that faithfully recapitulates the main genetic feature of primary diseases that may be used for novel diagnostics to predict drug responses as well as enable identification of effective therapeutic schemes

Conspicuous invisibility: A grounded theory approach to exploring the discovery and disclosure of violence against women attending general practice

Background: Violence against women is recognised as a common problem worldwide. In Ireland, 1:5 women experience emotional, sexual, physical, or financial violence from an intimate partner (Kelleher and O Connor 1995). However, little was known of how health professionals identify the issues, or how women make known their circumstances of domestic violence during general practice consultations. Aim: The aim of the study was twofold: a) to determine how the general practice team (GPT), discovered women who experience domestic violence from an intimate partner and, b) to determine how women were enabled (or not) to disclose their experiences of domestic violence when attending the clinical consultation. Participants and setting: Participants of the GPT included general practitioners, practice nurses and administrative staff working in urban general practices in the Republic of Ireland. All of the women participants had experienced intimate partner violence and had disclosed their experiences to others, but not always to the general practice team. Methodology: Using a grounded theory approach, 30 in-depth interviews were conducted with the GPT and women. Data were analysed in accordance with grounded theory methodology. Health professionals’ clinical experiences of discovering (or not) violence against women and women’s experiences of living in abusive relationships informed the data. Findings: The dynamics of general practice consultations were influenced by organisational factors and factors concerning the person: Firstly, choreographing the consultation in which the performance of engagement was explored through the iterative process of a choreography. Secondly, spiralling silences gave voice to the process of engagement (or not) with the issue of violence against women during clinical consultations. Thirdly, compartmentalising identified organisational factors in general practice that hindered, or enhanced, the discovery and disclosure of violence against women. Conclusion: This study advances a theory of conspicuous invisibility, which illuminates our understanding of women’s circumstances of disclosure and health professionals’ process of discovery of domestic violence. Underpinning the theory is a process of engagement, conceptualised as lifting the stones and seeing the slugs beneath. The model of engagement identified in this research illustrates three levels: level one, non-engagement; level two, first impression engagement or ‘on the face of it’ engagement; and level three, purposeful engagement

Association between falls in elderly women and chronic diseases and drug use: cross sectional study.

OBJECTIVE: To assess the associations between having had a fall and chronic diseases and drug use in elderly women. DESIGN: Cross sectional survey, using data from the British women's heart and health study. SETTING: General practices in 23 towns in Great Britain. PARTICIPANTS: 4050 women aged 60-79 years. MAIN OUTCOME MEASURE: Whether women had had falls in the previous 12 months. RESULTS: The prevalence of falling increased with increasing numbers of simultaneously occurring chronic diseases. However, no such relation with falling was found in the fully adjusted data for the number of drugs used. Circulatory disease, chronic obstructive pulmonary disease, depression, and arthritis were all associated with an increased odds of falling. The fully adjusted, population attributable risk of falling associated with having at least one chronic disease was 32.2% (95% confidence interval 19.6% to 42.8%). Only two classes of drugs (hypnotics and anxiolytics, and antidepressants) were independently associated with an increased odds of falling. Each class was associated with an increase of about 50% in the odds of falling, and each had a population attributable risk of < 5%. CONCLUSION: Chronic diseases and multiple pathology are more important predictors of falling than polypharmacy

Socioeconomic differences in childhood length/height trajectories in a middle-income country: a cohort study:a cohort study

Published: 8 September 2014Socioeconomic disadvantage is associated with shorter adult stature. Few studies have examined socioeconomic differences in stature from birth to childhood and the mechanisms involved, particularly in middle-income former Soviet settings.The sample included 12,463 Belarusian children (73% of the original cohort) born in 1996-1997, with up to 14 stature measurements from birth to 7 years. Linear spline multi-level models with 3 knots at 3, 12 and 34 months were used to analyse birth length and growth velocity during four age-periods by parental educational achievement (up to secondary school, advanced secondary/partial university, completed university) and occupation (manual, non-manual).Girls born to the most (versus least) educated mothers were 0.43 cm (95% confidence interval (CI): 0.28, 0.58) longer at birth; for boys, the corresponding difference was 0.30 cm (95% CI: 0.15, 0.46). Similarly, children of the most educated mothers grew faster from birth-3 months and 12-34 months (p-values for trend ≤ 0.08), such that, by age 7 years, girls with the most (versus least) educated mothers were 1.92 cm (95% CI: 1.47, 2.36) taller; after controlling for urban/rural and East/West area of residence, this difference remained at 1.86 cm (95% CI: 1.42, 2.31), but after additionally controlling for mid-parental height, attenuated to 1.10 cm (95% CI: 0.69, 1.52). Among boys, these differences were 1.95 cm (95% CI: 1.53, 2.37), 1.89 cm (95% CI: 1.47, 2.31) and 1.16 cm (95% CI: 0.77, 1.55), respectively. Additionally controlling for breastfeeding, maternal smoking and older siblings did not substantively alter these findings. There was no evidence that the association of maternal educational attainment with growth differed in girls compared to boys (p for interaction = 0.45). Results were similar for those born to the most (versus least) educated fathers, or who had a parent with a non-manual (versus manual) occupation.In Belarus, a middle-income former Soviet country, socioeconomic differences in offspring growth commence in the pre-natal period and generate up to approximately 2 cm difference in height at age 7 years. These associations are partly explained by genetic or other factors influencing parental stature.Current Controlled Trials: NCT01352247 assigned 9 Sept 2005; ClinicalTrials.gov. Identifier: NCT01561612 received 20 Mar 2012.Rita Patel, Kate Tilling, Debbie A Lawlor, Laura D Howe, Natalia Bogdanovich, Lidia Matush, Emily Nicoli, Michael S Kramer and Richard M Marti

Common Minimum Technical Standards and Protocols for Biobanks Dedicated to Cancer Research

Biological specimens collected, processed, and stored under optimal conditions increasingly provide a necessary foundation for cancer research. Information obtained from such samples opens opportunities to learn more about the causes, prevention, and treatment of the disease. International comparisons made possible by the study of sample collections from different parts of the world are also invaluable in the pursuit of the evidence base for cancer control. However, the above-mentioned opportunities are accompanied by many challenges and potential pitfalls. At times, pragmatic decisions have to be made in response to the constraints faced when conducting clinical or population-based studies. These constraints may be technical, may relate to infrastructure or finance, or may be ethical, legal, or social in nature. Being unaware of these types of risk to successful biobanking can place important scientific advances in jeopardy. In this context, it is a great pleasure to introduce this publication from the International Agency for Research on Cancer (IARC). The purpose of the text is to provide clear and practical advice on the common practices needed to create and maintain biobanks, recognizing that the circumstances faced by the curators of biobanks vary across the world. The international cooperation that went into formulating these Common Minimal Technical Standards provides confidence that the content is realistic, while at the same time maintaining the minimal standards needed in order for the biospecimens to be valid and to yield the reliable research data being sought. In providing this Foreword, I would like to place on record my thanks to all authors and reviewers who have contributed to this final product, as well as to all the contributors to Common Minimum Technical Standards and Protocols for Biological Resource Centres Dedicated to Cancer Research, known as the \u201cGreen Book\u201d, published by IARC in 2007. In publishing this book, my hope is for a balanced focus, not only on what goes into a biobank but also on what comes out. There is a risk that biobanks remain untouched or underexploited, a deposit that is rarely put to work for the common good. While this book aims to ensure that what goes into a biobank is of high quality and well managed, it has as its ultimate objective to drive the use of those same biospecimens in research. This will involve the analysis of biospecimens, but to maximize the benefits it will also require linkage to other well-documented epidemiological and clinical data sets. In this period of spiralling numbers of cancer cases and costs of cancer care, the failure to use stored samples to answer critical research questions is indefensible. In conclusion, I trust that readers will find this publication to be a support to successful biobanking and will find herein one important foundation for cancer research in the 21st century

The mutant p53-driven secretome has oncogenic functions in pancreatic ductal adenocarcinoma cells

The cancer secretome is a rich repository of useful information for both cancer biology and clinical oncology. A better understanding of cancer secretome is particularly relevant for pancreatic ductal adenocarcinoma (PDAC), whose extremely high mortality rate is mainly due to early metastasis, resistance to conventional treatments, lack of recognizable symptoms, and assays for early detection. TP53 gene is a master transcriptional regulator controlling several key cellular pathways and it is mutated in ~75% of PDACs. We report the functional effect of the hot-spot p53 mutant isoforms R175H and R273H on cancer cell secretome, showing their influence on proliferation, chemoresistance, apoptosis, and autophagy, as well as cell migration and epithelial-mesenchymal transition. We compared the secretome of p53-null AsPC-1 PDAC cells after ectopic over-expression of R175H-mutp53 or R273H-mutp53 to identify the differentially secreted proteins by mutant p53. By using high-resolution SWATH-MS technology, we found a great number of differentially secreted proteins by the two p53 mutants, 15 of which are common to both mutants. Most of these secreted proteins are reported to promote cancer progression and epithelial-mesenchymal transition and might constitute a biomarker secreted signature that is driven by the hot-spot p53 mutants in PDAC

Familial Associations of Adiposity: Findings from a Cross-Sectional Study of 12,181 Parental-Offspring Trios from Belarus

It is suggested that maternal adiposity has a stronger association with offspring adiposity than does paternal adiposity. Furthermore, a recent small study reported gender assortment in parental-offspring adiposity associations. We aimed to examine these associations in one of the largest studies to date using data from a low-middle income country that has recently undergone a major political and economic transition.In a cross-sectional study of 12,181 parental-offspring trios from Belarus (mean age (SD) of mothers 31.7 (4.9), fathers 34.1 (5.1) and children 6.6 (0.3) at time of assessment), we found positive graded associations of mother's and father's BMI with offspring adiposity. There was no evidence that these associations differed between mothers and fathers. For example, the odds ratio of offspring overweight or obesity (based on BMI) comparing obese and overweight mothers to normal weight mothers was 2.03 (95%CI 1.77, 2.31) in fully adjusted models; the equivalent result for father's overweight/obesity was 1.81 (1.58, 2.07). Equivalent results for offspring being in the top 10% waist circumference were 1.91 (1.67, 2.18) comparing obese/overweight to normal weight mothers and 1.72 (1.53, 1.95) comparing obese/overweight to normal weight fathers. Similarly, results for offspring being in the top 10% of percent fat mass were 1.58 (1.36, 1.84) and 1.76 (1.49, 2.07), for mother's and father's obese/overweight exposures respectively. There was no strong or consistent evidence of gender assortment--i.e. associations of maternal adiposity exposures with offspring outcomes were similar in magnitude for their daughters compared to equivalent associations in their sons and paternal associations were also similar in sons and daughters.These findings suggest that genetic and/or shared familial environment explain family clustering of adiposity. Interventions aimed at changing overall family lifestyle are likely to be important for population level obesity prevention

Life in Data”—Outcome of a Multi-Disciplinary, Interactive Biobanking Conference Session on Sample Data

©Sara Y. Nussbeck et al. 2016; Published by Mary Ann Liebert, Inc. This Open Access article is distributed under the terms of the Creative Commons Attribution Noncommercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited. The article attached is the publisher's pdf

Inferring structural variant cancer cell fraction.

We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone's performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity

IDH-wild type glioblastomas featuring at least 30% giant cells are characterized by frequent RB1 and NF1 alterations and hypermutation

: Giant cell glioblastoma (GC-GBM) is a rare variant of IDH-wt GBM histologically characterized by the presence of numerous multinucleated giant cells and molecularly considered a hybrid between IDH-wt and IDH-mutant GBM. The lack of an objective definition, specifying the percentage of giant cells required for this diagnosis, may account for the absence of a definite molecular profile of this variant. This study aimed to clarify the molecular landscape of GC-GBM, exploring the mutations and copy number variations of 458 cancer-related genes, tumor mutational burden (TMB), and microsatellite instability (MSI) in 39 GBMs dichotomized into having 30-49% (15 cases) or\u2009 65\u200950% (24 cases) GCs. The type and prevalence of the genetic alterations in this series was not associated with the GCs content (&lt;\u200950% or 65\u200950%). Most cases (82% and 51.2%) had impairment in TP53/MDM2 and PTEN/PI3K pathways, but a high proportion also featured TERT promoter mutations (61.5%) and RB1 (25.6%) or NF1 (25.6%) alterations. EGFR amplification was detected in 18% cases in association with a shorter overall survival (P\u2009=\u20090.004). Sixteen (41%) cases had a TMB\u2009&gt;\u200910 mut/Mb, including two (5%) that harbored MSI and one with a POLE mutation. The frequency of RB1 and NF1 alterations and TMB counts were significantly higher compared to 567 IDH wild type (P\u2009&lt;\u20090.0001; P\u2009=\u20090.0003; P\u2009&lt;\u20090.0001) and 26 IDH-mutant (P\u2009&lt;\u20090.0001; P\u2009=\u20090.0227; P\u2009&lt;\u20090.0001) GBMs in the TCGA PanCancer Atlas cohort. These findings demonstrate that the molecular landscape of GBMs with at least 30% giant cells is dominated by the impairment of TP53/MDM2 and PTEN/PI3K pathways, and additionally characterized by frequent RB1 alterations and hypermutation and by EGFR amplification in more aggressive cases. The high frequency of hypermutated cases suggests that GC-GBMs might be candidates for immune check-point inhibitors clinical trials