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Thawani R, Repetto M, Keddy C, Nicholson K, Jones K, Nusser K, Beach CZ, Harada G, Drilon A, Davare MA. TKI Type Switching Overcomes ROS1 L2086F in ROS1 Fusion-Positive Cancers. bioRxiv 2024:2024.01.16.575901. [PMID: 38293020 PMCID: PMC10827145 DOI: 10.1101/2024.01.16.575901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Purpose Despite the robust efficacy of ROS1 tyrosine kinase inhibitors (TKIs) in ROS1-positive non-small cell lung cancer, TKI resistance continues to hamper durability of the therapeutic response. The resistance liabilities of next-generation ROS1 TKI are sparsely characterized. Design We compared the activity of type I TKIs (crizotinib, entrectinib, taletrectinib, lorlatinib, and repotrectinib) to the type II TKIs (cabozantinib and merestinib), and to the type I FLT3 inhibitor, gilteritinib, in CD74-ROS1 wildtype and F2004C, L2026M, G2032R, or L2086 mutant Ba/F3 cells. The findings from the Ba/F3 cell model were confirmed using NIH3T3 colony formation assays and in vivo tumor growth. CRISPR/Cas9 gene editing was used to generate isogenic wildtype and L2086F mutant TPM3-ROS1 expressing patient-derived cell lines. These lines were used to further evaluate TKI activity using cell viability and immunoblotting methods. Molecular modeling studies enabled the characterization of structural determinants of TKI sensitivity in wildtype and mutant ROS1 kinase domains. We also report clinical cases of ROS1 TKI resistance that were treated with cabozantinib. Results ROS1 L2086F mutant kinase is resistant to type I TKI including crizotinib, entrectinib, lorlatinib, repotrectinib, taletrectinib, while the type II TKI cabozantinib and merestinib retain activity. Additionally, we found that gilteritinib, a type I FLT3 inhibitor, inhibited wildtype and L2086F mutant ROS1, however ROS1 G2032R solvent front mutation imposed resistance. The specific binding poses adopted by cabozantinib in the DFG-out kinase conformation and gilteritinib in the DFG-in kinase, provide rationale for their activity in the ROS1 mutants. Clinical cases demonstrated response to cabozantinib in tumors developing TKI resistance due to the ROS1 L2086F mutation. Conclusion Cabozantinib and gilteritinib effectively inhibit ROS1 L2086F. Clinical activity of cabozantinib is confirmed in patients with TKI-resistant, ROS1 L2086F mutant NSCLC. Gilteritinib may offer an alternative with distinct off-target toxicities, however further studies are required. Since cabozantinib and gilteritinib are multi-kinase inhibitors, there is a persistent unmet need for more selective and better-tolerated TKI to overcome ROS1 L2086F kinase-intrinsic resistance. Translational relevance ROS1 L2086F is an emerging recurrent resistance mutation to type I ROS1 TKIs, including later generation TKIs. Here, we show corroborating preclinical and clinical evidence for the activity of the quinolone-based type II TKI, cabozantinib, in ROS1 L2086F resistance setting. In addition, we show activity of the pyrazine carboxamide-based type I TKI, gilteritinib, in ROS1 L2086F resistance, suggesting that gilteritinib could be another option for ROS1 L2086F TKI-resistant patients. This study represents the first comprehensive report of ROS1 L2086F in the context of later-generation TKIs, including the macrocyclic inhibitors.
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Iyer SR, Nusser K, Jones K, Shinde P, Keddy C, Beach CZ, Aguero E, Force J, Shinde U, Davare MA. Discovery of oncogenic ROS1 missense mutations with sensitivity to tyrosine kinase inhibitors. EMBO Mol Med 2023; 15:e17367. [PMID: 37587872 PMCID: PMC10565643 DOI: 10.15252/emmm.202217367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/18/2023] Open
Abstract
ROS1 is the largest receptor tyrosine kinase in the human genome. Rearrangements of the ROS1 gene result in oncogenic ROS1 kinase fusion proteins that are currently the only validated biomarkers for targeted therapy with ROS1 TKIs in patients. While numerous somatic missense mutations in ROS1 exist in the cancer genome, their impact on catalytic activity and pathogenic potential is unknown. We interrogated the AACR Genie database and identified 34 missense mutations in the ROS1 tyrosine kinase domain for further analysis. Our experiments revealed that these mutations have varying effects on ROS1 kinase function, ranging from complete loss to significantly increased catalytic activity. Notably, Asn and Gly substitutions at Asp2113 in the ROS1 kinase domain were found to be TKI-sensitive oncogenic variants in cell-based model systems. In vivo experiments showed that ROS1 D2113N induced tumor formation that was sensitive to crizotinib and lorlatinib, FDA-approved ROS1-TKIs. Collectively, these findings highlight the tumorigenic potential of specific point mutations within the ROS1 kinase domain and their potential as therapeutic targets with FDA-approved ROS1-TKIs.
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Affiliation(s)
- Sudarshan R Iyer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Kevin Nusser
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Kristen Jones
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Pushkar Shinde
- Department of Chemical PhysiologyOregon Health and Sciences UniversityORPortlandUSA
| | - Clare Keddy
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Catherine Z Beach
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Erin Aguero
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
| | - Jeremy Force
- Department of Medicine, Division of Medical Oncology, Duke Cancer InstituteDuke UniversityNCDurhamUSA
| | - Ujwal Shinde
- Department of Chemical PhysiologyOregon Health and Sciences UniversityORPortlandUSA
| | - Monika A Davare
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Papé Family Pediatric Research InstituteOregon Health and Sciences UniversityORPortlandUSA
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Keddy C, Neff T, Huan J, Nickerson JP, Beach CZ, Akkari Y, Ji J, Moore S, Nazemi KJ, Corless CL, Beadling C, Woltjer R, Cho YJ, Wood MD, Davare MA. Mechanisms of targeted therapy resistance in a pediatric glioma driven by ETV6-NTRK3 fusion. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a006109. [PMID: 34429303 PMCID: PMC8559620 DOI: 10.1101/mcs.a006109] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/26/2021] [Indexed: 11/24/2022] Open
Abstract
Chromosomal rearrangements of the NTRK genes generate kinase fusions that are targetable oncogenic drivers in diverse adult and pediatric malignancies. Despite robust clinical response to targeted NTRK inhibition, the emergence of therapeutic resistance poses a formidable clinical challenge. Here we report the characterization of an ETV6-NTRK3 fusion-driven pediatric glioma that progressed through NTRK-targeted treatments with entrectinib and selitrectinib. Genetic analysis of multifocal recurrent/resistant lesions identified a previously uncharacterized NTRK3 p.G623A and a known p.G623E resistance mutation, in addition to other alterations of potential pathogenic impact. Functional studies using heterologous reconstitution model systems and patient-derived tumor cell lines establish that NTRK3G623A and NTRK3G623E mutated kinases exhibit reduced sensitivity to entrectinib and selitrectinib, as well as other NTRK inhibitors tested herein. In summary, this genetic analysis of multifocal recurrent/resistant glioma driven by ETV6-NTRK3 fusion captured a cross section of resistance-associated alterations that, based on in vitro analysis, likely contributed to resistance to targeted therapy and disease progression.
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Affiliation(s)
- Clare Keddy
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Tanaya Neff
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Jianya Huan
- Department of Pathology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Joshua P Nickerson
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Catherine Z Beach
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Yassmine Akkari
- Legacy Health, Department of Cytogenetics, Portland, Oregon 97209, USA
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles and Keck School of Medicine at University of Southern California, Los Angeles, California 90033, USA
| | - Stephen Moore
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Kellie J Nazemi
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Christopher L Corless
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon 97239, USA.,Department of Pathology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Carol Beadling
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Randy Woltjer
- Department of Pathology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Yoon-Jae Cho
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Matthew D Wood
- Knight Diagnostic Laboratories, Oregon Health & Science University, Portland, Oregon 97239, USA.,Department of Pathology, Oregon Health & Science University, Portland, Oregon 97239, USA
| | - Monika A Davare
- Department of Pediatrics, Doernbecher Children's Hospital, Oregon Health & Science University, Portland, Oregon 97239, USA
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Dietz MS, Beach CZ, Barajas R, Parappilly MS, Sengupta SK, Baird LC, Ciporen JN, Han SJ, Loret de Mola R, Cho YJ, Nazemi KJ, McClelland S, Wong MH, Jaboin JJ. Measure Twice: Promise of Liquid Biopsy in Pediatric High-Grade Gliomas. Adv Radiat Oncol 2020; 5:152-162. [PMID: 32280814 PMCID: PMC7136635 DOI: 10.1016/j.adro.2019.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/07/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose To review and critique the current state of liquid biopsy in pHGG. Materials and Methods Published literature was reviewed for articles related to liquid biopsy in pediatric glioma and adult glioma with a focus on high-grade gliomas. Results This review discusses the current state of liquid biomarkers of pHGG and their potential applications for liquid biopsy development. Conclusions While nascent, the progress toward identifying circulating analytes of pHGG primes the field of neuro-oncoogy for liquid biopsy development.
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Affiliation(s)
- Matthew S Dietz
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Catherine Z Beach
- Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon
| | - Ramon Barajas
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, Oregon.,Advanced Imaging Research Center, Oregon Health & Science University, Portland, Oregon
| | - Michael S Parappilly
- Department of Diagnostic Radiology, Oregon Health & Science University, Portland, Oregon
| | - Sidharth K Sengupta
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Lissa C Baird
- Department of Neurological Surgery, Oregon Health & Science University, Portland, Oregon
| | - Jeremy N Ciporen
- Department of Neurological Surgery, Oregon Health & Science University, Portland, Oregon
| | - Seunggu J Han
- Department of Neurological Surgery, Oregon Health & Science University, Portland, Oregon
| | | | - Yoon Jae Cho
- Department of Neurology, Oregon Health & Science University, Portland, Oregon.,The Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Kellie J Nazemi
- Department of Pediatrics, Oregon Health & Science University, Portland, Oregon
| | - Shearwood McClelland
- Department of Radiation Oncology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Melissa H Wong
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, Portland, Oregon.,The Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Jerry J Jaboin
- Department of Radiation Medicine, Oregon Health & Science University, Portland, Oregon.,The Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
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5
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Smith NR, Swain JR, Davies PS, Gallagher AC, Parappilly MS, Beach CZ, Streeter PR, Williamson IA, Magness ST, Wong MH. Monoclonal Antibodies Reveal Dynamic Plasticity Between Lgr5- and Bmi1-Expressing Intestinal Cell Populations. Cell Mol Gastroenterol Hepatol 2018; 6:79-96. [PMID: 29928673 PMCID: PMC6008251 DOI: 10.1016/j.jcmgh.2018.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/26/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Continual renewal of the intestinal epithelium is dependent on active- and slow-cycling stem cells that are confined to the crypt base. Tight regulation of these stem cell populations maintains homeostasis by balancing proliferation and differentiation to support critical intestinal functions. The hierarchical relation of discrete stem cell populations in homeostasis or during regenerative epithelial repair remains controversial. Although recent studies have supported a model for the active-cycling leucine-rich repeat-containing G-protein-coupled receptor 5 (Lgr5)+ intestinal stem cell (ISC) functioning upstream of the slow-cycling B lymphoma Mo-MLV insertion region 1 homolog (Bmi1)-expressing cell, other studies have reported the opposite relation. Tools that facilitate simultaneous analyses of these populations are required to evaluate their coordinated function. METHODS We used novel monoclonal antibodies (mAbs) raised against murine intestinal epithelial cells in conjunction with ISC-green fluorescent protein (GFP) reporter mice to analyze relations between ISC populations by microscopy. Ex vivo 3-dimensional cultures, flow cytometry, and quantitative reverse-transcription polymerase chain reaction analyses were performed. RESULTS Two novel mAbs recognized distinct subpopulations of the intestinal epithelium and when used in combination permitted isolation of discrete Lgr5GFP and Bmi1GFP-enriched populations with stem activity. Growth from singly isolated Lgr5GFP ISCs gave rise to small spheroids. Spheroids did not express Lgr5GFP and instead up-regulated Bmi1GFP expression. Conversely, Bmi1-derived spheroids initiated Lgr5GFP expression as crypt domains were established. CONCLUSIONS These data showed the functional utility of murine mAbs in the isolation and investigation of Lgr5GFP and Bmi1GFP ISC-enriched populations. Ex vivo analyses showed hierarchical plasticity between different ISC-expressing states; specifically Lgr5GFP ISCs gave rise to Bmi1GFP cells, and vice versa. These data highlight the impact of temporal and physiological context on unappreciated interactions between Lgr5GFP and Bmi1GFP cells during crypt formation.
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Key Words
- 3D, 3-dimensional
- 4-OHT, 4-hydroxytamoxifen
- APC, allophycocyanin
- Bmi1
- Bmi1, B lymphoma Mo-MLV insertion region 1 homolog
- Egf, epidermal growth factor
- FACS, fluorescence-activated cell sorting
- GFP, green fluorescent protein
- HBSS, Hank’s balanced salt solution
- Hierarchy
- ISC, intestinal stem cell
- Intestinal Stem Cells
- Lgr5
- Lgr5, leucine-rich repeat-containing G-protein–coupled receptor 5
- Lyz, lysozyme
- OHSU, Oregon Health and Science University
- PBS, phosphate-buffered saline
- PE, Phycoerythrin
- Plasticity
- Rspo1, R-spondin1
- TdT, tdTomato
- Wnt, wingless-type MMTV (mouse mammary tumor virus) integration site
- cDNA, complementary DNA
- mAb, monoclonal antibody
- mRNA, messenger RNA
- qRT-PCR, quantitative reverse-transcription polymerase chain reaction
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Affiliation(s)
- Nicholas R. Smith
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - John R. Swain
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Paige S. Davies
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Alexandra C. Gallagher
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Michael S. Parappilly
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Catherine Z. Beach
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon
| | - Philip R. Streeter
- Department of Pediatrics, Oregon Health and Science University, Portland, Oregon,Oregon Health & Science University Stem Cell Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Ian A. Williamson
- Department of Biomedical Engineering, Department of Medicine, Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina
| | - Scott T. Magness
- Department of Biomedical Engineering, Department of Medicine, Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina
| | - Melissa H. Wong
- Department of Cell, Developmental and Cancer Biology, Oregon Health and Science University, Portland, Oregon,Oregon Health & Science University Stem Cell Center, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon,Correspondence Address correspondence to: Melissa H. Wong, PhD, Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Mail Code L215, Portland, Oregon 97239. fax: (503) 494-4253.
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