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Aydın E, Tokat ÜM, Adibi A, Özgü E, Bilgiç ŞN, Demiray M. Case report: Precision guided reactive cancer management: molecular complete response in heavily pretreated metastatic CRC by dual immunotherapy and sorafenib. Front Oncol 2024; 14:1405170. [PMID: 39011472 PMCID: PMC11246968 DOI: 10.3389/fonc.2024.1405170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/13/2024] [Indexed: 07/17/2024] Open
Abstract
Background Metastatic colon adenocarcinoma presents significant challenges in treatment, particularly when resistant to standard therapies. Precision oncology, guided by multidisciplinary tumor boards (MTBs), offers a promising way for individualized therapeutic approaches. Integration of comprehensive genomic profiling (CGP) and minimal residual disease (MRD) testing strengthens treatment decision-making, yet challenges persist in identifying and overcoming resistance mechanisms. FLT3 amplification can be one of those resistance/escape mechanisms that needs to be targeted. Case presentation This case report presents a 58-year-old male diagnosed with metastatic colon adenocarcinoma with liver metastasis, resistant to conventional treatments. Utilizing CGP and MRD testing, our multidisciplinary MTB identified a complex mutational profile, including APC, DAXX, TP53 mutations, and CDK8 and FLT3 amplifications. With a tumor mutational burden of 10 muts/mb and TPS, CPS scores of 0, immunotherapy was considered, employing dual immune checkpoint inhibitors alongside mebendazole and Lenvatinib targeting the WNT and VEGF/angiogenesis pathways. MRD testing revealed early treatment failure. Re-evaluation identified high copied FLT3 amplification (62 copies) as a resistance mechanism, prompting modification to incorporate sorafenib and dual immunotherapy with mebendazole. Subsequent MRD assessments and radiological scans demonstrated a remarkable therapeutic response, with sustained efficacy and absence of detectable residual disease. Conclusion This case highlights the successful application of precision oncology principles, facilitated by dynamic MTB-guided treatment strategies. Integration of MRD testing provided early detection of treatment inefficacy, allowing for timely intervention and adaptation of the treatment plan. Additionally, the case highlights the educational value of rare molecular alterations, emphasizing continual learning and refinement of treatment approaches in precision oncology.
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Affiliation(s)
- Esranur Aydın
- Precision Oncology Center, Medicana Health Group, Istanbul, Türkiye
| | - Ünal Metin Tokat
- Precision Oncology Center, Medicana Health Group, Istanbul, Türkiye
| | - Ashkan Adibi
- Precision Oncology Center, Medicana Health Group, Istanbul, Türkiye
- Department of Basic Oncology, Division of Cancer Genetics, Institute of Oncology, University of Istanbul, Istanbul, Türkiye
| | - Eylül Özgü
- Precision Oncology Center, Medicana Health Group, Istanbul, Türkiye
| | | | - Mutlu Demiray
- Precision Oncology Center, Medicana Health Group, Istanbul, Türkiye
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2
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Pino JC, Posso C, Joshi SK, Nestor M, Moon J, Hansen JR, Hutchinson-Bunch C, Gritsenko MA, Weitz KK, Watanabe-Smith K, Long N, McDermott JE, Druker BJ, Liu T, Tyner JW, Agarwal A, Traer E, Piehowski PD, Tognon CE, Rodland KD, Gosline SJC. Mapping the proteogenomic landscape enables prediction of drug response in acute myeloid leukemia. Cell Rep Med 2024; 5:101359. [PMID: 38232702 PMCID: PMC10829797 DOI: 10.1016/j.xcrm.2023.101359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/19/2024]
Abstract
Acute myeloid leukemia is a poor-prognosis cancer commonly stratified by genetic aberrations, but these mutations are often heterogeneous and fail to consistently predict therapeutic response. Here, we combine transcriptomic, proteomic, and phosphoproteomic datasets with ex vivo drug sensitivity data to help understand the underlying pathophysiology of AML beyond mutations. We measure the proteome and phosphoproteome of 210 patients and combine them with genomic and transcriptomic measurements to identify four proteogenomic subtypes that complement existing genetic subtypes. We build a predictor to classify samples into subtypes and map them to a "landscape" that identifies specific drug response patterns. We then build a drug response prediction model to identify drugs that target distinct subtypes and validate our findings on cell lines representing various stages of quizartinib resistance. Our results show how multiomics data together with drug sensitivity data can inform therapy stratification and drug combinations in AML.
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Affiliation(s)
- James C Pino
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Camilo Posso
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Michael Nestor
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jamie Moon
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Joshua R Hansen
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chelsea Hutchinson-Bunch
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K Weitz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kevin Watanabe-Smith
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Nicola Long
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Jason E McDermott
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Tao Liu
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA; Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Paul D Piehowski
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D Rodland
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA; Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
| | - Sara J C Gosline
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.
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3
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Gosline SJC, Tognon C, Nestor M, Joshi S, Modak R, Damnernsawad A, Posso C, Moon J, Hansen JR, Hutchinson-Bunch C, Pino JC, Gritsenko MA, Weitz KK, Traer E, Tyner J, Druker B, Agarwal A, Piehowski P, McDermott JE, Rodland K. Proteomic and phosphoproteomic measurements enhance ability to predict ex vivo drug response in AML. Clin Proteomics 2022; 19:30. [PMID: 35896960 PMCID: PMC9327422 DOI: 10.1186/s12014-022-09367-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/22/2022] [Indexed: 11/23/2022] Open
Abstract
Acute Myeloid Leukemia (AML) affects 20,000 patients in the US annually with a five-year survival rate of approximately 25%. One reason for the low survival rate is the high prevalence of clonal evolution that gives rise to heterogeneous sub-populations of leukemic cells with diverse mutation spectra, which eventually leads to disease relapse. This genetic heterogeneity drives the activation of complex signaling pathways that is reflected at the protein level. This diversity makes it difficult to treat AML with targeted therapy, requiring custom patient treatment protocols tailored to each individual's leukemia. Toward this end, the Beat AML research program prospectively collected genomic and transcriptomic data from over 1000 AML patients and carried out ex vivo drug sensitivity assays to identify genomic signatures that could predict patient-specific drug responses. However, there are inherent weaknesses in using only genetic and transcriptomic measurements as surrogates of drug response, particularly the absence of direct information about phosphorylation-mediated signal transduction. As a member of the Clinical Proteomic Tumor Analysis Consortium, we have extended the molecular characterization of this cohort by collecting proteomic and phosphoproteomic measurements from a subset of these patient samples (38 in total) to evaluate the hypothesis that proteomic signatures can improve the ability to predict response to 26 drugs in AML ex vivo samples. In this work we describe our systematic, multi-omic approach to evaluate proteomic signatures of drug response and compare protein levels to other markers of drug response such as mutational patterns. We explore the nuances of this approach using two drugs that target key pathways activated in AML: quizartinib (FLT3) and trametinib (Ras/MEK), and show how patient-derived signatures can be interpreted biologically and validated in cell lines. In conclusion, this pilot study demonstrates strong promise for proteomics-based patient stratification to assess drug sensitivity in AML.
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Affiliation(s)
| | - Cristina Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | | | - Sunil Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Rucha Modak
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alisa Damnernsawad
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Camilo Posso
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Jamie Moon
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | | | | | - James C Pino
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | | | - Karl K Weitz
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Jeffrey Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Division of Oncological Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | | | - Jason E McDermott
- Pacific Northwest National Laboratory, Seattle, WA, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Karin Rodland
- Pacific Northwest National Laboratory, Seattle, WA, USA.
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA.
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Senapati J, Kadia TM. Which FLT3 Inhibitor for Treatment of AML? Curr Treat Options Oncol 2022; 23:359-380. [PMID: 35258791 DOI: 10.1007/s11864-022-00952-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 12/17/2022]
Abstract
OPINION STATEMENT Treatment options in acute myeloid leukemia (AML) have improved significantly over the last decade with better understanding of disease biology and availability of a multitude of targeted therapies. The use of FLT3 inhibitors (FLT3i) in FLT3-mutated (FLT3mut) AML is one such development; however, the clinical decisions that govern their use and dictate the choice of the FLT3i are evolving. Midostaurin and gilteritinib are FDA-approved in specific situations; however, available data from clinical trials also shed light on the utility of sorafenib maintenance post-allogeneic stem cell transplantation (allo-SCT) and quizartinib as part of combination therapy in FLT3mut AML. The knowledge of the patient's concurrent myeloid mutations, type of FLT3 mutation, prior FLT3i use, and eligibility for allo-SCT helps to refine the choice of FLT3i. Data from ongoing studies will further precisely define their use and help in making more informed choices. Despite improvements in FLT3i therapy, the definitive aim is to enable the eligible patient with FLT3mut AML (esp. ITD) to proceed to allo-SCT with regimens containing FLT3i incorporated prior to SCT and as maintenance after SCT.
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Affiliation(s)
- Jayastu Senapati
- Department of Leukemia, MD Anderson Cancer Center, 1515 Holcombe Blvd. - Unit 428, Houston, 77030, USA
| | - Tapan Mahendra Kadia
- Department of Leukemia, MD Anderson Cancer Center, 1515 Holcombe Blvd. - Unit 428, Houston, 77030, USA.
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5
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Phosphoproteomic Characterization of Primary AML Samples and Relevance for Response Toward FLT3-inhibitors. Hemasphere 2021; 5:e606. [PMID: 34136754 PMCID: PMC8202661 DOI: 10.1097/hs9.0000000000000606] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/20/2021] [Indexed: 11/26/2022] Open
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