Next Generation Sequencing (NGS): A Revolutionary Technology in Pharmacogenomics and Personalized Medicine in Cancer.

Following the completion of the Human Genome Project in 2003, research in oncology has progressively focused on the sequencing of cancer genomes, with the aim of better understanding the genetic basis of oncogenesis and identifying actionable alterations. The development of next-generation-sequencing (NGS) techniques, commercially available since 2006, allowed for a cost- and time-effective sequencing of tumor DNA, leading to a "genomic era" of cancer research and treatment. NGS provided a significant step forward in Personalized Medicine (PM) by enabling the detection of somatic driver mutations, resistance mechanisms, quantification of mutational burden, germline mutations which settled the foundation of a new approach in cancer care. In this chapter we discuss the history, available techniques and applications of NGS in oncology, with a particular referral to the PM approach and the emerging role of the research field of pharmacogenomics.

Caloric restriction leads to druggable LSD1-dependent cancer stem cells expansion.

Caloric Restriction (CR) has established anti-cancer effects, but its clinical relevance and molecular mechanism remain largely undefined. Here, we investigate CR's impact on several mouse models of Acute Myeloid Leukemias, including Acute Promyelocytic Leukemia, a subtype strongly affected by obesity. After an initial marked anti-tumor effect, lethal disease invariably re-emerges. Initially, CR leads to cell-cycle restriction, apoptosis, and inhibition of TOR and insulin/IGF1 signaling. The relapse, instead, is associated with the non-genetic selection of Leukemia Initiating Cells and the downregulation of double-stranded RNA (dsRNA) sensing and Interferon (IFN) signaling genes. The CR-induced adaptive phenotype is highly sensitive to pharmacological or genetic ablation of LSD1, a lysine demethylase regulating both stem cells and dsRNA/ IFN signaling. CR + LSD1 inhibition leads to the re-activation of dsRNA/IFN signaling, massive RNASEL-dependent apoptosis, and complete leukemia eradication in ~90% of mice. Importantly, CR-LSD1 interaction can be modeled in vivo and in vitro by combining LSD1 ablation with pharmacological inhibitors of insulin/IGF1 or dual PI3K/MEK blockade. Mechanistically, insulin/IGF1 inhibition sensitizes blasts to LSD1-induced death by inhibiting the anti-apoptotic factor CFLAR. CR and LSD1 inhibition also synergize in patient-derived AML and triple-negative breast cancer xenografts. Our data provide a rationale for epi-metabolic pharmacologic combinations across multiple tumors.

Evidence for interleukin 17 involvement in severe immune-related neuroendocrine toxicity.

AIM: Severe neurological and endocrine toxicities are well recognised adverse events of immune checkpoint inhibitors. However, the underlying pathophysiology is poorly understood, and classical circulating markers are often non-informative, making it difficult to obtain a precise diagnosis and to initiate timely and effective treatment. Here we investigated immune-modulating activity in the plasma of a mesothelioma patient who developed fatal neuroendocrine toxicity characterised by insulin-dependent diabetes, hypophisitis and a myasthenia-like syndrome while on treatment with the dual PD1 and TIM3 blockade. METHODS: We used an in vitro functional assay for unbiased detection of plasma dendritic cell-modulating activity, followed by cytokine quantification by the Cytokine Bead Array. RESULTS: Immunosuppressive treatment as per established guidelines could not prevent the fatal outcome. Patient's plasma contained a dendritic cell-stimulating activity that induced specific markers (CD25+) compatible with T-helper 17 stimulation. Consistently, elevated levels of interleukin 17 (IL17A), but no other cytokines, were identified in the patient's plasma but not in controls (healthy volunteers and patients treated with immunotherapy without neuroendocrine toxicities). CONCLUSION: If confirmed in larger series, these data suggest IL17 as a candidate diagnostic and therapeutic target in the management of high-grade neuroendocrine immune-related adverse events.

Semantic and Geographical Analysis of COVID-19 Trials Reveals a Fragmented Clinical Research Landscape Likely to Impair Informativeness.

Background: The unprecedented impact of the COVID-19 pandemic on modern society has ignited a "gold rush" for effective treatment and diagnostic strategies, with a significant diversion of economic, scientific, and human resources toward dedicated clinical research. We aimed to describe trends in this rapidly changing landscape to inform adequate resource allocation. Methods: We developed an online repository (COVID Trial Monitor) to analyze in real time the growth rate, geographical distribution, and characteristics of COVID-19 related trials. We defined structured semantic ontologies with controlled vocabularies to categorize trial interventions, study endpoints, and study designs. Analyses are publicly available at https://bioinfo.ieo.it/shiny/app/CovidCT. Results: We observe a clear prevalence of monocentric trials with highly heterogeneous endpoints and a significant disconnect between geographic distribution and disease prevalence, implying that most countries would need to recruit unrealistic percentages of their total prevalent cases to fulfill enrolment. Conclusions: This geographically and methodologically incoherent growth casts doubts on the actual feasibility of locally reaching target sample sizes and the probability of most of these trials providing reliable and transferable results. We call for the harmonization of clinical trial design criteria for COVID-19 and the increased use of larger master protocols incorporating elements of adaptive designs. COVID Trial Monitor identifies critical issues in current COVID-19-related clinical research and represents a useful resource with which researchers and policymakers can improve the quality and efficiency of related trials.

Homologous recombination deficiency in triple negative breast cancer.

Triple negative breast cancer (TNBC) represents a heterogeneous subtype of breast cancer characterized by an unfavorable prognosis due to its aggressive biology. The median overall survival (OS) for patients with metastatic TNBC is around 9-12 months with conventional cytotoxic agents. Considering this suboptimal outcome, which is induced despite of medical treatment, new therapeutic strategies would be urgently needed. The ultimate goal of precision medicine is to identify specific molecular alterations that permit considering effective targeted drug(s). Germline BRCA mutations occur in 10-20% of TNBC patients while somatic mutations occur in 3-5% of them. Alterations in the homologous recombination (HR) system are typical of BRCA mutant tumors, but can also be identified in tumors that do not carry this mutation, defining a subgroup of patients referred to as BRCAness. In this review, we focus on the role of homologous recombination deficiency (HRD) as both predictive and prognostic factor in different settings of TNBC patients treated with DNA damaging drugs and poly ADP ribose polymerase (PARP) inhibitors.

Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life.

The finalization of the Human Genome Project in 2003 paved the way for a deeper understanding of cancer, favouring a faster progression towards "personalized" medicine. Research in oncology has progressively focused on the sequencing of cancer genomes, to better understand the genetic basis of tumorigenesis and identify actionable alterations to guide cancer therapy. Thanks to the development of next-generation-sequencing (NGS) techniques, sequencing of tumoral DNA is today technically easier, faster and cheaper. Commercially available NGS panels enable the detection of single or global genomic alterations, namely gene mutation and mutagenic burden, both on germline and somatic DNA, potentially predicting the response or resistance to cancer treatments. Profiling of tumor DNA is nowadays a standard in cancer research and treatment. In this review we discuss the history, techniques and applications of NGS in cancer care, under a "personalized tailored therapy" perspective.

The evolving landscape of 'next-generation' immune checkpoint inhibitors: A review.

'First-generation' immune checkpoint inhibitors targeting Cytotoxic T-Lymphocyte Antigen 4 (CTLA4) and Programmed death-ligand 1 (PD(L)1) have undoubtedly revolutionised the treatment of multiple cancers in the advanced setting. Targeting signalling pathways other than core inhibitory modules may strongly impact the outcome of the antitumour immune response. Drugs targeting these pathways ('next-generation' immune modulators, NGIMs) constitute a major frontier in translational research and have generated unprecedented scientific and financial investment. Here, we systematically reviewed published literature, abstracts from major cancer conferences and pharma pipelines to identify NGIMs that have reached clinical development. We identified 107 molecules targeting 16 pathways, which we classified into 6 groups according to function (inhibitory vs stimulatory) and cell of predominant expression (lymphoid, non-lymphoid and natural killer). We identified all registered past and ongoing clinical trials (n = 428). We summarise the preclinical rationale for these targets, extracting translationally relevant information, and review published and preliminary clinical results. Some targets like indoleamine-2,3-dioxygenase 1, lymphocyte activation gene-3 and IL15 have experienced exceptional growth of interest, measured in terms of activated studies and expected patient enrolment over time. We conclude that in this vast and rapidly changing drug development landscape, novel trial designs and better biomarker identification are necessary to optimise resource allocation.

Opportunities and challenges of implementing Pharmacogenomics in cancer drug development.

Cancer drug development is a time and resources consuming process. Around 90% of drugs entering clinical trials fail due to lack of efficacy and/or safety issues, more often after conspicuous research and economic efforts. Part of the discarded drugs might be beneficial only in a subgroup of the study patients, and some adverse events might be prevented by identifying those patients more vulnerable to toxicities. The implementation of pharmacogenomic biomarkers allows the categorization of patients, to predict efficacy and toxicity and to optimize the drug development process. Around seventy FDA approved drugs currently present one or more genetic biomarker to keep in consideration, and with the progress of Precision Medicine tailoring therapies on individuals' genomic landscape promises to become a new standard of cancer care. In the current article we review the role of pharmacogenomics in cancer drug development, underlying the advantages and challenges of their implementation.

Targeting the microenvironment in solid tumors.

Tumorigenesis is a complex and dynamic process involving different cellular and non-cellular elements composed of tumor microenvironment (TME). The interaction of TME with cancer cells is responsible for tumor development, progression and drug resistance. TME consists of non malignant cells of the tumor such as cancer associated fibroblasts (CAFs), endothelial cells and pericytes composing tumor vasculature, immune and inflammatory cells, bone marrow derived cells, and the extracellular matrix (ECM) establishing a complex cross-talk with tumor. These interactions contribute towards proliferation and invasion of the tumor by producing growth factors, chemokines and matrix-degrading enzymes. ECM is a complex system containing macromolecules with distinctive physical, biochemical and biomechanical properties. During tumorigenesis this system is deregulated favoring the generation of tumorigenic microenvironment enhancing tumor-associated angiogenesis and inflammation. An important step of anticancer treatment is the identification of the biological alterations present in TME in order to target these key molecular players. Multitargeted approaches, providing a simultaneous inhibition of TME components, may offer a more efficient way to treat cancer. In this manuscript we overview the function of each components of TME and the treatments targeting the key players.

Clinical efficacy of ribociclib as a first-line therapy for HR-positive, advanced breast cancer.

INTRODUCTION: Breast cancer (BC) remains the most frequently diagnosed cancer and the most common cause of cancer death among women of all races worldwide. Over 80% of BC cases are hormone receptor (HR)-positive, comprised of luminal A and luminal B per molecular subtypes, imposing an urgent need to fully understand the mechanisms behind progression. Ribociclib is a selective cycline-dependent kinase 4 and 6 inhibitor. A phase 1 and a phase 3 trial have established a definitive role of ribociclib as frontline in the treatment of endocrine-sensitive advanced BC. Areas covered: Herein, the authors provide an overview of the data on ribociclib covering all aspects of the drug from its pharmacokinetics to efficacy and safety. The authors also provide their perspectives for the future. Expert opinion: Ribociclib is offering an opportunity to explore a new compound at the crossroads of different molecular activity and cell targets, which focus on endocrine-resistance reversal in multiple settings including early BC. Moreover, its activity against different subtypes of BC is being studied as is its immune-modulating effect. One cautionary note is that, in a market of concomitant similar competitors, a financial discussion will be mandatory.

Corrigendum to "Public versus Private Healthcare Systems following Discharge from the ICU: A Propensity Score-Matched Comparison of Outcomes".

[This corrects the article DOI: 10.1155/2016/6568531.].

Mortality of Adult Critically Ill Subjects With Cancer.

BACKGROUND: Cancer patients may require intensive care support for postoperative care, complications associated with underlying malignancy, or toxicities related to cancer therapy. The higher mortality rates found in this population than in the population of ICU patients without cancer may be attributable to confounding due to a higher prevalence of multiple organic dysfunctions at ICU admission in patients with malignancy; however, data regarding this hypothesis are scarce. Accordingly, we performed the present study to compare the crude and propensity score-matched mortality rates between adult subjects with and without cancer admitted to a mixed medical-surgical ICU. METHODS: We conducted a retrospective analysis of a comprehensive longitudinal ICU database in a tertiary referral hospital in Southern Brazil. All adult subjects who were admitted to the ICU from January 2008 to December 2014 were evaluated. Crude and propensity score-matched all-cause 30-d mortality rates of critically ill subjects with cancer were compared with those of critically ill subjects without cancer. RESULTS: A total of 4,221 subjects were evaluated. The survival analysis revealed that the crude mortality rate was higher among subjects with cancer than among subjects without cancer (18.7% vs 10.2%, P < .001). However, after matching by propensity score, the 30-d mortality rates of subjects with and without cancer were similar (18.5% vs 15.2%, P = .17). CONCLUSIONS: The present study failed to show an association between malignancy and all-cause 30-d mortality rate in adult subjects admitted to a mixed medical-surgical ICU. The propensity score-matched analysis showed no evidence of excessive mortality due to cancer diagnosis.

Public versus Private Healthcare Systems following Discharge from the ICU: A Propensity Score-Matched Comparison of Outcomes.

Purpose. The long-term outcomes of patients after discharge from tertiary ICUs as they relate to the public versus private healthcare systems in Brazil have not yet been evaluated. Materials and Methods. A multicenter prospective cohort study was conducted to compare the all-cause mortality and the physical functional status (PFS) 24 months after discharge from the ICU between adult patients treated in the public and private healthcare systems. A propensity score- (PS-) matched comparison of all causes of mortality and PFS 24 months after discharge from the ICU was performed. Results. In total, 928 patients were discharged from the ICU including 172 (18.6%) patients in the public and 756 (81.4%) patients in the private healthcare system. The results of the PS-matched comparison of all-cause mortality revealed higher mortality rates among the patients of the public healthcare system compared to those of the private healthcare system (47.3% versus 27.6%, P = 0.003). The comparison of the PS-matched Karnofsky performance and Lawton activities of daily living scores between the ICU survivors of the public and private healthcare systems revealed no significant differences. Conclusions. The patients of private healthcare system exhibited significantly greater survival rates than the patients of the public healthcare system with similar PFS following ICU discharge.

Locoregional recurrence in patients with HER2 positive breast cancer.

Literature shows that HER2/neu positive breast cancer cells are more sensitive to radiation-induced apoptosis by targeting the epidermal growth factor receptor family tyrosine kinase. We selected 466 patients with pT1-2 HER2/neu positive tumors who received adjuvant trastuzumab for primary invasive breast cancer. Patients were divided into three groups [Quadrantectomy followed by conventional radiotherapy vs Quadrantectomy followed by Intra-operative radiotherapy with electrons vs Mastectomy without radiotherapy]. After a median follow-up of 52 months, the 5-year cumulative incidence of locoregional recurrence (LRR) was 1.9%, 11.5% and 5.0% respectively (p < 0.01). At the multivariate analysis, extensive perivascular invasion, Luminal B HER2/Progesterone Receptor (PgR) negative status and Quadrantectomy followed by Intra-operative radiotherapy with electrons have significantly increased the risk of LRR. Our results suggest that HER2/neu positive breast cancer might have better outcomes when treated simultaneously with external radiotherapy and trastuzumab. Moreover, we underline the importance of PgR and further new stratification of risk among luminal subtypes.