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Le Q, Hadland B, Smith JL, Leonti A, Huang BJ, Ries R, Hylkema TA, Castro S, Tang TT, McKay CN, Perkins L, Pardo L, Sarthy J, Beckman AK, Williams R, Idemmili R, Furlan S, Ishida T, Call L, Srivastava S, Loeb AM, Milano F, Imren S, Morris SM, Pakiam F, Olson JM, Loken MR, Eidenschink Brodersen L, Riddell SR, Tarlock K, Bernstein ID, Loeb KR, Meshinchi S. CBFA2T3-GLIS2 model of pediatric acute megakaryoblastic leukemia identifies FOLR1 as a CAR T cell target. J Clin Invest 2022; 132:157101. [PMID: 36136600 DOI: 10.1172/jci157101] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Fusion oncoproteins are the initiating event in the pathogenesis of many pediatric AML. The CBFA2T3-GLIS2 (C/G) fusion is a product of a cryptic translocation primarily seen in infants and early childhood and is associated with dismal outcome. Here, we demonstrate that the expression of the C/G oncogenic fusion protein promotes the transformation of human cord blood hematopoietic stem/progenitor cells (CB HSPCs) in an endothelial cell (EC) co-culture system, that recapitulates the transcriptome, morphology and immunophenotype of C/G AML and induces highly aggressive leukemia in xenograft models. Interrogating the transcriptome of C/G-CB cells and primary C/G AML identified a library of C/G fusion-specific genes that are potential targets for therapy. We developed chimeric antigen receptor (CAR) T cells directed against one of the targets, FOLR1, and demonstrated their pre-clinical efficacy against C/G AML using in vitro and xenograft models. FOLR1 is also expressed in renal and pulmonary epithelium, raising concerns for toxicity that must be addressed for the clinical application of this therapy. Our findings underscore the role of the endothelial niche in promoting leukemic transformation of C/G-transduced CB HSPCs. Furthermore, this work has broad implications for studies of leukemogenesis applicable to a variety of oncogenic fusion-driven pediatric leukemias, providing a robust and tractable model system to characterize the molecular mechanisms of leukemogenesis and identify biomarkers for disease diagnosis and targets for therapy.
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Affiliation(s)
- Quy Le
- Clincial Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Brandon Hadland
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jenny L Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Amanda Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Benjamin J Huang
- Department of Pediatrics, University of California, San Francisco, San Francisco, United States of America
| | - Rhonda Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Tiffany A Hylkema
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Sommer Castro
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Thao T Tang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Cyd N McKay
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - LaKeisha Perkins
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Laura Pardo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Jay Sarthy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Amy K Beckman
- Department of Laboratory Medicine and Pathology, The University of Minnesota, Minneapolis, United States of America
| | - Robin Williams
- Department of Laboratory Medicine and Pathology, The University of Minnesota, Minneapolis, United States of America
| | - Rhonda Idemmili
- Department of Laboratory Medicine and Pathology, The University of Minnesota, Minneapolis, United States of America
| | - Scott Furlan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Takashi Ishida
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Lindsey Call
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Shivani Srivastava
- Program in Immunology, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Anisha M Loeb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Filippo Milano
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Suzan Imren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Shelli M Morris
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, United States of America
| | - Fiona Pakiam
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Insitute, Seattle, United States of America
| | - James M Olson
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Insitute, Seattle, United States of America
| | | | | | - Stanley R Riddell
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Katherine Tarlock
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Irwin D Bernstein
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Keith R Loeb
- Department of Pathology, Fred Hutchinson Cancer Research Center, Seattle, United States of America
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States of America
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Robinson L, Leonti A, Alonzo TA, Wang YC, Redell MS, Ries RE, Smith JL, Hylkema TA, Le Q, Kolb EA, Aplenc R, Ma X, Klco J, Tarlock K, Meshinchi S. Abstract 3479: UBTF tandem duplications (UBTF-TD) in childhood AML: Enrichment in FLT3-ITD and association with clinical outcome. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Childhood AML is an aggressive disease with high rates of failures and poor survival. We have demonstrated that the molecular landscape of AML in children is distinct, and co-occurrence of variants modulate outcomes. Recent discovery of tandem duplication (TD) of the UBTF gene in AML, with enrichment in FLT3-ITD has implicated yet another mutation whose cooperation with FLT3-ITD may modify outcome. Here, we provide a comprehensive evaluation of UBTF-TD in de novo AML and define its clinical implications within FLT3-ITD patients. Initial interrogation of transcriptome data from 1,158 children enrolled on COG AAML1031 identified 50 cases of UBTF-TD (4.3%). Overwhelming majority of UBTF-TD cases were observed in FLT3-ITD cases (77%), vs. that of 1.2% in those without FLT3-ITD (p<0.001). Given extreme enrichment of UBTF-TD in FLT3-ITD, we inquired whether cooperation of UBTF-TD and FLT3-ITD creates a distinct clinical entity. To this end we screened diagnostic DNA from 400 FLT3-ITD patients treated on three consecutive CCG/COG trials (COG AAML1031, COG AAML0531, and CCG-2961) by PCR and fragment analysis. UBTF-TD was identified in 61 FLT3-ITD cases (15.3%).
The data presented here forth focuses on evaluation of implications of UBTF-TD in FLT3-ITD positive patients only. Within the FLT3-ITD patients, initial correlation of UBTF-TD with demographics, disease characteristics, and associated genomic variants was conducted. Patients with and without UBTF-TD had a similar median age at diagnosis (p=0.322), lower diagnostic WBC (p=0.010) and higher marrow blast % (p<0.001). There was a stark paucity of cooperating variants that commonly co-occur with FLT3-ITD, with a single NPM1 mutation (1.6% vs. 29%, p<0.001) and no NUP98 fusions (0% vs. 23%, p<0.001). There was a significant enrichment of WT1 mutations, with 45% UBTF-TD patients with a WT1 mutation (FLT3-ITD/UBTF-TD/WT1), vs. 11% in UBTF-WT (p<0.001). Trisomy 8 (Tri8) was seen in 15% of UBTF-TD. Patients with UBTF-TD had a lower CR rate (44% vs. 60%, p = 0.018), and Higher MRD rate (38% vs. 21%, p<0.001). Patients with and without UBTF-TD had an EFS of 28% vs. 42% (p=0.047) with a corresponding OS of 40% and 57% (p=0.019). Given enrichment of WT1 mutations and Tri8 in patients with UBTF-TD, we studied the outcome UBTF-TD patients in the context of these two variants. FLT3-ITD/UBTF-TD/WT1 patients had a 5-year EFS of 17% vs. 38% for similar patients without WT1 mutations (p=0.0062). Patients with UBTF-TD with additional Tri8 had a similarly poor outcome with an EFS of 23% with a corresponding OS of 33%, providing a distinct high risk UBTF-TD cohort (+WT1 or Tri8), whereas the remaining UBTF-TD patients had a more favorable outcome with EFS and OS of 64% and 86%, respectively (p<0.0001, and p<0.0001). UBTF-TD is a novel genomic entity with high enrichment in patients with FLT3-ITD and a distinct clinical outcome driven by cooperating WT1 mutation and Tri8.
Citation Format: Leila Robinson, Amanda Leonti, Todd A. Alonzo, Yi-Cheng Wang, Michele S. Redell, Rhonda E. Ries, Jenny L. Smith, Tiffany A. Hylkema, Quy Le, E Anders Kolb, Richard Aplenc, Xiaotu Ma, Jeffrey Klco, Katherine Tarlock, Soheil Meshinchi. UBTF tandem duplications (UBTF-TD) in childhood AML: Enrichment in FLT3-ITD and association with clinical outcome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3479.
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Affiliation(s)
| | - Amanda Leonti
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | | | | | - Quy Le
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - E Anders Kolb
- 4Nemours Alfred I. duPont Hospital for Children, Wilmington, DE
| | | | - Xiaotu Ma
- 6St. Jude Children's Research Hospital, Memphis, TN
| | - Jeffrey Klco
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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Tarlock K, Lamble AJ, Wang YC, Gerbing RB, Ries RE, Loken MR, Brodersen LE, Pardo L, Leonti A, Smith JL, Hylkema TA, Woods WG, Cooper TM, Kolb EA, Gamis AS, Aplenc R, Alonzo TA, Meshinchi S. CEBPA-bZip mutations are associated with favorable prognosis in de novo AML: a report from the Children's Oncology Group. Blood 2021; 138:1137-1147. [PMID: 33951732 PMCID: PMC8570058 DOI: 10.1182/blood.2020009652] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/03/2021] [Indexed: 11/20/2022] Open
Abstract
Biallelic CEBPA mutations are associated with favorable outcomes in acute myeloid leukemia (AML). We evaluated the clinical and biologic implications of CEBPA-basic leucine zipper (CEBPA-bZip) mutations in children and young adults with newly diagnosed AML. CEBPA-bZip mutation status was determined in 2958 patients with AML enrolled on Children's Oncology Group trials (NCT00003790, NCT0007174, NCT00372593, NCT01379181). Next-generation sequencing (NGS) was performed in 1863 patients (107 with CEBPA mutations) to characterize the co-occurring mutations. CEBPA mutational status was correlated with disease characteristics and clinical outcomes. CEBPA-bZip mutations were identified in 160 (5.4%) of 2958 patients, with 132 (82.5%) harboring a second CEBPA mutation (CEBPA-double-mutated [CEBPA-dm]) and 28 (17.5%) had a single CEBPA-bZip only mutation. The clinical and laboratory features of the 2 CEBPA cohorts were very similar. Patients with CEBPA-dm and CEBPA-bZip experienced identical event-free survival (EFS) of 64% and similar overall survival (OS) of 81% and 89%, respectively (P = .259); this compared favorably to EFS of 46% and OS of 61% in patients with CEBPA-wild-type (CEBPA-WT) (both P < .001). Transcriptome analysis demonstrated similar expression profiles for patients with CEBPA-bZip and CEBPA-dm. Comprehensive NGS of patients with CEBPA mutations identified co-occurring CSF3R mutations in 13.1% of patients and GATA2 mutations in 21.5% of patients. Patients with dual CEBPA and CSF3R mutations had an EFS of 17% vs 63% for patients with CEBPA-mutant or CSF3R-WT (P < .001) with a corresponding relapse rate (RR) of 83% vs 22%, respectively (P < .001); GATA2 co-occurrence did not have an impact on outcome. CEBPA-bZip domain mutations are associated with favorable clinical outcomes, regardless of monoallelic or biallelic status. Co-occurring CSF3R and CEBPA mutations are associated with a high RR that nullifies the favorable prognostic impact of CEBPA mutations.
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Affiliation(s)
- Katherine Tarlock
- Division of Hematology/Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Adam J Lamble
- Division of Hematology/Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
| | | | | | - Rhonda E Ries
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Amanda Leonti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jenny L Smith
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Tiffany A Hylkema
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - William G Woods
- Aflac Cancer, Children's Healthcare of Atlanta, Emory University, Atlanta, GA
| | - Todd M Cooper
- Division of Hematology/Oncology, Seattle Children's Hospital, University of Washington, Seattle, WA
| | - E Anders Kolb
- Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Alan S Gamis
- Children's Mercy Hospital and Clinics, Kansas City, MO
| | - Richard Aplenc
- The Children's Hospital of Philadelphia, Philadelphia, PA; and
| | - Todd A Alonzo
- Children's Oncology Group, Monrovia, CA
- University of Southern California Keck School of Medicine, Los Angeles, CA
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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