Hybrid Modeling of Cancer Drug Resistance Mechanisms

Cancer is a multi-scale disease and its overwhelming complexity depends upon the multiple interwind events occurring at both molecular and cellular levels, making it very difficult for therapeutic advancements in cancer research. The resistance to cancer drugs is a significant challenge faced by scientists nowadays. The roots of the problem reside not only at the molecular level, due to multiple type of mutations in a single tumor, but also at the cellular level of drug interactions with the tumor. Tumor heterogeneity is the term used by oncologists for the involvement of multiple mutations in the development of a tumor at the sub-cellular level. The mechanisms for tumor heterogeneity are rigorously being explored as a reason for drug resistance in cancer patients. It is important to observe cell interactions not only at intra-tumoral level, but it is also essential to study the drug and tumor cell interactions at cellular level to have a complete picture of the mechanisms underlying drug resistance. The multi-scale nature of cancer drug resistance problem require modeling approaches that can capture all the multiple sub-cellular and cellular interaction factors with respect to dierent scales for time and space. Hybrid modeling offers a way to integrate both discrete and continuous dynamics to overcome this challenge. This research work is focused on the development of hybrid models to understand the drug resistance behaviors in colorectal and lung cancers. The common thing about the two types of cancer is that they both have dierent mutations at epidermal growth factor receptors (EGFRs) and they are normally treated with anti-EGFR drugs, to which they develop resistances with the passage of time. The acquiring of resistance is the sign of relapse in both kind of tumors. The most challenging task in colorectal cancer research nowadays is to understand the development of acquired resistance to anti-EGFR drugs. The key reason for this problem is the KRAS mutations appearance after the treatment with monoclonal antibodies (moAb). A hybrid model is proposed for the analysis of KRAS mutations behavior in colorectal cancer with respect to moAb treatments. The colorectal tumor hybrid model is represented as a single state automata, which shows tumor progression and evolution by means of mathematical equations for tumor sub-populations, immune system components and drugs for the treatment. The drug introduction is managed as a discrete step in this model. To evaluate the drug performance on a tumor, equations for two types of tumors cells are developed, i.e KRAS mutated and KRAS wild-type. Both tumor cell populations were treated with a combination of moAb and chemotherapy drugs. It is observed that even a minimal initial concentration of KRAS mutated cells before the treatment has the ability to make the tumor refractory to the treatment. Moreover, a small population of KRAS mutated cells has a strong influence on a large number of wild-type cells by making them resistant to chemotherapy. Patient's immune responses are specifically taken into considerations and it is found that, in case of KRAS mutations, the immune strength does not affect medication efficacy. Finally, cetuximab (moAb) and irinotecan (chemotherapy) drugs are analyzed as first-line treatment of colorectal cancer with few KRAS mutated cells. Results show that this combined treatment could be only effective for patients with high immune strengths and it should not be recommended as first-line therapy for patients with moderate immune strengths or weak immune systems because of a potential risk of relapse, with KRAS mutant cells acquired resistance involved with them. Lung cancer is more complicated then colorectal cancer because of acquiring of multiple resistances to anti-EGFR drugs. The appearance of EGFR T790M and KRAS mutations makes tumor resistant to a geftinib and AZD9291 drugs, respectively. The hybrid model for lung cancer consists of two non-resistant and resistant states of tumor. The non-resistant state is treated with geftinib drug until resistance to this drug makes tumor regrowth leading towards the resistant state. The resistant state is treated with AZD9291 drug for recovery. In this model the complete resistant state due to KRAS mutations is ignored because of the unavailability of parameter information and patient data. Each tumor state is evaluated by mathematical differential equations for tumor growth and progression. The tumor model consists of four tumor sub-population equations depending upon the type of mutations. The drug administration in this model is also managed as a discrete step for exact scheduling and dosages. The parameter values for the model are obtained by experiments performed in the laboratory. The experimental data is only available for the tumor progression along with the geftinib drug. The model is then fine tuned for obtaining the exact tumor growth patterns as observed in clinic, only for the geftinib drug. The growth rate for EGFR T790M tumor sub-population is changed to obtain the same tumor progression patterns as observed in real patients. The growth rate of mutations largely depends upon the immune system strength and by manipulating the growth rates for different tumor populations, it is possible to capture the factor of immune strength of the patient. The fine tuned model is then used to analyze the effect of AZD9291 drug on geftinib resistant state of the tumor. It is observed that AZD9291 could be the best candidate for the treatment of the EGFR T790M tumor sub-population. Hybrid modeling helps to understand the tumor drug resistance along with tumor progression due to multiple mutations, in a more realistic way and it also provides a way for personalized therapy by managing the drug administration in a strict pattern that avoid the growth of resistant sub-populations as well as target other populations at the same time. The only key to avoid relapse in cancer is the personalized therapy and the proposed hybrid models promises to do that

New findings on primary and acquired resistance to anti-EGFR therapy in metastatic colorectal cancer: Do all roads lead to RAS?

none13Anti-epidermal growth factor receptor therapy with the monoclonal antibodies cetuximab and panitumumab is the main targeted treatment to combine with standard chemotherapy for metastatic colorectal cancer. Many clinical studies have shown the benefit of the addition of these agents for patients without mutations in the EGFR pathway. Many biomarkers, including KRAS and NRAS mutations, BRAF mutations, PIK3CA mutations, PTEN loss, AREG and EREG expression, and HER-2 amplification have already been identified to select responders to anti-EGFR agents. Among these alterations KRAS and NRAS mutations are currently recognized as the best predictive factors for primary resistance. Liquid biopsy, which helps to isolate circulating tumor DNA, is an innovative method to study both primary and acquired resistance to anti- EGFR monoclonal antibodies. However, high-sensitivity techniques should be used to enable the identification of a wide set of gene mutations related to resistance.openBronte G.; Silvestris N.; Castiglia M.; Galvano A.; Passiglia F.; Sortino G.; Cicero G.; Rolfo C.; Peeters M.; Bazan V.; Fanale D.; Giordano A.; Russo A.Bronte, G.; Silvestris, N.; Castiglia, M.; Galvano, A.; Passiglia, F.; Sortino, G.; Cicero, G.; Rolfo, C.; Peeters, M.; Bazan, V.; Fanale, D.; Giordano, A.; Russo, A

EPMA position paper in cancer:current overview and future perspectives

At present, a radical shift in cancer treatment is occurring in terms of predictive, preventive, and personalized medicine (PPPM). Individual patients will participate in more aspects of their healthcare. During the development of PPPM, many rapid, specific, and sensitive new methods for earlier detection of cancer will result in more efficient management of the patient and hence a better quality of life. Coordination of the various activities among different healthcare professionals in primary, secondary, and tertiary care requires well-defined competencies, implementation of training and educational programs, sharing of data, and harmonized guidelines. In this position paper, the current knowledge to understand cancer predisposition and risk factors, the cellular biology of cancer, predictive markers and treatment outcome, the improvement in technologies in screening and diagnosis, and provision of better drug development solutions are discussed in the context of a better implementation of personalized medicine. Recognition of the major risk factors for cancer initiation is the key for preventive strategies (EPMA J. 4(1):6, 2013). Of interest, cancer predisposing syndromes in particular the monogenic subtypes that lead to cancer progression are well defined and one should focus on implementation strategies to identify individuals at risk to allow preventive measures and early screening/diagnosis. Implementation of such measures is disturbed by improper use of the data, with breach of data protection as one of the risks to be heavily controlled. Population screening requires in depth cost-benefit analysis to justify healthcare costs, and the parameters screened should provide information that allow an actionable and deliverable solution, for better healthcare provision

A cost-effectiveness analysis of two anti-EGFR monoclonal antibodies (cetuximab and panitumumab) plus best supportive care versus best supportive care alone as third-line treatment of advanced chemorefractory metastatic colorectal cancer

ABSTRACT Introduction The National Cancer Institute of Canada Clinical Trials Group CO. 17 trial and the Open-Label Phase III trial showed that the addition of new anti-EGFR monoclonal antibodies (cetuximab andpanitumumab) to best supportive care as third-line treatments prolong the life of patients with advanced metastatic colorectal cancer, but have also introduced a unique set of toxicities and increased costs. In a resource constrained environment this prompts the need for tools to identify the patients who are likely to benefit from these therapies in a more efficient and cost-effective way. We developed an economic model using analytic decision modeling to assess the cost-effectiveness of two anti-EGFR monoclonal antibodies (cetuximab and panitumumab) plus best supportive care versus best supportive care alone as third-line treatment in advanced chemorefractory metastatic colorectal cancer. Methods We constructed a Markov model based on the efficacy data obtained from the National Cancer Institute of Canada Clinical Trials Group CO. 17 trial and the Open-Label Phase III trial studies. Costs for physician visits, blood products, emergency department visits, hospitalizations and toxicity management were obtained published literature and expert opinion. Drug costs were obtained from London Health Sciences Center (LHSC) drug formulary intranet. The primary outcome of the model is the incremental cost-utility ratio of adding anti-EGFR monoclonal antibodies (panitumumab and cetuximab) to best supportive care as third-line therapies in treatment of advanced metastatic chemo-refractory colorectal cancer, expressed as cost per quality-adjusted life year (QALY) gained. A series of deterministic and probabilistic sensitivity analyses were also performed to account for uncertainty in the model parameters. Results Adding panitumumab to best supportive care (with KRAS test) resulted in a mean gain of 0.087 QALYs with a mean incremental cost utility ratio of $269,703 per QALY gained (95$135,432 to $766,072 per QALY gained). The addition of cetuximab to best supportive care (with KRAS test) resulted in a mean gain of 0.068 QALYs with a mean incremental cost-utility ratio of$352,046 per QALY gained (95% Cl = $151,916 to$949,342 per QALY gained). In subset of patients with wild-type KRAS, the addition of panitumumab to best supportive care resulted in a mean gain of 0.16 QALYs with a mean incremental cost-utility ratio of $236,469 per QALY gained (95$125,259 to $557,750 per QALY gained). Conclusions From a health economic perspective, both anti-EFGR therapies (panitumumab and cetuximab) showed very high Incremental cost-utility ratios and were not cost-effective at a willingness-to-pay threshold of$100,000 per QALY. The cost-utility ratios were much more favorable in subset of patients with wild-type KRAS. This suggests that personalizing advanced metastatic colorectal cancer treatment based on KRAS mutation status could not only save health care system substantial sums but also spare thousands of patients with metastatic colorectal cancer from side effects of the anti-EGFR therapies that are unlikely to benefit from the treatment

Knowledge Management Approaches for predicting Biomarker and Assessing its Impact on Clinical Trials

The recent success of companion diagnostics along with the increasing regulatory pressure for better identification of the target population has created an unprecedented incentive for the drug discovery companies to invest into novel strategies for stratified biomarker discovery. Catching with this trend, trials with stratified biomarker in drug development have quadrupled in the last decade but represent a small part of all Interventional trials reflecting multiple co-developmental challenges of therapeutic compounds and companion diagnostics. To overcome the challenge, varied knowledge management and system biology approaches are adopted in the clinics to analyze/interpret an ever increasing collection of OMICS data. By semi-automatic screening of more than 150,000 trials, we filtered trials with stratified biomarker to analyse their therapeutic focus, major drivers and elucidated the impact of stratified biomarker programs on trial duration and completion. The analysis clearly shows that cancer is the major focus for trials with stratified biomarker. But targeted therapies in cancer require more accurate stratification of patient population. This can be augmented by a fresh approach of selecting a new class of biomolecules i.e. miRNA as candidate stratification biomarker. miRNA plays an important role in tumorgenesis in regulating expression of oncogenes and tumor suppressors; thus affecting cell proliferation, differentiation, apoptosis, invasion, angiogenesis. miRNAs are potential biomarkers in different cancer. However, the relationship between response of cancer patients towards targeted therapy and resulting modifications of the miRNA transcriptome in pathway regulation is poorly understood. With ever-increasing pathways and miRNA-mRNA interaction databases, freely available mRNA and miRNA expression data in multiple cancer therapy have created an unprecedented opportunity to decipher the role of miRNAs in early prediction of therapeutic efficacy in diseases. We present a novel SMARTmiR algorithm to predict the role of miRNA as therapeutic biomarker for an anti-EGFR monoclonal antibody i.e. cetuximab treatment in colorectal cancer. The application of an optimised and fully automated version of the algorithm has the potential to be used as clinical decision support tool. Moreover this research will also provide a comprehensive and valuable knowledge map demonstrating functional bimolecular interactions in colorectal cancer to scientific community. This research also detected seven miRNA i.e. hsa-miR-145, has-miR-27a, has- miR-155, hsa-miR-182, hsa-miR-15a, hsa-miR-96 and hsa-miR-106a as top stratified biomarker candidate for cetuximab therapy in CRC which were not reported previously. Finally a prospective plan on future scenario of biomarker research in cancer drug development has been drawn focusing to reduce the risk of most expensive phase III drug failures

The significance of the EGFR pathway in malignant pleural mesothelioma

IntroductionEGFR, MTOR and COX2 are up regulated in malignant pleural mesothelioma (MPM). In this study we aimed to determine the expression of Lipoxygenase enzymes (LOX), absence of PTEN protein expression and the cytotoxic effect of EGFR, MTOR and COX2 inhibitors in MPM.Materials and MethodsImmunohistochemical analysis was performed in 93 archival MPM tissue samples to determine the expression of 5-LOX and 12-LOX and PTEN protein. The COX-2 positive cell lines MSTO-211H, NCI-H2052, NCI-H2452 (mesothelioma) and A549 (lung cancer) were utilised. All cell lines were tested for EGFR, KRAS and BRAF mutations. Cells were incubated with Cetuximab, Gefitinib, Rapamycin, Ku0063794 (MTOR kinase inhibitor) and Celecoxib as single agents and in combinations and analysed using the MTS assay.ResultsPositive 5-LOX expression was seen in 73% and positive 12-LOX expression was seen in 83% of MPM samples. PTEN protein expression was absent in 27% of the samples. A549 cells had a KRAS missense mutation at codon 12. No other EGFR, KRAS and BRAF mutations were identified in any of the cell lines. Cetuximab showed 50% cell growth inhibition in MSTO-211H cells at a concentration of 1.6 μM. All other cell lines were resistant to Cetuximab. All cell lines were resistant to Gefitinib. Rapamycin and Ku0063794 demonstrated 50% cell growth inhibition in NCI-H2052, NCI-H2452 and A549. Celecoxib demonstrated 50% cell growth inhibition in all cell lines. Cetuximab and Gefitinib were combined in turn with Rapamycin, Ku0063794 and Celecoxib. Cetuximab when combined with Celecoxib (NCI-H2052, NCI-H2452 and A549 cells) and Ku0063794 (MSTO-211H cells) demonstrated significant growth inhibition.ConclusionsOur study suggests that 5LOX and 12LOX are expressed in the majority and PTEN protein expression is absent is a significant proportion of MPM tissue samples. Inhibition of MTOR pathway may be an important therapeutic strategy in patients with MPM

The origin and properties of pro-oncogenic fields in the intestinal epithelium

Abstract: The intestinal epithelium is maintained by intestinal stem cells that replace each other stochastically over time. Stem cells that are excluded from the stem cell pool will differentiate into the absorptive or secretory cell lineages. However, intestinal cell-fate specification is not always restrictive and early secretory progenitors can revert back to the stem cell pool. Human colon cancer develops by acquisition of oncogenic mutations in the colonic epithelium throughout life. As secretory progenitors have unexpectedly been shown to be a significant source of colonic stem cells, they could serve a cell of origin for tumorigenesis. Furthermore, it has been speculated that tumours could arise in fields that encode pro-oncogenic mutations prior to overt tumour development. Mutations in KRAS can be found in 10% of healthy human colons in fields of up to 100 crypts that may be the cause of a subset of colorectal tumours. The extent to which such fields are predisposed to colorectal cancer development is unknown. The aims of this PhD project were to characterise the cell of origin and stem cell behaviour of KrasG12D fields and to develop new tools to recapitulate sequential mutations in vivo. Cre mediated lineage tracing of Atoh1 expressing early secretory progenitors carrying KrasG12D mutations demonstrated that KrasG12D expression does not change cell fate choices in homeostasis but appears to increase Atoh1+ stem cell contribution in the small intestine after Lgr5 depletion. In addition, Atoh1 derived KrasG12D stem cells have a competitive bias and Atoh1 derived KrasG12D crypts can multiply over time to create fields and polyps in the colonic epithelium. In addition, a mouse model that utilises Flp and Cre to temporally separate intestinal KrasG12D recombination from lineage-tracing was developed to study stem cell behaviour in KrasG12D fields. Lineage tracing in this model shows that crypts in KrasG12D epithelium have a markedly higher monoclonal conversion rate and accumulate an increased mutation load over time compared to WT crypts. Furthermore, the faster monoclonal conversion rate is shown to be dependent on Mek signalling downstream of Kras. Thus, KrasG12D fields may fix secondary mutations at an accelerated rate and so represent pro-oncogenic areas. Lastly, in this thesis a Rosa26 DrePr mouse model, that allows for recombination independently of other recombinases, is developed and used to initiate lineage tracing in a sequential model of Cre activated intestinal tumorigenesis. Collectively, the data presented in this thesis allows in-dept investigation of the cell of origin and stem cell behaviour in pro-oncogenic KrasG12D fields and contributes to the understanding of how such fields might lead to colon cancer

The emerging role of nimotuzumab in the treatment of non-small cell lung cancer

Current non-small cell lung cancer (NSCLC) chemotherapy and radiotherapy regimens, although showing definite survival benefit, still leave patients with a disappointing 15% 5-year overall survival rate. Because of the need to improve traditional outcomes, research has focused on identifying specific tumorigenic pathways that may serve as therapeutic targets. The most successful strategies to date are those aimed at the epidermal growth factor receptor (EGFR), which is found to be upregulated in 40%–80% of NSCLC. Several tyrosine kinase inhibitors and monoclonal antibodies (mAbs) have been developed that inhibit the EGFR receptor and have demonstrated clinical benefit in trials as single agents and in combination regimens. Here we discuss one such agent, the mAb nimotuzumab, the background of its development, its clinical experience in NSCLC thus far, and the rationale for expanding its use to other NSCLC treatment settings

Neutral evolution of drug resistant colorectal cancer cell populations is independent of their KRAS status

Emergence of tumor resistance to an anti-cancer therapy directed against a putative target raises several questions including: (1) do mutations in the target/pathway confer resistance? (2) Are these mutations pre-existing? (3) What is the relative fitness of cells with/without the mutation? We addressed these questions in patients with metastatic colorectal cancer (mCRC). We conducted an exhaustive review of published data to establish a median doubling time for CRCs and stained a cohort of CRCs to document mitotic indices. We analyzed published data and our own data to calculate rates of growth (g) and regression (d, decay) of tumors in patients with CRC correlating these results with the detection of circulating MT-KRAS DNA. Additionally we estimated mathematically the caloric burden of such tumors using data on mitotic and apoptotic indices. We conclude outgrowth of cells harboring intrinsic or acquired MT-KRAS cannot explain resistance to anti-EGFR (epidermal growth factor receptor) antibodies. Rates of tumor growth with panitumumab are unaffected by presence/absence of MT-KRAS. While MT-KRAS cells may be resistant to anti-EGFR antibodies, WT-KRAS cells also rapidly bypass this blockade suggesting inherent resistance mechanisms are responsible and a neutral evolution model is most appropriate. Using the above clinical data on tumor doubling times and mitotic and apoptotic indices we estimated the caloric intake required to support tumor growth and suggest it may explain in part cancer-associated cachexia

Noninvasive biomarkers of colorectal cancer: role in diagnosis and personalised treatment perspectives

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide. It has been estimated that more than one-third of patients are diagnosed when CRC has already spread to the lymph nodes. One out of five patients is diagnosed with metastatic CRC. The stage of diagnosis influences treatment outcome and survival. Notwithstanding the recent advances in multidisciplinary management and treatment of CRC, patients are still reluctant to undergo screening tests because of the associated invasiveness and discomfort (e.g., colonoscopy with biopsies). Moreover, the serological markers currently used for diagnosis are not reliable and, even if they were useful to detect disease recurrence after treatment, they are not always detected in patients with CRC (e.g., CEA). Recently, translational research in CRC has produced a wide spectrum of potential biomarkers that could be useful for diagnosis, treatment, and follow-up of these patients. The aim of this review is to provide an overview of the newer noninvasive or minimally invasive biomarkers of CRC. Here, we discuss imaging and biomolecular diagnostics ranging from their potential usefulness to obtain early and less-invasive diagnosis to their potential implementation in the development of a bespoke treatment of CRC