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  • 1
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 1893-1893
    Abstract: Background: Multiple myeloma (MM) is an incurable and heterogeneous haematological malignancy in which immune suppression and complex biology affect the disease and its response to treatment. Several new treatments have been approved for MM in recent years providing numerous options for patients with relapsed/refractory disease. However, there is no validated method for selecting the best treatment combination for each patient, making patient management difficult. The ability to predict treatment response based on disease characteristics could improve clinically outcomes. Aim: This was a validation of a genomics-informed response prediction using computational biology modelling (CBM) in patients with relapsed/refractory MM. Methods: Input data from fluorescence in-situ hybridization (FISH), karyotype, and a MM specific next generation sequencing capture array were analysed using CBM. This was a retrospective review of patients which were treated with different combinations based on patient/physician choice. The CBM uses PubMed and other online resources to generate patient-specific protein network maps of activated and inactivated pathways. The specific drug combination for each patient was simulated and the quantitative drug effect was measured on a composite MM disease inhibition score (i.e., cell proliferation, viability, apoptosis and paraproteins). The predicted outcomes were then compared to the clinical response (≥PR or 〈 PR per IMWG) to assess the accuracy of this CBM predictive approach. Results: 27 patients were selected for the study; 3 failed CBM due to missing inputs and in 3 clinical response was not able to be assessed, leaving 21 eligible for the analysis. The median age at presentation was 57 years (range 37-76) and 52% were male. The median prior lines of MM therapy was 5 (range 1-15). 38% were refractory to bortezomib, 62% to lenalidomide, 52% to carfilzomib, 57% to pomalidomide, and 43% to daratumumab. 81% had a prior autologous stem cell transplant. The treatments modelled included IMiD-based regimens (n = 9), PI-based regimens (n = 6), chemo-based regimens (n = 3), selinexor (n = 2), PI/IMiD combination regimens (n = 1). Sixteen were clinical responders and 5 were non-responders. CBM predictions matched for 17 of 21 treatments overall, 15 of 16 clinical responders and 2 of 5 non-responders. The statistics of prediction accuracy against clinical outcome are presented in Table 1. Interestingly, the CBM identified drugs within the combination regimens which may not have impacted efficacy. For example, the CBM predicted that one patient treated with bortezomib, venetoclax, and dexamethasone would have had similar response if venetoclax had been omitted from the regimen. Conclusion: We have demonstrated that a CBM approach, which incorporates genomics, can help predict response in patients with relapsed or refractory MM. Prospective studies using the CBM as part of treatment decision-making will help determine its application into clinical settings. Disclosures Vij: Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Jazz Pharmaceuticals: Honoraria, Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Karyopharma: Honoraria, Membership on an entity's Board of Directors or advisory committees; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Honoraria, Membership on an entity's Board of Directors or advisory committees; Jansson: Honoraria, Membership on an entity's Board of Directors or advisory committees. Singh:Cellworks Research India Private Limited: Employment. Sauban:Cellworks Research India Private Limited: Employment. Husain:Cellworks Research India Private Limited: Employment. Lakshminarayana:Cellworks Research India Private Limited: Employment. Talawdekar:Cellworks Research India Private Limited: Employment. Mitra:Cellworks Research India Private Limited: Employment. Abbasi:Cell Works Group Inc.: Employment. Vali:Cell Works Group Inc.: Employment.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
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  • 2
    In: Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 32, No. 15_suppl ( 2014-05-20), p. e19582-e19582
    Type of Medium: Online Resource
    ISSN: 0732-183X , 1527-7755
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    Language: English
    Publisher: American Society of Clinical Oncology (ASCO)
    Publication Date: 2014
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  • 3
    In: International Journal of Radiation Oncology*Biology*Physics, Elsevier BV, Vol. 108, No. 3 ( 2020-11), p. 716-724
    Type of Medium: Online Resource
    ISSN: 0360-3016
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
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  • 4
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2013
    In:  Cancer Research Vol. 73, No. 8_Supplement ( 2013-04-15), p. 2104-2104
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 2104-2104
    Abstract: Background: Drug repositioning - the application of marketed drugs to new diseases - is a time and cost effective alternative to de novo drug development. Thalidomide is a hallmark example of drug repositioning success. Withdrawn from the market in 1961 after causing thousands of severe birth defects, its newly discovered anti-angiogenic and immunomodulatory properties cleared the way for Food and Drug Administration (FDA) approval in 2006 for multiple myeloma (MM). Although thalidomide has demonstrated remarkable success in the treatment of MM, responses are typically short-lived with the emergence of resistance. For complex diseases like cancer, multi-target therapeutics are well suited to address efficacy and drug resistance challenges. Here we have designed a novel therapeutic combination of drugs for MM that impacts all disease phenotypes. Methods: Using a computer modeling system from Cellworks that mimics and simulates cancer disease physiology to predict clinical outcomes, we identified AT101 (Bcl2 antagonoist) and tesaglitazar (PPAR α/γ agonist) as a potentially effective drug combination for MM. This combination was shortlisted from over two hundred pharmacodynamic dose-response simulation studies using criteria of efficacy and synergy. Computer modeling predicted that this drug combination mechanistically targets apoptotic pathways and the combination of the agents provides greater than additive activity. These predictive findings were assessed in vitro using OPM2 and U266 human MM cell lines. AT101 and tesaglitazar growth inhibition was evaluated using the MTT assay and analysis of synergy was determined using the Bliss Independence model. Apoptotic induction was analyzed by immunoblotting for cleaved forms of caspases and PARP. Results: 10 μM tesaglitazar and 2 μM AT101 display minimal and moderate growth inhibition respectively as single agents in OPM2 and U266 MM cell lines. Growth inhibition in these cell lines is dramatically enhanced when the drugs are used in combination, reducing cellular viability by 88% and 77% in OPM2 and U266 cells, respectively. Based upon the Bliss Independence model, the relationship between tesaglitazar and AT-101 is synergistic in both cell lines. Combination treatment in both cell lines results in increased apoptosis as indicated by enhanced cleavage of PARP and caspase 3 and 9. Conclusions: Not only do these experiments identify AT101 and tesaglitazar as a potentially effective drug combination for the treatment of MM, these results also validate the use of rationally based, computer modeling to design effective therapeutics and predict clinical outcomes. Future studies will evaluate the mechanism of action for the synergistic interaction between tesaglitazar and AT101 in MM. Citation Format: Nicole A. Doudican, Shireen Vali, Shweta Kapoor, Anay Talawdekar, Zeba Sultana, Taher Abbasi, Gautam Sethi, Seth J. Orlow, Amitabha Mazumder. In vitro validation of rationally designed therapeutic based on drug repositioning and combinations. [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 2104. doi:10.1158/1538-7445.AM2013-2104
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 5
    In: Leukemia Research, Elsevier BV, Vol. 77 ( 2019-02), p. 42-50
    Type of Medium: Online Resource
    ISSN: 0145-2126
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
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  • 6
    In: Blood, American Society of Hematology, Vol. 120, No. 21 ( 2012-11-16), p. 5022-5022
    Abstract: Abstract 5022 Background: The extremely long development time and low success rate for new drug development programs has translated into limited clinical options in the treatment of cancer. The challenge is further compounded by drug resistance seen in clinical settings for approved standard of care therapeutic options like chemotherapy and targeted drugs like Bortezomib in Multiple Myeloma (MM). This has accelerated the need for initiatives and strategies which promote innovation but drastically reduce drug development failures through prediction of clinical outcomes. We present here a methodology and rationally designed therapeutic program for MM. This program has novel first-in-class mechanism of action and has been developed using a strategy of re-purposing and combinations based on National Center for Advanced Translational Sciences (NCATS) library of industry-provided drugs. Methods: The therapy design and development was completed using validated proprietary technology from Cellworks which enables simulation of cancer disease physiology computationally for predicting clinical outcomes. The comprehensive integrated representation of signaling and metabolic networks across all disease phenotypes and functional proteomics abstraction facilitated a large number of predictive studies in weeks with quantitative transparency into the network. The predictive cancer technology was customized to four MM profiles: OPM2, RPM1, SKMM2 and U266. Ten of the molecularly targeted drugs from the NCATS library were digitally screened alone and in combinations of two across the four MM profiles at four concentrations (C, C/2, C/4, and C/8). Based on screening of over six thousand predictive studies, three designed therapeutics hits were intelligently shortlisted based on synergistic impact on viability and proliferation. Results: The focused therapeutic candidate hit was selected based on synergy using viability endpoints and apoptosis markers such as caspase 3, PARP1 at sub-therapeutic doses. The proposed therapeutic regimen is a sub-therapeutic combination of AT101 and AVE0847. AT101 is a BCL2 inhibitor and AVE0847 is a PPAR alpha and gamma agonist agent. The concentration of each drug used in the designed therapy was close to IC30. The predictive results showed a synergistic increase in apoptotic markers caspase 3 and PARP1 cleaved form. This hit candidate is being pre-clinically validated experimentally across four MM profiles and results will be presented. Conclusion: The design of first in class mechanism of action based therapeutic strategies of drug rescue/repurposing has been used to identify AT101 and AVE0847 as a promising drug combination for use in MM which predicatively results in a synergistic increase in apoptosis. These results are currently being validated in vitro. The inherent multi target mechanism of action predicted by this combination could potentially eliminate the drug resistance challenges of single target therapeutics. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2012
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  • 7
    In: Blood, American Society of Hematology, Vol. 132, No. Supplement 1 ( 2018-11-29), p. 4034-4034
    Abstract: Background: Pediatric AML (pAML) treatment outcomes can vary due to genomic heterogeneity. Thus, selecting the right drugs for a given patient is challenging. There is a need for a priori means of predicting treatment responses based on tumor "omics". Computational biology modeling (CBM) is a precision medicine approach by which biological pathways of tumorigenesis are mapped using mathematical principles to yield a virtual, interactive tumor model. This model can be customized based on a patient's omics and analyzed virtually for response to therapies. Aim: To define prediction values of a CBM precision medicine approach in matching clinical response to ADE therapy in a cohort of pAML patients. Methods: Thirty pAML patients that were treated ADE chemotherapy were utilized with information on the clinical, genomic (cytogenetics, mutations) and protein expression data from this cohort of pAML patients used for the CBM. From cytogenetics results, gene copy number variations were coded as either knocked-down (KD) or over-expressed (OE). From NGS results (2 gene panel - CEBPA, NPM1), gene mutations were coded as either loss or gain of function (LOF or GOF). For protein expression data, proteins that were 〉 2sigma from the mean were coded as KD if their value was 〈 0 or OE if their value was 〉 0. Proteins with values 〈 2sigma from the mean were not included in the CBM as perturbed. The LOF, GOF, KD, OE data was input in the CBM software system (Cellworks Group) to generate patient-specific maps of AML. Each map showed unique interplay of dysregulated networks for the patient's AML. Digital drug simulations were then conducted in each map to measure the impact of cytarabine, daunorubicin and etoposide alone and in combination to predict AML disease inhibition score (DIS) (composite of cell proliferation, viability, apoptosis and impact on patient-specific biomarkers). Response to treatment is determined based on a threshold DIS range derived through AML training datasets comprising omics and clinical outcome. Clinical outcome data for these pAML patients treated with ADE was compared with CBM predictions. Clinical response was defined as complete response at the end of consolidation therapy as per International Working Group 2006 criteria. Results: Assessment was made for 30 patients, 14 female, median age 14 years, all of which achieved CR, with predictions made for all but one which lacked sufficient genomic inputs. CBM accurately predicted the clinical outcomes of 28 of 29 responders, with an accuracy and positive predictive value of 96 %. Multivariate analysis of predictive score with age at diagnosis, DFS and OS is positively correlated with Pearson coefficient of 0.22, 0.54 and 0.49. Analysis of the individual drug responses of each patient indicated that some of the drugs were predicted to be non-responsive based on the patient-disease pathway characteristics, and could have been eliminated from the treatment, thus reducing the overall adverse impact of the very intensive therapy regimen. There were profiles in which AraC was a responder due to decreased mismatch repair pathway in the disease network resulting from presence of aberrations such as KMT2A-AFDN, RUNX1-RUNX1T1, CEBPA LOF, KDM1A OE, MSH2 KD etc., while Daunorubicin and Etoposide were predicted as non-responders due to presence of an intact homologous DNA repair pathway as a result of absence of aberrations in HR pathway genes. CBM analysis of patient "omics" driven disease characteristics could have eliminated additional drugs for such patients. Conclusion: The CBM prediction of ADE in pAML patients based on genomic, proteomic and clinical data showed high predictive accuracy of 96.55%. CBM analysis of patients' genomics and proteomics driven disease characteristics and individual drug response prediction indicated that the intensive therapy regimen can be tailored for each patient to minimize toxicity by removing non-responsive drugs. The study validates the approach to a priori predict response and identify optimal therapy option for the patient. Disclosures Cogle: Celgene: Other: Steering Committee Member of Connect MDS/AML Registry. Abbasi:Cell Works Group Inc.: Employment. Singh:Cellworks Research India Private Limited: Employment. Sauban:Cellworks Research India Private Limited: Employment. Raman:Cellworks Research India Private Limited: Employment. Vidva:Cellworks Research India Private Limited: Employment. Tyagi:Cellworks Research India Private Limited: Employment. Talawdekar:Cellworks Research India Private Limited: Employment. Das:Cellworks Research India Private Limited: Employment. Vali:Cell Works Group Inc.: Employment.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2018
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  • 8
    In: Blood, American Society of Hematology, Vol. 122, No. 21 ( 2013-11-15), p. 4219-4219
    Abstract: Background The unique signature of a patient’s tumor mandates the need to rationally design personalized therapies employing N=1 segmentation conceptually. Repurposing of existing drug agents with validated clinical safety and pharmacokinetics data provides a rapid translational path to clinic which otherwise would require years of development time and associated new chemical risks. By focusing on rationally designed personalized treatment mechanisms, our strategy targets multiple key pathways to address the clinical problem of emergence of single therapy resistance. In order to overcome MM resistance, we have (1) employed predictive simulation modeling based upon patient genetic and environment profiling to design patient context specific combinatorial therapeutic regimens using library of drug agents from across indications with prior clinical data and (2) validating designed therapy ex-vivo in patient derived cell lines. Methods Clinical patient samples were analyzed for chromosome evaluation and molecular cytogenetic analysis by NYU. Using this information, an in silico simulation avatar of the patient was created. To identify effective personalized therapeutics, we focused our study on compounds from the National Center for Advanced Translational Science (NCATS) and other molecularly targeted agents. The predictive simulation based approach from Cellworks provides a comprehensive representation of MM disease physiology incorporating signaling and metabolic networks with an integrated phenotype view. This extensively validated simulation model predicts clinical outcomes with phenotype and bio-marker assays. Hits were shortlisted from over thousand pharmacodynamic dose-response simulation studies using criteria of efficacy and synergy. Computer modeling predicted that therapeutic combination mechanistically targets apoptotic pathways and the combination of the agents provides greater than additive activity. These predictive findings are in the process of being assessed ex vivo and retrospectively validated. Results The analysis detected loss of chromosome 13 signal consistent with monosomy 13 and loss of TP53 signal consistent with deletion of TP53; all other probes contained normal signal patterns. The shortlisted therapeutic combination identified from predictive simulation-based screening was BEZ235 (PI3K/mTOR inhibitor) and ABT-199 (BCL2 inhibitor). IC30 concentrations of the single agents resulted in a 56% inhibition of proliferation and 49% inhibition of viability in predictive simulations. The apoptotic markers CASP3, CASP9, Cleaved-PARP1 and BAK1 increased by 74% (1.75 fold), 132% (2.32 fold), 81% (1.8 fold), 217% (3.17 fold), respectively. The proposed mechanism of action using simulation model identified the p53 deletion as responsible for increased BCL2 activity and levels of activated AKT. Deletion of p53 increased levels of activated AKT via decreases in PTEN and IGFBP3. Hence, a mechanism that targets the PI3K/AKT/mTOR and BCL2 family showed efficacy in the simulation avatar of the patient and are currently being validated ex-vivo in patient cells. Conclusions This study demonstrates and validates simulation approaches and technologies to leverage big data from patient genomic analysis to create a simulation avatar for rational design of personalized therapeutics. This level of personalization, beyond linking point mutations to associated drugs targeting the same mutations, truly incorporates the broad patient tumor signature in translational path forward. Disclosures: No relevant conflicts of interest to declare.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2013
    detail.hit.zdb_id: 1468538-3
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  • 9
    In: Blood Advances, American Society of Hematology, Vol. 3, No. 12 ( 2019-06-25), p. 1837-1847
    Abstract: Patients with myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML) are generally older and have more comorbidities. Therefore, identifying personalized treatment options for each patient early and accurately is essential. To address this, we developed a computational biology modeling (CBM) and digital drug simulation platform that relies on somatic gene mutations and gene CNVs found in malignant cells of individual patients. Drug treatment simulations based on unique patient-specific disease networks were used to generate treatment predictions. To evaluate the accuracy of the genomics-informed computational platform, we conducted a pilot prospective clinical study (NCT02435550) enrolling confirmed MDS and AML patients. Blinded to the empirically prescribed treatment regimen for each patient, genomic data from 50 evaluable patients were analyzed by CBM to predict patient-specific treatment responses. CBM accurately predicted treatment responses in 55 of 61 (90%) simulations, with 33 of 61 true positives, 22 of 61 true negatives, 3 of 61 false positives, and 3 of 61 false negatives, resulting in a sensitivity of 94%, a specificity of 88%, and an accuracy of 90%. Laboratory validation further confirmed the accuracy of CBM-predicted activated protein networks in 17 of 19 (89%) samples from 11 patients. Somatic mutations in the TET2, IDH1/2, ASXL1, and EZH2 genes were discovered to be highly informative of MDS response to hypomethylating agents. In sum, analyses of patient cancer genomics using the CBM platform can be used to predict precision treatment responses in MDS and AML patients.
    Type of Medium: Online Resource
    ISSN: 2473-9529 , 2473-9537
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
    detail.hit.zdb_id: 2876449-3
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  • 10
    In: Journal of Translational Medicine, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2015), p. 43-
    Type of Medium: Online Resource
    ISSN: 1479-5876
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
    detail.hit.zdb_id: 2118570-0
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