Understanding XPO1 target networks using systems biology and mathematical modeling

The nuclear transport protein Exportin 1 (XPO1), also called chromosome region maintenance 1 (CRM1), is over-expressed 2- 4 fold in cancer. XPO1 is one of seven nuclear exporter proteins, and is solely responsible for the transport of the major tumor suppressor proteins (TSPs) from the nucleus to the cytoplasm. XPO1 exports any protein that carries a leucine-rich, hydrophobic nuclear export sequence (NES). A number of inhibitors have been discovered that block XPO1 function and thereby restore TSPs to the nucleus of both malignant and normal cells. However, natural product, irreversible XPO1 antagonists such as leptomycin B (LMB) have proven toxic in both preclinical models and in the clinic. Recently, orally bioavailable, drug-like small molecule, potent and selective inhibitors of XPO1 mediated nuclear export ("SINE") have been designed and are undergoing clinical evaluations in both humans and canines with cancer. The breadth of clinical applicability and long-term viability of an XPO1 inhibition strategy requires a deeper evaluation of the consequence of global re-organization of proteins in cancer and normal cells. Unfortunately, most of the studies on XPO1 inhibitors have focused on evaluating a limited number of TSPs or other proteins. Because XPO1 carries ~220 mammalian proteins out of the nucleus, such reductionism has not permitted a global understanding of cellular behavior upon drug-induced disruption of XPO1 function. The consequence of XPO1 inhibition requires holistic investigations that consider the entire set of XPO1 targets and their respective pathways modulated without losing key details. Systems biology is one such holistic approach that can be applied to understand XPO1 regulated proteins along with the downstream players involved. This review provides comprehensive evaluations of the different computational tools that can be utilized in the better understanding of XPO1 and its target. We anticipate that such holistic approaches can allow for the development of a clinically successful XPO1 targeted therapeutic strategy against cancer.

Small molecule inhibitors of bcl-2 family proteins for pancreatic cancer therapy

Pancreatic cancer (PC) has a complex etiology and displays a wide range of cellular escape pathways that allow it to resist different treatment modalities. Crucial signaling molecules that function downstream of the survival pathways, particularly at points where several of these pathways crosstalk, provide valuable targets for the development of novel anti-cancer drugs. Bcl-2 family member proteins are anti-apoptotic molecules that are known to be overexpressed in most cancers including PC. The anti-apoptotic machinery has been linked to the observed resistance developed to chemotherapy and radiation and therefore is important from the targeted drug development point of view. Over the past ten years, our group has extensively studied a series of small molecule inhibitors of Bcl-2 against PC and provide solid preclinical platform for testing such novel drugs in the clinic. This review examines the efficacy, potency, and function of several small molecule inhibitor drugs targeted to the Bcl-2 family of proteins and their preclinical progress against PC. This article further focuses on compounds that have been studied the most and also discusses the anti-cancer potential of newer class of Bcl-2 drugs.

Association of PPARγ2 gene variant Pro12Ala polymorphism with hypertension and obesity in the aboriginal Qatari population known for being consanguineous

AIM

The aim of this study was to investigate the association of the Pro12Ala polymorphism of the human peroxisome proliferator-activated receptor gamma 2 (PPARγ2) gene with hypertension and obesity in a highly consanguineous aboriginal Qatari population.

DESIGN

A cross-sectional survey conducted from January 2011-December 2012.

SETTING

Primary health care clinics.

SUBJECTS

A random sample of 1,528 Qatari male and female population older than 20 years of age.

MATERIALS AND METHODS

Data on age, sex, income, level of education, occupation status, body mass index, and blood pressure and lipid profile were obtained. The Pro12Ala in the PPARγ2 gene was detected on the LightCycler® using two specific probes: (Sensor [G] 5'-CTC CTA TTG ACG CAG AAA GCG-FL and PPAR Anchor 5' LC Red 640- TCC TTC ACT GAT ACA CTG TCT GCA AAC ATA TC-PH). Univariate and multivariate logistic regression were performed.

RESULT

Out of a total 1,528 participants, 220 were diagnosed with essential hypertension, and 420 were obese. Participants with consanguinity were significantly higher among hypertensive than normotensive (41.9% versus 30.8%; P=0.001). Altogether, more than three-fourths (89%) of the participants had a wild genotype (Pro12Pro), 9.8% were heterozygous with Pro12Ala, and only 1.2% was homozygous with the Ala12Ala genotype. The frequency of the Pro allele was 94.5% in normotensive versus 90.5% in hypertensive, while the distribution of the Ala allele was 5.5% in normotensive versus 9.5% in the hypertensive group (P=0.001). The odds of hypertension were 1.7 times higher among the participants with the Ala allele as compared to those with the Pro, while adjusting for other potential confounders (adjusted odds ratio 1.69; 95% confidence interval 1.12-2.55; P=0.012). There was no association between the PPARγ2Ala allele and obesity (P=0.740).

CONCLUSION

The current study revealed an association between the PPARγ2Ala allele and hypertension in Qatar's population. On the other hand, this study found no association between the Ala allele and obesity.

Systems analysis reveals a transcriptional reversal of the mesenchymal phenotype induced by SNAIL-inhibitor GN-25

Background

HMLEs (HMLE-SNAIL and Kras-HMLE, Kras-HMLE-SNAIL pairs) serve as excellent model system to interrogate the effect of SNAIL targeted agents that reverse epithelial-to-mesenchymal transition (EMT). We had earlier developed a SNAIL-p53 interaction inhibitor (GN-25) that was shown to suppress SNAIL function. In this report, using systems biology and pathway network analysis, we show that GN-25 could cause reversal of EMT leading to mesenchymal-to-epithelial transition (MET) in a well-recognized HMLE-SNAIL and Kras-HMLE-SNAIL models.

Results

GN-25 induced MET was found to be consistent with growth inhibition, suppression of spheroid forming capacity and induction of apoptosis. Pathway network analysis of mRNA expression using microarrays from GN-25 treated Kras-HMLE-SNAIL cells showed an orchestrated global re-organization of EMT network genes. The expression signatures were validated at the protein level (down-regulation of mesenchymal markers such as TWIST1 and TWIST2 that was concurrent with up-regulation of epithelial marker E-Cadherin), and RNAi studies validated SNAIL dependent mechanism of action of the drug. Most importantly, GN-25 modulated many major transcription factors (TFs) such as inhibition of oncogenic TFs Myc, TBX2, NR3C1 and led to enhancement in the expression of tumor suppressor TFs such as SMAD7, DD1T3, CEBPA, HOXA5, TFEB, IRF1, IRF7 and XBP1, resulting in MET as well as cell death.

Conclusions

Our systems and network investigations provide convincing pre-clinical evidence in support of the clinical application of GN-25 for the reversal of EMT and thereby reducing cancer cell aggressiveness.

Nuclear export mediated regulation of microRNAs: potential target for drug intervention

MicroRNAs (miRNAs) are short non-coding RNAs that have been recognized to regulate the expression of uncountable number of genes. Their aberrant expression has been found to be linked to the pathology of many diseases including cancer. There is a drive to develop miRNA targeted therapeutics for different diseases especially cancer. Nevertheless, reining in these short non-coding RNAs is not as straightforward as originally thought. This is in view of the recent discoveries that miRNAs are under epigenetic regulations at multiple levels. Exportin 5 protein (XPO5) nuclear export mediated regulation of miRNAs is one such important epigenetic mechanism. XPO5 is responsible for exporting precursor miRNAs through the nuclear membrane to the cytoplasm, and is thus a critical step in miRNA biogenesis. A number of studies have shown that variations in components of the miRNA biogenesis pathways, particularly the aberrant expression of XPO5, increase the risk of developing cancer. In addition to XPO5, the Exportin 1 protein (XPO1) or chromosome region maintenance 1 (CRM1) can also carry miRNA export function. These findings are supported by pathway analyses that reveal certain miRNAs as direct interaction partners of CRM1. An in depth understanding of miRNA export mediated regulatory mechanisms is important for the successful design of clinically viable therapeutics. In this review, we describe the current knowledge on the mechanisms of miRNA nuclear transport mediated regulation and propose strategies to selectively block this important mechanism in cancer.

Selective inhibitors of nuclear export for the treatment of non-Hodgkin's lymphomas

The nuclear export protein chromosome maintenance region 1, found to be elevated in non-Hodgkin's lymphomas, controls localization of critical tumor suppressor proteins. Nuclear localization of tumor suppressor proteins is necessary for their cell surveillance function. However, their nuclear exclusion by chromosome maintenance region 1 renders them ineffective making this nuclear transporter an attractive therapeutic target. We have identified selective inhibitors of nuclear export that lock tumor suppressor proteins in the cell nucleus leading to apoptosis of lymphoid but not normal cells. Our inhibitors induce tumor suppressor protein nuclear retention-dependent growth inhibition and apoptosis in a panel of non-Hodgkin's lymphoma cell lines. Western blot of nuclear protein fraction and confocal microscopy analysis demonstrated retention of major tumor suppressor proteins in the cell nucleus. Co-immunoprecipitation studies showed disruption of the tumor suppressor protein-chromosome maintenance region 1 interaction. Small inhibitor RNA knockdown of two major tumor suppressor proteins, p53 in wild-type protein-53 and protein 73 in mutant-protein-53, abrogated inhibitor activity. Oral administration of related inhibitor at 75 and 150 mg/kg resulted in 65 and 70% tumor reduction, respectively and subcutaneous injections of inhibitor (25 and 75 mg/kg) resulted in 70 and 74% suppression of non-Hodgkin's lymphoma tumor growth with no toxicity; residual tumors showed activation of the protein 73 pathway. Our study verifies chromosome maintenance region 1 as a therapeutic target in non-Hodgkin's lymphoma, indicating that this nuclear export protein warrants further clinical investigations.

Network insights into the genes regulated by hepatocyte nuclear factor 4 in response to drug induced perturbations: a review

Transcription factors (TFs) play central role in normal cellular physiology and their aberrant expression is linked to different diseases. Hepatocyte Nuclear Factors (HNFs) are TFs that have been recognized to play multiple roles in liver physiology. Emerging research has highlighted their function in the sustenance of solid tumors, indicating that HNFs could serve as possible therapeutic targets in cancer. Although, there have been many attempts to develop HNF targeted drugs, the myriad downstream targets associated with these transcription factors, some of which are critical for normal cell homeostasis, led to the realization that HNFs are not easily druggable. Therefore, identifying and optimizing drugs that can selectively inactivate HNFs is a challenge to the pharmaceutical industry. To achieve this, a more in-depth understanding is required of the HNFs binding partners, the protein interaction networks it regulates and the resulting phenotype. This calls for network analysis of the pathways regulated by HNFs and how chemical perturbations can selectively activate or suppress their functions. Network biology is an emerging field of research that is finding applications in cancer drug discovery. Specifically, network pharmacology is cementing its position in cancer research and has various applications such as biomarker identification, in determining synergistic drug pairs and in drug repurposing. Developing a network understanding of HNFs, the target it hits and responses thereof can enhance our ability to design drugs against these TFs. This article reviews how network pharmacology can help in the identification of druggable avenues in TFs and also allow the selection of drugs and their synergistic pairs against HNFs for cancer therapy.

Network pharmacology: reigning in drug attrition?

In the process of drug development, there has been an exceptionally high attrition rate in oncological compounds entering late phases of testing. This has seen a concurrent reduction in approved NCEs (new chemical entities) reaching patients. Network pharmacology has become a valuable tool in understanding the fine details of drug-target interactions as well as painting a more practical picture of phenotype relationships to patients and drugs. By utilizing all the tools achieved through molecular medicine and combining it with high throughput data analysis, interactions and mechanisms can be elucidated and treatments reasonably tailored to patients expressing specific phenotypes (or genotypes) of disease, essentially reigning in the phenomenon of drug attrition.

Abstract 3445: Specific inhibitors of nuclear export (SINE) for cancer therapy: from bench to bedside

Nuclear protein transport is an evolutionary conserved mechanism that controls aberrant cell proliferation through balanced nuclear expression of tumor suppressor proteins (TSPs). In cancers, overexpression of exportin protein chromosome region maintenance 1 (CRM-1) disrupts this balance leading to nuclear exclusion of TSPs leading to the low efficacy of traditional anti-cancer drugs. Our recent screening of pancreatic, colon, triple negative breast cancer (TNBC) and non-Hodgkin's lymphoma (NHL) patient samples showed over-expression of CRM-1. These important finding suggests that therapeutic targeting of CRM-1 leading to restoration of TSPs in the nucleus is an attractive strategy against cancer. Earlier attempts to develop CRM-1 inhibitor were not successful as exemplified by the failure of the Leptomycin B in a single clinical trial due to severe off-target toxicity. Since then the field has not witnessed any serious attempts to develop newer classes of CRM-1 inhibitors that could be used clinically. We have developed specific inhibitors of nuclear export (SINE) that are highly specific, orally active drugs with excellent pharmacokinetic parameters. We tested SINEs as targeted inhibitors of CRM-1, in a panel of pancreatic, colon, prostate, breast, NHL cell lines. SINE showed cancer selectivity (IC50s in low nano molar range in cancer cells and >20 micro Molar in normal lymphocytes, fibroblasts and NIH-3T3 cells). SINE induces global re-alignment of important tumor suppressors such as IKB, FOXO, p53, p73 and p27. SINEs were ineffective in killing cancer cells that were transduced with cys528 mut-CRM-1 proteins (a binding site for SINE) confirming the drugs selectivity. In in vivo studies, the clinical grade SINE induced significant tumor growth inhibition in subcutaneous and orthotopic solid and disseminated NHL xenografts. Our new class of SINEs has excellent pharmacokinetic parameters and has passed advanced toxicity profiling. Based on our strong preclinical data, SINE has entered clinical trials for both solid tumors and hematological malignancies.

Citation Format: Asfar S. Azmi, Bin Bao, Michael Kauffman, Sharon Shacham, Ramzi M. Mohammad. Specific inhibitors of nuclear export (SINE) for cancer therapy: from bench to bedside. [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 3445. doi:10.1158/1538-7445.AM2013-3445

Abstract 5234: Network interrogations on SNAIL inhibitor GN-25 induced perturbations in HMLE-SNAIL cell line models

HMLEs (HMLE-SNAIL and Kras-HMLE-SNAIL pairs) serve as excellent model system to interrogate the effect of SNAIL targeted agents that reverse epithelial-to-mesenchymal transition (EMT). We developed a SNAIL-p53 interaction inhibitor (GN-25) that was shown to suppress SNAIL function. In this report, using pathway network analysis, we show that GN-25 induces the reversal of EMT to mesenchymal-to-epithelial transition (MET) in well recognized HMLE-SNAIL and Kras-HMLE-SNAIL models. GN-25 induced MET was found to be concurrent with growth inhibition, suppression of spheroid forming capacity and induction of apoptosis. We performed systems and pathway network analysis on mRNA expression by microarrays from GN-25 treated Kras-HMLE-SNAIL cells that showed an orchestrated global re-organization of EMT network genes. The expression signatures were validated at the protein level using confocal microscopy, western blot analysis and time lapse videography, and we found down-regulation of mesenchymal markers such as TWIST1, TWIST2, ZEB-1 concurrently with up-regulation of epithelial marker E-Cadherin. Additionally, RNAi studies validated SNAIL dependent mechanism of action of the drug. Most importantly, GN-25 deregulated many major transcription factors (TFs) such as inhibition of oncogenic TFs Myc, TBX2, NR3C1 and enhancement in tumor suppressor TFs such as SMAD7, DD1T3, CEBPA, HOXA5, TFEB, IRF1, IRF7 and XBP1, resulting in MET as well as induction of cell death. Our systems and network investigations provide solid pre-clinical supportive evidence for clinical application of GN-25 for the reversal of EMT phenotype to MET in aggressive cancers.

Citation Format: Asfar S. Azmi, Aliccia Bollig-Fisher, Bin Bao, Bum Joon-Park, SH Lee, Gyu-Yong Song, Ramzi M. Mohammad, Fazlul H. Sarkar. Network interrogations on SNAIL inhibitor GN-25 induced perturbations in HMLE-SNAIL cell line models. [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 5234. doi:10.1158/1538-7445.AM2013-5234

Abstract 3438: Selective inhibitors of Mcl-1 with potent activity against multiple myeloma patient cells and animal xenografts

To date most of the studies targeting apoptotic machinery have focused on inhibiting Bcl2 and BclXL proteins that have shown limited clinical utility. This could be in part due to the over-expression of Myeloid Leukemia-1 (Mcl-1) that carries similar anti-apoptotic functions. Our recent evaluations of Multiple Myeloma (MM) patient derived samples have shown consistent over-expression of Mcl-1 suggesting that it is an attractive therapeutic target. We have discovered a novel druggable site in Mcl-1 protein. Using structure based drug design we have developed small molecule inhibitors (SMIs) of Mcl-1 that bind with high affinity to the BH-3 hydrophobic groove of the protein thereby displacing different pro-apoptotic partners such as Bax, Bak, Bok and Bid with activity against MM cells (IC50 5 μM) and anti-tumor activity in animal xenografts. The lead SMI (UMI-77) inhibits growth and induces apoptosis in MM cells. Molecular analysis of MM cells reveals activation of pro-apoptotic factors post UMI-77 treatment. Co-immunoprecipitation studies show that UMI-77 disrupts the Mcl-1-Bax and Mcl-1-Bak interactions. The drug synergizes with standard proteasome inhibitor Velcade (5 nM) and Carfilosimib (1 nM). In patient derived MM cells (n=45), UMI-77 inhibits growth and induces apoptosis that is concurrent with induction of Bax, Bak and enhancement in cleaved fractions of caspases 3 and 9. At similar concentrations UMI-77 does not affect normal peripheral lymphocytes. UMI-77 is well tolerated by animals at MTD (60 mg/kg i.v.). In a mice lymphoma model, oral administration of UMI-77 significantly reduced tumor growth and histological examination of tumors revealed suppression of Mcl-1 protein expression along with enhancement of pro-apoptotic markers. Our novel Mcl-1 inhibitors provide a new therapeutic option for cancers for MM that overexpress Mcl-1 that have failed standard therapies.

Citation Format: Asfar S. Azmi, Zaneta Nikolovka-Coleska, Muneer Abidi, Kelley Marsack, Ashiq Masood, Hiroshi Yano, Silvana Pregja, Jeffrey Zonder, Ramzi M. Mohammad. Selective inhibitors of Mcl-1 with potent activity against multiple myeloma patient cells and animal xenografts. [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 3438. doi:10.1158/1538-7445.AM2013-3438

Selective inhibitors of nuclear export block pancreatic cancer cell proliferation and reduce tumor growth in mice

BACKGROUND & AIMS

Tumor-suppressor proteins are inactivated by many different mechanisms, including nuclear exclusion by chromosome region maintenance (CRM)-1. Increased tumor levels of CRM-1 have been correlated with poor prognosis of patients with pancreatic cancer, making it a therapeutic target. Selective inhibitors of nuclear export (SINEs) bind to CRM-1 to irreversibly inhibit its ability to export proteins; we investigated a new class of SINEs in pancreatic cancer cells.

METHODS

We studied the effects of SINE analogs in a panel of pancreatic cancer cell lines and nontransformed human pancreatic ductal epithelial cells using proliferation, apoptosis, immunoblot, co-immunoprecipitation, small inhibitor RNA, and fluorescence microscopy analyses. The effects of the SINEs also were investigated in mice with subcutaneous and orthotopic tumors.

RESULTS

SINEs (KPT-185, KPT-127, KPT-205, and KPT-227) inhibited proliferation and promoted apoptosis of pancreatic cancer cells, but did not affect human pancreatic ductal epithelial cells. The nuclei of cells incubated with KPT-185 accumulated tumor-suppressor proteins (p27, FOXO, p73, and prostate apoptosis response-4 [PAR-4]) and inhibited interactions between CRM-1 and these proteins. Mutations in the region of CRM-1 that bind to SINEs (Cys-528), or small inhibitor RNA knockdown of PAR-4, prevented the ability of KPT-185 to block proliferation and induce apoptosis of pancreatic cancer cells. Oral administration of KPT-330 to mice reduced growth of subcutaneous and orthotopic xenograft tumors without major toxicity. Analysis of tumor remnants showed that KPT-330 disrupted the interaction between CRM-1 and PAR-4, activated PAR-4 signaling, and reduced proliferation of tumor cells.

CONCLUSIONS

We identified SINEs that inhibit CRM-1 and promote nuclear accumulation of tumor-suppressor proteins in pancreatic cancer cells. Oral administration of the drug to mice reduces growth of xenograft tumors.

Systems and Network Pharmacology Approaches to Cancer Stem Cells Research and Therapy

The cancer stem cell (CSC) hypothesis is increasingly being accepted as a model to explain for the functional heterogeneity that is commonly observed in solid tumors. According to this hypothesis, there exists a hierarchical organization of cells within the tumor, in which a differential subpopulation of stem-like cells is responsible for sustaining and recurrence of tumor growth. CSCs have been shown to exist in a variety of solid tumors especially those with known resistant phenotypes such as breast, prostate and pancreatic adenocarcinoma (PDAC). In all these models, the commonality of deregulation of three crucial pathways; Wnt, notch and hedgehog that maintain CSC self-renewal capacity is emerging. Collectively these major pathways and have been linked to the observed resistance of CSC to chemotherapy and radiotherapy. The existing lack of knowledge and our incomplete understanding of the molecular signatures associated with CSCs highlight the need for better approaches in both isolation and identification of unique pathways associated with these cells. In this direction, computational biology, especially systems and network approaches, have proven to be of great utility in unraveling pathway complexities such as those associated with CSCs. With highlights on the most up-to-date molecular, network, cellular, clinical, and therapeutic cancer research findings, this article tends to provide a wealth of insights on systems and network biology approaches to CSC marker identification, the mechanism through which they evade treatment as well as therapeutic approaches that will help in conquering these elusive cells in incurable and refractory malignancies.

HDM2 antagonist MI-219 (spiro-oxindole), but not Nutlin-3 (cis-imidazoline), regulates p53 through enhanced HDM2 autoubiquitination and degradation in human malignant B-cell lymphomas

Background

Lymphomas frequently retain wild-type (wt) p53 function but overexpress HDM2, thereby compromising p53 activity. Therefore, lymphoma is a suitable model for studying the therapeutic value of disrupting the HDM2-p53 interaction by small-molecule inhibitors (SMIs). HDM2 have been developed and are under various stages of preclinical and clinical investigation. Previously, we examined the anti-lymphoma activity of MI-319, the laboratory grade of a new class of HDM2 SMI, the spiro-oxindole, in follicular lymphoma. Since then, MI-219, the clinical grade has become readily available. This study further examines the preclinical effects and mechanisms of MI-219 in a panel of human lymphoma cell lines as well as a cohort of patient-derived B-lymphcytes for its potential clinical use.

Results

Preclinical assessment of MI-219 was evaluated by means of an in vitro and ex vivo approach and compared to Nutlin-3, the gold standard. Characterization of p53 activity and stability were assessed by quantitative PCR, Western blot, and immunoprecipitation. Biological outcome was measured using Trypan blue exclusion assay, Annexin V/PI, PARP and caspase-3 cleavage. Surprisingly, the overall biological effects of Nutlin-3 were more delayed (48 h) while MI-219 triggered an earlier response (12-24 h), predominantly in the form of apoptotic cell death. Using a cell free autoubiquitination assay, neither agent interfered with HDM2 E3 ligase function. MI-219 was more effective in upregulating wt-p53 stabilization compared to Nutlin-3. MI-219, but not Nutlin-3, enhanced the autoubiquitination and degradation of HDM2.

Conclusions

Our data reveals unexpected differences between MI-219 and the well-studied Nutlin-3 in lymphoma cell lines and patient samples. We suggest a novel mechanism for MI-219 that alters the functional activity of HDM2 through enhanced autoubiquitination and degradation. Additionally, this mechanism appears to correspond to biological outcome. Our results provide evidence that different classes of HDM2 SMIs elicit molecular events that extend beyond HDM2-p53 dissociation which may be of biological and potentially therapeutic importance.

Abstract A1: SNAIL inhibitor GN-25 induces MET through Global Reprograming of EMT Network Genes: a Systems and Network Analysis

Epithelial-to-mesenchymal transition (EMT) is a complex mechanism that arises through a cohesive and intricate biological cross-talk between numerous cancer-related networks. Among them sonic hedgehog directed snail network is one of the major components that drives EMT. This has led to strategies targeting either hedgehog signaling or snail protein using highly specific agents. However, it is needless to say that removal of individual components through single protein-targeted drug (here snail) from robust EMT networks may surprisingly have little functional consequence in cancer. We propose that, to have an impact, interventions within EMT network need to be multiple but highly selective. Further, predicting the functional outcome of interventions, such as those originating from single pathway targeted drug treatment, is not as straightforward as originally thought and computational/integrated tools are needed. The emergence of computational network biology has enhanced our knowledge of multi-pathway interactions in cancer and helped in making sense of drug response signature datasets that collectively decode the complex mechanisms of drug action. These holistic approaches have laid the foundation of the emerging concepts of “network pharmacology” that is solidifying its position in cancer medicine. Unlike earlier reductionist one-drug, one-target approaches, network pharmacology invokes the idea of drug promiscuity often engages a fortuitous combination of appropriate high-value targets in cancer cells to produce treatment success. Network pharmacology is being used in the identification of weak nodes in global cancer networks, predicting drug toxicity, drug repurposing, identifying multiscale mechanisms of drug action and in the rational design of potent anticancer drug combinations. To this end, we had earlier developed a novel snail-p53 interaction inhibitor (GN-25) that was shown to suppress snail function. However, this drug was not investigated for its effects against EMT pathways. Here using network pharmacology drug repurposing principles, we show that our novel SNAIL inhibitor (GN-25), through its promiscuous action induces mesenchymal-to-epithelial transition (MET) in well-recognized HMLE-snail cell line model developed by Dr. Weinberg. Network modeling of microarray gene expression profiling data from GN-25 treated cells showed an orchestrated global reorganization of EMT network genes. Most importantly, the expression signatures were validated both at the mRNA and protein expression levels, and mechanistically studied by RNA interference which provided unequivocal evidence on the role of GN-25 targeting EMT specific genes. This proof-of-concept investigation shows that computational biology and network pharmacology can be very powerful tools for rational design and development of agents that are typically promiscuous like the snail inhibitor as a candidate EMT-targeting drug.

Citation Format: Asfar S. Azmi, Ramzi M. Mohammad, Fazlul H. Sarkar. SNAIL inhibitor GN-25 induces MET through Global Reprograming of EMT Network Genes: a Systems and Network Analysis [abstract]. In: Proceedings of the AACR Special Conference on Chemical Systems Biology: Assembling and Interrogating Computational Models of the Cancer Cell by Chemical Perturbations; 2012 Jun 27-30; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2012;72(13 Suppl):Abstract nr A1.

Aberrant epigenetic grooming of miRNAs in pancreatic cancer: a systems biology perspective

Pancreatic cancer (PC) is a complex disease harboring a myriad of genetic and epigenetic changes. The dismal survival of patients diagnosed with PC is in part due to de novo and acquired resistance to conventional therapeutics, resulting from deregulated signaling including aberrant expression of small nc miRNAs. Emerging research in this area has lead to the identification and characterization of deregulated miRNAs, which have generated a renewed interest and hope in that novel targeting of miRNAs may lead to a better clinical outcome for patients diagnosed with PC. However, recent evidence suggests that miRNAs are also under a highly coordinated system of epigenetic regulation emphasizing the fact that the design of miRNAs as targeted therapy may not be as simple as originally anticipated. For a successful miRNA-based therapeutic regimen, a holistic integrated approach may be required to take into account because of these emerging epigenetic regulatory mechanisms. In this article, we will discuss miRNA epigenetics, it's significance in PC and the use of a systems science to identify these aberrant epigenetically groomed miRNAs, and we believe that such knowledge would likely benefit further research to realize the dream of miRNA-based targeted therapy for human malignancies.

Abstract 1825: Novel small molecule CRM-1 inhibitor for Non Hodgkin's Lymphoma

Recent evidence demonstrates that Non Hodgkin's Lymphoma (NHL) tumors have elevated expression of the XPO1 gene. XPO1 codes for the nuclear exporter protein CRM-1 that controls localization of critical tumor suppressors including p53 family members. For apoptosis and cell cycle regulation, p53/p73 nuclear localization and DNA binding are highly critical making CRM-1 an attractive therapeutic target for NHL; a disease that carries >90% wild type/functional p53 and only rare mutations in p73. Earlier strategies to develop CRM-1 targeted agents such as Leptomycin B failed in the clinic due to off target toxicity. As a significant advancement to the field, we have identified novel small molecule inhibitors of CRM-1 (KPTs) that bind irreversibly and lock tumor suppressors (including p53 and p73) in cancer cell nucleus leading to apoptosis selectively in tumor cells. The KPTs show minimal toxicity to normal tissues, and possess clinically acceptable pharmacokinetic parameters. Here we demonstrate for the first time that KPTs can induce apoptosis in resistant NHL cell lines and corresponding xenograft models. The most potent CRM-1 inhibitor (KPT-185 and not its inactive analog KPT-Tran) induced growth inhibition, cell cycle arrest and apoptosis in a panel of NHL cell lines with a median IC50 ∼25 nM. The drug does not have growth inhibitory or apoptotic effects against normal peripheral lymphocytes (IC50 ∼20 µM). Fluorescent microscopy, western blot ad co-immunoprecipitation analyses demonstrated that KPT-185 treatment resulted in nuclear localization as well as dissociation of CRM-1-p53 in wt-p53 and CRM-1-p73 in mut-p53 cell lines. Additionally, we observed KPT-185 mediated activation of p21 and Bax that are known downstream executioners of p53/p73 mediated cell cycle control and apoptosis, respectively. Most significantly, knockdown of p53 in wt-p53 WSU-FSCCL and p73 in mut-p53 WSU-DLCL2 abrogated the apoptotic potential of KPT-185, confirming that these were indeed p53/p73 dependent apoptotic events. KPT-185 showed a substantial enhancement in apoptosis when combined with genotoxic p53/p73 re-activating regimen CHOP. Using WSU-DLCL2 SCID models, we further show that oral administration of related CRM-1 inhibitor KPT-276 (75 and 150 mg/Kg p.o) resulted in 65 and 70% tumor reduction, respectively and subcutaneous injections of KPT-251 (25 and 75 mg/Kg) resulted in 70 and 74% suppression of tumor growth with no observed toxicity to the host. Remnant tumor tissue analysis (histology and protein markers) fell in line with our in vitro results with clear activation of p73 pathway. Additionally, Co-immunoprecipitation studies showed dissociation of CRM-1-p73 interaction in KPT treated animal tumors. Our study verifies CRM-1 as a potential therapeutic target in NHL irrespective of the functional status of p53. These results build a strong case for the clinical use of our novel CRM-1 inhibitors either as single agent or in combination with CHOP.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1825. doi:1538-7445.AM2012-1825

Abstract 1815: CRM-1 as a potential therapeutic target in pancreatic cancer

CRM-1 exportin protein encoded by the XPO-1 gene maintains cancer cells through nuclear export signal (NES)-dependent protein exclusion of tumor suppressor proteins (TSPs). High CRM-1 expression has been correlated with poor prognosis in pancreatic cancer making it an attractive therapeutic target. Numerous attempts have been made in the past to develop specific CRM-1 inhibitors; however, earlier inhibitors such as Leptomycin B failed in the clinic due to acute off target toxicity. Using structure based drug design; we have identified new class of selective inhibitors of nuclear export (SINE) that irreversibly inhibits CRM1 and lock TSPs in cancer cell nucleus leading to cancer cell selective apoptosis. The inhibitors have excellent pharmacokinetic parameters and minimal toxicity to normal tissue. Here, we tested SINEs against pancreatic cancer, a disease that urgently needs novel and effective therapies. CRM-1 inhibitors [(KPT-185 (most potent analog), KPT-127, KPT-205, KPT-227 as well as Leptomycin B (as positive control) and not its inactive analog KPT-Tran (as negative control)] induced growth inhibition (MTT) and apoptosis (Annexin V and Histone DNA ELISA) in five cell lines (IC50 ∼150 nM). KPT-SINEs did not have any effect on normal HPDE cells (IC50>5 µM). Mechanistically, KPT-185 mediated apoptosis was found to be through activation, phosphorylation and nuclear localization of a TSP prostate apoptosis response 4 (PAR-4). PAR-4 has earlier been established by our laboratory as a therapeutic target in pancreatic cancer. Co-immunoprecipitation studies demonstrated that KPT-185 dissociated CRM-1-PAR-4 and CRM-1-p-PAR-4 interaction. Further, PAR-4 siRNA knockdown abrogated KPT-SINEs ability to induce growth inhibition or apoptosis. In normal cells PAR-4 localization or phosphorylation was not observed and this was associated with low basal expression of PAR-4 and its phosphorylation inducer protein kinase A protein. Role of other TSPs such as p53 and p27 was also explored, however, our investigations directly point to a PAR-4 specific mechanism. KPT-251 (structurally very similar to KPT-185 with improved pharmacokinetics properties) was well tolerated in SCID mice upto 150 mg/kg, p.o. Oral administration of analog KPT-251 at 25 and 150 mg/kg daily for two weeks reduced pancreatic tumors significantly (p<0.01). Histological examination of remnant tumors showed enhanced staining of PAR-4 and reduced Ki67. Tumor tissue lysates were probed for protein expression using western blotting that revealed activation of PAR-4 signaling and co-immunoprecipitation assay demonstrated dissociation of CRM-1-PAR-4 in tumors as well. In conclusion, discovery of our novel non-toxic KPTs can significantly impact the advancement of the field of CRM-1 inhibitors and could become effective anti-cancer therapeutics for pancreatic cancer as well as other solid tumors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1815. doi:1538-7445.AM2012-1815

Resveratrol-induced apoptosis is enhanced in low pH environments associated with cancer

Many critical factors such as hypoxia, nutrient deficiency, activation of glycolytic pathway/Warburg effect contribute to the observed low pH in tumors compared to normal tissue. Studies suggest that such tumor specific acidic environment can be exploited for the development of therapeutic strategies against cancer. Independent observations show reduction in pH of mammalian cells undergoing internucleosomal DNA fragmentation and apoptosis. As such, our group has extensively demonstrated that anticancer mechanisms of different plant polyphenols involve mobilization of endogenous copper and consequent internucleosomal DNA breakage. Copper is redox active metal, an essential component of chromatin and is sensitive to subtle pH changes in its microenvironment. Here we explored whether, acidic pH promotes growth inhibition, apoptosis, and DNA damaging capacity of chemopreventive agent resveratrol. Our results reveal that growth inhibition and internucleosomal DNA fragmentation induced apoptosis in Capan-2 and Panc-28 pancreatic cancer cell lines (and not in normal HPDE cells) by resveratrol is enhanced at lower pH. Using comet assay, we further demonstrate that DNA breakage by resveratrol is enhanced with acidification. Membrane permeable copper specific chelator neocuproine (and not iron chelator orthophenanthroline) abrogated growth inhibition and apoptosis by resveratrol. Western blot results show enhanced activation of DNA laddering marker H2.aX by resveratrol at acidic pH that was reversed by neocuproine and not by orthophenanthroline. Our findings provide irrevocable proof that low pH environment can be turned into tumor weakness and assist in eradication of cancer cells by resveratrol.

Novel small-molecule CRM-1 inhibitor for GI cancer therapy

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Background: Pancreatic (PC) and Colon (CC) cancer remain deadly diseases despite the advent of novel targeted and cytotoxic therapies. Therefore, identification of new targets and development of novel agents against these targets are urgently needed. CRM-1 is a nuclear export protein encoded by the XPO1 (exportin 1) gene that mediates leucine-rich nuclear export signal ( NES )-dependent protein export. Elevated CRM-1 expression has been correlated with poor prognosis in PC and CC making it an attractive therapeutic target.

Methods: Using structure based drug design, we have identified novel, irreversible small molecule inhibitors of CRM-1 that lock target proteins, including TSP, in the nucleus. Normal cells undergo cell cycle arrest, but most cancer cells initiate apoptosis. Thus, the drugs selectively kill cancer cells with minimal toxicity to normal tissue and possess clinically acceptable pharmacokinetic parameters. In this report, using multiple molecular biological techniques, we have evaluated the role of CRM-1 inhibition on nuclear localization and apoptosis by PAR-4.

Results: The most potent small molecule CRM-1 inhibitor (KPT-185) induced growth inhibition and apoptosis in a panel of PC and CC cell lines with IC50’s <150 nM. Western blot and confocal microscopy analyses demonstrated that KPT-185 treatment resulted in TSP and PAR-4 nuclear localization (a pre-requisite for PAR-4 mediated apoptosis). Most significantly, siRNA knockdown of PAR-4 abrogated the apoptotic potential of KPT-185 in BxPC-3 and Colo-357 (PC) and HCT-116 and HT-29 (CC) cell lines, confirming that this was indeed a PAR-4 dependent apoptotic mechanism. KPT-185 showed synergistically enhanced apoptosis when combined with oxaliplatin in all the tested cell lines. Human genomic expression microarray profiling using HT-12 arrays are underway. Additionally, animal xenograft studies involving single agent KPT-185 and combination with oxaliplatin are currently ongoing.

Conclusions: This is the first report demonstrating CRM-1 as a potential therapeutic target in both PC and CC, perhaps by enhancing PAR-4 function. The drugs KPT-185 and related CRM1-inhibitors warrant further clinical investigations for this deadly malignancy.

Network perspectives on HDM2 inhibitor chemotherapy combinations

The discovery of small molecule inhibitors of HDM2-p53 interaction is considered one of the most significant therapeutic developments in the area p53 research. Intensive work on different classes of HDM2 inhibitors has proven their therapeutic utility as activators of p53 in multiple tumor models. Many laboratories have shown that HDM2 inhibitors can synergize with chemotherapeutic agents resulting in enhanced efficacy through both p53-dependent and independent mechanisms. In our hands HDM2 inhibitor and platinum drug combination showed remarkable antitumor activity that led tumor free survival in one of the most resistant and complex pancreatic xenograft models. Although antitumor efficacy of such combinations has been studied in detail, not much is known on the molecular mechanisms governing this synergy. This is partly due to complexity of multiple pathways modulated by p53 and HDM2. We are of the view that in order to decode this complexity, an integrated approach is needed that considers both HDM2 and p53 as components of a network and not in isolation. This review highlights recent advancements in our understanding of HDM2 inhibitor combination therapy based on network modeling and systems biology driven science. Our recent findings support such a network view as integrated gene expression profiling and pathway network modeling on MI-219-oxaliplatin treated cells revealed activation of multiple and closely knit biological networks. We anticipate that in the near future such network-centric approaches will benefit clinical development of HDM2 inhibitors for genetically predefined subsets of cancer patients and this will be a step towards personalized medicine.

Network modeling of CDF treated pancreatic cancer cells reveals a novel c-myc-p73 dependent apoptotic mechanism

Systems biology and molecular network modeling are important tools that are finding application in anti-cancer drug discovery. These technologies can be utilized to map and evaluate the entire set of pathways modulated by drugs in cancer cells without loosing key details. Such integrated approaches are especially useful in understanding the mechanism of action of agents that do not have a defined target. Our novel compound CDF (a synthetic analogue of curcumin), is one such multi-targeted agent with proven anti-cancer activity in vitro and in vivo. However, its mechanism of action is not fully understood, and thus a thorough analysis of key pathways targeted by CDF would be important for developing targeted and tailored therapy in the future. Applying Ingenuity Pathway Analysis (IPA), we have mapped the pathways altered by CDF treatment of BxPC-3 pancreatic cancer (PC) cells. Illumina HT-12 microar-rays were performed on RNA extracted from CDF treated cells. IPA analysis of gene expression at early time point (24 hrs) revealed deregulation of genes in the c-Myc hub. Western blot analysis validated the activation of c-Myc, p73 and its downstream pro-apoptotic effector Bax with simultaneous down-regulation of Bcl-2 in two distinct pancreatic cancer cell lines (BxPC-3 and Colo-357). In order to further delineate the role of c-Myc in inducing apoptosis, siRNA silencing technology was used. As expected, c-Myc siRNA knockdown resulted in abrogation of the growth inhibitory and apoptotic potential of CDF. In conclusion, our results demonstrate a novel c-Myc driven apoptotic network activated by CDF in PC cells that is independent of wild-type p53, and thus warrants further investigation on the clinical utility of CDF.