Genetics and personal genomics for personalized breast cancer surgery: progress and challenges in research and clinical practice

Copy Number Profiling of MammaPrint™ Genes Reveals Association with the Prognosis of Breast Cancer Patients

Purpose

The MammaPrint™ gene signature, currently used in clinical practice, provides prognostic information regarding the recurrence and potential metastasis in breast cancer patients. However, the prognostic information of the 70 genes included can only be estimated at the RNA expression level. In this study, we investigated whether copy number information of MammaPrint™ genes at the DNA level can be used as a prognostic tool for breast cancer, as copy number variations (CNVs) are major contributors to cancer progression.

Methods

We performed CNV profiling of MammaPrint™ genes in 59 breast cancer cell lines and 650 breast cancer patients, using publicly available data in The Cancer Genome Atlas (TCGA) database. Statistical analyses including Fisher exact test, chi-square test, and Kaplan-Meier survival analyses were performed.

Results

All MammaPrint™ genes showed recurrent CNVs, particularly in TCGA cohort. CNVs of 32 and 36 genes showed significant associations with progesterone receptor and estrogen rector, respectively. No genes showed a significant association with human epidermal growth factor receptor 2 status and lymph node status. In addition, only six genes were associated with tumor stages. RFC4, HRASLS, NMU, GPR126, SCUBE2, C20orf46, and EBF4 were associated with reduced survival and RASSF7 and ESM1 were associated with reduced disease-free survival.

Conclusion

Based on these findings, a concordance of CNV-based genomic rearrangement with expression profiling of these genes and their putative roles in disease tumorigenesis was established. The results suggested that the CNV profiles of the MammaPrint™ genes can be used to predict the prognosis of breast cancer patients. In addition, this approach may lead to the development of new cancer biomarkers at the DNA level.

Assessment of DNA methylation profiling and copy number variation as indications of clonal relationship in ipsilateral and contralateral breast cancers to distinguish recurrent breast cancer from a second primary tumour

BACKGROUND

Patients with breast cancer have an increased risk of developing subsequent breast cancers. It is important to distinguish whether these tumours are de novo or recurrences of the primary tumour in order to guide the appropriate therapy. Our aim was to investigate the use of DNA methylation profiling and array comparative genomic hybridization (aCGH) to determine whether the second tumour is clonally related to the first tumour.

METHODS

Methylation-sensitive high-resolution melting was used to screen promoter methylation in a panel of 13 genes reported as methylated in breast cancer (RASSF1A, TWIST1, APC, WIF1, MGMT, MAL, CDH13, RARβ, BRCA1, CDH1, CDKN2A, TP73, and GSTP1) in 29 tumour pairs (16 ipsilateral and 13 contralateral). Using the methylation profile of these genes, we employed a Bayesian and an empirical statistical approach to estimate clonal relationship. Copy number alterations were analysed using aCGH on the same set of tumour pairs.

RESULTS

There is a higher probability of the second tumour being recurrent in ipsilateral tumours compared with contralateral tumours (38 % versus 8 %; p <0.05) based on the methylation profile. Using previously reported recurrence rates as Bayesian prior probabilities, we classified 69 % of ipsilateral and 15 % of contralateral tumours as recurrent. The inferred clonal relationship results of the tumour pairs were generally concordant between methylation profiling and aCGH.

CONCLUSION

Our results show that DNA methylation profiling as well as aCGH have potential as diagnostic tools in improving the clinical decisions to differentiate recurrences from a second de novo tumour.

Nipple-sparing mastectomy and immediate reconstruction in ductal carcinoma in situ: a critical assessment with 41 patients

BACKGROUND

Nipple-sparing mastectomy (NSM) is increasingly popular for the treatment of select breast cancers and prophylactic mastectomy. This study aimed to analyze the authors' 11-year experience with NSM and breast reconstruction in cases of ductal carcinoma in situ (DCIS) with an emphasis on indications, complications, and cancer recurrence rate.

METHODS

Between January 2000 and December 2010, 41 NSMs were performed in 41 women for DCIS. The mean age of the women was 49.7±8.7 years (range, 33-66 years). The indications for NSM were tumor size greater than 3 cm (18 cases), multifocal tumor (16 cases), and tumor recurrence (7 cases). In all cases, the tumor was located more than 2 cm from the nipple-areola complex (NAC), as shown by preoperative radiologic imaging. Histologic results, secondary NAC resection, complications, and cancer recurrence rates were recorded.

RESULTS

The NAC was lost in seven cases (17%) due to postoperative necrosis. In another 10 patients (25%), the NAC was secondarily removed due to proximity of the tumor to the resection margin. Five patients were lost to follow-up evaluation (12%). The authors report the long-term follow-up data for the remaining 19 patients (46%). In this group, they observed one local recurrence (5.3%) and one case of ovarian cancer.

CONCLUSION

Despite the low locoregional recurrence rate for DCIS, NSM remains controversial because of the nipple necrosis observed and the irradical tumor excisions. Given the ethical impossibility of conducting randomized controlled studies to compare NSM with conventional or skin-sparing mastectomy in DCIS, only long-term follow-up evaluations can demonstrate the safety of NSM.

LEVEL OF EVIDENCE IV

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Genome-based approaches for the diagnosis of breast cancer: a review with perspective

SUMMARY Despite progress with microarray-based gene expression profiling of multiple genes concurrently, solid biomarkers or molecular classification have not been established as a result of Phase III randomized trials. Conventional clinicopathological characteristics and single-gene defect-based molecular tools based on the old dogma of reductionist approaches and linear experimentation that have created our knowledge in biology over the past century, and still today represent the basis for the prevention, diagnosis and treatment of all diseases in clinical medicine, are saving the lives of tens of thousands of patients with breast cancer. Almost 5000 manuscripts have been published on next-generation technologies in MEDLINE in the last 3 years, with 100 of them regarding breast cancer. This review considers evidence published after 2010 and up until October 2013 of the latest studies published using high-throughput next-generation techniques in significant numbers of samples from patients with breast cancer and data from trials enrolled on ClinicalTrials.gov website. A perspective estimation of the potential and challenges of modern approaches are also explained in detail.

Identifying potential cancer driver genes by genomic data integration

Cancer is a genomic disease associated with a plethora of gene mutations resulting in a loss of control over vital cellular functions. Among these mutated genes, driver genes are defined as being causally linked to oncogenesis, while passenger genes are thought to be irrelevant for cancer development. With increasing numbers of large-scale genomic datasets available, integrating these genomic data to identify driver genes from aberration regions of cancer genomes becomes an important goal of cancer genome analysis and investigations into mechanisms responsible for cancer development. A computational method, MAXDRIVER, is proposed here to identify potential driver genes on the basis of copy number aberration (CNA) regions of cancer genomes, by integrating publicly available human genomic data. MAXDRIVER employs several optimization strategies to construct a heterogeneous network, by means of combining a fused gene functional similarity network, gene-disease associations and a disease phenotypic similarity network. MAXDRIVER was validated to effectively recall known associations among genes and cancers. Previously identified as well as novel driver genes were detected by scanning CNAs of breast cancer, melanoma and liver carcinoma. Three predicted driver genes (CDKN2A, AKT1, RNF139) were found common in these three cancers by comparative analysis.

Association between cytotoxic T lymphocyte antigen-4 +49A/G, -1722T/C, and -1661A/G polymorphisms and cancer risk: a meta-analysis

Cytotoxic T lymphocyte antigen-4 (CTLA-4), a key gene that contributes to the susceptibility and clinical course of cancer, is an important down-regulator of T cell activation and proliferation. The +49A/G polymorphism is commonly studied because of its association with cancer risks. However, other polymorphisms, such as -1722T/C and -1661A/G, have not been studied in detail. We performed a meta-analysis using 43 eligible case-control studies with a total of 19,089 patients and 21,388 controls to examine the association between CTLA-4 +49A/G, -1722T/C, and -1661A/G polymorphisms and cancer risk. We searched the PubMed and EMBASE databases for all articles published up to July 17, 2013. Individuals with the +49 A allele (AA/AG vs. GG, odds ratio (OR) = 1.21, 95% confidence interval (95% CI) = 1.16-1.27) and -1661 G allele (AG/GG vs. AA, OR = 1.52, 95% CI = 1.34-1.73) had increased cancer risk. However, no significant association between cancer risk and the -1722T/C polymorphism was found (CC/CT vs. TT, OR = 1.04, 95% CI = 0.92-1.16). In subgroup analysis for the +49A/G polymorphism, increased cancer risk remained in the subgroups of Asians (OR = 1.25, 95 % CI = 1.18-1.31), patients with breast cancer (OR = 1.28, 95% CI = 1.15-1.42), and patients with lung cancer (OR = 1.20, 95 % CI = 1.07-1.35). For the -1661A/G polymorphism, increased cancer risk remained in the subgroups of Asians (OR = 1.52, 95% CI = 1.34-1.73), patients with breast cancer (OR = 1.48, 95% CI = 1.07-2.03), and patients with oral cancer (OR = 3.16, 95% CI = 1.84-5.45). However, no significant increase in cancer risk was found in the subgroups for the -1722T/C polymorphism. In conclusion, the results suggest that +49A/G and -1661A/G polymorphisms in CTLA-4 are risk factors for cancers, whereas the -1722T/C polymorphism is not associated with an increased risk of cancer.

Positive association between lymphotoxin-alpha variation rs909253 and cancer risk: a meta-analysis based on 36 case-control studies

Lymphotoxin-alpha (LTA) polymorphism rs909253 has been reported to be a risk factor for cancers, but some results are inconsistent. To establish a more conclusive association, we performed a meta-analysis of this variant with cancers. A systematic search was performed for informative case-control studies of rs909253 with cancers among literature databases, including PubMed, Web of Science, Embase, China National Knowledge Infrastructure (CNKI), and Wanfang Chinese Periodical Database. After a comprehensive filtration procedure, 36 publications involved with 35,677 participants were selected for the current meta-analysis. Stratified factors, such as cancer type, populations, and source of control, were used for a better interpretation of this variant. Minimal heterogeneity was shown in the current meta-analysis (I (2) = 0.0%, P = 0.48). Our results show a significant association of rs909253 and cancer risk (odds ratio (OR) = 1.12, P (z) < 0.001). In the subgroup analysis, significant association of rs909253 was found in adenocarcinoma (OR = 1.16, P (z) < 0.001) and hematological malignancy (OR = 1.10, P (z) < 0.001). Our meta-analyses established a significant association of rs909253 with cancer risk among multiple populations including North Americans, Asians, and Europeans.

Occult primary breast cancer at a comprehensive cancer center

BACKGROUND

Management of occult primary breast cancer (OPBC), that is, breast cancer that first presents through regional nodal or distant disease without clinical or mammographic evidence of disease in the breast, has been controversial and inconsistent. Here, we review OPBC patients treated at our institution.

METHODS

We conducted a retrospective review of women diagnosed with a first primary breast cancer between March 1999 and September 2010 to identify patients who presented with isolated axillary lymphadenopathy proven to be histologically consistent with primary breast malignancy but had no evidence of a breast mass on physical examination, mammography, or ultrasound. Descriptions of treatments received, recurrence, morbidity, and mortality as of October 2012 are reported.

RESULTS

Of 5533 patients reviewed, seven (0.1%) patients were identified. The median age was 65 y old (range, 40-72), and the median length of follow-up was 86 mo (range, 42-124). Four patients underwent modified radical mastectomy, one patient had a lumpectomy and axillary lymph node dissection, and two patients had axillary lymph node dissection without breast surgery. Four patients received adjuvant radiation therapy. All seven patients received chemotherapy. Three patients received endocrine therapy, and two patients received anti-HER2 therapy. At the last follow-up, all seven patients were alive with no evidence of disease.

CONCLUSIONS

Although there was some variation in the management of OPBC at our institution, our patients had excellent outcomes after multimodal treatment. Our results support a curative intent approach to the treatment of OPBC and illustrate the need for individualized treatment algorithms based on tumor biology and extent of the disease at diagnosis.

Multilevel research and the challenges of implementing genomic medicine

Advances in genomics and related fields promise a new era of personalized medicine in the cancer care continuum. Nevertheless, there are fundamental challenges in integrating genomic medicine into cancer practice. We explore how multilevel research can contribute to implementation of genomic medicine. We first review the rapidly developing scientific discoveries in this field and the paucity of current applications that are ready for implementation in clinical and public health programs. We then define a multidisciplinary translational research agenda for successful integration of genomic medicine into policy and practice and consider challenges for successful implementation. We illustrate the agenda using the example of Lynch syndrome testing in newly diagnosed cases of colorectal cancer and cascade testing in relatives. We synthesize existing information in a framework for future multilevel research for integrating genomic medicine into the cancer care continuum.

Optimizing targeted cancer therapy: towards clinical application of systems biology approaches

In cancer, genetic and epigenetic alterations ultimately culminate in discordant activation of signal transduction pathways driving the malignant process. Pharmacological or biological inhibition of such pathways holds significant promise with respect to devising rational therapy for cancer. Thus, technical concepts pursuing robust characterization of kinase activity in tissue samples from cancer patients have been subject of investigation. In the present review we provide a comprehensive overview of these techniques and discuss their advantages and disadvantages for systems biology approaches to identify kinase targets in oncological disease. Recent advances in the development and application of array-based peptide-substrate kinase activity screens show great promise in overcoming the discrepancy between the evaluation of aberrant cell signaling in specific malignancies or even individual patients and the currently available ensemble of highly specific targeted treatment strategies. These developments have the potential to result in a more effective selection of kinase inhibitors and thus optimize mechanism-based patient-specific therapeutic strategies. Given the results from current research on the tumor kinome, generating network views on aberrant tumor cell signaling is critical to meet this challenge.

Personal genomic testing as part of the complete breast cancer risk assessment: a case report

Patient access and utilization of personal genomic testing is becoming increasingly common. We present a case of a patient's personal genomic screening results leading to early detection of infiltrating breast ductal cell carcinoma via MRI scan. This case exemplifies the successful integration of personal genomic testing into the primary care setting, with the guidance and support of genetic counseling services. We discuss the scientific basis of the patient's genome scan results and risk assessment, and how this informed her decision-making and subsequent screening. We also expound upon the role of personal genomic testing as compared to other screening tests in the complete breast cancer risk assessment.

Identifying gaps in the locoregional management of early breast cancer: highlights from the Kyoto Consensus Conference

A consensus conference was held to investigate issues related to the local management of early breast cancer. Here, we highlight the major topics discussed at the conference and propose ideas for future studies. Regarding axillary management, we examined three major issues. First, we discussed whether the use of axillary reverse mapping could clarify the lymphatic system of breast and whether the ipsilateral arm might help avoid lymphedema. Second, the use of an indocyanine green fluorescent navigation system was discussed for intraoperative lymphatic mapping. These new issues should be examined further in practice. Finally, some agreement was reached on the importance of "four-node diagnosis" to aid in the diagnostic accuracy of sentinel nodes. Regarding breast treatment, there was general agreement that the clinical value of surgical margins in predicting local failure was dependent on the tumor's intrinsic biology and subtypes. For patients treated with preoperative chemotherapy, less extensive excision may be feasible in those who respond to systemic therapy in an acceptable manner. Most trials of preoperative chemotherapy lack outcome data on local recurrence. Therefore, there is a need for such data for overview analysis. We also agreed that radiation after mastectomy may be beneficial in node-positive cases where more than four nodes are involved. Throughout the discussions for both invasive and noninvasive disease, the investigation of nomograms was justified for major issues in the decision-making process, such as the presence or absence of microinvasion and the involvement of nonsentinel nodes in sentinel node-positive patients.

Polymorphisms in the cytotoxic T-lymphocyte antigen 4 gene and cancer risk: a meta-analysis

BACKGROUND

Polymorphisms in the cytotoxic T-lymphocyte antigen 4 (CTLA-4) gene have been implicated in susceptibility to cancer, but the many published studies have reported inconclusive results. The objective of the current study was to conduct a meta-analysis investigating the association between polymorphisms in the CTLA-4 gene and the risk of cancer.

METHODS

The PubMed and EMBASE databases were searched for all articles published up to September 19, 2010 that addressed cancer and polymorphisms, variants, or mutations of CTLA-4. A statistical analysis was performed using proprietary statistical software.

RESULTS

Three polymorphisms (+49 adenine/guanine [+49A/G], -318 cytosine/thymine [-318C/T], and the +6230G/A polymorphism [CT60]) in 48 case-control studies from 27 articles were analyzed. The results indicated that individuals who carried the +49 G allele (AG + GG) had a 16% decreased risk of cancer compared with homozygotes (+49AA; odds ratio [OR], 0.84; 95% confidence interval [CI], 0.74-0.95). However, there was no significant association between the risk of cancer and the -318C/T polymorphism or the CT60 polymorphism (-318C/T: OR, 1.23; 95% CI, 0.99-1.54 for TT + TC vs CC; CT60: OR, 1.02; 95% CI, 0.80-1.29 for AA + AG vs GG). In further stratified analyses for the +49A/G and -318C/T polymorphisms, the decreased risk of cancer remained in subgroups of Europeans, patients with breast cancer, and patients with lung cancer for the +49A/G polymorphism; whereas an increased risk of cancer was observed among Europeans for the -318C/T polymorphism.

CONCLUSIONS

Results from the current meta-analysis suggested that the +49A/G and -318C/T polymorphisms in CTLA-4 are risk factors for cancer. To further evaluate gene-gene and gene-environment interactions between CTLA-4 polymorphisms and the risk of cancer, more studies with larger groups of patients will be required.

Personalized medicine: marking a new epoch in cancer patient management

Personalized medicine (PM) is defined as "a form of medicine that uses information about a person's genes, proteins, and environment to prevent, diagnose, and treat disease." The promise of PM has been on us for years. The suite of clinical applications of PM in cancer is broad, encompassing screening, diagnosis, prognosis, prediction of treatment efficacy, patient follow-up after surgery for early detection of recurrence, and the stratification of patients into cancer subgroup categories, allowing for individualized therapy. PM aims to eliminate the "one size fits all" model of medicine, which has centered on reaction to disease based on average responses to care. By dividing patients into unique cancer subgroups, treatment and follow-up can be tailored for each individual according to disease aggressiveness and the ability to respond to a certain treatment. PM is also shifting the emphasis of patient management from primary patient care to prevention and early intervention for high-risk individuals. In addition to classic single molecular markers, high-throughput approaches can be used for PM including whole genome sequencing, single-nucleotide polymorphism analysis, microarray analysis, and mass spectrometry. A common trend among these tools is their ability to analyze many targets simultaneously, thus increasing the sensitivity, specificity, and accuracy of biomarker discovery. Certain challenges need to be addressed in our transition to PM including assessment of cost, test standardization, and ethical issues. It is clear that PM will gradually continue to be incorporated into cancer patient management and will have a significant impact on our health care in the future.