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1.
Wiley Interdiscip Rev Syst Biol Med ; 8(4): 314-36, 2016 07.
Article in English | MEDLINE | ID: mdl-27240214

ABSTRACT

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.


Subject(s)
Colorectal Neoplasms/therapy , Models, Theoretical , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Cell Cycle Checkpoints , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Humans , MicroRNAs/metabolism , Polymorphism, Single Nucleotide , Practice Guidelines as Topic , RNA, Messenger/metabolism
2.
Methods Mol Biol ; 1386: 181-219, 2016.
Article in English | MEDLINE | ID: mdl-26677185

ABSTRACT

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.


Subject(s)
Decision Support Systems, Clinical , Medical Oncology , Models, Biological , Neoplasms , Signal Transduction , Systems Biology , Computational Biology/methods , Computer Simulation , Databases, Genetic , Humans , Medical Oncology/methods , Neoplasms/etiology , Neoplasms/metabolism , Neoplasms/therapy , Precision Medicine/methods , Research Design , Systems Biology/methods
3.
Clin Cancer Res ; 21(17): 3934-45, 2015 Sep 01.
Article in English | MEDLINE | ID: mdl-25964294

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 (ΔΨ(m)), 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 ΔΨ(m) 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.


Subject(s)
Acrylamides/pharmacology , Antineoplastic Agents/pharmacology , Cyclosporine/pharmacology , Endoplasmic Reticulum Stress/drug effects , Leukemia/metabolism , Mitochondria/drug effects , Mitochondria/metabolism , Piperidines/pharmacology , ATP Binding Cassette Transporter, Subfamily B/antagonists & inhibitors , ATP Binding Cassette Transporter, Subfamily B/metabolism , Adenosine Triphosphate/metabolism , Aged , Apoptosis/drug effects , Cell Line, Tumor , Cell Survival/drug effects , Chromosome Aberrations , Drug Resistance, Neoplasm , Drug Synergism , Female , Gene Expression , Humans , Immunoglobulin Heavy Chains/genetics , Leukemia/genetics , Leukemia/mortality , Leukemia/pathology , Male , Membrane Potential, Mitochondrial/drug effects , Middle Aged , Mutation , NAD/metabolism , Neoplasm Staging , Niacin/pharmacology , Niacinamide/pharmacology , Nicotinamide Phosphoribosyltransferase/antagonists & inhibitors , Nicotinamide Phosphoribosyltransferase/genetics , Nicotinamide Phosphoribosyltransferase/metabolism , Primary Cell Culture , Prognosis , Tumor Cells, Cultured , Unfolded Protein Response/drug effects
4.
Oncotarget ; 6(7): 5041-58, 2015 Mar 10.
Article in English | MEDLINE | ID: mdl-25671297

ABSTRACT

The interconnected network of pathways downstream of the TGFß, 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.


Subject(s)
Colorectal Neoplasms/drug therapy , Colorectal Neoplasms/metabolism , Models, Biological , Neoplasm Proteins/metabolism , Cell Line, Tumor , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Epidermal Growth Factor/genetics , Epidermal Growth Factor/metabolism , G1 Phase/physiology , HCT116 Cells , HT29 Cells , Humans , Molecular Targeted Therapy , Neoplasm Proteins/genetics , Resting Phase, Cell Cycle/physiology , Transforming Growth Factor beta/genetics , Transforming Growth Factor beta/metabolism , Wnt Signaling Pathway/drug effects , Wnt Signaling Pathway/physiology
5.
Tumori ; 100(2): 128-35, 2014.
Article in English | MEDLINE | ID: mdl-24852855

ABSTRACT

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.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Breast Neoplasms/drug therapy , Carcinoma/drug therapy , Lymph Node Excision , Lymph Nodes/pathology , Mastectomy , Adult , Aged , Antineoplastic Combined Chemotherapy Protocols/administration & dosage , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Axilla , Biomarkers, Tumor/analysis , Breast Neoplasms/surgery , Carcinoma/surgery , Chemotherapy, Adjuvant , Cyclophosphamide/administration & dosage , Docetaxel , Drug Administration Schedule , Epirubicin/administration & dosage , Feasibility Studies , Female , Fluorouracil/administration & dosage , Granulocyte Colony-Stimulating Factor/therapeutic use , Humans , In Situ Hybridization, Fluorescence , Italy , Lymph Nodes/surgery , Lymphatic Metastasis , Mastectomy/methods , Middle Aged , Neoplasm Staging , Receptor, ErbB-2/analysis , Taxoids/administration & dosage , Treatment Outcome
6.
Leuk Res ; 38(6): 649-59, 2014 Jun.
Article in English | MEDLINE | ID: mdl-24726781

ABSTRACT

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.


Subject(s)
Leukemia, Myeloid, Acute/genetics , Leukemia, Myeloid, Acute/therapy , Mutation , CCAAT-Enhancer-Binding Proteins/genetics , DNA (Cytosine-5-)-Methyltransferases/genetics , DNA Methyltransferase 3A , DNA-Binding Proteins/genetics , Dioxygenases , Genotype , Humans , Leukemia, Myeloid, Acute/mortality , Nuclear Proteins/genetics , Nucleophosmin , Prognosis , Proto-Oncogene Proteins/genetics , WT1 Proteins/genetics , fms-Like Tyrosine Kinase 3/genetics
7.
Thromb Haemost ; 111(2): 308-22, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24196571

ABSTRACT

Pharmacological 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.


Subject(s)
Acrylamides/pharmacology , Anti-Inflammatory Agents/pharmacology , Atherosclerosis/drug therapy , Carotid Arteries/drug effects , Carotid Artery Diseases/drug therapy , Chemokine CXCL1/metabolism , Cytokines/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Neutrophil Infiltration/drug effects , Nicotinamide Phosphoribosyltransferase/antagonists & inhibitors , Piperidines/pharmacology , Plaque, Atherosclerotic , Animals , Apolipoproteins E/deficiency , Apolipoproteins E/genetics , Atherosclerosis/enzymology , Atherosclerosis/genetics , Atherosclerosis/immunology , Atherosclerosis/pathology , Carotid Arteries/enzymology , Carotid Arteries/immunology , Carotid Arteries/pathology , Carotid Artery Diseases/enzymology , Carotid Artery Diseases/genetics , Carotid Artery Diseases/immunology , Carotid Artery Diseases/pathology , Cells, Cultured , Collagen/metabolism , Cytokines/metabolism , Diet, High-Fat , Disease Models, Animal , Human Umbilical Vein Endothelial Cells/drug effects , Human Umbilical Vein Endothelial Cells/enzymology , Human Umbilical Vein Endothelial Cells/immunology , Humans , Matrix Metalloproteinase 9/metabolism , Mice , Mice, Inbred C57BL , Mice, Knockout , Nicotinamide Phosphoribosyltransferase/metabolism , Signal Transduction/drug effects , Time Factors , Transcription Factor RelA/metabolism
8.
Haematologica ; 98(9): 1335-43, 2013 Sep.
Article in English | MEDLINE | ID: mdl-24006406

ABSTRACT

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 anti-cancer 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.


Subject(s)
Autophagy/physiology , Hematologic Neoplasms/metabolism , Hematologic Neoplasms/therapy , Animals , Clinical Trials as Topic/methods , Hematologic Neoplasms/diagnosis , Humans , Signal Transduction/physiology
10.
Curr Cancer Drug Targets ; 13(7): 711-23, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23906052

ABSTRACT

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.


Subject(s)
Antineoplastic Agents/therapeutic use , Drug Design , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Molecular Targeted Therapy , Protein Kinase Inhibitors/therapeutic use , Animals , Antineoplastic Agents/adverse effects , Antineoplastic Agents/chemistry , Disease Progression , Drug Resistance, Neoplasm , Fusion Proteins, bcr-abl/antagonists & inhibitors , Fusion Proteins, bcr-abl/genetics , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology , Neoplastic Stem Cells/drug effects , Neoplastic Stem Cells/enzymology , Neoplastic Stem Cells/pathology , Protein Kinase Inhibitors/adverse effects , Protein Kinase Inhibitors/chemistry , Signal Transduction/drug effects , Treatment Outcome
11.
Curr Cancer Drug Targets ; 13(7): 779-90, 2013 Sep.
Article in English | MEDLINE | ID: mdl-23906053

ABSTRACT

Chronic myeloid leukemia (CML) is a hematological disease accounting for about 15-20% of all adult leukemias. The clinical and biologic advances achieved in such a malignancy, represent one of the best successes obtained by translational medicine. Indeed, identification of the fusion oncogene BCR-ABL has allowed using of small molecule inhibitors of its tyrosine kinase activity which, in turn, have literally revolutionized the treatment of CML. Importantly the successfully clinical management was also realized on appropriate diagnosis, disease monitoring as well as early identification of such mutations causing drug resistance. Notably the recent availability of refined laboratory equipments represented by the Next Generation Sequencing (NGS) and genomic analyses has further contributed to gain ground towards the cure of this tumor. These issues are discussed here together with an overview on how patients treated with tyrosine kinase inhibitors should be monitored.


Subject(s)
Antineoplastic Agents/therapeutic use , Fusion Proteins, bcr-abl/antagonists & inhibitors , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Protein Kinase Inhibitors/therapeutic use , Animals , DNA Mutational Analysis , Drug Monitoring , Fusion Proteins, bcr-abl/genetics , Fusion Proteins, bcr-abl/metabolism , Genetic Testing , Genomics/methods , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/enzymology , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology , Molecular Diagnostic Techniques , Molecular Targeted Therapy , Mutation , Patient Selection , Precision Medicine , Predictive Value of Tests , Signal Transduction/drug effects , Treatment Outcome
12.
Blood ; 122(7): 1243-55, 2013 Aug 15.
Article in English | MEDLINE | ID: mdl-23823317

ABSTRACT

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.


Subject(s)
Antineoplastic Agents/pharmacology , Boronic Acids/pharmacology , Multiple Myeloma/drug therapy , NAD/metabolism , Neoplasm Recurrence, Local/drug therapy , Nicotinamide Phosphoribosyltransferase/metabolism , Pyrazines/pharmacology , Acrylamides/pharmacology , Animals , Antineoplastic Combined Chemotherapy Protocols , Apoptosis/drug effects , Autophagy/drug effects , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Blotting, Western , Bortezomib , Case-Control Studies , Caspases/genetics , Caspases/metabolism , Cell Proliferation/drug effects , Drug Synergism , Female , Fluorescent Antibody Technique , Gene Expression Profiling , Humans , Male , Mice , Mice, SCID , Multiple Myeloma/metabolism , Multiple Myeloma/mortality , NF-kappa B/genetics , NF-kappa B/metabolism , Neoplasm Recurrence, Local/metabolism , Neoplasm Recurrence, Local/mortality , Nicotinamide Phosphoribosyltransferase/antagonists & inhibitors , Nicotinamide Phosphoribosyltransferase/genetics , Oligonucleotide Array Sequence Analysis , Piperidines/pharmacology , Poly(ADP-ribose) Polymerases/genetics , Poly(ADP-ribose) Polymerases/metabolism , Prognosis , RNA, Messenger/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , Survival Rate , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
13.
Math Biosci Eng ; 10(1): 103-20, 2013 Feb.
Article in English | MEDLINE | ID: mdl-23311364

ABSTRACT

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 bio-medical 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.


Subject(s)
Breast Neoplasms/pathology , Signal Transduction/physiology , Systems Biology/methods , Breast Neoplasms/metabolism , Computer Simulation , ErbB Receptors/metabolism , Extracellular Signal-Regulated MAP Kinases/metabolism , Female , Gene Expression Regulation , Humans , MAP Kinase Signaling System , Mathematics , Models, Biological , Nucleic Acids/metabolism , Proteins/physiology , Software , beta Catenin/metabolism
14.
Leuk Lymphoma ; 54(2): 342-52, 2013 Feb.
Article in English | MEDLINE | ID: mdl-22762548

ABSTRACT

Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder characterized by the expansion of a leukemic stem cell (LSC) clone, carrying a Philadelphia translocation, able to overcome the non-malignant hematopoietic stem cells. The tyrosine kinase inhibitors (TKIs) imatinib, nilotinib and dasatinib are gold-standard for CML treatment. Each shows an impressive rate of complete cytogenetic response in chronic phase (CP)-CML. However, relapse and treatment failure are major problems with long-term use of TKIs. A polymerase chain reaction (PCR) assay to detect the mRNA expression of BCR-ABL1 represents the main molecular approach to monitoring response to treatment. However, using this analysis it is currently not possible to prospectively identify patients whose disease will relapse due to LSC reappearance. The aim of our study was to investigate whether the mRNA expression analysis of two Hedgehog (Hh) stemness signaling molecules, Smoothened (SMO) and Patched-1 (PTCH1), could predict upcoming molecular relapse. At the time of diagnosis, patients with high Sokal risk (n = 12) showed higher and lower levels of SMO and PTCH1, respectively (p = 0.0132), compared with patients with different Sokal scores (p = 0.0316 for intermediate risk and p = 0.0340 for low risk). These data suggest that Hh signaling was functionally more active in this risk group at the time of diagnosis. Furthermore, the kinetics of Hh signaling activity during the individual medical history correlated with BCR-ABL1 mRNA level and with upcoming molecular relapse. Also, mutation analysis of BCR-ABL1 revealed that activation of Hh signaling precedes molecular relapse by several months, mostly in patients carrying the gatekeeper mutation T315I. Importantly, in vitro data showed a synergistic effect of chemical inhibitors of Hh signaling and TKIs in both wild-type and resistant (T315I) CML cell lines. Collectively our data show that monitoring Hh pathway activity contemporaneously with BCR-ABL1 mRNA level may improve the chance of early detection of patients who will experience a relapse (mainly in the high Sokal risk group), paving the way for an innovative management of this hematologic malignancy.


Subject(s)
Antineoplastic Agents/pharmacology , Hedgehog Proteins/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology , Protein Kinase Inhibitors/pharmacology , Signal Transduction/drug effects , Adult , Aged , Aged, 80 and over , Antineoplastic Agents/therapeutic use , Antineoplastic Agents/toxicity , Cell Line, Tumor , Female , Fusion Proteins, bcr-abl/genetics , Gene Expression Regulation, Leukemic , Humans , Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy , Leukocytes, Mononuclear/metabolism , Leukocytes, Mononuclear/pathology , Male , Middle Aged , Mutation , Patched Receptors , Patched-1 Receptor , Protein Kinase Inhibitors/therapeutic use , Protein Kinase Inhibitors/toxicity , Receptors, Cell Surface/genetics , Receptors, G-Protein-Coupled/genetics , Recurrence , Smoothened Receptor , Treatment Outcome , Young Adult
15.
Antioxid Redox Signal ; 18(6): 630-41, 2013 Feb 20.
Article in English | MEDLINE | ID: mdl-22452634

ABSTRACT

AIMS: Nicotinamide phosphoribosyltransferase (Nampt) is a key enzyme for nicotinamide adenine dinucleotide (NAD(+)) biosynthesis, and recent evidence indicates its role in inflammatory processes. Here, we investigated the potential effects of pharmacological Nampt inhibition with FK866 in a mouse myocardial ischemia/reperfusion model. In vivo and ex vivo mouse myocardial ischemia/reperfusion procedures were performed. RESULTS: Treatment with FK866 reduced myocardial infarct size, neutrophil infiltration, and reactive oxygen species (ROS) generation within infarcted hearts in vivo in a mouse model of ischemia and reperfusion. The benefit of FK866 was not shown in the Langendorff model (ex vivo model of working heart without circulating leukocytes), suggesting a direct involvement of these cells in cardiac injury. Sera from FK866-treated mice showed reduced circulating levels of the neutrophil chemoattractant CXCL2 and impaired capacity to prime migration of these cells in vitro. The release of CXCL8 (human homolog of murine chemokine CXCL2) by human peripheral blood mononuclear cells (PBMCs) and Jurkat cells was also reduced by FK866, as well as by sirtuin (SIRT) inhibitors and SIRT6 silencing, implying a pivotal role for this NAD(+)-dependent deacetylase in the production of this chemokine. INNOVATION: The pharmacological inhibition of Nampt might represent an effective approach to reduce neutrophilic inflammation- and oxidative stress-mediated tissue damage in early phases of reperfusion after a myocardial infarction. CONCLUSIONS: Nampt inhibition appears as a new strategy to dampen CXCL2-induced neutrophil recruitment and thereby reduce neutrophil-mediated tissue injury in mice.


Subject(s)
Acrylamides/administration & dosage , Myocardial Infarction , Neutrophil Infiltration/drug effects , Nicotinamide Phosphoribosyltransferase , Piperidines/administration & dosage , Animals , Chemokine CXCL2/metabolism , Humans , Male , Mice , Myocardial Infarction/drug therapy , Myocardial Infarction/enzymology , Myocardial Infarction/pathology , Myocardial Reperfusion Injury/drug therapy , Myocardial Reperfusion Injury/pathology , NAD/biosynthesis , Nicotinamide Phosphoribosyltransferase/antagonists & inhibitors , Nicotinamide Phosphoribosyltransferase/metabolism , Oxidative Stress/drug effects , Reactive Oxygen Species/metabolism , Signal Transduction
16.
Autophagy ; 9(3): 410-2, 2013 Mar.
Article in English | MEDLINE | ID: mdl-23221771

ABSTRACT

Multiple myeloma (MM) is a clonal B-cell malignancy characterized by the proliferation of plasma cells in the bone marrow. Despite recent therapeutic advances, MM remains an incurable disease. Therefore, research has focused on defining new aspects in MM biology that can be therapeutically targeted. Compelling evidence suggests that malignant cells have a higher nicotinamide adenine dinucleotide (NAD+) turnover rate than normal cells, suggesting that this biosynthetic pathway represents an attractive target for cancer treatment. We recently reported that an intracellular NAD(+)-depleting agent, FK866, exerts its anti-MM effect by triggering autophagic cell death via transcriptional-dependent (transcription factor EB, TFEB) and -independent (PI3K-MTORC1) mechanisms. Our findings link intracellular NAD(+) levels to autophagy in MM cells, providing the rationale for novel targeted therapies in MM.


Subject(s)
Autophagy/physiology , Multiple Myeloma/metabolism , NAD/metabolism , Acrylamides/pharmacology , Apoptosis , Cell Death , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Gene Transfer Techniques , Humans , Lentivirus/genetics , Multiple Myeloma/pathology , Piperidines/pharmacology , Transcription, Genetic
17.
Curr Pharm Des ; 19(4): 734-44, 2013.
Article in English | MEDLINE | ID: mdl-23016853

ABSTRACT

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.


Subject(s)
Antineoplastic Agents/pharmacology , Histone Deacetylase Inhibitors/pharmacology , Multiple Myeloma/drug therapy , Antineoplastic Agents/therapeutic use , Drug Synergism , Epigenesis, Genetic , Gene Expression Regulation, Neoplastic , Histone Deacetylase Inhibitors/therapeutic use , Humans , Hydroxamic Acids/pharmacology , Hydroxamic Acids/therapeutic use , Indoles/pharmacology , Indoles/therapeutic use , Molecular Targeted Therapy , Multiple Myeloma/enzymology , Multiple Myeloma/genetics , Panobinostat , Tumor Microenvironment , Vorinostat
18.
J Biol Chem ; 287(49): 40924-37, 2012 Nov 30.
Article in English | MEDLINE | ID: mdl-23086953

ABSTRACT

Cytokine secretion by cancer cells contributes to cancer-induced symptoms and angiogenesis. Studies show that the sirtuin SIRT6 promotes inflammation by enhancing TNF expression. Here, we aimed to determine whether SIRT6 is involved in conferring an inflammatory phenotype to cancer cells and to define the mechanisms linking SIRT6 to inflammation. We show that SIRT6 enhances the expression of pro-inflammatory cyto-/chemokines, such as IL8 and TNF, and promotes cell migration in pancreatic cancer cells by enhancing Ca(2+) responses. Via its enzymatic activity, SIRT6 increases the intracellular levels of ADP-ribose, an activator of the Ca(2+) channel TRPM2. In turn, TRPM2 and Ca(2+) are shown to be involved in SIRT6-induced TNF and IL8 expression. SIRT6 increases the nuclear levels of the Ca(2+)-dependent transcription factor, nuclear factor of activated T cells (NFAT), and cyclosporin A, a calcineurin inhibitor that reduces NFAT activity, reduces TNF and IL8 expression in SIRT6-overexpressing cells. These results implicate a role for SIRT6 in the synthesis of Ca(2+)-mobilizing second messengers, in the regulation of Ca(2+)-dependent transcription factors, and in the expression of pro-inflammatory, pro-angiogenic, and chemotactic cytokines. SIRT6 inhibition may help combat cancer-induced inflammation, angiogenesis, and metastasis.


Subject(s)
Calcium/metabolism , Gene Expression Regulation, Enzymologic , Gene Expression Regulation, Neoplastic , Histone Deacetylases/metabolism , NAD/metabolism , Pancreatic Neoplasms/metabolism , Sirtuins/metabolism , Animals , Cell Line, Tumor , Cell Movement , Cytokines/metabolism , Humans , Inflammation , Interleukin-8/metabolism , Mice , NF-kappa B/metabolism , RNA, Small Interfering/metabolism , Retroviridae/metabolism , Signal Transduction , Tumor Necrosis Factor-alpha/metabolism
19.
Blood ; 120(17): 3519-29, 2012 Oct 25.
Article in English | MEDLINE | ID: mdl-22955917

ABSTRACT

Malignant cells have a higher nicotinamide adenine dinucleotide (NAD(+)) turnover rate than normal cells, making this biosynthetic pathway an attractive target for cancer treatment. Here we investigated the biologic role of a rate-limiting enzyme involved in NAD(+) synthesis, Nampt, in multiple myeloma (MM). Nampt-specific chemical inhibitor FK866 triggered cytotoxicity in MM cell lines and patient MM cells, but not normal donor as well as MM patients PBMCs. Importantly, FK866 in a dose-dependent fashion triggered cytotoxicity in MM cells resistant to conventional and novel anti-MM therapies and overcomes the protective effects of cytokines (IL-6, IGF-1) and bone marrow stromal cells. Nampt knockdown by RNAi confirmed its pivotal role in maintenance of both MM cell viability and intracellular NAD(+) stores. Interestingly, cytotoxicity of FK866 triggered autophagy, but not apoptosis. A transcriptional-dependent (TFEB) and independent (PI3K/mTORC1) activation of autophagy mediated FK866 MM cytotoxicity. Finally, FK866 demonstrated significant anti-MM activity in a xenograft-murine MM model, associated with down-regulation of ERK1/2 phosphorylation and proteolytic cleavage of LC3 in tumor cells. Our data therefore define a key role of Nampt in MM biology, providing the basis for a novel targeted therapeutic approach.


Subject(s)
Acrylamides/pharmacology , Antineoplastic Agents/pharmacology , Cytokines/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Mitogen-Activated Protein Kinase 1/antagonists & inhibitors , Mitogen-Activated Protein Kinase 3/antagonists & inhibitors , Multiple Myeloma/drug therapy , NAD/metabolism , Nicotinamide Phosphoribosyltransferase/antagonists & inhibitors , Piperidines/pharmacology , Proteins/antagonists & inhibitors , Animals , Autophagy/drug effects , Autophagy/genetics , Cell Line, Tumor , Cell Survival , Cytokines/genetics , Cytokines/metabolism , Dose-Response Relationship, Drug , Drug Resistance, Neoplasm/drug effects , Drug Resistance, Neoplasm/genetics , Gene Expression Regulation, Neoplastic/drug effects , Humans , Mechanistic Target of Rapamycin Complex 1 , Mice , Mitogen-Activated Protein Kinase 1/genetics , Mitogen-Activated Protein Kinase 1/metabolism , Mitogen-Activated Protein Kinase 3/genetics , Mitogen-Activated Protein Kinase 3/metabolism , Molecular Targeted Therapy , Multiple Myeloma/genetics , Multiple Myeloma/metabolism , Multiprotein Complexes , NAD/antagonists & inhibitors , Nicotinamide Phosphoribosyltransferase/genetics , Nicotinamide Phosphoribosyltransferase/metabolism , Organ Specificity , Proteins/genetics , Proteins/metabolism , RNA, Small Interfering/genetics , Signal Transduction/drug effects , Signal Transduction/genetics , TOR Serine-Threonine Kinases , Xenograft Model Antitumor Assays
20.
Semin Hematol ; 49(3): 270-6, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22726551

ABSTRACT

Accumulating evidence supports the potential of proteasome inhibitors as immunosuppressants. Proteasome inhibitors interfere with antigen processing and presentation, as well as with the signaling cascades involved in immune cell function and survival. Both myeloma and healthy plasma cells appear to be highly susceptible to proteasome inhibitors due to impaired proteasomal activity in both cell types. As a consequence, these agents can be used to reduce antibody production and thus prevent antibody-induced tissue damage. Several clinical studies have explored the potential of bortezomib, a peptide boronate proteasome inhibitor, for treating immune disorders, such as antibody-mediated organ rejection and graft-versus-host disease (GVHD), with encouraging results. Here, we discuss the biological rationale for the use of proteasome inhibitors as immunosuppressive agents and review the clinical experience with bortezomib in immune-mediated diseases.


Subject(s)
Graft Rejection/drug therapy , Graft vs Host Disease/drug therapy , Immunosuppressive Agents/immunology , Immunosuppressive Agents/therapeutic use , Proteasome Endopeptidase Complex/metabolism , Proteasome Inhibitors/immunology , Proteasome Inhibitors/therapeutic use , Animals , Antibodies/immunology , Boronic Acids/immunology , Boronic Acids/therapeutic use , Bortezomib , Graft Rejection/enzymology , Graft Rejection/immunology , Graft vs Host Disease/enzymology , Graft vs Host Disease/immunology , Humans , Pyrazines/immunology , Pyrazines/therapeutic use
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