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Supplemental Figures 1-8. Figure 1S: A) Nampt locus (human chromosome 7q22.3) copy number heatmap for lines included in the Cancer Cell Line Encyclopedia. B) mRNA Nampt expression plotted vs. DNA copy number (log2 ratio). Figure 2S: effect of APO866 combined plus FK506 on Mec.1 cell lines. Figure 3S: intracellular APO866 determination in primary B-CLL cell extract. Figure 4S: anti-tumor activity of APO866 combined with Pg-p inhibitors (CsA, Verapamil and Nilotinib) on primary B-CLL and AML cells. Figure 5S: effects of drugs combination on healthy PBPCs (A) and PBMCs (B) cells. Figure 6S: intracellular NAD+(H) and ATP levels measured in AML cells following drugs combination. Figure 7S: relative expression of WBs showed in Figure 6B. Figure 8S: effects of NA addition on anti-tumor activity of APO866 combined with PgP inhibitors and schematic representation of proposed model.

Two different perspectives are the main focus of this book chapter: (1) A perspective that looks to the future, with the goal of devising rational associations of targeted inhibitors against distinct altered signaling-network pathways. This goal implies a sufficiently in-depth molecular diagnosis of the personal cancer of a given patient. A sufficiently robust and extended dynamic modeling will suggest rational combinations of the abovementioned oncoprotein inhibitors. The work toward new selective drugs, in the field of medicinal chemistry, is very intensive. Rational associations of selective drug inhibitors will become progressively a more realistic goal within the next 3-5 years. Toward the possibility of an implementation in standard oncologic structures of technologically sufficiently advanced countries, new (legal) rules probably will have to be established through a consensus process, at the level of both diagnostic and therapeutic behaviors. (2) The cancer patient of today is not the patient of 5-10 years from now. How to support the choice of the most convenient (and already clinically allowed) treatment for an individual cancer patient, as of today? We will consider the present level of artificial intelligence (AI) sophistication and the continuous feeding, updating, and integration of cancer-related new data, in AI systems. We will also report briefly about one of the most important projects in this field: IBM Watson US Cancer Centers. Allowing for a temporal shift, in the long term the two perspectives should move in the same direction, with a necessary time lag between them.

Current colorectal cancer (CRC) treatment guidelines are primarily based on clinical features, such as cancer stage and grade. However, outcomes may be improved using molecular treatment guidelines. Potentially useful biomarkers include driver mutations and somatically inherited alterations, signaling proteins (their expression levels and (post) translational modifications), mRNAs, micro-RNAs and long noncoding RNAs. Moving to an integrated system is potentially very relevant. To implement such an integrated system: we focus on an important region of the signaling network, immediately above the G1-S restriction point, and discuss the reconstruction of a Molecular Interaction Map and interrogating it with a dynamic mathematical model. Extensive model pretraining achieved satisfactory, validated, performance. The model helps to propose future target combination priorities, and restricts drastically the number of drugs to be finally tested at a cellular, in vivo, and clinical-trial level. Our model allows for the inclusion of the unique molecular profiles of each individual patient's tumor. While existing clinical guidelines are well established, dynamic modeling may be used for future targeted combination therapies, which may progressively become part of clinical practice within the near future. WIREs Syst Biol Med 2016, 8:314-336. doi: 10.1002/wsbm.1342 For further resources related to this article, please visit the WIREs website.

Transcription factors (TFs) represent key regulators of gene-expression patterns controlling cell behavior. TFs are active at nuclear – chromatin levels. TFs do not act in isolation; small sets of TFs cooperate toward the transcription of sets of mRNAs and consequently the translation of new proteins (the molecular phenotypes of a cell). Most TFs are activated through a cascade of biochemical reactions mediated by receptors expressed on the target cell surface. Nuclear Receptors (NRs) are transcription factors activated instead by small hydrophobic molecules capable of crossing the plasma membrane. The convergence of different pathways on TFs and their posttranslational modifications ensure that the external stimuli generate appropriate and integrated responses. The reconstruction of the molecular anatomy of these pathways through Molecular Interactions Maps (MIMs) can depict these intricate interactions. A mathematical modeling approach simulates/mimics their mechanism of action in normal and pathological conditions. We can simulate the effect of virtual hits in neoplastic transformation as mutations/alterations in these pathways. We can also simulate the effect of targeted inhibitors on these deregulated pathways. This strategy can help to guide an appropriate combination of targeted drugs in the treatment of a cancer patient, a major innovative perspective of incoming years.

Abstract Purpose: The nicotinamide phosphoribosyltransferase (NAMPT) inhibitor, APO866, has been previously shown to have antileukemic activity in preclinical models, but its cytotoxicity in primary leukemia cells is frequently limited. The success of current antileukemic treatments is reduced by the occurrence of multidrug resistance, which, in turn, is mediated by membrane transport proteins, such as P-glycoprotein-1 (Pgp). Here, we evaluated the antileukemic effects of APO866 in combination with Pgp inhibitors and studied the mechanisms underlying the interaction between these two types of agents. Experimental Design: The effects of APO866 with or without Pgp inhibitors were tested on the viability of leukemia cell lines, primary leukemia cells (AML, n = 6; B-CLL, n = 19), and healthy leukocytes. Intracellular nicotinamide adenine dinucleotide (NAD+) and ATP levels, mitochondrial transmembrane potential (ΔΨm), markers of apoptosis and of endoplasmic reticulum (ER) stress were evaluated. Results: The combination of APO866 with Pgp inhibitors resulted in a synergistic cytotoxic effect in leukemia cells, while sparing normal CD34+ progenitor cells and peripheral blood mononuclear cells. Combining Pgp inhibitors with APO866 led to increased intracellular APO866 levels, compounded NAD+ and ATP shortage, and induced ΔΨm dissipation. Notably, APO866, Pgp inhibitors and, to a much higher extent, their combination induced ER stress and ER stress inhibition strongly reduced the activity of these treatments. Conclusions: APO866 and Pgp inhibitors show a strong synergistic cooperation in leukemia cells, including acute myelogenous leukemia (AML) and B-cell chronic lymphocytic leukemia (B-CLL) samples. Further evaluations of the combination of these agents in clinical setting should be considered. Clin Cancer Res; 21(17); 3934–45. ©2015 AACR.

AIM:The aim of present study was to investigate the feasibility of a densified sequence of FEC75 (5-fluorouracil 600 mg/m2, epirubicin 75 mg/m2, cyclophosphamide 600 mg/m2) and docetaxel 100 mg/m2 (D100) in patients with primary operable high-risk breast cancer.METHODS:Fifty-one consecutive patients with resectable breast cancer and 4 or more positive axillary lymph nodes were enrolled. After a common regimen of 4 cycles of FEC75 given every 14 days, patients received 4 cycles of D100 every 14 days. Prophylactic granulocyte colony-stimulating factor was administered subcutaneously at 5 mg/kg daily from days 5 to 10 to each patient.RESULTS:The primary endpoint was the proportion of subjects receiving at least 85% of the relative dose intensity (rDI) both in the FEC and docetaxel parts of the regimen. In view of the high percentage of grade 3-4 skin toxicity (32%) observed in the first 25 patients (Group A) during D100 treatment, it was decided to continue the study using a docetaxel dose reduced by 15% (85 mg/m2; D85). This second group of 26 patients was defined as Group B. Of the total 51 patients, 38 (75%) received docetaxel rDI ≥85%, 23/26 patients (88.5%) and 15/25 patients (60.0%) in Group B and Group A, respectively. The observed grade 3-4 hematological and nonhematological toxicities were in line with data from the literature. The only significant difference was the higher percentage of grade 3-4 skin toxicity experienced with D100.CONCLUSION:This study failed to demonstrate the feasibility of a dose-dense FEC-D regimen with docetaxel 100 mg/m2. Docetaxel 85 mg/m2 seems to allow a higher rDI than docetaxel 100 mg/m2 but this should be confirmed in a larger cohort of patients.

Acute myeloid leukemia (AML) is the most common form of acute leukemia affecting adults. Although it is a complex disease driven by numerous genetic and epigenetic abnormalities, nearly 50% of patients exhibit a normal karyotype (CN-AML) with an intermediate cytogenetic risk. However, a widespread genomic analysis has recently shown the recurrence of genomic aberrations in this category (mutations of FLT3, CEBPA, NPM1, RUNX1, TET2, IDH1/2, DNMT3A, ASXL1, MLL and WT1) thus revealing its marked genomic heterogeneity. In this perspective, a global gene expression analysis of AML patients provides an independent prognostic marker to categorize each patient into clinic-pathologic subgroups based on its molecular genetic defects. Consistently such classification, taking into account the uniqueness of each AML patient, furnishes an individualized treatment approach leading a step closer to personalized medicine. Overall the genome-wide analysis of AML patients, by providing novel insights into biology of this tumor, furnishes accurate prognostic markers as well as useful tools for selecting the most appropriate treatment option. Moreover it provides novel therapeutic targets useful to enhance efficacy of the current anti-AML therapeutics. Here we describe the prognostic relevance of such new genetic data and discuss how this approach can be used to improve survival and treatment of AML patients.

SummaryPharmacological treatments targeting CXC chemokines and the associated neutrophil activation and recruitment into atherosclerotic plaques hold promise for treating cardiovascular disorders. Therefore, we investigated whether FK866, a nicotinamide phosphoribosyltransferase (NAMPT) inhibitor with anti-inflammatory properties that we recently found to reduce neutrophil recruitment into the ischaemic myocardium, would exert beneficial effects in a mouse atherosclerosis model. Atherosclerotic plaque formation was induced by carotid cast implantation in ApoE-/- mice that were fed with a Western-type diet. FK866 or vehicle were administrated intraperitoneally from week 8 until week 11 of the diet. Treatment with FK866 reduced neutrophil infiltration and MMP-9 content and increased collagen levels in atherosclerotic plaques compared to vehicle. No effect on other histological parameters, including intraplaque lipids or macrophages, was observed. These findings were associated with a reduction in both systemic and intraplaque CXCL1 levels in FK866-treated mice. In vitro, FK866 did not affect MMP-9 release by neutrophils, but it strongly reduced CXCL1 production by endothelial cells which, in the in vivo model, were identified as a main CXCL1 source at the plaque level. CXCL1 synthesis inhibition by FK866 appears to reflect interference with nuclear factor-κB signalling as shown by reduced p65 nuclear levels in endothelial cells pre-treated with FK866. In conclusion, pharmacological inhibition of NAMPT activity mitigates inflammation in atherosclerotic plaques by reducing CXCL1-mediated activities on neutrophils. These results support further assessments of NAMPT inhibitors for the potential prevention of plaque vulnerability.

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.

e13511 Background: The ALK inhibitor crizotinib is the standard of care of patients with ALK+, advanced NSCLC. However, its clinical benefit is limited by the development of resistance. Cycles of fasting enhance the activity of chemo-radiotherapy in preclinical cancer models and dietary approaches based on fasting are explored in oncological clinical trials. Whether combining fasting with molecularly targeted agents, such as crizotinib, is going to be potentially beneficial remains unknown. Methods: H3122 (ALK+) NSCLC cells were treated in vitro with crizotinib (80-400 nM) in regular culture conditions or in fasting-mimicking conditions (FMCs: 1% FBS, 0.5g/L glucose). Viability was assessed in sulforodhamine B assays. P-Erk and total Erk levels were assessed by WB. H3122 cells were engineered to overexpress HRAS, HRASV12 or a control plasmid. Subcutaneous H3122 xenografts were established in nude mice. Mice were given 25 mg/kg crizotinib (or vehicle) daily for five days a week (Mon-Fri) for a total of three weeks. Fasting cycles of two days (water only; Sun, Mon) were done in animals treated with crizotinib or with vehicle. Tumor size and mouse weight were monitored daily. Results: In vitro, FMCs synergistically increased the activity of crizotinib in H3122 cells. Crizotinib administration in FMCs inhibited Erk activation to a higher extent compared to its administratin in standard conditions. HRAS or HRASV12 overexpression induced resistance to crizotinib, FMCs or their combination, consistent with inhibition of the MAPK pathway playing a key role in the anticancer activity of these treatments. Both fasting cycles and crizotinib effectively reduced the growth of H3122 xenografts in vivo with no difference in terms of efficacy between the two approaches. The combination crizotinib+fasting was more active than either type of treatment alone (p<0.05). Fasted mice exhibited transient weight losses, but fully recovered their weight between one cycle and the next. Conclusions: In an ALK+ NSCLC model, fasting cycles have similar anticancer activity compared to crizotinib and potentiate its activity when used in combination. Fasting cycles (or fasting-mimicking diets) could improve the efficacy of crizotinib in suitable patients.

Multiple Myeloma (MM) is a common hematologic malignancy of plasma cells representing an excellent model of epigenomics dysregulation in human disease. Importantly, these findings, in addition to providing a better understanding of the underlying molecular changes leading to this malignance, furnish the basis for an innovative therapeutic approach. Histone deacetylase inhibitors (HDACIs), including Vorinostat and Panobinostat, represent a novel class of drugs targeting enzymes involved in epigenetic regulation of gene expression, which have been evaluated also for the treatment of multiple myeloma. Although the clinical role in this setting is evolving and their precise utility remains to be determined, to date that single-agent anti-MM activity is modest. More importantly, HDACIs appear to be synergistic both in vitro and in vivo when combined with other anti-MM agents, mainly proteasome inhibitors including bortezomib. The molecular basis underlying this synergism seems to be multifactorial and involves interference with protein degradation as well as the interaction of myeloma cells with microenvironment. Here we review molecular events underling antitumor effects of HDACIs and the most recent results of clinical trials in relapsed and refractory MM.

Over the past decades the prognosis of patients with Chronic Myeloid Leukemia (CML) has radically changed due to groundbreaking scientific and translational studies that have revealed the biologic basis of such a hematologic malignancy. These studies have led to the rapid development of many BCR-ABL specific tyrosine kinase inhibitors (TKIs), such as Imatinib, Nilotinib and Dasatinib, which have improved 10-years survival to more than 80%. Although these therapies represent a landmark step in the race for the cure of CML, they did not change the progression in advanced phase of disease. Therefore unravel the molecular mechanisms and the biological basis of CML, especially during the advanced stage, is of seminal importance as this would result in the design of more effective and less toxic therapies. In such a scenario, several novel drugs designed to specifically target biological features of CML cells are currently in clinical trials with promising results that would provide not only improve the therapeutic armamentarium but also to overcome drug resistance of this tumor. Here we review recent advances in biology of CML and their therapeutic implications.

We recently demonstrated that Nicotinamide phosphoribosyltransferase (Nampt) inhibition depletes intracellular NAD⁺ content leading, to autophagic multiple myeloma (MM) cell death. Bortezomib has remarkably improved MM patient outcome, but dose-limiting toxicities and development of resistance limit its long-term utility. Here we observed higher Nampt messenger RNA levels in bortezomib-resistant patient MM cells, which correlated with decreased overall survival. We demonstrated that combining the NAD⁺ depleting agent FK866 with bortezomib induces synergistic anti-MM cell death and overcomes bortezomib resistance. This effect is associated with (1) activation of caspase-8, caspase-9, caspase-3, poly (ADP-ribose) polymerase, and downregulation of Mcl-1; (2) enhanced intracellular NAD⁺ depletion; (3) inhibition of chymotrypsin-like, caspase-like, and trypsin-like proteasome activities; (4) inhibition of nuclear factor κB signaling; and (5) inhibition of angiogenesis. Furthermore, Nampt knockdown significantly enhances the anti-MM effect of bortezomib, which can be rescued by ectopically overexpressing Nampt. In a murine xenograft MM model, low-dose combination FK866 and Bortezomib is well tolerated, significantly inhibits tumor growth, and prolongs host survival. Taken together, these findings indicate that intracellular NAD⁺ level represents a major determinant in the ability of bortezomib to induce apoptosis in MM cells and provide proof of concept for the combination with FK866 as a new strategy to enhance sensitivity or overcome resistance to bortezomib.

We started offering an introduction to very basic aspects of molecular biology, for the reader coming from computer sciences, information technology, mathematics. Similarly we offered a minimum of information about pathways and networks in graph theory, for a reader coming from the biomedical sector. At the crossover about the two different types of expertise, we offered some definition about Systems Biology. The core of the article deals with a Molecular Interaction Map (MIM), a network of biochemical interactions involved in a small signaling-network sub-region relevant in breast cancer. We explored robustness/sensitivity to random perturbations. It turns out that our MIM is a non-isomorphic directed graph. For non physiological directions of propagation of the signal the network is quite resistant to perturbations. The opposite happens for biologically significant directions of signal propagation. In these cases we can have no signal attenuation, and even signal amplification. Signal propagation along a given pathway is highly unidirectional, with the exception of signal-feedbacks, that again have a specific biological role and significance. In conclusion, even a relatively small network like our present MIM reveals the preponderance of specific biological functions over unspecific isomorphic behaviors. This is perhaps the consequence of hundreds of millions of years of biological evolution.

Autophagy is a cell recycling process the molecular apparatus of which has been identified over the past decade. Autophagy allows cells to survive starvation and inhospitable conditions and plays a key role in numerous physiological functions, including hematopoiesis and immune responses. In hematologic malignancies, autophagy can either act as a chemo-resistance mechanism or have tumor suppressive functions, depending on the context. In addition, autophagy is involved in other important aspects of blood cancers as it promotes immune competence and anticancer immunity, and may even help enhance patient tolerance to standard treatments. Approaches exploiting autophagy, either to activate or inhibit it, could find broad application in hematologic malignancies and contribute to improved clinical outcomes. These aspects are discussed here together with a brief introduction to the molecular machinery of autophagy and to its role in blood cell physiology.

Abstract Background: Immunohistochemistry (IHC) and fluorescence-in-situ hybridization (FISH) are the standard methods to assess human epidermal growth factor receptor 2 (HER-2) status in breast cancer (BC) patients. Real-time quantitative polymerase-chain-reaction (Q-PCR) and quantitative reverse transcriptase PCR (qRT-PCR) allow quantitative determination of gene copy number and gene expression on, respectively, DNA and RNA. These molecular methods are available to assess HER-2 amplification/overexpression but their use remains controversial. Here we performed a parallel comparison of these four methods to define their concordance rates and evaluate their relative role in HER-2 status determination. Patients and Methods: HER-2 status was determined by IHC, FISH, Q-PCR and qRT-PCR in a retrospectively assessed cohort of 130 BC patients. The studied set was enriched in cases scoring as 3+ by standard IHC analysis. Tests were performed blindly in parallel. Western blotting was performed on a subset of equivocal cases. Kappa statistics and ROC curves were used as appropriate, and concordance analyses were interpreted according to the ASCO/CAP guidelines. Results: Of the 130 enrolled patients, 47 (36%) were classified as positive and 27 (21%) as equivocal by IHC. With FISH, 50 patients (38%) were HER-2 amplified, while 80 (62%) were not. The overall agreement between FISH and Q-PCR was 98.5% (95% CI, 94.6% to 99.6%) with a k value of 0.97 (95% CI, 0.92 to 1). Assuming FISH as the standard reference, Q-PCR showed a sensitivity of 98% (95% CI, 89.5% to 99.6%) and a specificity of 98.8% (95% CI, 93.3% to 99.8%), with a global accuracy of 98%. The overall agreement between FISH and qRT-PCR was 96.9% (95% CI, 92.3% to 98.8%) with a k value of 0.94 (95% CI, 0.87 to 1). For both comparisons, the observed concordance values were greater than the 95% threshold required by the ASCO/CAP guidelines to validate novel approaches for HER-2 testing. 3% of samples showed HER-2 overexpression only by qRT-PCR analysis, in all cases belonging to the equivocal range as defined by either IHC or FISH. In these patients, WB confirmed higher HER-2 protein levels compared to healthy diploid controls. Conclusions: The high concordance between FISH and both Q-PCR and qRT-PCR supports the use of molecular tests as an alternative to current standard methods. Present results also suggest that qRT-PCR may be able to unequivocally classify patients belonging to the IHC/FISH equivocal range. Non-amplified HER-2 overexpressing BCs may account for the rare trastuzumab-responders observed in phase III trials, where trastuzumab response was assessed in HER-2-amplified vs. non-amplified cases. Citation Format: Gabriele Zoppoli, Anna Garuti, Ilaria Rocco, Claudia Palermo, Gabriella Cirmena, Enrico Carminati, Daniele Friedman, Ludovica Verdun di Cantogno, Anna Sapino, Franco Patrone, Alberto Ballestrero. Agreement of immunohistochemistry, fluorescence in situ hybridization, real-time quantitative polymerase-chain reaction, and quantitative reverse transcriptase PCR for Her-2/Neu status assessment in breast cancer patients: a single center, retrospective m [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 49. doi:10.1158/1538-7445.AM2013-49