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Supplementary Table 2. Results of the statistical analyses in BRCA mutation carriers.

Supplementary Table 1. The 3,248 SNPs included in the study

Supplementary Table 3. Results of the statistical analyses of SNPs from project 12 in BRCA-mutation carriers affected or non-affected with breast cancer and according to their estrogen receptor status.

Background:BRCA1 and BRCA2 mutation carriers are at substantially increased risk for developing breast and ovarian cancer. The incomplete penetrance coupled with the variable age at diagnosis in carriers of the same mutation suggests the existence of genetic and nongenetic modifying factors. In this study, we evaluated the putative role of variants in many candidate modifier genes.Methods: Genotyping data from 15,252 BRCA1 and 8,211 BRCA2 mutation carriers, for known variants (n = 3,248) located within or around 445 candidate genes, were available through the iCOGS custom-designed array. Breast and ovarian cancer association analysis was performed within a retrospective cohort approach.Results: The observed P values of association ranged between 0.005 and 1.000. None of the variants was significantly associated with breast or ovarian cancer risk in either BRCA1 or BRCA2 mutation carriers, after multiple testing adjustments.Conclusion: There is little evidence that any of the evaluated candidate variants act as modifiers of breast and/or ovarian cancer risk in BRCA1 or BRCA2 mutation carriers.Impact: Genome-wide association studies have been more successful at identifying genetic modifiers of BRCA1/2 penetrance than candidate gene studies. Cancer Epidemiol Biomarkers Prev; 24(1); 308–16. ©2014 AACR.

Metabolite profiling using 1H nuclear magnetic resonance (NMR) spectroscopy was used to investigate the metabolic changes associated with deletion of the gene for the transcriptional coactivator p300 in the human colon carcinoma cell line HCT116. Multivariate statistical methods were used to distinguish between metabolite patterns that were dependent on cell growth conditions and those that were specifically associated with loss of p300 function. In the absence of serum, wild-type cells showed slower growth, which was accompanied by a marked decrease in phosphocholine concentration, which was not observed in otherwise isogenic cell lines lacking p300. In the presence of serum, several metabolites were identified as being significantly different between the two cell types, including glutamate and glutamine, a nicotinamide-related compound and glycerophosphocholine (GPC). However, in the absence of serum, these metabolites, with the exception of GPC, were not significantly different, leading us to conclude that most of these changes were context dependent. Transcript profiling, using DNA microarrays, showed changes in the levels of transcripts for several enzymes involved in choline metabolism, which might explain the change in GPC concentration. Localized in vivo 1H NMR measurements on the tumors formed following s.c. implantation of these cells into mice showed an increase in the intensity of the peak from choline-containing compounds in the p300− tumors. These data show that NMR-based metabolite profiling has sufficient sensitivity to identify the metabolic consequences of p300 gene deletion in tumor cells in vitro and in vivo. (Cancer Res 2006; 66(15): 7606-14)

Supplementary Table 1 from Metabolic Consequences of p300 Gene Deletion in Human Colon Cancer Cells

Background Breast cancer (BC) is the most frequently diagnosed cancer and a leading cause of death among women worldwide. Early BC is potentially curable, but the mortality rates still observed among BC patients demonstrate the urgent need of novel and more effective diagnostic and therapeutic options. Limitless self-renewal is a hallmark of cancer, governed by telomere maintenance. In around 95% of BC cases, this process is achieved by telomerase reactivation through upregulation of the human telomerase reverse transcriptase (hTERT). The hypermethylation of a specific region within the hTERT promoter, termed TERT hypermethylated oncological region (THOR) has been associated with increased hTERT expression in cancer. However, its biological role and clinical potential in BC have never been studied to the best of our knowledge. Therefore, we aimed to investigate the role of THOR as a biomarker and explore the functional impact of THOR methylation status in hTERT upregulation in BC. Results THOR methylation status in BC was assessed by pyrosequencing on discovery and validation cohorts. We found that THOR is significantly hypermethylated in malignant breast tissue when compared to benign tissue (40.23% vs. 12.81%, P TERT core promoter alone (P TERT transcription, targeted THOR demethylation was performed using novel technology based on CRISPR-dCas9 system and significant THOR demethylation was achieved. Cells previously demethylated on THOR region did not develop a histologic cancer phenotype in in vivo assays. Additional studies are required to validate these observations and to unravel the causality between THOR hypermethylation and hTERT upregulation in BC. Conclusions THOR hypermethylation is an important epigenetic mark in breast tumorigenesis, representing a promising biomarker and therapeutic target in BC. We revealed that THOR acts as a repressive regulatory element of hTERT and that its hypermethylation is a relevant mechanism for hTERT upregulation in BC.

BackgroundBreast cancer (BC) genome-wide association studies (GWAS) have identified hundreds of risk-loci that require novel approaches to reveal the causal variants and target genes within them. As causal variants are most likely regulators of gene expression, we hypothesize that their identification is facilitated by pinpointing the variants with greater regulatory potential within risk-loci.MethodsWe performed genome-wide differential allelic expression (DAE) analysis using microarrays data from 64 normal breast tissue samples. Then, we mapped the variants associated with DAE (daeQTLs) and intersected these with GWAS data to reveal candidate risk regulatory variants. Finally, we validated our approach by functionally analysing the 5q14.1 breast cancer risk-locus.ResultsWe found widespread gene expression regulation by cis-acting variants in breast tissue, with 80% of coding and non-coding expressed genes displaying DAE (daeGenes). We identified over 23K daeQTLs for 2753 (16%) daeGenes, including at 154 known BC risk- loci. And in 31 of these risk-loci, we found risk-associated variant(s) and daeQTLs in strong linkage disequilibrium suggesting that the risk-causing variants are cis-regulatory, and in 27 risk-loci we propose 37 candidate target genes. As validation, we identified five candidate causal variants at the 5q14.1 risk-locus targeting the ATG10, RPS23, and ATP6AP1L genes, likely via modulation of miRNA binding, alternative transcription, and transcription factor binding.ConclusionOur study shows the power of DAE analysis and daeQTL mapping to identify causal regulatory variants and target genes at BC risk loci, including those with complex regulatory landscapes, and provides a genome-wide resource of variants associated with DAE for future functional studies.

For two decades, GWAS identified individual variants associated with risk for complex diseases. These associations can be combined into polygenic scores (PGS) aiming at quantifying an individual’s risk to disease, inform on prognosis and even treatment response (Lambert et al., 2019). Broadly, PGS use summary statistics produced by GWAS to calculate a weighted sum of trait-associated alleles carried by each individual, in which the weights correspond to the per-allele size effects. Initially used to validate associations with disease and uncover interactions between variants, PGS have been more challenging to implement in the clinic. In 2020, over 1400 publications on PGS appeared in PubMed, raising the need for a standardized distribution of studies’ key data, assuring their wide evaluation and accurate use. The Polygenic Score (PGS) Catalog, created in 2019, is a publicly available, manually curated database of PGS and relevant metadata, that responds to this need (Lambert et al., 2020). Its current release [date 2021-02-03] includes data from 133 publications and 721 PGS associated with 194 traits. Currently, data is accessed via three ways: (i) the web graphical user interface (GUI); (ii) by downloading database dumps; and (iii) the recent PGS Catalog representational state transfer (REST) application programming interface (API), the preferred method for batch analyses. info:eu-repo/semantics/publishedVersion

Introduction: Translation of genome-wide association study (GWAS) findings into preventive approaches is challenged by the identification of the causal risk variants and the understanding of the biological mechanisms by which they act. We present using allelic expression (AE) ratios to perform quantitative caseecontrol analysis as a novel approach to identify risk associations, causal regulatory variants, and target genes. Methods: Using the breast cancer (BC) risk locus 17q22 to validate this approach, we measured AE ratios in normal breast tissue samples from controls and cases, as well as from unmatched blood samples. Then we used in-silico and in-vitro analysis to map and functionally characterised candidate causal variants. Results: We found a significant shift in the AE patterns of STXBP4 (rs2628315) and COX11 (rs17817901) in the normal breast tissue of cases and healthy controls. Preferential expression of the G-rs2628315 and A-rs17817901 alleles, more often observed in cases, was associated with an increased risk for BC. Analysis of blood samples from cases and controls found a similar association. Furthermore, we identified two putative cis-regulatory variants - rs17817901 and rs8066588 - that affect a miRNA and a transcription factor binding site, respectively. Conclusion: We propose causal variants and target genes for the 17q22 BC risk locus and show that using AE ratios in caseecontrol association studies is helpful in identifying risk and mapping causal variants. info:eu-repo/semantics/publishedVersion

PIK3CA mutations are the most common in breast cancer, particularly in the estrogen receptor positive cohort, but the benefit of PI3K inhibitors has had limited success compared with approaches targeting other less common mutations. We found allelic imbalances in the expression of PIK3CA in normal breast tissue and mapped a germline candidate regulatory variant. An imbalance was also frequently observed in the expression of the missense mutant and wild-type PIK3CA alleles in breast tumors from METABRIC and TCGA projects. Moreover, although 60% of tumors preferentially expressed the mutant allele, 10% did preferentially express the wild-type allele. Mechanistically, we show that these imbalances are more frequently due to regulatory variants in cis than altered copy-number and predict that somatic variants have a more significant role than germline ones. We further found that imbalanced allelic expression between mutant and wild-type alleles due to cis-regulatory variants associated with poor prognosis (p=0.0081).Interestingly, ER+, PR+, and Her2− tumors expressing very low levels of the mutant allele had the poorest prognosis (DSS + and PR+ tumors and − tumors). Hence, our work provides compelling evidence to support the clinical utility of PIK3CA allelic expression in breast cancer in identifying this cohort of low mutant allele expressing patients of poorer prognosis, who will unlikely benefit from PI3K inhibitors. Furthermore, our work establishes a new model of differential regulation of critical cancer-promoting genes.

Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil (Lens culinarisMedik. subsp.culinaris) was first cultivated in Southwest Asia (SWA) 8000–10,000 years ago but archeological evidence is unclear as to how many times it may have been independently domesticated, in which SWA region(s) this may have happened, and whether wild species within theLensgenus have contributed to the cultivated gene pool. In this study, we combined genotyping-by-sequencing (GBS) of 190 accessions from wild (67) and domesticated (123) lentils from the Old World with archeological information to explore the evolutionary history, domestication, and diffusion of lentils to different environments. GBS led to the discovery of 87,647 single-nucleotide polymorphisms (SNPs), which allowed us to infer the phylogeny of genusLens. We confirmed previous studies proposing four groups within it. The only gene flow detected was between cultivated varieties and their progenitor (L. culinarissubsp.orientalis) albeit at very low levels. Nevertheless, a few putative hybrids or naturalized cultivars were identified. Within cultivated lentil, we found three geographic groups. Phylogenetics, population structure, and archeological data coincide in a scenario of protracted domestication of lentils, with two domesticated gene pools emerging in SWA. Admixed varieties are found throughout their range, suggesting a relaxed selection process. A small number of alleles involved in domestication and adaptation to climatic variables were identified. Both novel mutation and selection on standing variation are presumed to have played a role in adaptation of lentils to different environments. The results presented have implications for understanding the process of plant domestication (past), the distribution of genetic diversity in germplasm collections (present), and targeting genes in breeding programs (future).

PurposeTriple-negative breast cancer (TNBC) has a higher incidence, a younger age of onset, and a more aggressive behavior in African-ancestry women. Biological disparities have been suggested as an important factor influencing the ancestry-associated TNBC discrepancy. In this study, we sought to identify ancestry-associated differential gene and protein expression between African-ancestry and White TNBC patients, controlling for patients’ menopause status and pathological staging at diagnosis.MethodsDifferential gene expression analyses (DGEA) were performed using RNA-sequencing data from The Cancer Genome Atlas (TCGA). Gene set enrichment analysis (GSEA) and Ingenuity Pathway Analysis (IPA), with focus on network design, were performed to highlight candidate genes for further validation through immunohistochemistry of TNBC samples from patients followed in Portugal.ResultsWith 52 African-American and 90 White TNBC patients included, TCGA’s data corroborate that African-American patients have a higher TNBC incidence (28.42% vs 11.89%, pConclusionsWe found ancestry-associated gene expression patterns between African-ancestry and White TNBCs, particularly when controlling for menopause status or staging. EGFR, Myc, Bcl2 and β-catenin gene and protein differential expression matching results in distinct populations suggest these markers as being important indicators of TNBC’s ancestry-associated development.

Advances in genomic technologies in the last decade have revolutionised the field of medicine, especially in cancer, by producing a large amount of genetic information, often referred to as Big Data. The identification of genetic predisposition changes, prognostic signatures, and cancer driver genes, which when mutated can act as genetic biomarkers for both targeted treatments and disease monitoring, has greatly advanced our understanding of cancer. However, there are still many challenges, such as more sophisticated analysis tools and higher processing capacity, along with cheaper storage, faster and more efficient data transfer, that must be overcome before personalised medicine finally becomes a reality.

Most breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms—TargetScan and miRanda—to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant ($$P\le 5\times {10}^{-8}$$ P ≤ 5 × 10 − 8 ) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3′-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.

Recent genome-wide association studies (GWAS) have revealed the association of hundreds of single nucleotide polymorphisms (SNPs) with breast cancer (BC) risk, which mostly locate in non-coding regions, suggesting regulatory roles to the causal variants. Functional characterisation of GWAS loci has been biased towards the effect of regulatory SNPs on transcription factor binding. Here we set out to determine the extent of the contribution of breast cancer risk-associated SNPs to alternative splicing (AS).We screened genome-wide significant (P≤ 5 × 10−8) BC risk SNPs for association with AS, using expression and genotype data from normal breast samples, from the GTEx project. We identified four splicing quantitative trait loci (sQTL). In locus 6p22.1,rs6456883is a significant cis-sQTL for the expression ofZNF311gene isoforms. Three SNPs in locus 8p23.3,rs6682326,rs3008282andrs2906324, were also identified as significant cis-sQTLs/svQTLs for the expression ofRPL23AP53gene isoforms. In-silico functional analysis revealed that these variants can potentially alter enhancer splicing elements within the target genes.Our work shows that BC risk-associated variants at two loci are associated with AS isoforms in normal breast tissue, thus demonstrating that AS plays an important role in breast cancer susceptibility. Furthermore, it supports that all cis-regulatory mechanisms should be considered in the functional characterisation of risk loci.

// Ines Faleiro 1,2,3 , Ricardo Leao 4,5 , Alexandra Binnie 1,2,3 , Ramon Andrade de Mello 1,2,3 , Ana-Teresa Maia 1,2,3 and Pedro Castelo-Branco 1,2,3 1 Regenerative Medicine Program, Department of Biomedical Sciences and Medicine, University of Algarve, Faro, Portugal 2 Centre for Biomedical Research, University of Algarve, Faro, Portugal 3 Algarve Biomedical Center, Campus Gambelas, Edificio 2. Faro, Portugal 4 Department of Surgery, Princess Margaret Cancer Center, Division of Urology, University of Toronto, Toronto, Canada 5 Renal Transplantation and Urology Service, Coimbra University Hospital Center EPE, Faculty of Medicine, University of Coimbra, Portugal Correspondence to: Pedro Castelo-Branco, email: // Keywords : epigenetic therapy, urologic cancers, clinical trials Received : October 26, 2016 Accepted : December 13, 2016 Published : December 26, 2016 Abstract Epigenetic dysregulation is one of many factors that contribute to cancer development and progression. Numerous epigenetic alterations have been identified in urologic cancers including histone modifications, DNA methylation changes, and microRNA expression. Since these changes are reversible, efforts are being made to develop epigenetic drugs that restore the normal epigenetic patterns of cells, and many clinical trials are already underway to test their clinical potential. In this review we analyze multiple clinical trials ( n =51) that test the efficacy of these drugs in patients with urologic cancers. The most frequently used epigenetic drugs were histone deacetylase inhibitors followed by antisense oligonucleotides, DNA methyltransferase inhibitors and histone demethylase inhibitors, the last of which are only being tested in prostate cancer. In more than 50% of the clinical trials considered, epigenetic drugs were used as part of combination therapy, which achieved the best results. The epigenetic regulation of some cancers is still matter of research but will undoubtedly open a window to new therapeutic approaches in the era of personalized medicine. The future of therapy for urological malignancies is likely to include multidrug regimens in which epigenetic modifying drugs will play an important role.

publishersversion published

Background: A synonymous single nucleotide polymorphism (SNP) rs172378 (A>G, Gly−>Gly) in the complement component C1QA has been proposed to be associated with distant breast cancer metastasis. We previously reported overexpression of this gene to be significantly associated with better prognosis in oestrogen-receptor-negative tumours. The purpose of this study was to investigate the association of rs172378 with expression of C1QA and breast cancer survival. Methods: We analysed the gene expression pattern of rs172378 in normal and tumour tissue samples, and further explored its involvement in relation to mortality in 2270 women with breast cancer participating in Studies of Epidemiology and Risk factors in Cancer Heredity, a population-based case–control study. Results: We found that although rs172378 showed differential allelic expression significantly different between normal (preferentially expressing the G allele) and tumour tissue samples (preferentially expressing the A allele), there was no significant difference in survival by rs172378 genotype (per allele hazard ratio (HR) 1.02, 95% CI: 0.88–1.19, P=0.78 for all-cause mortality; HR 1.03, 95% CI: 0.87–1.22, P=0.72 for breast-cancer-specific mortality). Conclusion: Our study results show that rs172378 is linked to a cis-regulatory element affecting gene expression and that allelic preferential expression is altered in tumour samples, but do not support an association between genetic variation in C1QA and breast cancer survival.

The imprinted insulin-like growth factor 2 (IGF2) gene is expressed predominantly from the paternal allele. Loss of imprinting (LOI) associated with hypomethylation at the promoter proximal sequence (DMR0) of the IGF2 gene was proposed as a predisposing constitutive risk biomarker for colorectal cancer. We used pyrosequencing to assess whether IGF2 DMR0 methylation is either present constitutively prior to cancer or whether it is acquired tissue-specifically after the onset of cancer. DNA samples from tumour tissues and matched non-tumour tissues from 22 breast and 42 colorectal cancer patients as well as peripheral blood samples obtained from colorectal cancer patients [SEARCH (n=case 192, controls 96)], breast cancer patients [ABC (n=case 364, controls 96)] and the European Prospective Investigation of Cancer [EPIC-Norfolk (n=breast 228, colorectal 225, controls 895)] were analysed. The EPIC samples were collected 2-5 years prior to diagnosis of breast or colorectal cancer. IGF2 DMR0 methylation levels in tumours were lower than matched non-tumour tissue. Hypomethylation of DMR0 was detected in breast (33%) and colorectal (80%) tumour tissues with a higher frequency than LOI indicating that methylation levels are a better indicator of cancer than LOI. In the EPIC population, the prevalence of IGF2 DMR0 hypomethylation was 9.5% and this correlated with increased age not cancer risk. Thus, IGF2 DMR0 hypomethylation occurs as an acquired tissue-specific somatic event rather than a constitutive innate epimutation. These results indicate that IGF2 DMR0 hypomethylation has diagnostic potential for colon cancer rather than value as a surrogate biomarker for constitutive LOI.

PurposeThe prognosis of breast cancer varies considerably among individuals, and inherited genetic factors may help explain this variability. Of particular interest are genes involved in defense against reactive oxygen species (ROS) because ROS are thought to cause DNA damage and contribute to the pathogenesis of cancer.Patients and MethodsWe examined associations between 54 polymorphisms that tag the known common variants (minor allele frequency > 0.05) in 10 genes involved in oxidative damage repair (CAT, SOD1, SOD2, GPX1, GPX4, GSR, TXN, TXN2, TXNRD1, and TXNRD2) and survival in 4,470 women with breast cancer.ResultsTwo single nucleotide polymorphisms (SNPs) in GPX4 ( rs713041 and rs757229 ) were associated with all-cause mortality even after adjusting for multiple hypothesis testing (adjusted P = .0041 and P = .0035). These SNPs are correlated with each other (r2= 0.61). GPX4 rs713041 is located near the selenocysteine insertion sequence element in the GPX4 3′ untranslated region, and the rare allele of this SNP is associated with an increased risk of death, with a hazard ratio of 1.27 per rare allele carried (95% CI, 1.13 to 11.43). This effect was not attenuated after adjusting for tumor stage, grade, or estrogen receptor status. We found that the common allele is preferentially expressed in normal lymphocytes, normal breast, and breast tumors compared with the rare allele, but there were no differences in total levels of GPX4 mRNA across genotypes.ConclusionThese data provide strong support for the hypothesis that common variation in GPX4 is associated with prognosis after a diagnosis of breast cancer.

Previous studies involving identical twins with concordant leukemia and retrospective scrutiny of archived neonatal blood spots have shown that common chromosome translocations of pediatric leukemia frequently arise before birth. The IGH/TCR clonotypic sequences used as surrogate molecular markers suggest this is also likely to be true for hyperdiploid acute lymphoblastic leukemia (ALL). Yet evidence that hyperdiploidy itself is an early or initiating event occurring prenatally has been limited. Now, however, we can provide direct evidence of this from our identification of CD34+/CD19+ B-lineage progenitor cells with triploid chromosomes in the stored cord blood of an individual who subsequently developed hyperdiploid ALL.

A unique case of ALL in three monozygotic triplets diagnosed at the age of 24, 27 and 37 months is described. Archived bone marrow smears were available for molecular analysis of immunoglobulin heavy chain (IGH) and IGK genes and T-cell receptor (TCR)-delta and gamma gene rearrangements. A shared IGH rearrangement was found in triplets "A" and "B", and an identical rearrangement of TCR-delta in triplets "B" and "C". These data suggest a common, monoclonal initiation of ALL in one of these three triplets, followed by dissemination of clonal progeny to the other twins via vascular anastomoses within the single, monochorionic placenta that they shared in utero. Differences in IGH rearrangements in diagnostic samples also indicates divergent subclonal evolution of the original "pre-leukaemic" clone.

Studies in identical twins and with neonatal blood spots (Guthrie cards) have backtracked the origin of childhood acute leukemia and their associated chromosomal translocations to before birth. High hyperdiploidy is the most common genetic abnormality in childhood acute lymphoblastic leukemia (ALL). Evidence for an in utero initiation of this important genetic event in ALL is available from blood spots but remains limited. Twin children with hyperdiploid ALL have not hitherto been reported. We describe a pair of 2-year-old monozygotic twins with concordant B-cell precursor ALL and hyperdiploid karyotypes. One twin's leukemic cells had two rearranged TCRD alleles and one of these was a clonotypic Vdelta2-Ddelta3 sequence shared with leukemic cells of the other twin. The twins' leukemic cells had several different IGH V(H)-J(H) rearrangements but shared two common D(H)-J(H) 'stem' sequences. We conclude that ALL in these twins is likely to have originated prenatally in one fetus before spreading to the other via intraplacental anastomoses. It is likely that one or more additional postnatal genetic events was required for overt leukemogenesis.

No contexto da globalização dos negócios e da ênfase dada às relações Portugal‑China, afigura-se como pertinente o estudo do processo de comunicação entre empresas portuguesas e empresas chinesas. Devido às diferenças culturais entre Portugal e a China, é importante perceber quais as necessidades de comunicação específicas e quais as medidas que as empresas estão dispostas a implementar para dar resposta a essas necessidades, de forma a estabelecerem relações de negócios apoiadas na comunicação intercultural consciente e eficaz. É feita uma apresentação das relações entre os dois países, o processo de comunicação no contexto empresarial internacional e a análise de necessidades referentes a este tipo de comunicação. Pretende-se também entender o conceito de cultura e a sua interdependência com o fenómeno da comunicação, pondo em relevo a importância da comunicação intercultural para o sucesso das empresas. Através de quatro casos de estudo de empresas da região de Aveiro é feita uma análise à realidade da comunicação entre empresas portuguesas e os seus parceiros chineses, denotando processos, dificuldades e desafios sentidos, bem como as estratégias adotadas para a superação dos obstáculos comunicativos., RUA-L: Revista da Universidade de Aveiro. Letras, n.º 4 (2015): Línguas e culturas nas relações empresariais

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics The purpose of this work project is to analyze the concept of commoditization in the information technology industry (IT). It is based on a case study that describes how IBM, a successful company for more than seventy years, was affected by the commoditization of the personal computer segment in the early 1990s and the strategic transformation undertook by the company to overcome this problem. Furthermore, it is also emphasized IBM’s decisions to exit commoditized segments and to shift its portfolio towards services and software, due to their major contribution in bringing the company back to its leading position in the marketplace.

TOX3 maps to 16q12, a region commonly lost in breast cancers and recently implicated in the risk of developing breast cancer. However, not much is known of the role of TOX3 itself in breast cancer biology. This is the first study to determine the importance of TOX3 mutations in breast cancers. We screened TOX3 for mutations in 133 breast tumours and identified four mutations (three missense, one in-frame deletion of 30 base pairs) in six primary tumours, corresponding to an overall mutation frequency of 4.5%. One potentially deleterious missense mutation in exon 3 (Leu129Phe) was identified in one tumour (genomic DNA and cDNA). Whilst copy number changes of 16q12 are common in breast cancer, our data show that mutations of TOX3 are present at low frequency in tumours. Our results support that TOX3 should be further investigated to elucidate its role in breast cancer biology. Breast Cancer Research Foundation grant; University of Cambridge; Cancer Research UK; Hutchison Whampoa Limited; NIHR Cambridge Biomedical Research Centre; Marie Curie Career Integration Grant; Cancer Research UK [16942]; National Institute for Health Research [NF-SI-0611-10154]

Analysis of 4,405 variants in 89,050 European subjects from 41 case-control studies identified three independent association signals for estrogen-receptor-positive tumors at 11q13. The strongest signal maps to a transcriptional enhancer element in which the G allele of the best candidate causative variant rs554219 increases risk of breast cancer, reduces both binding of ELK4 transcription factor and luciferase activity in reporter assays, and may be associated with low cyclin D1 protein levels in tumors. Another candidate variant, rs78540526, lies in the same enhancer element. Risk association signal 2, rs75915166, creates a GATA3 binding site within a silencer element. Chromatin conformation studies demonstrate that these enhancer and silencer elements interact with each other and with their likely target gene, CCND1. © 2013 The American Society of Human Genetics.

Introduction: Cis-acting regulatory single nucleotide polymorphisms (SNPs) at specific loci may modulate penetrance of germline mutations at the same loci by introducing different levels of expression of the wild-type allele. We have previously reported that BRCA2 shows differential allelic expression and we hypothesize that the known variable penetrance of BRCA2 mutations might be associated with this mechanism. Methods: We combined haplotype analysis and differential allelic expression of BRCA2 in breast tissue to identify expression haplotypes and candidate cis-regulatory variants. These candidate variants underwent selection based on in silico predictions for regulatory potential and disruption of transcription factor binding, and were functionally analyzed in vitro and in vivo in normal and breast cancer cell lines. SNPs tagging the expression haplotypes were correlated with the total expression of several genes in breast tissue measured by Taqman and microarray technologies. The effect of the expression haplotypes on breast cancer risk in BRCA2 mutation carriers was investigated in 2,754 carriers. Results: We identified common haplotypes associated with differences in the levels of BRCA2 expression in human breast cells. We characterized three cis-regulatory SNPs located at the promoter and two intronic regulatory elements which affect the binding of the transcription factors C/EBP alpha, HMGA1, D-binding protein (DBP) and ZF5. We showed that the expression haplotypes also correlated with changes in the expression of other genes in normal breast. Furthermore, there was suggestive evidence that the minor allele of SNP rs4942440, which is associated with higher BRCA2 expression, is also associated with a reduced risk of breast cancer (per-allele hazard ratio (HR) = 0.85, 95% confidence interval (CI) = 0.72 to 1.00, P-trend = 0.048). Conclusions: Our work provides further insights into the role of cis-regulatory variation in the penetrance of disease-causing mutations. We identified small-effect genetic variants associated with allelic expression differences in BRCA2 which could possibly affect the risk in mutation carriers through altering expression levels of the wild-type allele. Core Genomics team at Cambridge Research Institute; Breast Cancer Research Foundation; University of Cambridge; Cancer Research UK [C1287/A10118, C1287/A11990, C5047/A8385]; Hutchison Whampoa Limited; NIHR Cambridge Biomedical Research Centre; Cancer Genetics Network; Marjorie Cohen Foundation; NIHR; Royal Marsden NHS Foundation Trust; Ligue National Contre le Cancer; Association for International Cancer Research [AICR-07-0454]; Association "Le cancer du sein, parlons-en!"; Helsinki University Central Hospital; Academy of Finland [132473]; Finnish Cancer Society; Sigrid Juselius Foundation; NIH [CA128978]; Breast Cancer Specialized Program of Research Excellence (SPORE) [CA116167]; Komen Foundation for the Cure; Eileen Stein Jacoby Fund; University of Kansas Cancer Center; Kansas Bioscience Authority; Tumour Tuscany Institute [AOOGRT/0011780/Q.30.11]; NHMRC; National Breast Cancer Foundation; Cancer Australia [628333]; Queensland Cancer Fund; Cancer Council of New South Wales; Cancer Council of Victoria; Cancer Council of Tasmania; Cancer Council South Australia; Cancer Foundation of Western Australia; [U01CA69631]; [5U01CA113916]; Cancer Research UK [19275, 11022, 10118, 19556, 11174]; National Institute for Health Research [NF-SI-0611-10154, NF-SI-0510-10096]

Recent genome-wide association studies have identified a breast cancer susceptibility locus on 16q12 with an unknown biological basis. We used a set of single nucleotide polymorphism (SNP) markers to generate a fine-scale map and narrowed the region of association to a 133 kb DNA segment containing the largely uncharacterized hypothetical gene LOC643714, a short intergenic region and the 5' end of TOX3. Re-sequencing this segment in European subjects identified 293 common polymorphisms, including a set of 26 highly correlated candidate causal variants. By evaluation of these SNPs in five breast cancer case-control studies involving more than 23 000 subjects from populations of European and Southeast Asian ancestry, all but 14 variants could be excluded at odds of

The recent whole-genome scan for breast cancer has revealed the FGFR2 (fibroblast growth factor receptor 2) gene as a locus associated with a small, but highly significant, increase in the risk of developing breast cancer. Using fine-scale genetic mapping of the region, it has been possible to narrow the causative locus to a haplotype of eight strongly linked single nucleotide polymorphisms (SNPs) spanning a region of 7.5 kilobases (kb) in the second intron of the FGFR2 gene. Here we describe a functional analysis to define the causative SNP, and we propose a model for a disease mechanism. Using gene expression microarray data, we observed a trend of increased FGFR2 expression in the rare homozygotes. This trend was confirmed using real-time (RT) PCR, with the difference between the rare and the common homozygotes yielding a Wilcox p-value of 0.028. To elucidate which SNPs might be responsible for this difference, we examined protein–DNA interactions for the eight most strongly disease-associated SNPs in different breast cell lines. We identify two cis-regulatory SNPs that alter binding affinity for transcription factors Oct-1/Runx2 and C/EBPβ, and we demonstrate that both sites are occupied in vivo. In transient transfection experiments, the two SNPs can synergize giving rise to increased FGFR2 expression. We propose a model in which the Oct-1/Runx2 and C/EBPβ binding sites in the disease-associated allele are able to lead to an increase in FGFR2 gene expression, thereby increasing the propensity for tumour formation., Author Summary Recently, a number of whole-genome association studies have identified genes that predispose individuals to common diseases such as cancer. The challenge now is to understand how the identified risk loci contribute to disease, since the majority of these loci are located within introns (which are discarded after transcription) and intergenic regions, and therefore do not change the coding region of nearby genes. This manuscript describes how two single–base pair changes in intron 2 of the FGFR2 (fibroblast growth factor receptor 2) gene, “the top hit” of the breast cancer susceptibility study, exert their function. We find that the changes alter the binding of two transcription factors and cause an increase in FGFR2 gene expression, thus providing a molecular explanation for the risk phenotype. This is the first functional study, to our knowledge, of the risk loci identified for breast cancer in a whole-genome scan and demonstrates that these studies can be used as valid starting points for studying the underlying biology of cancer., Recent whole-genome scans have identified novel risk genes for many common diseases, challenging researchers to determine how these genes contribute to disease. A new study provides molecular insights into a breast cancer risk factor.

Mestrado em Línguas e Relações Empresariais No actual contexto de globalização das transacções comerciais esta dissertação tem como objectivo estudar o processo de comunicação entre empresas portuguesas e empresas chinesas. Devido às diferenças culturais patentes entre Portugal e a China é importante perceber quais as necessidades específicas de comunicação existentes e quais as medidas que as empresas estão dispostas a implementar para dar resposta a essas necessidades, de forma a estabelecerem relações de negócios apoiadas na comunicação intercultural consciente e eficaz. Procura elucidar-se como se desenrola o processo de comunicação, as suas barreiras, a comunicação específica do contexto organizacional e a análise de necessidades referentes a este tipo de comunicação. Como componente essencial da comunicação entre dois países diferentes, pretende-se também entender o conceito de cultura e a sua interdependência com o fenómeno da comunicação, pondo em relevo a importância da comunicação intercultural para o sucesso das empresas. Através de questionários e entrevistas a várias empresas da região de Aveiro, é feita uma análise à realidade da comunicação intercultural entre empresas portuguesas e os seus parceiros chineses, denotando que, apesar de haver consciência da importância fulcral das competências interculturais, na generalidade, não há um pensamento estratégico a priori, que deriva da falta de informação, de oferta formativa e de apoios institucionais sentida pelas empresas portuguesas. ABSTRACT: In today’s globalized commercial exchange context, this dissertation aims at studying the communication process between Portuguese and Chinese companies. Due to the cultural differences between Portugal and China it is important to understand specific communication needs and the measures companies are willing to implement in order to establish business relations supported by a conscientious and effective intercultural communication. It is important to understand the functioning of the communication process, its barriers, the specific organizational communication and the needs analysis that refers to this kind of communication. As an essential component of the communication between two countries, it is also relevant to understand the concept of culture and its interdependence with the communication phenomenon, highlighting the importance of intercultural communication to the success of businesses. Through questionnaires and interviews conducted in several companies of the Aveiro region, we analyse the reality of intercultural communication between Portuguese companies and its Chinese counterparts. Despite being aware of the key importance of intercultural competences, generally there is not a prior strategic planning, which derives from the lack of information, of training opportunities and institutional support felt by the Portuguese companies.

Breast cancer is the most common cancer affecting women in the developed world. However, the current knowledge of breast cancer genetic risk cannot explain as much as two-thirds of cases. While successful, GWAS have not: (1) contributed to explain the genetic causality of risk; (2) provided an indication of the biological mechanisms involved. Based on our previous results demonstrating that cis-regulatory variation is involved in breast cancer risk, we have performed whole-genome differential allelic expression (DAE) analysis of sixty-four normal breast tissue samples. We integrated this genome-wide DAE map with published breast cancer GWAS risk loci according to chromosome location, and linkage disequilibrium between DAE SNPs and GWAS associated SNPs. We found 15 loci (20%) displaying GWAS associated SNPs in strong linkage disequilibrium with SNPs displaying DAE. Potential regulatory SNPs in top two candidate loci are being currently mapped and functionally studied. We are now integrating the DAE whole-genome map with unpublished GWAS data, to test the efficiency of this approach to help prioritise loci for further risk-association validation. The large overlap between GWAS and DAE data confirms the importance of cis-regulation in the biology of breast cancer risk and provides a new powerful tool to prioritise and functionally analyse risk loci identified through GWAS. Citation Format: Joana Xavier, Roslin Russell, Bernardo P. Almeida, Nordiana Rosli, Catia Rocha, Shamith Samarajiwa, Suet-Feung Chin, Carlos Caldas, Bruce AJ Ponder, Ana-Teresa Maia. Integrative differential allelic expression analysis efficiently reveals the biology underlying risk to breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A31.

Studies of monozygotic twins with concordant leukemia and scrutiny of archived neonatal blood by polymerase chain reaction (PCR) indicated that many pediatric leukemias are initiated prenatally by chromosomal translocation followed by a variable postnatal period before diagnosis of disease. The latter is thought to reflect a persistent preleukemic stage and a requirement for secondary genetic events. We sought to examine this further by examination of blood spots in rare cases of MLL fusion-positive or ETV6/RUNX1 (TEL-AML1) fusion gene-positive acute leukemia that were diagnosed at ages beyond the normal age range. We present evidence that the duration of the postnatal preleukemic state can occasionally be very protracted in these biological subtypes of pediatric leukemia, and we discuss its biological significance.

Identical infant twins with concordant leukemia were first described in 1882, and since that time many such pairs of infants and older children have been described. It has long been recognized that this situation offers a unique opportunity to identify aspects of the developmental timing, natural history, and molecular genetics of pediatric leukemia in general. We reviewed both the older literature and more recent molecular biologic studies that have uncovered the basis of concordance of leukemia. Molecular markers of clonality, including unique, genomic fusion gene sequences, have provided unequivocal evidence that twin pairs of leukemia have a common clonal origin. The only plausible basis for this, first suggested more than 40 years ago, is that following initiation of leukemia in one twin fetus, clonal progeny spread to the co-twin via vascular anastomoses within a single, monochorionic placenta. This explanation has been endorsed by the identification of clonotypic gene fusion sequences in archived neonatal blood spots of individuals who subsequently developed leukemia. These analyses of twin leukemias have thrown considerable light on the natural history of disease. They reveal a frequent prenatal origin and an early or initiating role for chromosome translocations. Further, they provide evidence for a variable and often protracted latency and the need, in childhood acute lymphoblastic leukemia (ALL)/acute myeloblastic leukemia (AML), for further postnatal exposures and/or genetic events to produce clinical disease. We argue that these insights provide a very useful framework for attempts to understand etiologic mechanisms. (Blood. 2003;102:2321-2333)

The occurrence of childhood acute lymphoblastic leukemia (ALL) in 2 of 3 triplets provided a unique opportunity for the investigation of leukemogenesis and the natural history of ALL. The 2 leukemic triplets were monozygotic twins and shared an identical, acquiredTEL-AML1 genomic fusion sequence indicative of a single-cell origin in utero in one fetus followed by dissemination of clonal progeny to the comonozygotic twin by intraplacental transfer. In accord with this interpretation, clonotypic TEL-AML1 fusion sequences could be amplified from the archived neonatal blood spots of the leukemic twins. The blood spot of the third, healthy, dizygotic triplet was also fusion gene positive in a single segment, though at age 3 years, his blood was found negative by sensitive polymerase chain reaction (PCR) screening for the genomic sequence and by reverse transcription–PCR. Leukemic cells in both twins had, in addition toTEL-AML1 fusion, a deletion of the normal, nonrearrangedTEL allele. However, this genetic change was found by fluorescence in situ hybridization to be subclonal in both twins. Furthermore, mapping of the genomic boundaries of TELdeletions using microsatellite markers indicated that they were individually distinct in the twins and therefore must have arisen as independent and secondary events, probably after birth. These data support a multihit temporal model for the pathogenesis of the common form of childhood leukemia.

Gliomas are the most frequent primary tumours of the central nervous system and several types of gliomas are histopathologically recognized. Loss of the whole chromosome 10, or part of it, is the most prevalent genetic abnormality in astrocytic tumours, particularly in glioblastomas, in which it is observed in up to 80% of all cases [1]. In an attempt to localize a common region of loss in these tumours, we carried out an allelotyping analysis of 25 glioblastomas multiforme, 6 astrocytomas, 4 oligodendrogliomas and 2 ependymomas using highly polymorphic DNA markers, located in the q26 region of chromosome 10. Two meningioma samples have also been analysed. Loss of heterozygosity was found in 76% (19/25) of the glioblastomas, 50% (3/6) of the astrocytomas, 50% (2/4) of the oligodendrogliomas and 100% (2/2) of the ependymomas. None of the two meningiomas showed evidence of loss in this region. The allelotyping results revealed a minimal common region of loss, bordered by the D10S1236 and D10S186 markers, spanning 8.88 Mb, which may be a possible location for a tumour suppressor gene involved in human glioma progression. This region may also be associated to glioma tumorigenesis, since it also appears deleted in early stage gliomas. The fact that microsatellite instability (MSI) screening of gliomas has rendered only one positive sample shows that there is little evidence of MSI for one of the analysed markers, suggesting that this is not a significant event in the tumorigenesis of these malignancies.

INTRODUCTION: Normal gene expression variation is thought to play a central role in inter-individual variation and susceptibility to disease. Regulatory polymorphisms in cis-acting elements result in the unequal expression of alleles. Differential allelic expression (DAE) in heterozygote individuals could be used to develop a new approach to discover regulatory breast cancer susceptibility loci. As access to large numbers of fresh breast tissue to perform such studies is difficult, a suitable surrogate test tissue must be identified for future studies. METHODS: We measured differential allelic expression of 12 candidate genes possibly related to breast cancer susceptibility (BRCA1, BRCA2, C1qA, CCND3, EMSY, GPX1, GPX4, MLH3, MTHFR, NBS1, TP53 and TRXR2) in breast tissue (n = 40) and fresh blood (n = 170) of healthy individuals and EBV-transformed lymphoblastoid cells (n = 19). Differential allelic expression ratios were determined by Taqman assay. Ratio distributions were compared using t-test and Wilcoxon rank sum test, for mean ratios and variances respectively. RESULTS: We show that differential allelic expression is common among these 12 candidate genes and is comparable between breast and blood (fresh and transformed lymphoblasts) in a significant proportion of them. We found that eight out of nine genes with DAE in breast and fresh blood were comparable, as were 10 out of 11 genes between breast and transformed lymphoblasts. CONCLUSIONS: Our findings support the use of differential allelic expression in blood as a surrogate for breast tissue in future studies on predisposition to breast cancer.