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Castro MP, Khanlou N, Fallah A, Pampana A, Alam A, Lala DA, Roy KGG, Amara ARR, Prakash A, Singh D, Behura L, Kumar A, Kapoor S. Targeting chromosome 12q amplification in relapsed glioblastoma: the use of computational biological modeling to identify effective therapy-a case report. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1289. [PMID: 36618786 PMCID: PMC9816820 DOI: 10.21037/atm-2022-62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/20/2022] [Indexed: 11/17/2022]
Abstract
Background Relapsed glioblastoma (GBM) is often an imminently fatal condition with limited therapeutic options. Computation biological modeling, i.e., biosimulation, of comprehensive genomic information affords the opportunity to create a disease avatar that can be interrogated in silico with various drug combinations to identify the most effective therapies. Case Description We report the outcome of a GBM patient with chromosome 12q amplification who achieved substantial disease remission from a novel therapy using this approach. Following next generation sequencing (NGS) was performed on the tumor specimen. Mutation and copy number changes were input into a computational biologic model to create an avatar of disease behavior and the malignant phenotype. In silico responses to various drug combinations were biosimulated in the disease network. Efficacy scores representing the computational effect of treatment for each strategy were generated and compared to each other to ascertain the differential benefit in drug response from various regimens. Biosimulation identified CDK4/6 inhibitors, nelfinavir and leflunomide to be effective agents singly and in combination. Upon receiving this treatment, the patient achieved a prompt and clinically meaningful remission lasting 6 months. Conclusions Biosimulation has utility to identify active treatment combinations, stratify treatment options and identify investigational agents relevant to patients' comprehensive genomic abnormalities. Additionally, the combination of abemaciclib and nelfinavir appear promising for GBM and potentially other cancers harboring chromosome 12q amplification.
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Affiliation(s)
- Michael P. Castro
- Beverly Hills Cancer Center and Personalized Cancer Medicine, PLLC, Beverly Hills, CA, USA;,Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Negar Khanlou
- Department of Pathology, Ronald Reagan UCLA Medical Center, Los Angeles, CA, USA
| | - Aria Fallah
- Department of Neurosurgery, Ronald Reagan UCLA Medical Center, Los Angeles, CA, USA
| | - Anusha Pampana
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Aftab Alam
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Deepak Anil Lala
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Kunal Ghosh Ghosh Roy
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Anish Raju R. Amara
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Annapoorna Prakash
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Divya Singh
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Liptimayee Behura
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Ansu Kumar
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
| | - Shweta Kapoor
- Cellworks Group, Inc., S. San Francisco, CA, USA;,Cellworks Group, Inc., Bangalore, India
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Radhachandran A, Garikipati A, Iqbal Z, Siefkas A, Barnes G, Hoffman J, Mao Q, Das R. A machine learning approach to predicting risk of myelodysplastic syndrome. Leuk Res 2021; 109:106639. [PMID: 34171604 DOI: 10.1016/j.leukres.2021.106639] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/18/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Early myelodysplastic syndrome (MDS) diagnosis can allow physicians to provide early treatment, which may delay advancement of MDS and improve quality of life. However, MDS often goes unrecognized and is difficult to distinguish from other disorders. We developed a machine learning algorithm for the prediction of MDS one year prior to clinical diagnosis of the disease. METHODS Retrospective analysis was performed on 790,470 patients over the age of 45 seen in the United States between 2007 and 2020. A gradient boosted decision tree model (XGB) was built to predict MDS diagnosis using vital signs, lab results, and demographics from the prior two years of patient data. The XGB model was compared to logistic regression (LR) and artificial neural network (ANN) models. The models did not use blast percentage and cytogenetics information as inputs. Predictions were made one year prior to MDS diagnosis as determined by International Classification of Diseases (ICD) codes, 9th and 10th revisions. Performance was assessed with regard to area under the receiver operating characteristic curve (AUROC). RESULTS On a hold-out test set, the XGB model achieved an AUROC value of 0.87 for prediction of MDS one year prior to diagnosis, with a sensitivity of 0.79 and specificity of 0.80. The XGB model was compared against LR and ANN models, which achieved an AUROC of 0.838 and 0.832, respectively. CONCLUSIONS Machine learning may allow for early MDS diagnosis MDS and more appropriate treatment administration.
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Ex vivo drug screening defines novel drug sensitivity patterns for informing personalized therapy in myeloid neoplasms. Blood Adv 2021; 4:2768-2778. [PMID: 32569379 DOI: 10.1182/bloodadvances.2020001934] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
Precision medicine approaches such as ex vivo drug sensitivity screening (DSS) are appealing to inform rational drug selection in myelodysplastic syndromes (MDSs) and acute myeloid leukemia, given their marked biologic heterogeneity. We evaluated a novel, fully automated ex vivo DSS platform that uses high-throughput flow cytometry in 54 patients with newly diagnosed or treatment-refractory myeloid neoplasms to evaluate sensitivity (blast cytotoxicity and differentiation) to 74 US Food and Drug Administration-approved or investigational drugs and 36 drug combinations. After piloting the platform in 33 patients, we conducted a prospective feasibility study enrolling 21 patients refractory to hypomethylating agents (HMAs) to determine whether this assay could be performed within a clinically actionable time frame and could accurately predict clinical responses in vivo. When assayed for cytotoxicity, ex vivo drug sensitivity patterns were heterogeneous, but they defined distinct patient clusters with differential sensitivity to HMAs, anthracyclines, histone deacetylase inhibitors, and kinase inhibitors (P < .001 among clusters) and demonstrated synergy between HMAs and venetoclax (P < .01 for combinations vs single agents). In our feasibility study, ex vivo DSS results were available at a median of 15 days after bone marrow biopsy, and they informed personalized therapy, which frequently included venetoclax combinations, kinase inhibitors, differentiative agents, and androgens. In 21 patients with available ex vivo and in vivo clinical response data, the DSS platform had a positive predictive value of 0.92, negative predictive value of 0.82, and overall accuracy of 0.85. These data demonstrate the utility of this approach for identifying potentially useful and often novel therapeutic drugs for patients with myeloid neoplasms refractory to standard therapies.
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Hellström-Lindberg E, Tobiasson M, Greenberg P. Myelodysplastic syndromes: moving towards personalized management. Haematologica 2020; 105:1765-1779. [PMID: 32439724 PMCID: PMC7327628 DOI: 10.3324/haematol.2020.248955] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
The myelodysplastic syndromes (MDS) share their origin in the hematopoietic stem cell but have otherwise very heterogeneous biological and genetic characteristics. Clinical features are dominated by cytopenia and a substantial risk for progression to acute myeloid leukemia. According to the World Health Organization, MDS is defined by cytopenia, bone marrow dysplasia and certain karyotypic abnormalities. The understanding of disease pathogenesis has undergone major development with the implementation of next-generation sequencing and a closer integration of morphology, cytogenetics and molecular genetics is currently paving the way for improved classification and prognostication. True precision medicine is still in the future for MDS and the development of novel therapeutic compounds with a propensity to markedly change patients' outcome lags behind that for many other blood cancers. Treatment of higher-risk MDS is dominated by monotherapy with hypomethylating agents but novel combinations are currently being evaluated in clinical trials. Agents that stimulate erythropoiesis continue to be first-line treatment for the anemia of lower-risk MDS but luspatercept has shown promise as second-line therapy for sideroblastic MDS and lenalidomide is an established second-line treatment for del(5q) lower-risk MDS. The only potentially curative option for MDS is hematopoietic stem cell transplantation, until recently associated with a relatively high risk of transplant-related mortality and relapse. However, recent studies show increased cure rates due to better tools to target the malignant clone with less toxicity. This review provides a comprehensive overview of the current status of the clinical evaluation, biology and therapeutic interventions for this spectrum of disorders.
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Affiliation(s)
- Eva Hellström-Lindberg
- Karolinska Institutet, Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Tobiasson
- Karolinska Institutet, Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Greenberg
- Stanford Cancer Institute, Division of Hematology, Stanford University School of Medicine, Stanford, CA, USA
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Identification of Lenalidomide Sensitivity and Resistance Mechanisms in Non-Del(5q) Myelodysplastic Syndromes. Int J Mol Sci 2020; 21:ijms21093323. [PMID: 32397113 PMCID: PMC7246771 DOI: 10.3390/ijms21093323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
Whereas lenalidomide is an effective therapy for del(5q) MDS patients, a minority of non-del(5q) MDS patients achieve hematologic improvement with lenalidomide. We used computational biology modeling and digital drug simulation to examine genomic data from 56 non-del(5q) MDS patients treated with lenalidomide, and then matched treatment response with molecular pathways. The computer inferred genomic abnormalities associating with lenalidomide treatment response in non-del(5q) MDS to include trisomy 8, del(20q), or RUNX1 loss of function mutations. Genomic abnormalities associating with lenalidomide resistance in non-del(5q) MDS patients included mutations in SF3B1, TET2, WNT3A amplification, MCL1 amplification, and/or PSEN2 amplification. These results may inform protocols for determining appropriateness of lenalidomide in non-del(5q) MDS.
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Vizirianakis IS, Miliotou AN, Mystridis GA, Andriotis EG, Andreadis II, Papadopoulou LC, Fatouros DG. Tackling pharmacological response heterogeneity by PBPK modeling to advance precision medicine productivity of nanotechnology and genomics therapeutics. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019. [DOI: 10.1080/23808993.2019.1605828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ioannis S. Vizirianakis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Androulla N. Miliotou
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George A. Mystridis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleftherios G. Andriotis
- Laboratory of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis I. Andreadis
- Laboratory of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Lefkothea C. Papadopoulou
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios G. Fatouros
- Laboratory of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Stevens B, Winters A, Gutman JA, Fullerton A, Hemenway G, Schatz D, Miltgen N, Wei Q, Abbasi T, Vali S, Singh NK, Drusbosky L, Cogle CR, Hammes A, Abbott D, Jordan CT, Smith C, Pollyea DA. Sequential azacitidine and lenalidomide for patients with relapsed and refractory acute myeloid leukemia: Clinical results and predictive modeling using computational analysis. Leuk Res 2019; 81:43-49. [PMID: 31009835 DOI: 10.1016/j.leukres.2019.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/04/2019] [Accepted: 04/08/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Patients with relapsed and refractory (R/R) acute myeloid leukemia (AML) have limited treatment options. Genomically-defined personalized therapies are only applicable for a minority of patients. Therapies without identifiable targets can be effective but patient selection is challenging. The sequential combination of azacitidine with high-dose lenalidomide has shown activity; we aimed to determine the efficacy of this genomically-agnostic regimen in patients with R/R AML, with the intention of applying sophisticated methods to predict responders. METHODS Thirty-seven R/R AML/myelodysplastic syndrome patients were enrolled in a phase 2 study of azacitidine with lenalidomide. The primary endpoint was complete remission (CR) and CR with incomplete blood count recovery (CRi) rate. A computational biological modeling (CBM) approach was applied retrospectively to predict outcomes based on the understood mechanisms of azacitidine and lenalidomide in the setting of each patients' disease. FINDINGS Four of 37 patients (11%) had a CR/CRi; the study failed to meet the alternative hypothesis. Significant toxicity was observed in some cases, with three treatment-related deaths and a 30-day mortality rate of 14%. However, the CBM method predicted responses in 83% of evaluable patients, with a positive and negative predictive value of 80% and 89%, respectively. INTERPRETATION Sequential azacitidine and high-dose lenalidomide is effective in a minority of R/R AML patients; it may be possible to predict responders at the time of diagnosis using a CBM approach. More efforts to predict responses in non-targeted therapies should be made, to spare toxicity in patients unlikely to respond and maximize treatments for those with limited options.
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Affiliation(s)
- Brett Stevens
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Amanda Winters
- University of Colorado Children's Hospital, Aurora CO, United States
| | - Jonathan A Gutman
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Aaron Fullerton
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Gregory Hemenway
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Derek Schatz
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Nicholas Miltgen
- University of Colorado Children's Hospital, Aurora CO, United States
| | - Qi Wei
- University of Colorado Children's Hospital, Aurora CO, United States
| | | | | | | | | | | | - Andrew Hammes
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado, Aurora, CO, United States
| | - Diana Abbott
- Center for Innovative Design and Analysis, Department of Biostatistics and Informatics, University of Colorado, Aurora, CO, United States
| | - Craig T Jordan
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Clayton Smith
- University of Colorado Division of Hematology, Aurora, CO, United States
| | - Daniel A Pollyea
- University of Colorado Division of Hematology, Aurora, CO, United States.
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