Comprehensive analysis of the ATM, CHEK2 and ERBB2 genes in relation to breast tumour characteristics and survival: a population-based case-control and follow-up study

Impact on breast cancer susceptibility and clinicopathological traits of common genetic polymorphisms in TP53, MDM2 and ATM genes in Sardinian women

Common variants of genes involved in DNA damage correction [tumor protein p53 (TP53), murine double 2 homolog oncoprotein (MDM2) and ataxia-telengiectasia mutated (ATM)] may serve a role in cancer predisposition. The purpose of the present study was to investigate the association of five variants in these genes with breast cancer risk and clinicopathological traits in a cohort of 261 women from northern Sardinia. Polymorphic variants in TP53 (rs17878362, rs1042522 and rs1625895), MDM2 (rs2279744) and ATM (rs1799757) were determined by PCR and TaqMan single nucleotide polymorphism assay in patients with breast cancer (n=136) and healthy controls (n=125). Association with clinicopathological (e.g., age at diagnosis, lymph node involvement, clinical stage) and lifestyle factors (e.g., smoking status, alcohol intake, contraceptive use) was also evaluated. TP53 rs17878362 and rs1625895 polymorphisms were associated with decreased risk of BC diagnosis in patients older than 50 years (codominant and recessive models) and post-menopause (recessive model). Furthermore, there was a significant association between lymph node status (positive vs. negative) and ATM rs1799757-delT in dominant and additive models and between MDM2 rs2279744-allele and use of oral contraceptives. This analysis suggested that TP53 rs17878362 and rs1625895 may affect age of onset of breast cancer and ATM rs1799757 and MDM2 rs2279744 may be associated with lymph node status and prolonged use of oral contraceptives, respectively.

mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer

Intrinsic and acquired resistance to the monoclonal antibody drug trastuzumab is a major problem in the treatment of HER2-positive breast cancer. A deeper understanding of the underlying mechanisms could help to develop new agents. Our intention was to detect genes and single nucleotide polymorphisms (SNPs) affecting trastuzumab efficiency in cell culture. Three HER2-positive breast cancer cell lines with different resistance phenotypes were analyzed. We chose BT474 as model of trastuzumab sensitivity, HCC1954 as model of intrinsic resistance, and BTR50, derived from BT474, as model of acquired resistance. Based on RNA-Seq data, we performed differential expression analyses on these cell lines with and without trastuzumab treatment. Differentially expressed genes between the resistant cell lines and BT474 are expected to contribute to resistance. Differentially expressed genes between untreated and trastuzumab treated BT474 are expected to contribute to drug efficacy. To exclude false positives from the candidate gene set, we removed genes that were also differentially expressed between untreated and trastuzumab treated BTR50. We further searched for SNPs in the untreated cell lines which could contribute to trastuzumab resistance. The analysis resulted in 54 differentially expressed candidate genes that might be connected to trastuzumab efficiency. 90% of 40 selected candidates were validated by RT-qPCR. ALPP, CALCOCO1, CAV1, CYP1A2 and IGFBP3 were significantly higher expressed in the trastuzumab treated than in the untreated BT474 cell line. GDF15, IL8, LCN2, PTGS2 and 20 other genes were significantly higher expressed in HCC1954 than in BT474, while NCAM2, COLEC12, AFF3, TFF3, NRCAM, GREB1 and TFF1 were significantly lower expressed. Additionally, we inferred SNPs in HCC1954 for CAV1, PTGS2, IL8 and IGFBP3. The latter also had a variation in BTR50. 20% of the validated subset have already been mentioned in literature. For half of them we called and analyzed SNPs. These results contribute to a better understanding of trastuzumab action and resistance mechanisms.

Variations of the ataxia telangiectasia mutated gene in patients with chronic lymphocytic leukemia lack substantial impact on progression-free survival and overall survival: a Cancer and Leukemia Group B study

The impact of mutation of the ATM (ataxia telangiectasia mutated) gene in chronic lymphocytic leukemia (CLL) treatment outcome has not been examined. We studied ATM mutations in 73 patients treated with fludarabine and rituximab. ATM gene mutation analysis was performed using temperature gradient capillary electrophoresis. The impact of detected variants on overall survival (OS) and progression-free survival (PFS) was tested with proportional hazards models. None of the 73 patients demonstrated truncating ATM mutations; 17 (23%, 95% confidence interval 14-35%) had non-silent variants (ATM-NSVs), including 13 known ATM polymorphisms and four missense variants. ATM-NSVs were not significantly associated with any baseline characteristics including immunoglobulin heavy chain variable gene (IGVH) status. In multivariable models, no significant differences in complete response (p =0.70), PFS (p =0.59) or OS (p =0.13) were observed. Our data indicate that truncating ATM mutations are rare in patients with CLL. Furthermore, in this dataset, these non-silent variants had limited impact on PFS and OS.

Prognostic impact of polymorphisms in the MYBL2 interacting genes in breast cancer

MYBL2 is a transcription factor, which regulates the expression of genes involved in cancer progression. In this study, we investigated whether putative functional variants in genes regulating MYBL2 (E2F1, E2F3 and E2F4) or in genes, which are regulated by MYBL2 (BCL2, BIRC5, COL1A1, COL1A2, COL5A2, ERBB2, CLU, LIN9 and TOP2A) affect breast cancer (BC) susceptibility and clinical outcome. Twenty-eight SNPs were genotyped in a population-based series of 782 Swedish BC cases and 1,559 matched controls. BC-specific survival analysis of BIRC5 suggested that carriers of the minor allele of rs8073069 and rs1042489 have a worse survival compared with the major homozygotes (HR 2.46, 95% CI 1.39-4.36 and HR 1.81, 95% CI 1.01-3.25, respectively). The poor survival was observed especially in women with aggressive tumours. Multivariate analysis supported the role of rs8073069 as an independent prognostic marker. For BCL2, minor allele carriers of rs1564483 were more likely to have hormone receptor-positive tumours than the major homozygotes. Another SNP in BCL2, rs4987852, was associated with tumour stages II-IV and histologic grade 3. In CLU, the minor allele carriers of rs9331888 were more likely to have tumours with regional lymph node metastasis and stages II-IV than the major homozygotes. In conclusion, our study suggests a role of genetic variation in BIRC5, BCL2 and CLU as progression and prognostic markers for BC, supporting previous studies based on the expression of the genes.

Evaluation of functional genetic variants for breast cancer risk: results from the Shanghai breast cancer study

In previous studies among 1,144 cases and 1,256 controls recruited in stage 1 of the Shanghai Breast Cancer Study (SBCS I; 1996-1998), 18 known or potentially functional single nucleotide polymorphisms (SNPs) in 16 genes were found to be associated with breast cancer risk. The authors evaluated these associations among 1,918 cases and 1,819 controls recruited in stage 2 of the SBCS (SBCS II; 2002-2005) using genetic effect models and subgroup analyses predetermined from SBCS I results. Five SNPs (AHR rs2066853, ATM rs1003623, ESR1 rs2234693, GSTP1 rs1695, and SHBG rs6259) showed generally consistent results in SBCS I and SBCS II and statistically significant associations with breast cancer risk in combined analyses, mostly in subgroups defined by age or menopausal status. Further, the relation between breast cancer risk and SHBG rs6259 was found to vary by body mass index (weight (kg)/height (m)(2)) (P for interaction = 0.003). The strongest reduction in risk associated with SHBG rs6259 was found for lean (body mass index <23) postmenopausal minor allele carriers (odds ratio = 0.6, 95% confidence interval: 0.5, 0.8; P = 4.6 × 10(-4)). This biologically plausible and highly significant finding provides strong evidence for a true association among Asian women. This study also highlights the value of gene-environment interaction analyses in evaluating genetic factors for complex diseases.

Lack of replication for the association between HER2 I655V polymorphism and breast cancer risk: a systematic review and meta-analysis

BACKGROUND

Multiple epidemiological studies have investigated rs1136201, a non-synonymous polymorphism of the human epidermal growth factor receptor-2 gene (HER2) resulting in the substitution of valine for isoleucine at codon 655 (Ile655Val) of the HER2 protein, as a risk factor for breast cancer.

METHODS

We searched multiple databases to identify genetic association studies investigating the effect of rs1136201 on breast cancer risk. For each study we calculated unadjusted odds ratios (ORs) with their variance under additive, dominant, recessive and allele-frequency genetic models. Summary ORs with their corresponding confidence interval (CI) were calculated using random effects models.

RESULTS

Based on the 33 case-control studies reporting data for the additive genetic model (20,461 cases/23,832 controls) we did not find evidence of an association between rs1136201 and breast cancer, OR=1.05 (95% CI, 0.99-1.11), with significant between-study heterogeneity (p(Q)<0.001; I(2)=49%). Smaller studies produced more extreme results compared to larger studies (p=0.001). Studies in which genotyping was not blind to case-control status (p=0.01), studies not reporting the use of genotyping quality control (p=0.01), and studies using RFLP-based methods (p=0.01) produced significant associations. Meta-regression results confirmed that there was a significant interaction between lack of quality control (p=0.04) and lack of blinding (p=0.04) and the genetic effect of rs1136201 on breast cancer risk.

CONCLUSIONS

It is unlikely that HER2 rs1136201 is a risk factor for breast cancer. Laboratory artifacts, lack of genotyping quality control or blinding and publication bias appear to have influenced the results published to date and need to be addressed in the design of future studies.

HER2/neu protein expression and fine needle breast aspiration from Argentinean patients with non-palpable breast lesions

The objective of this pilot project was to investigate whether the breast fine needle aspiration (FNA) technique is a useful tool for determining the increased risk of breast cancer in patients with non-palpable breast lesions. FNA is a minimally invasive technique that isolates mammary epithelial cells from breast cells in the suspicious region. In this study, two FNA samples were collected from 12 patients. The level of HER2/neu expression at the mRNA level (in serum) was measured in each patient. As gene amplification is characteristic of cancer cells and may assist in diagnosis and prognostic assessment, it is crucial that gene amplification of HER2/neu in patients with non-palpable breast lesions is compared to breast biopsy results. In serum, the level of HER2/neu was determined by ELISA assay. Gene amplification was determined by PCR and confirmed by IHC employing monoclonal ERRB2 in the FNA sample. The results indicate that FNA has a good correlation with breast biopsy. FNA combined with mammographic imaging is a strong tool for determining favorable treatment options for patients.

Variants in the ATM gene and breast cancer susceptibility

It has been established that heterozygous carriers of ataxia-telangiectasia-causing mutations in the ATM gene are at approximately two-fold higher risk of breast cancer. Several studies have attempted to assess the potential implication of the gene's more common variants in breast cancer susceptibility. Three large case-control studies have consistently found no evidence of association for variants with minor allele frequency greater than 5%. Other studies have evaluated associations for coding variants with intermediate frequency (1-5%), but the results are inconsistent. Larger and/or combined association studies are needed to clarify this issue.

Mining data, gathering variables and recombining information: the flexible architecture of epidemiological studies

Since the second half of the twentieth century, biomedical research has made increasing use of epidemiological methods to establish empirical evidence on a population level. This paper is about practices with data in epidemiological research, based on a case study in Denmark. I propose an epistemology of record linkage that invites exploration of epidemiological studies as heterogeneous assemblages. Focusing on data collecting, sampling and linkage, I examine how data organisation and processing become productive beyond the context of their collection. The case study looks at how a local population database established in 1976 to investigate possibilities for the prevention of cardiovascular disease is used thirty years later to test hypotheses on the aetiology of breast cancer. For two breast cancer investigations based on the same core data set, I follow the underlying record linkage practice and describe how research objects such as molecular markers become relevant with respect to public health through information networking. Epidemiological association studies function as tools that performatively enrol different contexts into statistical risk estimation, thereby configuring options for research as well as for clinical testing and public health policy.

Variants in the ATM gene associated with a reduced risk of contralateral breast cancer

Between 5% and 10% of women who survive a first primary breast cancer will subsequently develop a second primary cancer in the contralateral breast. The Women's Environment, Cancer, and Radiation Epidemiology Study was designed to identify genetic and environmental determinants of contralateral breast cancer (CBC). In this study, 708 women with asynchronous CBC served as cases and 1,397 women with unilateral breast cancer served as controls. ATM, a serine-threonine kinase, controls the cellular response to DNA double-strand breaks, and has been implicated in breast cancer risk. Complete mutation screening of the ATM gene in all 2,105 study participants identified 240 distinct sequence variants; only 15 were observed in >1% of subjects. Among the rare variants, deleterious alleles resulting in loss of ATM function were associated with a nonsignificant increase in risk of CBC. In contrast, carriers of common variants had a statistically significant reduction in risk of CBC. Four of these 15 variants were individually associated with a significantly decreased risk of second primary breast cancer [c.1899-55T>G, rate ratio (RR), 0.5; 95% confidence interval (CI), 0.3-0.8; c.3161C>G, RR, 0.5; 95% CI, 0.3-0.9; c.5558A>T, RR, 0.2; 95% CI, 0.1-0.6; c.6348-54T>C RR, 0.2; 95% CI, 0.1-0.8]. These data suggest that some alleles of ATM may exert an antineoplastic effect, perhaps by altering the activity of ATM as an initiator of DNA damage responses or a regulator of p53.

Focus on ERBB2

The ERBB2 (HER2) gene codes for a tyrosine kinase receptor that activates pathways involved in cell division, differentiation and apoptosis. Gene amplification, and as a result protein overexpression, are commonly seen in breast tumors and correlate with poor prognosis. The overexpressed protein is the target of trastuzumab, a monoclonal antibody routinely used in clinical practice. A new tyrosine kinase inhibitor, lapatinib, is already an alternative in women progressing despite treatment with trastuzumab. Using comprehensive tagging approaches, highly-powered association studies concluded that ERBB2 was unlikely to be a breast cancer predisposition gene. ERBB2 pharmacogenomics are of little relevance at present, since we have no knowledge of polymorphisms in the gene that could affect the binding, efficacy or tolerability of trastuzumab or lapatinib. There is minor contribution from hepatic cytochrome CYP2C19 to the metabolism of lapatinib, whereas in vitro studies have shown the drug to be a substrate for the transporter P-glycoprotein. If, and how, the pharmacokinetics of lapatinib would be altered in individuals carrying polymorphisms in CYP2C19 or ABCB1 – the gene that codes for the P-glycoprotein – is yet to be determined.

ESR1 and EGF genetic variation in relation to breast cancer risk and survival

Introduction

Oestrogen exposure is a central factor in the development of breast cancer. Oestrogen receptor alpha (ESR1) is the main mediator of oestrogen effect in breast epithelia and has also been shown to be activated by epidermal growth factor (EGF). We sought to determine if common genetic variation in the ESR1 and EGF genes affects breast cancer risk, tumour characteristics or breast cancer survival.

Methods

We genotyped 157 single nucleotide polymorphisms (SNPs) in ESR1 and 54 SNPs in EGF in 92 Swedish controls and selected haplotype tagging SNPs (tagSNPs) that could predict both single SNP and haplotype variation in the genes with an R² of at least 0.8. The tagSNPs were genotyped in 1,590 breast cancer cases and 1,518 controls, and their association with breast cancer risk, tumour characteristics and survival were assessed using unconditional logistic regression models, Cox proportional hazard models and haplotype analysis.

Results

The single tagSNP analysis did not reveal association evidence for breast cancer risk, tumour characteristics, or survival. A multi-locus analysis of five adjacent tagSNPs suggested a region in ESR1 (between rs3003925 and rs2144025) for association with breast cancer risk (p = 0.001), but the result did not withstand adjustment for multiple comparisons (p = 0.086). A similar region was also implicated by haplotype analyses, but its significance needs to be verified by follow-up analysis.

Conclusion

Our results do not support a strong association between common variants in the ESR1 and EGF genes and breast cancer risk, tumour characteristics or survival.

Single nucleotide polymorphism D1853N of the ATM gene may alter the risk for breast cancer

PURPOSE

Various ATM (ataxia telangiectasia-mutated) mutations and polymorphisms have been reported to be associated with an increased breast cancer risk. Recent studies have produced contradictory results regarding the association between ATM genetic variants and breast cancer risk.

MATERIALS AND METHODS

The common ATM polymorphism 5557G>A (p.D1853N) (rs1801516), previously suggested to be associated with bilateral breast cancer, was analyzed using real-time PCR in 514 unselected patients with breast cancer and 511 age-matched healthy control individuals. DNA was obtained from peripheral blood draw.

RESULTS

The ATM genotype was weakly associated with the risk for breast cancer (P = 0.04 for the overall test). The odds ratio for women with a heterozygous genotype was 0.70 (95% CI, 0.52-0.94) and for the homozygous variant 0.63 (95% CI, 0.27-1.49). Disease-free survival and overall survival showed no significant association with specific genotypes.

CONCLUSIONS

The results of this study might suggest a minor association between polymorphism 5557G>A and a reduced risk of breast cancer.

In search of breast cancer culprits: suspecting the suspected and the unsuspected

I would like to welcome breast cancer research community to the first editorial of our newest journal "Breast Cancer: Basic and Clinical Research". In pursuit of breast cancer culprits, we have come a long way since the early 90's when the first breast cancer susceptibility gene BRCA1 was mapped and cloned. In the past few years, several new loci associated with the various degree of breast cancer risk have been identified using "Candidate Gene Association Study (CGAS) and Genome-Wide Association Study (GWAS)" approaches. This editorial is meant to quickly glance over recent findings of these population-based association studies.

In Search of Breast Cancer Culprits: Suspecting the Suspected and the Unsuspected

I would like to welcome breast cancer research community to the first editorial of our newest journal “Breast Cancer: Basic and Clinical Research”. In pursuit of breast cancer culprits, we have come a long way since the early 90's when the first breast cancer susceptibility gene BRCA1 was mapped and cloned. In the past few years, several new loci associated with the various degree of breast cancer risk have been identified using “Candidate Gene Association Study (CGAS) and Genome-Wide Association Study (GWAS)” approaches. This editorial is meant to quickly glance over recent findings of these population-based association studies.