7 results on '"Deepak Anil Lala"'
Search Results
2. Computational modeling of early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) to identify personalized therapy using genomics
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Leylah Drusbosky, Shireen Vali, Shahabuddin Usmani, Shivgonda C. Birajdar, Ansu Kumar, Christopher R. Cogle, P. R. K. Bhargav, Anuj Tyagi, Aftab Alam, Taher Abbasi, Amy Meacham, Deepak Anil Lala, Anusha Pampana, Kunal Ghosh Roy, Sumanth Vasista, Girish Chinnaswamy, Madeleine Turcotte, Swaminathan Rajagopalan, Manju Sengar, Bijal D. Shah, and Kabya Basu
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Drug ,Cancer Research ,NPM1 ,media_common.quotation_subject ,T cell ,Lymphoblastic Leukemia ,Genomics ,Computational biology ,Biology ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Sensitivity and Specificity ,03 medical and health sciences ,0302 clinical medicine ,Biomarkers, Tumor ,medicine ,Humans ,Computer Simulation ,Precision Medicine ,Personalized therapy ,media_common ,Computational Biology ,Myeloid leukemia ,Hematology ,medicine.disease ,Leukemia ,medicine.anatomical_structure ,Oncology ,030220 oncology & carcinogenesis ,Nucleophosmin ,030215 immunology - Abstract
Early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) is an aggressive hematological malignancy for which optimal therapeutic approaches are poorly characterized. Using computational biology modeling (CBM) in conjunction with genomic data from cell lines and individual patients, we generated disease-specific protein network maps that were used to identify unique characteristics associated with the mutational profiles of ETP-ALL compared to non-ETP-ALL (T-ALL) cases and simulated cellular responses to a digital library of FDA-approved and investigational agents. Genomics-based classification of ETP-ALL patients using CBM had a prediction sensitivity and specificity of 93% and 87%, respectively. This analysis identified key genomic and pathway characteristics that are distinct in ETP-ALL including deletion of nucleophosmin-1 (NPM1), mutations of which are used to direct therapeutic decisions in acute myeloid leukemia. Computational simulations based on mutational profiles of 62 ETP-ALL patient models identified 87 unique targeted combination therapies in 56 of the 62 patients despite actionable mutations being present in only 37% of ETP-ALL patients. Shortlisted two-drug combinations were predicted to be synergistic in 11 profiles and were validated by in vitro chemosensitivity assays. In conclusion, computational modeling was able to identify unique biomarkers and pathways for ETP-ALL, and identify new drug combinations for potential clinical testing.
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- 2019
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3. Biosimulation Using the Cellworks Computational Omics Biology Model (CBM) Identifies Immune Modulation As a Key Pathway for Predicting Azacitidine (AZA) Response in Myelodysplastic Syndromes (MDS)
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Shruthi Kulkarni, Yugandhara Narvekar, Scott C. Howard, Himanshu Grover, Rahul K Raman, Anusha Pampana, Anuj Tyagi, Prashant Ramachandran Nair, Michele Dundas Macpherson, Deepak Anil Lala, S. Mohapatra, Ansu Kumar, Kritika Sahni, Shweta Kapoor, Michael Castro, Nirjhar Mundkur, Vijayashree P Shyamasundar, Ashokraja Balla, Guido Marcucci, Mamatha Patil, Rakhi Purushothaman Suseela, James Christie, Divya Singh, Naga Ganesh Palaniyeppa, Veena Balakrishnan, and Sanjana Patel
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Myelodysplastic syndromes ,Immunology ,Azacitidine ,Cell Biology ,Hematology ,Computational biology ,Biology ,Immune modulation ,medicine.disease ,Omics ,Biochemistry ,Key (cryptography) ,medicine ,Biosimulation ,medicine.drug - Abstract
Background: DNA methyltransferase inhibition (DNMTi) with the hypomethylating agents (HMA) azacitidine (AZA) or decitabine, remains the mainstay of therapy for the majority of high-risk Myelodysplastic Syndromes (MDS) patients. Nevertheless, only 40-50% of MDS patients achieve clinical improvement with DNMTi. There is a need for a predictive clinical approach that can stratify MDS patients according to their chance of benefit from current therapies and that can identify and predict responses to new treatment options. Ideally, patients predicted to be non-responders (NR) could be offered alternative strategies while being spared protracted treatment with HMA alone that has a low likelihood of efficacy. Recently, an intriguing discovery of immune modulation by HMA has emerged. In addition to the benefits of unsilencing differentiation genes and tumor suppressor genes, HMA's reactivate human endogenous retroviral (HERV) genes leading to viral mimicry and upregulation of the immune response as a major mechanism of HMA efficacy. Although the PD-L1/PD1 blockade plus HMA has been recognized as a beneficial combination, there are no established markers to guide decision-making. We report here the utility of immunomic profiling of chromosome 9 copy number status as a significant mechanism of immune evasion and HMA resistance. Methods: 119 patients with known clinical responses to AZA were selected for this study. Publicly available data largely from TCGA and PubMed was utilized for this study. The aberration and copy number variations from individual cases served as input into the Cellworks Computation Omics Biology Model (CBM), a computational biology multi-omic software model, created using artificial intelligence heuristics and literature sourced from PubMed, to generate a patient-specific protein network map. Disease-biomarkers unique to each patient were identified within protein network maps. The Cellworks Biosimulation Platform has the capacity to biosimulate disease phenotypic behavior and was used to create a disease model and then conduct biosimulations to measure the effect of AZA on a cell growth score comprised of a composite of cell proliferation, viability, apoptosis, metastasis, and other cancer hallmarks. Biosimulation of drug response was conducted to identify and predict therapeutic efficacy. Results: Although AZA treatment increased tumor associated antigens and interferon signaling, it also increased PD-L1 expression to inactivate cytotoxic CD8(+) T cells. Copy number alterations of the chromosome 9p region were found to significantly drive PD-L1 expression with multiple genes such as CD274, IFNA1, IFNA2, JAK2, PDCD1LG and KDM4C playing a role in PD-L1 regulation further increasing immune suppression (Figure 1). Among 6 cases of chromosome 9p aberration in this dataset, 9p amp (n=2) were clinical non-responders (NR) while 9p del (n=4) were responders (R) to AZA. In principle, checkpoint immunotherapy could improve outcomes for patients with 9p abnormalities. Additionally, copy number variation loss of key genes located on chromosome 16 involved in antigen processing and presentation such as CIITA, CTCF, IRF8, PSMB10, NLRC5, and SOCS1 were found to negatively impact AZA sensitivity (NR=4; R=0); these patients would also be unlikely to respond to checkpoint immunotherapy. Also, aberrations in melanoma antigen gene (MAGE) family proteins (NR=2; R=O), and STT3A (NR=1; R=5) were found to impact AZA efficacy by decreasing antigen processing on tumor cells. Conclusion: Based on the results from the Cellworks Biosimulation Platform applied to the CBM, copy number variants of chromosome 9p and 16 can be converted into CBM-derived biomarkers for response to checkpoint immunotherapy in combination with HMA. Our results support a future prospective evaluation in larger cohorts of MDS patients. Figure 1 Figure 1. Disclosures Howard: Servier: Consultancy; Cellworks Group Inc.: Consultancy; Sanofi: Consultancy, Other: Speaker fees. Kumar: Cellworks Group Inc.: Current Employment. Castro: Bugworks: Consultancy; Exact sciences Inc.: Consultancy; Guardant Health Inc.: Speakers Bureau; Cellworks Group Inc.: Current Employment; Caris Life Sciences Inc.: Consultancy; Omicure Inc: Consultancy. Grover: Cellworks Group Inc.: Current Employment. Mohapatra: Cellworks Group Inc.: Current Employment. Kapoor: Cellworks Group Inc.: Current Employment. Tyagi: Cellworks Group Inc.: Current Employment. Nair: Cellworks Group Inc.: Current Employment. Suseela: Cellworks Group Inc.: Current Employment. Pampana: Cellworks Group Inc.: Current Employment. Lala: Cellworks Group Inc.: Current Employment. Singh: Cellworks Group Inc.: Current Employment. Shyamasundar: Cellworks Group Inc.: Current Employment. Kulkarni: Cellworks Group Inc.: Current Employment. Narvekar: Cellworks Group Inc.: Current Employment. Sahni: Cellworks Group Inc.: Current Employment. Raman: Cellworks Group Inc.: Current Employment. Balakrishnan: Cellworks Group Inc.: Current Employment. Patil: Cellworks Group Inc.: Current Employment. Palaniyeppa: Cellworks Group Inc.: Current Employment. Balla: Cellworks Group Inc.: Current Employment. Patel: Cellworks Group Inc.: Current Employment. Mundkur: Cellworks Group Inc: Current Employment. Christie: Cellworks Group Inc.: Current Employment. Macpherson: Cellworks Group Inc.: Current Employment. Marcucci: Abbvie: Other: Speaker and advisory scientific board meetings; Novartis: Other: Speaker and advisory scientific board meetings; Agios: Other: Speaker and advisory scientific board meetings.
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- 2021
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4. Biosimulation Using the Cellworks Computational Omics Biology Model (CBM) Predicted Novel Biomarkers for Hyper-CVAD (CVAD) Treatment Response and Combination of Rituximab and Cladribine (RC) in CVAD Resistant Cases of Mantle Cell Lymphoma (MCL)
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Mamatha Patil, Naga Ganesh Palaniyeppa, Diwyanshu Sahu, Yashaswini S Ullal, Kabya Basu, Jharana Mohanty, Vishwas Joseph, Upasana Mitra, Scott C. Howard, Mohammed Sauban, Ashokraja Balla, Vijayashree P Shyamasundar, S. Mohapatra, Annapoorna Prakash, Shweta Kapoor, Swati Khandelwal, Guido Marcucci, Liptimayee Behura, Deepak Anil Lala, Michele Dundas Macpherson, Sanjana Patel, Ansu Kumar, Karthik Sundara Raju, Michael Castro, and Ashish Kumar Agrawal
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Oncology ,Treatment response ,medicine.medical_specialty ,Immunology ,Hyper-CVAD ,Cell Biology ,Hematology ,Biology ,medicine.disease ,Omics ,Biochemistry ,Internal medicine ,medicine ,Rituximab ,Mantle cell lymphoma ,Biosimulation ,Cladribine ,medicine.drug - Abstract
Background: Mantle Cell Lymphoma (MCL) accounts for 3-10% of all non-Hodgkin lymphomas with a median overall survival of 3-4 years. Hyper-CVAD (CVAD) with or without Rituximab constitutes first line therapy for treatment of MCL, yet the use of this combination is associated with high toxicity and only modest efficacy. On the other hand, impressive clinical efficacy has been reported in relapsed MCL patients treated with rituximab and cladribine (RC). Prediction of response based on cancer genomics heterogeneity creates an opportunity to personalize treatment and avoid toxic therapy which has little chance of response. We conducted a study using the Cellworks Biosimulation Platform to identify novel genomic biomarkers associated with response to CVAD and RC among MCL patients. Method: Newly-diagnosed MCL patients were selected for this study based largely on genomic data (i.e. aberrations and copy number variations) published in PubMed and TCGA. The Cellworks Computational Omics Biology Model (CBM) is a computational multi-omic biology software model created using artificial intelligence heuristics and literature sourced from PubMed, to generate a patient-specific protein network map. Genomic data from each patient served as input for the CBM. Biomarkers unique to each patient were identified within protein network-maps. Drug impact on the disease network was biosimulated using the Cellworks Biosimulation Platform to determine a treatment efficacy value by measuring the treatment effects on the cell growth score, a composite of cell proliferation, viability, apoptosis, metastasis, DNA damage and other cancer hallmarks. The mechanism of action of each drug was mapped to each patient's CBM and the predicted biological consequences were used to determine response. Biosimulation of CVAD was applied to the patients in this cohort. RC was biosimulated on all CVAD non-responders. Results: Among the 94 MCL patients treated with CVAD, the Cellworks Biosimulation Platform identified novel biomarkers (Table 1) to predict treatment response or failure. The biosimulation also identified unique drug combinations for patients that were non-responders (NR) to both treatments. Of the 94 patients, 57 were deemed responders (R) and 37 non-responders (NR). ATM LOF/del, RAD51 del, LIG4A del, RB1 del, ERCC5 del, CARD11 amp, IKZF1 amp, and FANCC del were major predictors of CVAD response. These genes contributed to drug efficacy by impacting various pathways, including DNA repair, oxidative-stress, NFKB activation, spindle formation and mitotic-catastrophe. The frequency of aberration affecting these genes was high among the R group and was low in the NR group. Biosimulation was used to assess response to RC, and predicted, that 41 of 94 patients would respond and 53 would not respond. KMT2D LOF and SMAD4 del were associated with response to RC. Epigenetic dysregulation caused by KMT2D LOF decreased MSH6-mediated mismatch repair required for futile DNA repair leading to replication fork arrest and apoptosis. Interestingly, KMT2D LOF was identified in 20/41 R to RC. MYC amp, NOTCH 1 GOF, and NT5C2 amp were identified as key non-response markers for RC. In considering both regimens, 27 patients were predicted R to both CVAD and RC, 14 to RC but not to CVAD, 30 to CVAD but not RC, and 23 NR to both regimens. In the latter group, biosimulation predicted that a venetoclax-based combination would be effective in many cases due to the high incidence of TP53 GOF mutation within this subgroup. Conclusions: This pilot study highlights how the Cellworks Biosimulation Platform applied to the patient-specific CBM can identify treatment alternatives for patients with low likelihood of response to standard therapy or who may be ineligible for CVAD because of co-morbidities. RC responsiveness was either an equivalent but much less toxic option to CVAD or superior to CVAD. By using novel biomarkers derived from comprehensive mutational and copy number analysis, the CBM identified pathway-based, polygenic biomarkers that can be employed to determine optimal drug combinations for MCL patients. This biosimulation approach warrants prospective validation in a larger patient cohort. Figure 1 Figure 1. Disclosures Marcucci: Abbvie: Other: Speaker and advisory scientific board meetings; Agios: Other: Speaker and advisory scientific board meetings; Novartis: Other: Speaker and advisory scientific board meetings. Kumar: Cellworks Group Inc.: Current Employment. Castro: Bugworks: Consultancy; Caris Life Sciences Inc.: Consultancy; Omicure Inc: Consultancy; Guardant Health Inc.: Speakers Bureau; Cellworks Group Inc.: Current Employment; Exact sciences Inc.: Consultancy. Khandelwal: Cellworks Group Inc.: Current Employment. Mohapatra: Cellworks Group Inc.: Current Employment. Kapoor: Cellworks Group Inc.: Current Employment. Agrawal: Cellworks Group Inc.: Current Employment. Sauban: Cellworks Group Inc.: Current Employment. Basu: Cellworks Group Inc.: Current Employment. Shyamasundar: Cellworks Group Inc.: Current Employment. Lala: Cellworks Group Inc.: Current Employment. Raju: Cellworks Group Inc.: Current Employment. Palaniyeppa: Cellworks Group Inc.: Current Employment. Ullal: Cellworks Group Inc.: Current Employment. Joseph: Cellworks Group Inc.: Current Employment. Behura: Cellworks Group Inc.: Current Employment. Sahu: Cellworks Group Inc.: Current Employment. Prakash: Cellworks Group Inc.: Current Employment. Mitra: Cellworks Group Inc.: Current Employment. Balla: Cellworks Group Inc.: Current Employment. Patil: Cellworks Group Inc.: Current Employment. Mohanty: Cellworks Group Inc.: Current Employment. Patel: Cellworks Group Inc.: Current Employment. Macpherson: Cellworks Group Inc.: Current Employment. Howard: Sanofi: Consultancy, Other: Speaker fees; Servier: Consultancy; Cellworks Group Inc.: Consultancy.
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- 2021
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5. Therapy Biosimulation Using the Cellworks Computational Omics Biology Model (CBM) Is Predictive of Individual Acute Myeloid Leukemia (AML) Patient Probability of Clinical Response (CR) and Overall Survival (OS): Mycare-023
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Drew Watson, Yashaswini S Ullal, Scott C. Howard, Ashish Kumar Agrawal, Michael Castro, Diwyanshu Sahu, Mohammed Sauban, Kabya Basu, Shweta Kapoor, Anusha Pampana, Rakhi Purushothaman Suseela, Anuj Tyagi, Poornachandra G, Yugandhara Narvekar, Adity Ghosh, Prashant Ramachandran Nair, Deepak Anil Lala, Karthik Sundara Raju, Sanjana Patel, Samiksha Avinash Prasad, James Christie, Kunal Ghosh Roy, Nirjhar Mundkur, Swaminathan Rajagopalan, Aftab Alam, Guido Marcucci, and Michele Dundas Macpherson
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Oncology ,medicine.medical_specialty ,Internal medicine ,Immunology ,medicine ,Overall survival ,Myeloid leukemia ,Cell Biology ,Hematology ,Biology ,Biosimulation ,Omics ,Biochemistry - Abstract
Background: Although some genomic biomarkers have been integrated into therapeutic decision-making for the management of AML, the complete remission and cure rates have significant margin for improvement. Except for a few targeted therapies, genomic assessments offer limited guidance on treatment. Nevertheless, comprehensive molecular profiling of AML discloses a complex and heterogeneous disease network that impacts the efficacy of individual chemotherapeutics differently in individual patients. The Cellworks Computational Omics Biology Model (CBM) was developed using artificial intelligence heuristics and literature sourced from PubMed to generate a patient-specific protein network map. The Cellworks Biosimulation Platform uses the CBM to model each patient's unique cancer and predict personalized responses to standard AML drugs, identify novel drug combinations for treatment-refractory patients and optimize treatment selection to improve outcomes. Methods: A prospectively designed study involving observational data from 416 de novo AML patients was used to test the hypothesis that biosimulation using the Cellworks Biosimulation Platform predicts clinical response to individual drugs and estimates likelihood of response and survival better than physician prescribed treatment (PPT) alone. Cytogenetic and molecular data obtained from clinical trials including AMLSG 07-04, Beat AML, TCGA and PubMed publications was used to create personalized in silico models of each patient's AML and generate a Singula™ biosimulation report with a Therapy Response Index (TRI) to determine the efficacy of specific chemotherapeutic agents. The impact of specific AML agents on each patient's disease network was biosimulated to determine a treatment efficacy score by estimating the effect of chemotherapy on the cell growth score, a composite of cell proliferation, viability, apoptosis, metastasis, DNA damage and other cancer hallmarks. The mechanism of action of each drug was mapped to each patient's genome and biological consequences determined response. Multivariate logistic regression models for clinical response and likelihood ratio tests were used to assess the contribution of the Cellworks Biosimulation Platform beyond PPT. Similarly, multivariate Cox proportional hazards models were used to test the hypothesis that the Cellworks Biosimulation Platform is predictive of overall survival (OS) and provides predictive information beyond PPT alone. Scoring quantifies the benefit of each drug used to treat each patient's AML. Kaplan-Meier curves, associated log rank tests, and median OS are provided for patients predicted by predefined low and high treatment benefit groups. Results: The TRI Score, scaled from 0 to 100, predicted complete response (CR) (likelihood ratio χ 12 = 52.54, p < 0.0001). Specific leukemia therapies generated a variable likelihood of benefit for individual patients. Notably, Cellworks biosimulation was able to predict treatment benefit or failure better than PPT alone (likelihood ratio χ 12 = 14.86, p < 0.0001). The use of therapy biosimulation to select therapy is estimated to increase the odds of CR by 19% per every 25 units of the TRI Score. TRI was also a significant predictor of OS (likelihood ratio χ 12 = 80.41, p < 0.0001) and provides predictive information above and beyond PPT alone (likelihood ratio χ 12 = 58.70, p < 0.0001 ). Inclusion of the Cellworks Biosimulation Platform is estimated to reduce the hazard ratio for death above and beyond PPT alone by 16% per every 25 units of the TRI Score. Furthermore, predictiveness curves suggest that approximately 25% of de novo AML patients had low probabilities of CR resulting in lower OS and could benefit substantially from inclusion of drugs and combinations identified by biosimulation into frontline management. Conclusions: By predicting the impact of aberrations and copy number alterations on drug response, the Cellworks Biosimulation Platform can improve treatment outcomes for AML patients. The Cellworks TRI predicts response and OS beyond PPT alone, and the Cellworks Biosimulation Platform provides individualized, networked-based alternate treatment options for patients predicted to be non-responders to standard care. Disclosures Howard: Sanofi: Consultancy, Other: Speaker fees; Cellworks Group Inc.: Consultancy; Servier: Consultancy. Watson: Cellworks Group Inc.: Consultancy, Other: Advisor; CellMax Life: Consultancy, Other: Advisor; AlloVir: Consultancy, Membership on an entity's Board of Directors or advisory committees; BioAi Health: Consultancy, Membership on an entity's Board of Directors or advisory committees. Castro: Cellworks Group Inc.: Current Employment; Bugworks: Consultancy; Guardant Health Inc.: Speakers Bureau; Exact sciences Inc.: Consultancy; Caris Life Sciences Inc.: Consultancy; Omicure Inc: Consultancy. Kapoor: Cellworks Group Inc.: Current Employment. Nair: Cellworks Group Inc.: Current Employment. Prasad: Cellworks Group Inc.: Current Employment. Rajagopalan: Cellworks Group Inc.: Current Employment. Alam: Cellworks Group Inc.: Current Employment. Roy: Cellworks Group Inc.: Current Employment. Sahu: Cellworks Group Inc.: Current Employment. Lala: Cellworks Group Inc.: Current Employment. Basu: Cellworks Group Inc.: Current Employment. Ullal: Cellworks Group Inc.: Current Employment. Narvekar: Cellworks Group Inc.: Current Employment. Ghosh: Cellworks Group Inc.: Current Employment. Sauban: Cellworks Group Inc.: Current Employment. G: Cellworks Group Inc.: Current Employment. Agrawal: Cellworks Group Inc.: Current Employment. Tyagi: Cellworks Group Inc.: Current Employment. Suseela: Cellworks Group Inc.: Current Employment. Raju: Cellworks Group Inc.: Current Employment. Pampana: Cellworks Group Inc.: Current Employment. Patel: Cellworks Group Inc.: Current Employment. Mundkur: Cellworks Group Inc: Current Employment. Christie: Cellworks Group Inc.: Current Employment. Macpherson: Cellworks Group Inc.: Current Employment. Marcucci: Agios: Other: Speaker and advisory scientific board meetings; Novartis: Other: Speaker and advisory scientific board meetings; Abbvie: Other: Speaker and advisory scientific board meetings.
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- 2021
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6. Predicting Resistance to the Combination of ATO and ATRA in APL Patients with PML-Rara Fusions, Using a Computational Biology Modeling Approach: Mycare-021-01
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Poornachandra G, Pallavi Kumari, S. Mohapatra, Nirjhar Mundkur, Humera Azam, Scott C. Howard, Himanshu Grover, Neha Gupta, Michele Dundas Macpherson, Prashant Ramachandran Nair, Samiksha Avinash Prasad, Shweta Kapoor, Upasana Mitra, Deepak Anil Lala, and Anuj Tyagi
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Immunology ,Cell Biology ,Hematology ,Computational biology ,Biology ,Biochemistry - Abstract
Background: Acute promyelocytic leukemia (APL) is a biologically and clinically distinct subtype of acute myeloid leukemia (AML) with unique molecular pathogenesis, clinical manifestations, and treatment. APL is cytogenetically characterized by a balanced translocation t(15;17) (q24;q21), which involves the retinoic acid receptor alpha (RARA) gene on chromosome 17 and the promyelocytic leukemia (PML) gene on chromosome 15 that results in a PML-RARA fusion gene (PMID: 30575821). The PML-RARA fusion gene is the most critical event involved in the pathogenesis of APL, reported in 99% of APL patients (PMID: 32182684). The fusion confers a selective sensitivity to the targeted drugs, arsenic trioxide (ATO) and all-trans-retinoic acid (ATRA), with response rates over 90% (PMID: 31635329). However, the mechanism of resistance in the minority of non-responders is not well understood. This study used the Cellworks Omics Biology Model (CBM) to predict response to the combination of ATO-ATRA in patients harboring the PML-RARA fusion and identify mechanisms of resistance. Methods: Outcomes of 30 APL patients treated with ATRA or ATRA plus ATO were compared with outcomes predicted by CBM (Table 1). Genomic data from 6 publications (Table 2) derived from whole exome sequencing (WES), targeted next-generation sequencing (NGS), copy number variation (CNV) and/or karyotype data were used. All data was anonymized, de-identified and exempt from IRB review. The available genomic data for each profile was entered into the CBM which generates a patient-specific disease protein network model using PubMed and other online resources. The CBM predicts the patient-specific biomarker and phenotype response of a personalized diseased cell to drug agents, radiation and cell signaling. Disease biomarkers that are unique to each patient were identified within the protein network models. ATO and ATRA were simulated on all 30 patient cases. The treatment impact was assessed by quantitatively measuring the drug's effect on a cell growth score which is a composite of the quantified values for cell proliferation, survival, and apoptosis, along with the simulated impact on each patient-specific disease biomarker score. Each patient-specific model was also digitally screened to identify response to ATO and ATRA. Results: The CBM correctly predicted the response to ATO and ATRA in 28 of 30 cases. The overall prediction accuracy was 93% with a PPV of 100%, NPV of 60%, sensitivity of 93%, and specificity of 100%. In 2 of 30 patients who did not respond to ATO and ATRA, the CBM identified clinically relevant deletions to EZH2, KMT2E, and HIPK2 genes. All three genes are located on chromosome 7 and these non-responders had monosomy 7. Conclusions: The Cellworks Omics Biology Model predicted response to ATO and ATRA in APL patients harboring PML-RARA fusions. Predicting non-response to ATO and ATRA in patients with PML-RARA fusion up-front could prevent ineffective treatment, avoid unnecessary adverse events and reduce treatment costs. Additionally, computational modeling can identify new mechanisms of resistance and suggest alternative regimens for non-responding patients by targeting the patient-specific disease biomarkers unique to each. Disclosures Howard: Servier: Consultancy, Other: Speaker; Boston Scientific: Consultancy; Sanofi: Consultancy, Other: Speaker; EUSA Pharma: Consultancy; Cellworks: Consultancy. Nair:Cellworks Research India Private Limited: Current Employment. Grover:Cellworks Research India Private Limited: Current Employment. Tyagi:Cellworks Research India Private Limited: Current Employment. Kumari:Cellworks Research India Private Limited: Current Employment. Prasad:Cellworks Research India Private Limited: Current Employment. Mitra:Cellworks Research India Private Limited: Current Employment. Lala:Cellworks Research India Private Limited: Current Employment. Azam:Cellworks Research India Private Limited: Current Employment. Gupta:Cellworks Research India Private Limited: Current Employment. Mohapatra:Cellworks Research India Private Limited: Current Employment. G:Cellworks Research India Private Limited: Current Employment. Mundkur:Cellworks Group Inc.: Current Employment. Macpherson:Cellworks Group Inc.: Current Employment. Kapoor:Cellworks Research India Private Limited: Current Employment.
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- 2020
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7. Comparative Analysis for Differential Drug Response between Early T-Cell Precursor Acute Lymphoblastic Leukemia (ETP-ALL) and T-Cell Acute Lymphoblastic Leukemia (T-ALL) Patients Using the Cellworks Omics Biology Model (CBM): Mycare-021-03
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Scott C. Howard, Anuj Tyagi, Ansu Kumar, Yashaswini S Ullal, Vishwas Joseph, Prashant Ramachandran Nair, Pallavi Kumari, Veena Balakrishnan, Anusha Pampana, Nirjhar Mundkur, Michele Dundas Macpherson, Shweta Kapoor, Deepak Anil Lala, and Karthik Sundara Raju
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Oncology ,medicine.medical_specialty ,Myeloid ,Bortezomib ,Immunology ,Myeloid leukemia ,Cell Biology ,Hematology ,Biology ,Biochemistry ,Jurkat cells ,medicine.anatomical_structure ,Nilotinib ,Internal medicine ,medicine ,Cytarabine ,Idarubicin ,Exome sequencing ,medicine.drug - Abstract
Background:Early T-cell Precursor Acute Lymphoblastic Leukemia (ETP-ALL), an orphan disease, is a sub-type of T-Cell Acute Lymphoblastic Leukemia (T-ALL) with very poor prognosis and limited therapy options. ETP-ALL is a heterogeneous disease with many distinct genomic profiles, often with more myeloid than lymphoid characteristics. However, standard of care (SOC) drugs for acute myeloid leukemia (AML) have shown limited efficacy for ETP-ALL (PMID: 32733662, 25435716). The genomic profiles of ETP-ALL patients have more complex cytogenetics and larger numbers of genomic aberrations when compared to non-ETP-ALL (T-ALL) profiles (PMID: 22237106, 30641417). We present an alternative multi-gene analysis approach using the Cellworks Omics Biology Model (CBM) workflow to identify unique, intersecting protein pathways in patient-specific disease profiles. The CBM predictive workflow was used to design novel personalized therapy options for an ETP-ALL representative PEER human lymphoid cell line in comparison to a T-ALL JURKAT cell line. The predicted combination therapies were then validated in a lab model. Methods:A PEER cell line was selected to represent ETP-ALL and a JURKAT cell line was selected as a representative for non-ETP T-ALL. Next Generation Sequencing (NGS) was performed for the PEER cell line. For the JURKAT cell line, publicly available NGS whole exome sequencing from cBioPortal and Sanger, along with array CGH from Agilent, were used. The genomic data for the PEER and JURKAT cell lines were used as inputs to the CBM to generate dynamic patient-specific disease protein network maps. Biomarkers and pathway characteristics unique to the PEER and JURKAT cell lines were identified. A digital drug library of targeted FDA-approved agents was simulated on the disease models using both single drug agents and drug combinations at varying doses. The treatment impact was assessed by quantitatively measuring drug effect on a cell growth score, which is a composite of the quantified values of cell proliferation, survival and apoptosis along with impact on the patient-specific disease biomarker score. Comparative dose response studies were run to assess IC50 differences for both cell lines. Cellworks VenturaTM predicted novel therapy combinations for the ETP-ALL representative PEER cell line, which were then prospectively validated by in vitro experiments. The same therapy options were predicted to be less effective in the T-ALL representative JURKAT cell line, which was also confirmed by in vitro studies. Results:The CBM predicted three novel combination therapies for the ETP-ALL representative PEER cell line: nilotinib + cytarabine, bortezomib + cytarabine and bortezomib + idarubicin. All three therapies were predicted to be less effective in JURKAT cells. In vitro, PEER cells were sensitive to all 3 combinations, as predicted by the CBM; whereas, JURKAT cell lines were not sensitive to the first 2 combinations (as predicted), but were sensitive to bortezomib + idarubicin. The CBM analysis is supported by scientific rationales for these combinations based on the genomics-driven disease characteristics of the cell-line. The reasons for drug sensitivity and resistance were determined. These combinations were then prospectively validated in vitro on both cell lines and the experimental responses matched the predicted outcomes. Conclusion:The Cellworks Omics Biology Model integrates the multiple genomic abnormalities in a patient to identify disease network characteristics unlike other NGS analytic tools that attempt to interpret the impact of each genomic alteration in isolation. CBM identified 3 novel therapy options for ETP-ALL that were validated in vitro, similar to anecdotal experience in vivo. This predictive technology can improve clinical decision-making and identify novel treatment options. Disclosures Howard: Cellworks:Consultancy;Servier:Consultancy, Other: Speaker;EUSA Pharma:Consultancy;Sanofi:Consultancy, Other: Speaker;Boston Scientific:Consultancy.Kumar:Cellworks Research India Private Limited:Current Employment.Pampana:Cellworks Research India Private Limited:Current Employment.Ullal:Cellworks Research India Private Limited:Current Employment.Tyagi:Cellworks Research India Private Limited:Current Employment.Lala:Cellworks Research India Private Limited:Current Employment.Kumari:Cellworks Research India Private Limited:Current Employment.Joseph:Cellworks Research India Private Limited:Current Employment.Raju:Cellworks Research India Private Limited:Current Employment.Balakrishnan:Cellworks Research India Private Limited:Current Employment.Mundkur:Cellworks Group Inc.:Current Employment.Macpherson:Cellworks Group Inc.:Current Employment.Nair:Cellworks Research India Private Limited:Current Employment.Kapoor:Cellworks Research India Private Limited:Current Employment.
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- 2020
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