Demosthenes E Ziogas

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.

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.

Targeted therapy for colorectal cancer resistance to EGF receptor antibodies and new trends

Colorectal cancer (CRC) remains a major health problem worldwide despite substan -tial advances in multimodal treatment. High quality comparative–effectiveness research has standardized surgery, radio-therapy and systemic chemotherapy. But there is still controversy on the selection of the best chemotherapeutic regimen and tailored targeted therapy. For exam-ple, there is currently a debate on whether testing for microsatellite instability and/or for the multigene assays, ColoPrint and Oncotype Dx, should be used for adju-vant chemotherapy decision in localized CRC. In the metastatic setting, decisions on cetuximab versus panitumumab for patients with

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.

Novel translational therapeutic strategy by sequencing primary liver cancer genomes

Department of Surgery, Ioannina University Hospital, Ioannina, Greece Centre for Biosystems & Genome Network Medicine, Ioannina University, Ioannina, Greece Department of Surgery, ‘G. Hatzikosta’ General Hospital, Ioannina, Greece Department of Plastic Surgery, Ioannina University Hospital, Ioannina, Greece Unit of Systems Biology, Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece *Author for correspondence: Tel.: +302651005572; droukos@uoi.gr

Targeting dynamics of subclones of GI, liver and pancreatic cancers

Centre for Biosystems and Genomic Network Medicine, University of Ioannina, Ioannina, Greece; Department of Surgery, ‘G. Hatzikosta’ General Hospital, Ioannina, Greece; Department of Surgery, Ioannina University Hospital, Ioannina, Greece; 1st Department of Surgery, University of Athens School of Medicine, Laikon Hospital, Athens, Greece; Biomedical Research Foundation of the Academy of Athens (BRFAA), Athens, Greece

Intratumor heterogeneity: predicting and preventing therapeutic resistance

Despite dramatic advances and widespread clinical adoption of genetic testing for the identification of interpatient genetic variation, treatment with targeted drugs and temporary effectiveness, these agents only prolong survival for a few months [1]. Recent data suggest that shifting from single biopsybased testing to comprehensive intratumor diversity using next-generation sequencing (NGS) technologies could reduce tumor resistance to modern therapy. Could intratumor heterogeneity be used as a biomarker to predict primary tumor responsiveness and improve initial systemic treatment? Genetic testing to identify a single mutated or amplified gene has been established widely in the clinic as a basis for personalized prevention or treatment strategies. Sequencing BRCA1/BRCA2 genes, mismatch repair genes (MLH1, MSH2, MSH6 and PMS2) and CDH1 guide prophylactic surgery of hereditary breast-ovarian cancer, colorectal (Lynch) and diffuse gastric cancer syndromes, respectively [2].

Targeted therapy: overcoming drug resistance with clinical cancer genome

Most currently available targeted cancer drugs have been revealed by recent Phase III randomized trials to have a temporary effect limited to a few months and low or no antitumor activity. Although trastuzumab and imatinib show long-term therapeutic effects in gene defect-based selection of patients, curing many of them, they are also limited by acquired resistance in other patients, while vemurafenib response and overall survival benefit is fleeting, with acquired resistance after a mean duration of approximately 7 months. Besides this clinical success, for all other monoclonal antibodies (mAbs) and small-molecule tyrosine kinase inhibitors (TKIs) evidence suggests either a progression-free survival benefit without an overall survival benefit or no therapeutic effect [1]. How can these clinical results be explained despite highly promising data from the research arena? The revolutionary next-generation sequencing (NGS) technologies provide an unprecedented capacity for whole-genome sequencing (WGS), whole-exome sequencing (WES) and RNA sequencing-based transcriptome analysis. Can these genome-wide mapping technologies, applied in appropriately designed clinical trials, help to overcome resistance to current drugs and improve poor clinical outcomes by improving therapeutic approaches with the implementation of personalized oncology into the clinic? Advances & limitations of translational oncology Over the past decades, evidence-based standardization of surgery, radiotherapy and systemic chemotherapy has resulted in a substantial survival benefit for millions of cancer patients. However, despite multiple enthusiastic reports, the hard reality is reflected by the current US cancer statistics with cancer death rates remaining alarmingly high, particularly in advanced tumor stages III and IV [2]. In addition, the adverse effects of systemic chemotherapy have slowly been reduced, inf luencing quality of life. To increase the eff icacy regarding responsiveness and survival rates, pharma ceutical and biomolecular diagnostic research has been shifted from chemotherapy to signaling transduction inhibitor drug development and validation. Crucial cellular processes including survival, growth, differentiation, proliferation and apoptosis are regulated by signal transduction from the cell surface to the nucleus. Deregulation or amplification of this signal transmission by the accumulation of genetic and epigenetic changes and ultimately also gene expression dysfunction, collectively result in major diseases such as cancer, among others. Inhibiting or restoring deregulated signaling pathways and gene expression patterns in cancer Expert Rev. Anticancer Ther. 12(7), 861–864 (2012)

Risk factors and early detection of breast cancer: facts, questions, and genome-based perspectives

The Editor Current Oncology March 28, 2012 Substantial progress in detecting breast cancer at an early stage has been made over recent decades. Mammographic breast screening in the general population and BRCA1/2 mutation testing in the subpopulation of women with significant family history of breast and ovarian cancer represent two prime paradigms of clinical success. However, breast cancer continues to be the most common female cancer, and mortality remains high. In the October issue of Current Oncology, Narod 1, based on his large-scale experience in breast cancer and analyzing a huge body of genetic and non-genetic risk factors, provided a critical approach on early onset of the disease. Despite advances through classical biomedical reductionist research and genetic epidemiology in identifying lifestyle and environmental risk factors and the identification of many genes involved in breast cancer, grand challenges and unresolved questions are ahead of us. Identification of individual women at very high risk for personalized prevention is currently unrealistic for the vast preponderance of cases; only for a small percentage (5%–10% of annually diagnosed breast cancers with BRCA1/2 mutation) is such prediction feasible. Breast cancer is a heterogeneous disease that arises from complex genome–environment interactions and accumulation of genetic and epigenetic alterations. The high complexity involved in the understanding of how these driver mutations and epigenome events dys-regulate critical cell signalling pathways, biomolecular networks, and biologic systems homeostasis leading to tumorigenesis explains the current limitations in personalized risk assessment and prevention of the disease. Whether all these problems can be resolved by using next-generation sequencing for exome and whole-genome sequencing and rapid advances in systems and synthetic biology for predicting biomolecular networks will result in the discovery of novel robust biomarkers for early detection at a very early stage in asymptomatic women and new preventive drugs is still unknown 2–9.

Next-generation sequencing: from conventional applications to breakthrough genomic analyses and precision oncology

The validity, accuracy, and decreasing cost of genome analyses in health and disease [1,2] and their successful integration in the ENCODE project [3] have revolutionized life sciences. Progress in the research of major complex diseases, including neurodevelopmental and degenerative disorders, psychiatric syndromes, and particularly cancer has been slow. Rapid advances in next-generation sequencing (NGS) applications from static, conventional, single-biopsy NGS to dynamic, breakthrough, multiple-biopsy analyses, assessing genomic clone evolution in time and space, have laid the foundation of precision medicine [4]. Conventional NGS refers to singlebiopsy analyses at a single time point, while breakthrough NGS includes multi-regional analyses of the primary tumor for the identification of intratumor heterogeneity (ITH), as well as serial liquid biopsy analyses, using circulating cell-free DNA (cfDNA) followed by NGS (cfDNA-NGS). Here, we summarize the potential and challenges of NGS integration into appropriately designed studies, to achieve predictive, preventive, and therapeutic clinical implications. Common complex diseases remain an unresolved health problem. In some cases, such as cardiovascular disease, there has been substantial progress in prevention, although the management of these patients requires lifelong treatment and intensive follow-up [5]. Other diseases, such as neurodevelopmental and neurodegenerative disorders, schizophrenia, and cancer, remain incurable, lacking means of early and accurate diagnosis, as well as effective therapies, and featuring poor quality of life. Subsequently, it has become clear that, without understanding the germline and/or somatic mutational landscape underlying these complex diseases and how structural genome variants affect molecular networks, gene-expression profiles, transcription and translation, significant progress toward cure will never occur. The rapid evolution of NGS platforms during the past decade and their unprecedented potential to identify genetic and genomic aberrations in tissue and liquid biopsies have rendered these genomic analyses into the most accurate tool for precise diagnosis and individualized treatment. 2. NGS technologies and the revolution of life sciences