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Carbon nanotubes (CNTs) were discovered in 1991, and since then, have been one of the most intensely studied nanomaterials due to their improved functionalities and diversity of applications. Specifically, CNTs are entirely composed of carbon atoms connected through sp2 bonds structured in several condensed benzene rings rolled up into a cylinder form. Depending on the number of graphitic layers, CNTs can be classified into single-walled carbon nanotubes (SWCNTs) or multi-walled carbon nanotubes (MWCNTs). The specific structural properties of CNTs, leading to a strong loading capacity, high surface area, high strength, and enhanced chemical and thermal stability, make these nanomaterials very promising for biomedical applications. In this sense, this book chapter overviews the potential applications of CNTs in the biomedical field, highlighting their usage on: (1) diagnosis, by the development of CNTs-based biosensors and imaging methods; (2) tissue engineering; (3) delivery systems of several anticancer and antihypertensive drugs, corticosteroids, genes, nucleic acids, among others; and (4) target therapies, namely photothermal and photodynamic therapies. Additionally, particular attention is given to the CNTs potential toxicity and different strategies to overcome this controversial subject, namely by the adequate CNTs functionalization. published

People living with HIV (PLWH) with advanced immunosuppression who initiate antiretroviral therapy (ART) are susceptible to the occurrence of an immune reconstitution inflammatory syndrome (IRIS). Although ART is responsible for AIDS- associated Kaposi sarcoma (KS) improvement and resolution, new onset (unmasking KS-IRIS) or sudden progression of preexisting KS (paradoxical KS-IRIS) can occur after a time delay of between a few days and 6 months after the initiation or resumption of ART, even in patients with a low degree of immunocompromise. KS-IRIS incidence varies from 2.4% to 39%, depending on study design, populations, and geographic regions. Risk factors for developing KS-IRIS include advanced KS tumor stage (T1), pre-treatment HIV viral load >5 log10 copies/mL, detectable pre-treatment plasma-KSHV, and initiation of ART alone without concurrent chemotherapy. Both paradoxical and unmasking KS-IRIS have been associated with significant morbidity and mortality, and thrombocytopenia (

ROS proto-oncogene 1 (ROS1) rearrangements are reported in about 1–2% of non-squamous non-small-cell lung cancer (NSCLC). After efficacy of crizotinib was demonstrated, identification of ROS1 translocations in advanced disease became fundamental to give patients the chance of specific and effective treatment. Different methods are available for detection of rearrangements, and probably the real prevalence of ROS1 rearrangements is higher than that reported in literature, as our capacity to detect gene rearrangements is improving. In particular, with next generation sequencing (NGS) techniques, we are currently able to assess multiple genes simultaneously with increasing sensitivity. This is leading to overcome the “single oncogenic driver” paradigm, and in the very near future, the co-existence of multiple drivers will probably emerge more frequently and represent a therapeutic issue. Since recently, crizotinib has been the only available therapy, but today, many other tyrosine kinase inhibitors (TKI) are emerging and seem promising both in first and subsequent lines of treatment. Indeed, novel inhibitors are also able to overcome resistance mutations to crizotinib, hypothesizing a possible sequential strategy also in ROS1-rearranged disease. In this review, we will focus on ROS1 rearrangements, dealing with diagnostic aspects, new therapeutic options, resistance issues and the coexistence of ROS1 translocations with other molecular alterations.

Vaccines are a promising therapeutic alternative to monoclonal antibodies against HER-2+ breast cancer. We present the preclinical activity of an ES2B-C001, a VLP-based vaccine being developed for human breast cancer therapy. FVB mice challenged with HER-2+ mammary carcinoma cells QD developed progressive tumors, whereas all mice vaccinated with ES2B-C001+Montanide ISA 51, and 70% of mice vaccinated without adjuvant, remained tumor-free. ES2B-C001 completely inhibited lung metastases in mice challenged intravenously. HER-2 transgenic Delta16 mice developed mammary carcinomas by 4–8 months of age; two administrations of ES2B-C001+Montanide prevented tumor onset for >1 year. Young Delta16 mice challenged intravenously with QD cells developed a mean of 68 lung nodules in 13 weeks, whereas all mice vaccinated with ES2B-C001+Montanide, and 73% of mice vaccinated without adjuvant, remained metastasis-free. ES2B-C001 in adjuvant elicited strong anti-HER-2 antibody responses comprising all Ig isotypes; titers ranging from 1–10 mg/mL persisted for many months. Antibodies inhibited the 3D growth of human HER-2+ trastuzumab-sensitive and -resistant breast cancer cells. Vaccination did not induce cytokine storms; however, it increased the ELISpot frequency of IFN-γ secreting HER-2-specific splenocytes. ES2B-C001 is a promising candidate vaccine for the therapy of tumors expressing HER-2. Preclinical results warrant further development towards human clinical studies.

The recent identification of rearrangements of neurotrophic tyrosine receptor kinase (NTRK) genes and the development of specific fusion protein inhibitors, such as larotrectinib and entrectinib, have revolutionised the diagnostic and clinical management of patients presenting with tumours with these alterations. Tumours that harbour NTRK fusions are found in both adults and children; and they are either rare tumours with common NTRK fusions that may be diagnostic, or more prevalent tumours with rare NTRK fusions. To assess currently available evidence on this matter, three key Spanish medical societies (the Spanish Society of Medical Oncology (SEOM), the Spanish Society of Pathological Anatomy (SEAP), and the Spanish Society of Paediatric Haematology and Oncology (SEHOP) have brought together a group of experts to develop a consensus document that includes guidelines on the diagnostic, clinical, and therapeutic aspects of NTRK-fusion tumours. This document also discusses the challenges related to the routine detection of these genetic alterations in a mostly public Health Care System., SEOM, SEAP and SEHOP have received financial support for this project in the form of unrestricted collaboration in the logistics of expert meeting from Bayer and Roche.

Triple-negative breast cancer (TNBC) is characterized by the absence of hormone receptor and HER2 expression, and therefore a lack of therapeutic targets. Anthracyclines and taxane-based neoadjuvant chemotherapy have historically been the cornerstone of treatment of early TNBC. However, genomic and transcriptomic analyses have suggested that TNBCs include various subtypes, characterized by peculiar genomic drivers and potential therapeutic targets. Therefore, several efforts have been made to expand the therapeutic landscape of early TNBC, leading to the introduction of platinum and immunomodulatory agents into the neoadjuvant setting. This review provides a comprehensive overview of the currently available evidence regarding platinum agents and immune-checkpoint-inhibitors for the neoadjuvant treatment of TNBC, as well as the novel target therapies that are currently being evaluated in this setting. Taking into account the economic issues and the side effects of the expanding therapeutic options, we focus on the potential efficacy biomarkers of the emerging therapies, in order to select the best therapeutic strategy for each specific patient.

Hepatocellular carcinoma (HCC) is the main type of liver cancer. In the majority of cases, HCC is diagnosed at the advanced stage, leading to poor prognosis. In recent years, many efforts have been devoted to investigating potential new and more effective drugs and, indeed, the treatment armamentarium for advanced HCC has broadened tremendously, with targeted- and immune-therapies, and probably the combination of both, playing pivotal roles. Together with new established knowledge, many issues are emerging, with the role of neoadjuvant/adjuvant settings, the definition of the best transitioning time from loco-regional treatments to systemic therapy, the identification of potential predictive biomarkers, and radiomics being just some of the topics that will have to be further explored in the next future. Clearly, the current COVID-19 pandemic has influenced the management of HCC patients and some considerations about this topic will be elucidated.

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in childhood. Recently, we demonstrated the overexpression of both DNA methyltransferase 3A (DNMT3A) and 3B (DNMT3B) in RMS tumour biopsies and cell lines compared to normal skeletal muscle. Radiotherapy may often fail due to the abnormal expression of some molecules able to drive resistance mechanisms. The aim of this study was to analyse the involvement of DNMT3A and DNMT3B in radioresistance in RMS. RNA interference experiments against DNMT3A/3B were performed in embryonal RMS cells, upon ionizing radiation (IR) exposure and the effects of the combined treatment on RMS cells were analysed. DNMT3A and DNMT3B knocking down increased the sensitivity of RMS cells to IR, as indicated by the drastic decrease of colony formation ability. Interestingly, DNMT3A/3B act in two different ways: DNMT3A silencing triggers the cellular senescence program by up-regulating p16 and p21, whilst DNMT3B depletion induces significant DNA damage and impairs the DNA repair machinery (ATM, DNA-PKcs and Rad51 reduction). Our findings demonstrate for the first time that DNMT3A and DNMT3B overexpression may contribute to radiotherapy failure, and their inhibition might be a promising radiosensitizing strategy, mainly in the treatment of patients with metastatic or recurrent RMS tumours.

Next-generation sequencing (NGS) is progressively being used in clinical practice. However, several barriers preclude using this technology for precision oncology in most Latin American countries. To overcome some of these barriers, we have designed a 25-gene panel that contains predictive biomarkers for most current and near-future available therapies in Chile and Latin America. Library preparation was optimized to account for low DNA integrity observed in formalin-fixed paraffin-embedded tissue. The workflow includes an automated bioinformatic pipeline that accounts for the underrepresentation of Latin Americans in genome databases. The panel detected small insertions, deletions, and single nucleotide variants down to allelic frequencies of 0.05 with high sensitivity, specificity, and reproducibility. The workflow was validated in 272 clinical samples from several solid tumor types, including gallbladder (GBC). More than 50 biomarkers were detected in these samples, mainly in BRCA1/2, KRAS, and PIK3CA genes. In GBC, biomarkers for PARP, EGFR, PIK3CA, mTOR, and Hedgehog signaling inhibitors were found. Thus, this small NGS panel is an accurate and sensitive method that may constitute a more cost-efficient alternative to multiple non-NGS assays and costly, large NGS panels. This kind of streamlined assay with automated bioinformatics analysis may facilitate the implementation of precision medicine in Latin America.

Small cell lung cancer is a highly aggressive, difficult to treat neoplasm. Among all lung tumors, small cell lung cancers account for about 20%. Patients typically include heavy smokers in 70s age group, presenting with symptoms such as intrathoracic tumors growth, distant spread or paraneoplastic syndromes at the time of diagnosis. A useful and functional classification divides small cell lung cancers into limited disease and extensive disease. Concurrent chemo-radiotherapy is the standard treatment for limited disease, with improved survival when combined with prophylactic cranial irradiation. Platinum compounds (cisplatin/carboplatin) plus etoposide remain the cornerstone for extensive disease. Nevertheless, despite high chemo- and radio-sensitivity of this cancer, nearly all patients relapse within the first two years and the prognosis is extremely poor. A deeper understanding about small cell lung cancer carcinogenesis led to develop and test a considerable number of new and targeted agents but the results are currently weak or insufficient. To date, small cell lung cancer is still a challenge for researchers. In this review, key aspects of small cell lung cancer management and controversial points of standard and new treatments will be discussed.

microRNAs (miRNAs) regulate gene expression by modulating the translation of protein-coding RNAs. Their aberrant expression is involved in various human diseases, including cancer. Here, we summarize the experimental pieces of evidence that proved how dysregulated miRNA expression can lead to RAS (HRAS, KRAS, or NRAS) activation irrespective of their oncogenic mutations. These findings revealed relevant pathogenic mechanisms as well as mechanisms of resistance to target therapies. Based on this knowledge, potential approaches for the control of RAS oncogenic activation can be envisioned.

Introduction: Innate immune response and bone remodeling are key factors contributing to the pathogenesis of psoriatic arthritis (PsA). Moreover, the evidence of autoantibodies in patients' sera suggests an autoimmune side in PsA. Besides the immune pathways, studies strongly support the role of genetic risk alleles in affecting the clinical heterogeneity of PsA as well as the response to therapy. A good clinical response to treatment, indeed, represents a challenge in PsA patients and the identification of patient-targeted therapies is still a critical issue. Areas covered: We performed a systematic review aiming at describing new evidence on PsA pathogenesis and treatments. Reported items for systematic reviews (PRISMA checklist) were analyzed. Studies included from the PubMed database addressed the following items: innate immunity, autoimmunity, bone remodeling, and therapeutic targets in PsA; time frame of research 1970-2019. Specifically, we reviewed data on IL-17 inhibitors, abatacept, JAK inhibitors, ABT 122, and A (3) adenosine receptors agonist, CF101. Expert opinion: In PsA an intriguing pathogenetic network has been documented. Several biological and synthetic drugs are promising in terms of efficacy and safety profile.

The development of effective nanosystems for drug delivery represents a key challenge for the improvement of most current anticancer therapies. Recent progress in the understanding of structure and function of extracellular vesicles (EVs)—specialized membrane-bound nanocarriers for intercellular communication—suggests that they might also serve as optimal delivery systems of therapeutics. In addition to carrying proteins, lipids, DNA and different forms of RNAs, EVs can be engineered to deliver specific bioactive molecules to target cells. Exploitation of their molecular composition and physical properties, together with improvement in bio-techniques to modify their content are critical issues to target them to specific cells/tissues/organs. Here, we will discuss the current developments in the field of animal and plant-derived EVs toward their potential use for delivery of therapeutic agents in different pathological conditions, with a special focus on cancer.

Several new biological agents have been investigated as second line of treatment in advanced Hepatocellular Cancer (HCC). We performed a meta -analysis to assess the effect of targeted therapies in advanced HCC patients beyond the first line of treatment. A literature-based metaanalysis of randomized controlled trials was undertaken. The primary outcome was the overall survival. The secondary endpoints were the progression-free survival (PFS), the response rate (RR) and disease control rate (DCR) and the safety. Pooled analysis of targeted agents revealed a modest increase in overall survival compared with control arm (Hazard Ratio (HR) = 0.93, 95%CI: 0.83-1.04; P = 0.21). On the counterpart, all the secondary endpoints were in favoured to the targeted agents-based treatment (PFS: HR = 0.68, 95% CI:0.56–0.83; P = 0.0002; RR: 3.50,95% CI 1.81–6.76; P = 0.0002, DCR: RR:1.19, 95% CI 1.06–1.32; P = 0.002). To date, there is a clinical need of a more efficacious second line of therapy in treatment of the advanced HCC. This study showed some activity of the new targeted therapies in second line of treatment in advanced HCC.

The prognosis of patients affected by ovarian cancer has not substantially changed in the last decades and improving survival still remains a challenge. In the promising era of 'personalized therapy' several new biologic therapies are currently being investigated: in this setting, targeting the folate receptor (FR) has been considered a new potential strategy for biologic therapy. Areas covered: The aim of the current review is to summarize, giving a critical overview,promising folate receptor alpha antagonists under preclinical or early clinical development for ovarian cancer. Expert opinion: Two categories of therapeutics are included in this class: FRα targeted mAbs and FRα-binding-ADC (Antibody drug conjugates); both share the interesting possibility of selecting patients via a biomarker which is already available. In the first class, farletuzumab has reached the most advanced stage in clinical evaluation and results of a Phase II randomized trial are awaited to assess its efficacy in a specific patients' setting. MOv18 IgE represents a novel strategy to target FRα expressing cells, which has shown encouraging results in preclinical studies: further evaluation is needed in the clinical setting. IMGN 853 is an innovative FRα-binding ADC under development, with only preliminary results of a Phase I trial available.

The presence of mutations in the KRAS gene is a predictor of a poor clinical response to EGFR-targeted agents in patients affected by colorectal cancer (CRC), but its significance as a global prognostic factor remains unclear. The aim of the present study was to evaluate the impact of the KRAS mutational status on time to first metastasis (TTM) and overall survival (OS) in a cohort of Sardinian CRC patients. A total of 551 patients with metastatic CRC at the time of enrolment were included. Clinical and pathological features of the disease, including follow-up information, were obtained from medical records and cancer registry data. For mutational analysis formalin-fixed paraffin-embedded tissue samples were processed using a standard protocol. The coding sequence and splice junctions of exons 2 and 3 of the KRAS gene were screened for mutations by direct automated sequencing. Overall, 186 KRAS mutations were detected in 183/551 (33%) patients: 125 (67%) were located in codon 12, 36 (19%) in codon 13, and 18 (10%) in codon 61. The remaining mutations (7; 4%) were detected in uncommonly-affected codons. No significant correlation between KRAS mutations and gender, age, anatomical location and stage of the disease at the time of diagnosis was identified. Furthermore, no prognostic value of KRAS mutations was found considering either TTM or OS. When patients were stratified by KRAS mutational status and gender, males were significantly associated with a longer TTM. The results of the present study indicate that KRAS mutation correlated with a slower metastatic progression in males with CRC from Sardinia, irrespective of the age at diagnosis and the codon of the mutation.

With the ever-expanding therapeutic indications and ongoing clinical trials with Poly(adenosine diphosphate-ribose) Polymerase (PARP) inhibitors, it is of outmost importance to stop and rethink what we know and still do not know concerning one of the major revolutions in target therapies in the last decades. Indeed, many PARP inhibitors (PARPi) are able to bind multiple targets, with a plethora of potential interactions with cancer cell signaling, metabolism and the tumor microenvironment (TME). These interactions can mediate both response and resistance to PARPi, but also represent an opportunity for sequential and/or combinatorial therapies. Here we advocate a "look before you leap" approach in reviewing available clinical and preclinical evidence concerning PARPi, delving into this complex entanglement, trying to unravel the potential for innovative therapeutic strategies revolving on PARP inhibition.

Inflammatory Bowel Diseases (IBD), whose denomination comprehends Crohn's Disease (CD) and Ulcerative Colitis (UC), are intestinal chronic diseases that often require lifelong medical therapy. In the last two decades monoclonal antibodies against the cytokine TNF have become integral parts in the treatment of IBD patients, however there are unwanted side-effects and one third of patients show primary non-response while another subgroup loses response over time. Finding novel drugs which could act as therapies against precise pro-inflammatory molecular targets to avoid unwanted systemic side effects and additionally the process of immunization, represents an important aim for subsequent therapeutic approaches. Oligonucleotide based therapies represent a promising novel concept for the treatment of IBD. The molecular action of oligonucleotides ranges from inhibition of the translational process of mRNA transcripts of pro-inflammatory molecules, to mimicking bacterial DNA which can activate cellular targets for immunomodulation. Alicaforsen, selectively targets ICAM-1 mRNA. ICAM-1 is an adhesion molecule which is upregulated on endothelial cells during IBD, thereby mediating the adhesion and migration of leucocytes from blood to sites of active inflammation. In CD parenteral application of alicaforsen did not show therapeutic efficacy in phase II trials, but it demonstrated an improved efficacy as a topical enema in distal UC. Topical application of alicaforsen might represent a therapeutic perspective for refractory pouchitis as well. SMAD7 is a protein that inhibits the signaling of TGFβ, which is the mainstay of a regulatory counterpart in cellular immune responses. An antisense oligonucleotide against SMAD7 mRNA (mongersen) demonstrated pre-clinical and phase II efficacy in CD, but a phase III clinical trial was stopped due to lack of efficacy. Cobitolimod is a single strand oligonucleotide, which mimics bacterial DNA as its CpG dinucleotide sequences can be recognized by the Toll-like receptor 9 on different immune cells thereby causing induction of different cytokines, for example IL10 and IFNα. Topical application of cobitolimod was studied in UC patients. We will also discuss two other novel oligonucleotides which act on the GATA3 transcription factor (SB012) and on carbohydrate sulfotransferase 15 (STNM01), which could both represent novel promising therapeutic options for the treatment of UC.

The treatment of advanced disease (stage IIIb and IV) of non-small cell lung cancer (NSCLC) is based on systemic treatment with platinum-based chemotherapy or biological compounds depending on the disease molecular profile. In the last few years, intensive investigational efforts in anticancer therapy have led to the registration of new active chemotherapeutic agents, combination regimens, and biological drugs, expanding choices for customizing individual treatment. However, the introduction of new drugs in the clinical setting has led to several new toxicities, creating some difficulties in daily management. Among these, ocular toxicity is generally overlooked as more common toxicities such as myelosuppression, stomatitis, diarrhea, vomiting, “hand–foot syndrome”, and neurological alterations attract greater attention. Ophthalmic complications from cytotoxic chemotherapeutics are rare, transient, and of mild/moderate intensity but irreversible acute disorders are possible. The best way to prevent potential irreversible visual complications is an awareness of the potential for ocular toxicity because dose reductions or early drug cessation can prevent serious ocular complications in the majority of cases. However, given the novelty of many therapeutic agents and the complexity of ocular pathology, oncologists may be unfamiliar with these adverse effects of anticancer therapy. Although toxicities from chemotherapy are generally intense but short lasting, toxicities related to targeted drugs are often milder but longer lasting and can persist throughout treatment. Here we review the principal clinical presentations of ocular toxicity arising from chemotherapy [1–3], target therapies [4], and newly developed drugs and provide some recommendations for monitoring and management of ocular toxicity.

The integration between radiotherapy and drugs, from chemotherapy to recently available target therapies, continues to have a relevant role in the treatment of locally advanced and metastatic Non-small cell lung cancer (NSCLC). Aim of the present review is to evaluate the promising and emerging application of the best interaction between new drugs and new modalities of radiotherapy. Areas covered: We searched Medline, Google Scholar, PubMed, ProQuest Dissertation, and Theses databases for reports published in English. A study was included when it reported on cancer-related radiotherapy and included patients with NSCLC treated with chemo and/or target therapies. Review articles were excluded from the analysis. Expert commentary: Chemo-radiotherapy still represents the standard of choice in locally advanced NSCLC, while to date the addition of target therapies to chemo-radiotherapy did not demonstrate any robust advantage in this stage of disease. Considering the absence of randomized controlled trials, the role of target therapies in early stage adjuvant NSCLC is not yet recommended in clinical practice. On the contrary, in the setting of oligometastatic and oligoprogressive disease, new molecules demonstrated to be safe and effective, opening to a promising and emerging application of the best interaction between new drugs and new modalities of radiotherapy.

A main limitation of therapies that selectively target kinase signalling pathways is the emergence of secondary drug resistance. Cetuximab, a monoclonal antibody that binds the extracellular domain of epidermal growth factor receptor (EGFR), is effective in a subset of KRAS wild-type metastatic colorectal cancers. After an initial response, secondary resistance invariably ensues, thereby limiting the clinical benefit of this drug. The molecular bases of secondary resistance to cetuximab in colorectal cancer are poorly understood. Here we show that molecular alterations (in most instances point mutations) of KRAS are causally associated with the onset of acquired resistance to anti-EGFR treatment in colorectal cancers. Expression of mutant KRAS under the control of its endogenous gene promoter was sufficient to confer cetuximab resistance, but resistant cells remained sensitive to combinatorial inhibition of EGFR and mitogen-activated protein-kinase kinase (MEK). Analysis of metastases from patients who developed resistance to cetuximab or panitumumab showed the emergence of KRAS amplification in one sample and acquisition of secondary KRAS mutations in 60% (6 out of 10) of the cases. KRAS mutant alleles were detectable in the blood of cetuximab-treated patients as early as 10 months before radiographic documentation of disease progression. In summary, the results identify KRAS mutations as frequent drivers of acquired resistance to cetuximab in colorectal cancers, indicate that the emergence of KRAS mutant clones can be detected non-invasively months before radiographic progression and suggest early initiation of a MEK inhibitor as a rational strategy for delaying or reversing drug resistance.

Tumor heterogeneity is associated with the therapeutic failures of targeted therapies. To overcome such heterogeneity, a novel targeted therapy is proposed that could kill tumor populations with diverse phenotypes by delivering nonselective cytotoxins to target‐positive cells as well as to the surrounding tumor cells via a recurrent bystander killing effect. A representative prodrug is prepared that targets integrin αvβ3 and releases cytotoxins upon entering cells or by caspase‐3. This allows the prodrug to kill integrin αvβ3‐positive cells and upregulate caspase‐3, which in turn, activates the prodrug to release a cytotoxin that could subsequently diffuse into and kill the neighboring tumor cells. Apoptotic cells further upregulate and release caspase‐3, which activate more prodrugs leading to another round of adjacent cell death and caspase‐3 release. Thus, the bystander killing effect could occur repeatedly, leading to augmented and widespread anticancer activity. This strategy provides an avenue that could advance the current targeted therapy.

Background The study of cancer therapy is a key issue in the field of oncology research and the development of target therapies is one of the main problems currently under investigation. This is particularly relevant in different types of tumor where traditional chemotherapy approaches often fail, such as lung cancer. Results We started from the general definition of robustness introduced by Kitano and applied it to the analysis of dynamical biochemical networks, proposing a new algorithm based on moment independent analysis of input/output uncertainty. The framework utilizes novel computational methods which enable evaluating the model fragility with respect to quantitative performance measures and parameters such as reaction rate constants and initial conditions. The algorithm generates a small subset of parameters that can be used to act on complex networks and to obtain the desired behaviors. We have applied the proposed framework to the EGFR-IGF1R signal transduction network, a crucial pathway in lung cancer, as an example of Cancer Systems Biology application in drug discovery. Furthermore, we have tested our framework on a pulse generator network as an example of Synthetic Biology application, thus proving the suitability of our methodology to the characterization of the input/output synthetic circuits. Conclusions The achieved results are of immediate practical application in computational biology, and while we demonstrate their use in two specific examples, they can in fact be used to study a wider class of biological systems. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0216-5) contains supplementary material, which is available to authorized users.

The presence of mutations in the KRAS gene is a predictor of a poor clinical response to EGFR-targeted agents in patients affected by colorectal cancer (CRC), but its significance as a global prognostic factor remains unclear. The aim of the present study was to evaluate the impact of the KRAS mutational status on time to first metastasis (TTM) and overall survival (OS) in a cohort of Sardinian CRC patients. A total of 551 patients with metastatic CRC at the time of enrolment were included. Clinical and pathological features of the disease, including follow-up information, were obtained from medical records and cancer registry data. For mutational analysis formalin-fixed paraffin-embedded tissue samples were processed using a standard protocol. The coding sequence and splice junctions of exons 2 and 3 of the KRAS gene were screened for mutations by direct automated sequencing. Overall, 186 KRAS mutations were detected in 183/551 (33%) patients: 125 (67%) were located in codon 12, 36 (19%) in codon 13, and 18 (10%) in codon 61. The remaining mutations (7; 4%) were detected in uncommonly-affected codons. No significant correlation between KRAS mutations and gender, age, anatomical location and stage of the disease at the time of diagnosis was identified. Furthermore, no prognostic value of KRAS mutations was found considering either TTM or OS. When patients were stratified by KRAS mutational status and gender, males were significantly associated with a longer TTM. The results of the present study indicate that KRAS mutation correlated with a slower metastatic progression in males with CRC from Sardinia, irrespective of the age at diagnosis and the codon of the mutation.

Le neoplasie polmonari rappresentano la prima causa di morte per cancro al mondo; la loro incidenza e mortalità sono pressoché sovrapponibili ad indicare una scarsa curabilità di questo tipo di neoplasia. Nella maggior parte dei casi, si presentano alla diagnosi in stadio localmente avanzato o metastatico e pertanto non passibili di chirurgia. Circa l’80-85% di queste neoplasie rientrano nella categoria istologica “non a piccole cellule (NSCLC)”. Le neoplasie polmonari non a piccole cellule si presentano nel 50% dei casi in stadio avanzato alla diagnosi e, pertanto, trattabili con il solo trattamento medico. Negli ultimi anni sono aumentate le conoscenze circa la biologia del NSCLC che hanno portato a sviluppare nuove strategie terapeutiche, sia con nuovi farmaci chemioterapici sia con farmaci a target molecolare. Sebbene notevoli progressi siano stati fatti negli ultimi anni nel trattamento del NSCLC, questa malattia risulta ancora legata a cattiva prognosi nella maggior parte dei pazienti. Negli ultimi anni, in relazione al progressivo incremento delle conoscenze ed anche grazie all’introduzione delle terapie biologiche, sempre più si è andato ad affermando il concetto di personalizzazione del trattamento, secondo il quale una determinata terapia andrebbe somministrata ad un dato paziente a seconda delle caratteristiche specifiche della neoplasia di cui è affetto e delle caratteristiche proprie di quell’individuo. Nella pratica clinica, un dato schema terapeutico viene scelto tenendo conto di alcuni fattori come l’età, il performance status, la presenza di co-morbidità e valutando i profili di tossicità dei vari regimi, lontani quindi da una situazione di specifica individualizzazione. In quest’ottica, recenti evidenze suggeriscono la possibilità di individuare sottopopolazioni di pazienti che possono beneficiare di uno specifico trattamento rispetto ad altre. Proprio in questo ambito si inserisce il progetto che ho sviluppato in questi 4 anni, volto ad identificare fattori predittivi di risposta ai diversi tipi di trattamento (chemioterapico e biologico) impiegati nella terapia del NSCLC avanzato. Il mio progetto si è articolato in quattro sottoprogetti relativi a quattro differenti tipi di terapie impiegate nelle varie fasi del NSCLC avanzato. I quattro sottoprogetti sviluppati sono stati i seguenti: 1. Panel di marcatori molecolari predittivi nel trattamento con gefitinib di pazienti affetti da tumore polmonare non a piccole cellule in stadio avanzato; 2. Espressione immunoistochimica di ERCC1/BRCA1 e polimorfismi dei geni di riparo del DNA quali fattori predittivi nel trattamento chemioterapico a base di platino dei pazienti affetti da tumore polmonare non a piccole cellule in stadio avanzato; 3. Correlazione dei polimorfismi e della attività della citidina deaminasi con l’outcome dei pazienti affetti da carcinoma polmonare non a piccole cellule avanzato trattati con platino-gemcitabina; 4. Fattori biologici predittivi nel trattamento chemioterapico con pemetrexed nella neoplasia polmonare non a piccole cellule in stadio avanzato. Nel primo sottoprogetto è stato valutato il ruolo predittivo di un gruppo di marcatori molecolari comprendente le mutazioni dei geni codificanti per EGFR e per K-ras, l’amplificazione dei geni per EGFR ed HER2, l’espressione proteica della proteina EGFR ed i polimorfismi dell’introne 1 del gene EGFR, in 91 pazienti affetti da NSCLC in fase avanzata trattati con gefitinib, inibitore dell’attività tirosino-chinasica di EGFR. Il sesso (p = 0.005), lo stato di non fumatore (p = 0.010), la tossicità cutanea (p = 0.020), mutazioni del gene EGFR (p < 0.001) e la positività per EGFR FISH (p = 0.016) sono risultati associati alla risposta a gefitinib. La mutazione di K-ras è stata rilevata in soli 7 pazienti non-responder. La sopravvivenza mediana è stata di 10 mesi. Solo lo stato di non fumatore e il polimorfismo dell’introne 1 di EGFR hanno mostrato una correlazione statisticamente significativa con la sopravvivenza (p = 0.031 e 0.044, rispettivamente). In conclusione, abbiamo confermato il ruolo della mutazione del gene EGFR come fattore predittivo di risposta agli inibitori dell’attività tirosino-chinasica di EGFR. Inoltre, il numero di copie del gene EGFR e, potenzialmente, anche il polimorfismo dell’introne 1 di EGFR potrebbero aiutare a predire la responsività agli inibitori dell’attività tirosino-chinasica di EGFR nel NSCLC avanzato. Il secondo sottoprogetto è uno studio retrospettivo condotto su materiale istologico di archivio relativo a pazienti affetti da NSCLC in stadio IIIB-IV trattati in I linea all’interno del protocollo di chemioterapia FAST. Con tale studio si sono analizzati su 110 campioni tumorali fattori potenzialmente predittivi di risposta al cisplatino, quali l’espressione immunoistochimica di EGFR e BRCA1 e i polimorfismi di ERCC1, XPD, XRCC1 e 3. La casistica del protocollo FAST ha consentito valutare tali fattori in gruppo di pazienti che ha ricevuto chemioterapia a base di cisplatino ed in un gruppo che è stato trattato senza cisplatino. L’espressione immunoistochimica di ERCC1 e BRCA1 sono risultate positive in 58 e 56 pazienti, rispettivamente. Nel complesso, i pazienti ERCC1-negativi hanno mostrato un migliore tasso di risposta (p = 0.0015), più lunghe sopravvivenza libera da progressione (p = 0.023) e sopravvivenza globale (p = 0.012) rispetto a quelli positivi, con una interazione con il trattamento solo in termini di tasso di risposta (test di interazione, p = 0.076). Nel complesso, i pazienti BRCA1 positivi hanno mostrato un migliore outcome anche se in maniera non statisticamente significativa. I polimorfismi dei geni di riparo del DNA non hanno mostrato associazioni statisticamente significative con l’outcome dei pazienti. Questo studio dimostra il ruolo prognostico dell’espressione immunoistochimica ERCC1 in pazienti con NSCLC avanzato trattati con chemioterapia; tuttavia, l'espressione di ERCC1/BRCA1 e specifici polimorfismi dei geni di riparo del DNA non sembrano influenzare il beneficio clinico derivante dall’uso del cisplatino. La gemcitabina è un analogo della deossicitidina con provata attività nei confronti di un ampio spettro di tumori; la doppietta gemcitabina-cisplatino è uno dei regimi più ampiamente utilizzati nel trattamento del NSCLC in stadio avanzato. La citidina deaminasi (CDA) è il principale enzima inattivante di gemcitabina e il suo ruolo fondamentale nelle attività/tossicità della gemcitabina è stata dimostrata da diversi studi pre-clinici e clinici. L'obiettivo di questo terzo sottostudio è stato di valutare se tre polimorfismi a singolo nucleotide (SNP) nella regione codificante del CDA (CDA 79A>C, 208G>A, e CDA 435C>T) cosi come l’attività enzimatica potessero influenzare l’outcome di un gruppo di 126 pazienti con NSCLC trattati con chemioterapia a base di gemcitabina-platino. I pazienti con genotipi CDA A79A/A79C hanno mostrato un tempo alla progressione di malattia (6.0 vs 3.0 mesi, p = 0.001) e una sopravvivenza globale (11.0 vs 5.0 mesi, p = 0.001) significativamente più lunghi rispetto ai pazienti con genotipo C79C. I pazienti portatori dei genotipi CDA C435C/C435T hanno avuto una più lunga sopravvivenza globale (p = 0.025), ma non sono state osservate correlazioni con il tempo alla progressione di malattia. Al contrario, i pazienti con bassa attività CDA hanno mostrato un tasso di risposta (37.7% vs 13.8%, p = 0.006) e un beneficio clinico (91.8% vs 51.7%, p < 0.001) significativamente più alti, così come migliori tempo alla progressione (8.0 vs 3.0 mesi p < 0.001) e sopravvivenza globale (19.0 vs 6.0 mesi, p < 0.001). Inoltre, l'attività enzimatica è emerso come fattore indipendente del rischio di morte/progressione all'analisi multivariata. In conclusione, l'attività enzimatica di CDA sembra essere un fattore predittivo forte di attività e di efficacia di una chemioterapia a base di gemcitabina. Questo quarto sottostudio biologico rappresenta un’indagine di ricerca traslazionale condotta al fine di identificare gruppi di pazienti che presentano beneficio differente con trattamento a base di pemetrexed. E’ stato valutato il ruolo dei polimorfismi dei geni TS, MTHFR, RFC, GGH nel predire l’efficacia e la tossicità nei confronti del trattamento con pemetrexed in 208 pazienti affetti da NSCLC avanzato. Questo studio ha evidenziato una correlazione significativa fra l’allele MTHFR 677T e una maggiore sopravvivenza in pazienti trattati con pemetrexed. Tale differenza è risultata clinicamente rilevante dato che i pazienti con genotipo TT, che sono però solo il 17% della popolazione in studio, hanno mostrato sopravvivenze libera da progressione e globale quasi doppie rispetto ai pazienti con genotipo eterozigote o wild-type. In assenza di un gruppo di controllo non trattato con pemetrexed, non è possibile tuttavia definire il ruolo prognostico o predittivo del beneficio con pemetrexed di tale polimorfismo. In conclusione, questo progetto ha consentito di identificare alcuni fattori potenzialmente utili nel predire l’outcome dei pazienti con NSCLC avanzato. Le mutazioni di EGFR, come riscontrato anche nel primo sottostudio, rappresentano attualmente un fattore determinante nella scelta terapeutica del NSCLC. ERCC1 ha sicuramente un ruolo prognostico, come evidenziato nel secondo sottostudio, ma non può essere utilizzato come fattore predittivo nella comune pratica clinica. Visti gli interessanti risultati ottenuti, studi clinici prospettici dovrebbero essere condotti al fine di validare l’attività di CDA e il polimorfismo MTHFR 677T quali potenziali marcatori predittivi del trattamento con gemcitabina e pemetrexed rispettivamente nel NSCLC avanzato.

Malignant melanoma is an aggressive tumor of the skin with a poor prognosis for patients with advanced disease. It is resistant to current therapeutic approaches. In melanoma, both the Ras/Raf/MEK/ERK (MAPK) and the PI3K/AKT (AKT) signalling pathways are constitutively activated through multiple mechanisms. Mutations of BRAF have been proposed to contribute to melanoma development. Increased activity of the MAPK pathway prevents apoptosis and induces cell cycle progression. PTEN deletion results in Akt activation. Akt activation can result in the phosphorylation and inactivation of Raf. This decrease in downstream MEK and ERK activation may lead to loss of differentiation or senescence. This review summarizes the most relevant studies focused on the signalling pathways involved in melanomagenesis. New therapeutic strategies are also reported.

Standard treatment of cervical cancer (CC) consists of surgery in the early stages and of chemoradiation in locally advanced disease. Metastatic CC has a poor prognosis and is usually treated with palliative platinum-based chemotherapy. Current chemotherapeutic regimens are associated with significant adverse effects and only limited activity, making identification of active and tolerable novel targeted agents a high priority. Angiogenesis is a complex process that plays a crucial role in the development of many types of cancer. The dominant role of angiogenesis in CC seems to be directly related to human papillomavirus-related inhibition of p53 and stabilization of hypoxia-inducible factor-1α. Both of these mechanisms are able to increase expression of vascular endothelial growth factor (VEGF). Activation of VEGF promotes endothelial cell proliferation and migration, favoring formation of new blood vessels and increasing permeability of existing blood vessels. Since bevacizumab, a recombinant humanized monoclonal antibody binding to all isoforms of VEGF, has been demonstrated to significantly improve survival in gynecologic cancer, some recent clinical research has explored the possibility of using novel therapies directed toward inhibition of angiogenesis in CC too. Here we review the main results from studies concerning the use of antiangiogenic drugs that are being investigated for the treatment of CC.

Ovarian cancer is burdened by the highest mortality rate among gynecological cancers. Gold standard is represented by the association of platinum-taxane -based chemotherapy and radical surgery. Despite several adjustments occurred in cytotoxic drug in last decades, most patients continue to relapse, and no significant enhancement has been reached in the overall survival. The development of drug resistance and the recurrence of disease have prompted the investigations of other targets that can be used in the treatment of ovarian cancers. Among such targets, polyadenosine diphosphate-ribose polymerase (PARP) represents a novel way to target specific patways involved in tumor growth. PARP accelerates the reaction of the polyADP-ribosylation of proteins implicated in DNA repair. PARP inhibitors have shown activity in cancers with BRCA mutations, with other deficient DNA repair genes or signaling pathways that modulate DNA repair, or in association with DNA damaging agents not involved in DNA repair dysfunction. A number of inhibitors for PARP has been developed, and such drugs are under investigation in clinical trials to identify their impact in the treatment of ovarian cancers. This review aims to summarize the recent researches and clinical progress on PARP inhibitors as novel target agents in ovarian cancer.

// Lorenzo Tortolina 2,* , David J. Duffy 3,* , Massimo Maffei 1,* , Nicoletta Castagnino 1,* , Aimee M. Carmody 3,* , Walter Kolch 3 , Boris N. Kholodenko 3 , Cristina De Ambrosi 2 , Annalisa Barla 2 , Elia M. Biganzoli 4 , Alessio Nencioni 1,5 , Franco Patrone 1,5 , Alberto Ballestrero 1,5 , Gabriele Zoppoli 1,5 , Alessandro Verri 2 and Silvio Parodi 1 1 Department of Internal Medicine and Medical Specializations (DIMI), University of Genoa, Italy 2 Department of Informatics, Bioengineering, Robotics and Systems Engineering (DIBRIS), University of Genoa, Italy 3 Systems Biology Ireland, Conway Institute, University College Dublin, Belfield, Dublin, Ireland 4 Unit of Medical Statistics, Biometry and Bioinformatics “Giulio A. Maccacaro”, Department of Clinical Sciences and Community Health, University of Milan, Italy 5 Istituto a Carattere di Ricerca Clinic - Scientifico (IRCCS), Azienda Ospedaliera Universitaria San Martino, Istituto Nazionale Tumori (IST), Genoa, Italy * These authors contributed equally to this work Correspondence: Silvio Parodi, email: // Keywords : Colorectal cancer, Target therapies, Signaling-network, Dynamic modeling, Onco-protein inhibitors Received : December 17, 2014 Accepted : December 28, 2014 Published : December 31, 2014 Abstract The interconnected network of pathways downstream of the TGFβ, WNT and EGF-families of receptor ligands play an important role in colorectal cancer pathogenesis. We studied and implemented dynamic simulations of multiple downstream pathways and described the section of the signaling network considered as a Molecular Interaction Map (MIM). Our simulations used Ordinary Differential Equations (ODEs), which involved 447 reactants and their interactions. Starting from an initial “physiologic condition”, the model can be adapted to simulate individual pathologic cancer conditions implementing alterations/mutations in relevant onco-proteins. We verified some salient model predictions using the mutated colorectal cancer lines HCT116 and HT29. We measured the amount of MYC and CCND1 mRNAs and AKT and ERK phosphorylated proteins, in response to individual or combination onco-protein inhibitor treatments. Experimental and simulation results were well correlated. Recent independently published results were also predicted by our model. Even in the presence of an approximate and incomplete signaling network information, a predictive dynamic modeling seems already possible. An important long term road seems to be open and can be pursued further, by incremental steps, toward even larger and better parameterized MIMs. Personalized treatment strategies with rational associations of signaling-proteins inhibitors, could become a realistic goal.