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

BACKGROUND

The age of personal genomics is here. A flood of translational research discoveries may influence also surgeon oncologist. Breast-conserving surgery (BCS) is standard care in early breast cancer. Classic clinicopathologic factors are suboptimal to predict risk of ipsilateral breast cancer (IBC) recurrence and/or contralateral breast cancer (CBC). Human genetic variation may be involved in local failures.

OBJECTIVE

To describe the potential clinical utility of genetics, personal genomics, and epigenetics to identify IBC/CBC high-risk patients who might benefit from aggressive surgery (bilateral mastectomy).

DATA SOURCES AND SYNTHESIS

PubMed (MEDLINE) was searched (January 1990 to November 2008).

RESULTS

Even following current guidelines, IBC/CBC as isolated first event in a long-term aspect after treatment suggests a serious problem. Preclinical and clinical data reveal that at highest risk of IBC/CBC are patients with inherited BRCA1/2 mutations who benefited from bilateral mastectomy. Local failure risk prediction is currently unfeasible among familial non-BRCA1/2 (BRCA-test negative) and sporadic (no family history) breast cancer. Genome-wide association studies have already identified novel risk alleles with a series of tumor-initiating single-nucleotide polymorphisms (SNPs). Some of these variants and other novel SNPs and copy-number variants (CNVs) may also be relevant for local failures (IBC/CBC).

CONCLUSIONS

Beyond established risk factors, genetic testing allows identification of high-risk patients (BRCA mutation carriers) who may benefit from bilateral mastectomy rather than BCS. Human genetic variation (SNPs/CNVs) and DNA methylation may be relevant for local failures assessment. Technological revolution has opened a new avenue but multiple challenges should be overcome to integrate SNPs/CNVs as markers for IBC/CBC risk-stratification-based personalized surgery.

Radiation burden of patients undergoing endovascular abdominal aortic aneurysm repair

INTRODUCTION

Endovascular repair of abdominal aortic aneurysm (EVAR) requires the patient's extended exposure to x-rays, before, during, and after the intervention. The aim of this study was to determine the radiation exposure of patients undergoing EVAR and to assess the probability for the induction of both late and early radiation-related effects.

METHODS

During the period of May 2006 to December 2007 EVAR was carried out in 62 patients using a mobile C-arm unit. The following dosimetric quantities were assessed: fluoroscopy time, cumulative dose in air, dose-area product, field area, and peak skin dose.

RESULTS

The duration of fluoroscopy and the body mass index were found to be the main factors that influence the radiation burden in our hospital. The mean effective dose per procedure, 6.2 mSv, was between that from a planar coronary angiography and a coronary angioplasty. Taking into account the computed tomography (CT) procedure-related angiographies carried out during the first year, patients receive a total effective dose of about 62 mSv within the first year. In vivo dosimetry showed that the peak skin dose was linearly correlated with cumulative dose in air and did not exceed 1.0 Gy, ie, it was less than the threshold for any acute skin reaction.

CONCLUSION

Repair of abdominal aortic aneurysm results in substantial radiation burden. Radiation-related risks for carcinogenesis and skin injuries are factors that have to be taken into account in the selection of the strategy of each facility.

Drug resistance: origins, evolution and characterization of genomic clones and the tumor ecosystem to optimize precise individualized therapy

Progress in understanding and overcoming fatal intrinsic and acquired resistance is slow, with only a few exceptions. Despite advances in modern genome and transcriptome analysis, the controversy of the three different theories on drug resistance and tumor progression, namely dynamic intratumor heterogeneity, pre-existing minor genomic clones and tumor ecosystem, is unresolved. Moreover, evidence on transcriptional heterogeneity suggests the necessity of a drug bank for individualized, precise drug-sensitivity prediction. We propose a cancer type- and stage-specific clinicogenomic and tumor ecosystemic concept toward cancer precision medicine, focusing on early therapeutic resistance and relapse.

Dynamic genome and transcriptional network-based biomarkers and drugs: precision in breast cancer therapy

Despite remarkable progress in medium-term overall survival benefit in the adjuvant, neoadjuvant and metastatic settings, with multiple recent targeted drug approvals, acquired resistance, late relapse, and cancer-related death rates remain challenging. Integrated technological systems have been developed to overcome these unmet needs. The characterization of structural and functional noncoding genome elements through next-generation sequencing (NGS) systems, Hi-C and CRISPR/Cas9, as well as computational models, allows for whole genome and transcriptome analysis. Rapid progress in large-scale single-biopsy genome analysis has identified several novel breast cancer driver genes and oncotargets. The exploration of spatiotemporal tumor evolution has returned exciting while inconclusive data on dynamic intratumor heterogeneity (ITH) through multiregional NGS and single-cell DNA/RNA sequencing and circulating genomic subclones (cGSs) by serial circulating cell-free DNA NGS to predict and overcome intrinsic and acquired therapeutic resistance. This review discusses reliable breast cancer genome analysis data and focuses on two major crucial perspectives. The validation of ITH, cGSs, and intrapatient genetic/genomic heterogeneity as predictive biomarkers, as well as the valid discovery of novel oncotargets within patient-centric genomic trials, encouraging early drug development, could optimize primary and secondary therapeutic decision-making. A longer-term goal is to identify the individualized landscape of both coding and noncoding key mutations. This progress will enable the understanding of molecular mechanisms perturbating regulatory networks, shaping the pharmaceutical controllability of deregulated transcriptional biocircuits.

Multigene assays and isolated tumor cells for early breast cancer treatment: time for bionetworks

Despite advances with adjuvant endocrine treatment for hormone receptor-positive tumors and with trastuzumab for HER2-positive disease, overall, over 50% of women with early-stage breast cancer experience recurrence and die of the disease. Biomarkers for tailoring systemic adjuvant treatment to responder patients are needed. The multigene assays, 21-gene recurrence score (Oncotype DX [Genomic Health, CA, USA]) and 70-gene signature (MammaPrint [Agendia, CA, USA]), and the isolated tumor cells in sentinel lymph node(s) represent the latest advances for improving adjuvant chemotherapy decisions. This article evaluates how these new markers, added to current standard factors (age, tumor size, grade, hormone receptor status and HER2 status), could improve early breast cancer treatment decisions. Moreover, emerging evidence from the latest large-scale studies using next-generation DNA-sequencing technology reveals a high heterogeneity and complexity of breast cancer. This assessment now shapes a new research strategy towards completion of a breast cancer causal (driver) mutations catalog and understanding complex genetic interactions and signaling pathway networks. Despite multiple challenges, advances in cancer genomes and systems biology approaches promise the future development of robust biomarkers.

Highly elevated serum levels of CA 19-9 in choledocholithiasis: a case report

We present a case of a 79-year-old woman admitted to our hospital with pain in the right upper abdominal quadrate radiated to the back, jaundice, fever and chills. The laboratory tests showed serum carbohydrate antigen 19-9 levels of 99.070 U/ml (normal values: 0-37 U/ml). The rest of the biochemistry showed alkaline phosphatase of 550 IU/l, direct bilirubin: 17.5 mg/dl, total bilirubin: 28.4 mg/dl. Abdominal sonography demonstrated dilated common bile duct. Two weeks postoperatively, the carbohydrate antigen 19-9 fell to 970 U/ml and returned within normal range (31 U/ml) two months later. Furthermore, the magnetic resonance cholangiopancreatography performed postoperatively demonstrated normal configuration of the biliary tree and the common bile duct.

Bulk and Single-Cell Next-Generation Sequencing: Individualizing Treatment for Colorectal Cancer

The increasing incidence combined with constant rates of early diagnosis and mortality of colorectal cancer (CRC) over the past decade worldwide, as well as minor overall survival improvements in the industrialized world, suggest the need to shift from conventional research and clinical practice to the innovative development of screening, predictive and therapeutic tools. Explosive integration of next-generation sequencing (NGS) systems into basic, translational and, more recently, basket trials is transforming biomedical and cancer research, aiming for substantial clinical implementation as well. Shifting from inter-patient tumor variability to the precise characterization of intra-tumor genetic, genomic and transcriptional heterogeneity (ITH) via multi-regional bulk tissue NGS and emerging single-cell transcriptomics, coupled with NGS of circulating cell-free DNA (cfDNA), unravels novel strategies for therapeutic response prediction and drug development. Remarkably, underway and future genomic/transcriptomic studies and trials exploring spatiotemporal clonal evolution represent most rational expectations to discover novel prognostic, predictive and therapeutic tools. This review describes latest advancements and future perspectives of integrated sequencing systems for genome and transcriptome exploration to overcome unmet research and clinical challenges towards Precision Oncology.

From Clinical Standards to Translating Next-Generation Sequencing Research into Patient Care Improvement for Hepatobiliary and Pancreatic Cancers

Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA. It is a pity that multiple Phase III randomized control trials testing the efficacy of targeted agents have negative results. Failure in the development of effective drugs probably reflects the poor understanding of genome-wide alterations and molecular mechanisms orchestrating therapeutic resistance and recurrence. In the post-ENCODE (Encyclopedia of DNA Elements) era, cancer is referred to as a highly heterogeneous and systemic disease of the genome. The unprecedented potential of next-generation sequencing (NGS) technologies to accurately identify genetic and genomic variations has attracted major research and clinical interest. The applications of NGS include targeted NGS with potential clinical implications, while whole-exome and whole-genome sequencing focus on the discovery of both novel cancer driver genes and therapeutic targets. These advances dictate new designs for clinical trials to validate biomarkers and drugs. This review discusses the findings of available NGS studies on HBP cancers and the limitations of genome sequencing analysis to translate genome-based biomarkers and drugs into patient care in the clinic.

Discovering novel valid biomarkers and drugs in patient-centric genomic trials: the new epoch of precision surgical oncology

Despite standardization of multimodal treatment and approval of several targeted drugs for resectable, non-metastatic cancer (M0 patients), intrinsic and acquired resistance and relapse rates remain high, even in early-stage aggressive tumors. Genome analysis could overcome these unmet needs. Our comprehensive review underlines the controversy on stable or spatiotemporally evolving clones as well as promising yet inconclusive data on genome-based biomarkers and drug development. We propose clinicogenomic trials in M0 patients for the validation of intratumor heterogeneity (ITH), circulating genomic subclones (cGSs) and intra-patient genomic heterogeneity (IPGH) as biomarkers and simultaneous discovery of novel oncotargets. This evidence-based strategy highlights the coming of precision surgical oncology with a future perspective of understanding and disrupting deregulated transcriptional networks.

Research and clinical applications of cancer genome sequencing

PURPOSE OF REVIEW

To highlight the recent advances in cancer genome research and its clinical applications made possible by next-generation sequencing (NGS), with particular emphasis on gynecological and breast cancers is the purpose of the review.

RECENT FINDINGS

Through advances in NGS technologies, whole-exome sequencing and whole-genome sequencing (WGS) have been performed on various cancers, identifying in the process numerous recurrent mutations and highly mutated genes. These cancers include uterine serous carcinomas, high-grade serous ovarian adenocarcinomas and breast cancer. In contrast to identifying somatic mutations in sporadic cancers, a far smaller number of studies using NGS have been conducted to identify new causal mutations or genes for hereditary cancer syndromes. In addition to research discovery, diagnostic applications of NGS have also become increasingly evident. Thus, WGS has been applied in a diagnostic context to identify a complex chromosomal rearrangement in a patient with acute myeloid leukemia of unclear subtype. Similarly, the targeted sequencing of panels of known cancer genes using NGS has demonstrated its robustness in the context of identifying known pathological mutations.

SUMMARY

The research and clinical applications of cancer genome sequencing have progressed at an unprecedented pace over the last few years, and this promises to be accelerated with new developments of high-throughput NGS technologies and robust analytical tools.

Intestinal obstruction due to an anomalous congenital band

We report a case of a 20-year-old male who presented with symptoms and signs of intestinal obstruction. The patient reported no previous history of abdominal surgery or trauma while clinical and radiographic examinations were not diagnostic. An open laparotomy was subsequently performed and the intraoperative findings were consistent with a congenital band extending from the antimesenteric wall of the jejunum to the root of mesentery. The band was ligated and divided with an uneventful postoperative course. Congenital bands are extremely rare. Their exact incidence is still unknown and usually observed in childhood. This case, therefore, represents an unusual surgical problem in an older individual in which the diagnosis was clinically unexpected.