1
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Tian M, Wei JS, Shivaprasad N, Highfill SL, Gryder BE, Milewski D, Brown GT, Moses L, Song H, Wu JT, Azorsa P, Kumar J, Schneider D, Chou HC, Song YK, Rahmy A, Masih KE, Kim YY, Belyea B, Linardic CM, Dropulic B, Sullivan PM, Sorensen PH, Dimitrov DS, Maris JM, Mackall CL, Orentas RJ, Cheuk AT, Khan J. Preclinical development of a chimeric antigen receptor T cell therapy targeting FGFR4 in rhabdomyosarcoma. Cell Rep Med 2023; 4:101212. [PMID: 37774704 PMCID: PMC10591056 DOI: 10.1016/j.xcrm.2023.101212] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 06/12/2023] [Accepted: 09/06/2023] [Indexed: 10/01/2023]
Abstract
Pediatric patients with relapsed or refractory rhabdomyosarcoma (RMS) have dismal cure rates, and effective therapy is urgently needed. The oncogenic receptor tyrosine kinase fibroblast growth factor receptor 4 (FGFR4) is highly expressed in RMS and lowly expressed in healthy tissues. Here, we describe a second-generation FGFR4-targeting chimeric antigen receptor (CAR), based on an anti-human FGFR4-specific murine monoclonal antibody 3A11, as an adoptive T cell treatment for RMS. The 3A11 CAR T cells induced robust cytokine production and cytotoxicity against RMS cell lines in vitro. In contrast, a panel of healthy human primary cells failed to activate 3A11 CAR T cells, confirming the selectivity of 3A11 CAR T cells against tumors with high FGFR4 expression. Finally, we demonstrate that 3A11 CAR T cells are persistent in vivo and can effectively eliminate RMS tumors in two metastatic and two orthotopic models. Therefore, our study credentials CAR T cell therapy targeting FGFR4 to treat patients with RMS.
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Affiliation(s)
- Meijie Tian
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Jun S Wei
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Nityashree Shivaprasad
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Steven L Highfill
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Berkley E Gryder
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - David Milewski
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - G Tom Brown
- Artificial Intelligence Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Larry Moses
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Hannah Song
- Center for Cellular Engineering, Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Jerry T Wu
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Peter Azorsa
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Jeetendra Kumar
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Dina Schneider
- Lentigen Corporation, Miltenyi Bioindustry, 1201 Clopper Road, Gaithersburg, MD 20878, USA
| | - Hsien-Chao Chou
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Young K Song
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Abdelrahman Rahmy
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Katherine E Masih
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Yong Yean Kim
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA
| | - Brian Belyea
- Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Corinne M Linardic
- Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Boro Dropulic
- Caring Cross, 708 Quince Orchard Road, Gaithersburg, MD 20878, USA
| | - Peter M Sullivan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, 1100 Olive Way, Seattle, WA 98101, USA
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Dimiter S Dimitrov
- University of Pittsburgh Department of Medicine, Pittsburgh, PA 15261, USA
| | - John M Maris
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Crystal L Mackall
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rimas J Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, 1100 Olive Way, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Adam T Cheuk
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA.
| | - Javed Khan
- Genetics Branch, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892, USA.
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2
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Masih KE, Gardner RA, Chou HC, Abdelmaksoud A, Song YK, Mariani L, Gangalapudi V, Gryder BE, Wilson AL, Adebola SO, Stanton BZ, Wang C, Milewski D, Kim YY, Tian M, Cheuk ATC, Wen X, Zhang Y, Altan-Bonnet G, Kelly MC, Wei JS, Bulyk ML, Jensen MC, Orentas RJ, Khan J. A stem cell epigenome is associated with primary nonresponse to CD19 CAR T cells in pediatric acute lymphoblastic leukemia. Blood Adv 2023; 7:4218-4232. [PMID: 36607839 PMCID: PMC10440404 DOI: 10.1182/bloodadvances.2022008977] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 09/19/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023] Open
Abstract
CD19 chimeric antigen receptor T-cell therapy (CD19-CAR) has changed the treatment landscape and outcomes for patients with pre-B-cell acute lymphoblastic leukemia (B-ALL). Unfortunately, primary nonresponse (PNR), sustained CD19+ disease, and concurrent expansion of CD19-CAR occur in 20% of the patients and is associated with adverse outcomes. Although some failures may be attributable to CD19 loss, mechanisms of CD19-independent, leukemia-intrinsic resistance to CD19-CAR remain poorly understood. We hypothesize that PNR leukemias are distinct compared with primary sensitive (PS) leukemias and that these differences are present before treatment. We used a multiomic approach to investigate this in 14 patients (7 with PNR and 7 with PS) enrolled in the PLAT-02 trial at Seattle Children's Hospital. Long-read PacBio sequencing helped identify 1 PNR in which 47% of CD19 transcripts had exon 2 skipping, but other samples lacked CD19 transcript abnormalities. Epigenetic profiling discovered DNA hypermethylation at genes targeted by polycomb repressive complex 2 (PRC2) in embryonic stem cells. Similarly, assays of transposase-accessible chromatin-sequencing revealed reduced accessibility at these PRC2 target genes, with a gain in accessibility of regions characteristic of hematopoietic stem cells and multilineage progenitors in PNR. Single-cell RNA sequencing and cytometry by time of flight analyses identified leukemic subpopulations expressing multilineage markers and decreased antigen presentation in PNR. We thus describe the association of a stem cell epigenome with primary resistance to CD19-CAR therapy. Future trials incorporating these biomarkers, with the addition of multispecific CAR T cells targeting against leukemic stem cell or myeloid antigens, and/or combined epigenetic therapy to disrupt this distinct stem cell epigenome may improve outcomes of patients with B-ALL.
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Affiliation(s)
- Katherine E. Masih
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, Cambridge, England
- Medical Scientist Training Program, University of Miami Leonard M. Miller School of Medicine, Miami, FL
| | - Rebecca A. Gardner
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Center for Clinical and Translational Research, Seattle Children’s Research Institute, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Hsien-Chao Chou
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Abdalla Abdelmaksoud
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Young K. Song
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Luca Mariani
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Vineela Gangalapudi
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Berkley E. Gryder
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Ashley L. Wilson
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Serifat O. Adebola
- Immunodynamics Group, Cancer and Inflammation Program, Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Benjamin Z. Stanton
- Center for Childhood Cancer and Blood Diseases, Nationwide Children’s Hospital, Columbus, OH
| | - Chaoyu Wang
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - David Milewski
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yong Yean Kim
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Meijie Tian
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Adam Tai-Chi Cheuk
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Xinyu Wen
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yue Zhang
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Grégoire Altan-Bonnet
- Immunodynamics Group, Cancer and Inflammation Program, Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Michael C. Kelly
- Center for Cancer Research Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD
| | - Jun S. Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Martha L. Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Michael C. Jensen
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Rimas J. Orentas
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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3
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Tian M, Cheuk AT, Wei JS, Abdelmaksoud A, Chou HC, Milewski D, Kelly MC, Song YK, Dower CM, Li N, Qin H, Kim YY, Wu JT, Wen X, Benzaoui M, Masih KE, Wu X, Zhang Z, Badr S, Taylor N, Croix BS, Ho M, Khan J. An optimized bicistronic chimeric antigen receptor against GPC2 or CD276 overcomes heterogeneous expression in neuroblastoma. J Clin Invest 2022; 132:155621. [PMID: 35852863 PMCID: PMC9374382 DOI: 10.1172/jci155621] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Meijie Tian
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Adam T. Cheuk
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jun S. Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Abdalla Abdelmaksoud
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Hsien-Chao Chou
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - David Milewski
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Michael C. Kelly
- Single Cell Analysis Facility, Center for Cancer Research, NIH, Bethesda, Maryland, USA
| | - Young K. Song
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Christopher M. Dower
- Mouse Cancer Genetics Program, Center for Cancer Research, NCI, Frederick, Maryland, USA
| | - Nan Li
- Laboratory of Molecular Biology, Center for Cancer Research and
| | - Haiying Qin
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Yong Yean Kim
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jerry T. Wu
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Xinyu Wen
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Mehdi Benzaoui
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Katherine E. Masih
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Zhongmei Zhang
- Experimental Immunology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Sherif Badr
- Experimental Immunology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Naomi Taylor
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Brad St. Croix
- Mouse Cancer Genetics Program, Center for Cancer Research, NCI, Frederick, Maryland, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology, Center for Cancer Research and
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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4
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Masih KE, Islam Z, Aiyetan P, Kuznetsov IB, Hewitt SM, Catchpoole D, Wei JS, Bocik W, Khan J. Abstract LB062: Profiling of pediatric neuroblastoma reveals a dynamic and clinically significant tumor immune microenvironment. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb062] [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
Background: Neuroblastoma (NB) is the 3rd most common childhood cancer and accounts for 15% of all pediatric cancer deaths. Recently, immunotherapy using monoclonal antibodies targeting GD2 have improved survival rates for some patients with NB. Unfortunately, this response is not uniform across patients, which suggests an incomplete understanding of the underlying immune biology of this disease. Large-scale sequencing efforts of patient tumors have suggested that NB has diverse immune microenvironments (TMEs), which are associated with MYCN-amplification (A) and patient outcomes. While this is strong evidence, these results need to be further validated, specifically to determine whether the infiltrating immune cells can interact with tumor cells and if the TME is impacted by evolutionary pressures. We hypothesized the TME is dynamic, changing with therapy and metastasis, influenced by molecular subtype, and associated with patient outcomes.
Methods: To better understand the heterogeneity seen in NB TMEs, we obtained 93 clinically annotated tumors from 72 pediatric patients with neuroblastoma, consisting of high-risk primary and metastatic tumors both pre- and post- chemotherapy. We designed two highly multiplexed antibody panels targeting immune cells and performed either imaging mass cytometry (IMC) (n = 46) or NanoString GeoMx DSP (n = 47).
Results: We confirmed that MYCN-non amplified (NA) tumors display higher frequencies of lymphocytes including CD4 (p < 0.003) and CD8 (p < 0.005) T-cells. Using nearest neighbor analysis, we found that not only are both CD4 and CD8 T-cells more frequent in MYCN-NA samples, but they are significantly closer to tumor cells compared to MYCN-A tumors (p < 2.2E-16), suggesting increased interactions. We then investigated the effects of exposure to chemotherapy on the TME and discovered that MYCN-NA tumors displayed higher frequencies of T-cells (p < 0.0041) and B-cells (p = 0.047) prior to exposure to chemotherapy. We also revealed increased frequencies of macrophages (p = 0.0193) and antigen presentation in tumors post-treatment. Interestingly, we saw increased expression of the immune checkpoints CTLA-4 (p = 0.0432) and TIM-3 (p = 2.05E-5), but not PD-1, PD-L1, or PD-L2, suggesting targeted checkpoint blockade could improve response to therapy in these patients. Notably, high expression of CD56, a marker for both NK cells and NB, was associated with increase overall survival, indicating a potential role of NK cells in improving outcomes.
Conclusions: Using two independent protein-based profiling methods, we investigated the TME in clinically annotated patient NBs. We find that the TME in NB varies with tumor subtype and changes dynamically with chemotherapy. These results can inform future trials to optimize the timing and specificity of novel immunotherapeutic approaches for these high-risk patients.
Citation Format: Katherine E. Masih, Zahin Islam, Paul Aiyetan, Igor B. Kuznetsov, Stephen M. Hewitt, Daniel Catchpoole, Jun S. Wei, William Bocik, Javed Khan. Profiling of pediatric neuroblastoma reveals a dynamic and clinically significant tumor immune microenvironment [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 LB062.
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Affiliation(s)
- Katherine E. Masih
- 1Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Zahin Islam
- 1Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Paul Aiyetan
- 1Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Igor B. Kuznetsov
- 2Cancer Research Center and Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensellaer, NY
| | - Stephen M. Hewitt
- 3Experimental Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Daniel Catchpoole
- 4The Tumour Bank, Children’s Cancer Research Unit, Kids Research Institute, the Children’s Hospital at Weastmead, Weastmead, Australia
| | - Jun S. Wei
- 1Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - William Bocik
- 5Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Javed Khan
- 1Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
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5
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Masih KE, Gardner R, Chou HC, Abdelmaksoud A, Song YK, Mariani L, Gangalapudi V, Gryder BE, Wilson A, Adebola SO, Stanton BZ, Wang C, Wen X, Altan-Bonnet G, Kelly MC, Wei JS, Bulyk ML, Jensen MC, Orentas RJ, Khan J. Abstract 3581: Multi-omic analysis identifies mechanisms of resistance to CD19 CAR T-cell therapy in children with acute lymphoblastic leukemia. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3581] [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
Background: Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. Despite the survival rate of 90% for newly diagnosed children with ALL, the outcome for relapsed patients is historically poor with a less than 30% survival. CD19 CAR T-cell therapy (CART19) has shown remarkable response rates, between 80-90% in relapsed/refractory disease. Little is known about antigen-independent factors that predict initial resistance to CART19. We hypothesized that leukemias that are resistant to CART19 are distinct from sensitive leukemias and that these differences can be detected prior to therapy.
Methods: To interrogate differences between resistant and sensitive leukemias, we obtained pre-treatment bone marrow aspirates (BMAs) from patients enrolled in a clinical trial at Seattle Children’s Hospital (PLAT-02). Samples were categorized based on patient response, with non-response defined as not achieving and maintaining minimal residual disease negativity at Day +63. Our study included 7 resistant and 7 sensitive leukemias as controls. We performed whole exome sequencing, bulk RNA-seq, PacBio-seq of the CD19 locus, array-based methylation, ATAC-seq, scRNA-seq, and CyTOF.
Results: We found that non-response to CART19 is independent of leukemic subtype. Despite blasts being CD19+ in all patients by flow cytometry, we identified alternative splicing of CD19 in one non-responder, while the remaining non-responders expressed high levels of wildtype CD19. We discovered a distinctive DNA methylation pattern in the non-responders characterized by hypermethylation of PRC2 targets in embryonic and cancer stem cells (p = 8.15E-25) Furthermore, using gene set enrichment analysis of ATAC-seq data, we found increased accessibility of chromatin at regions associated with stem cell proliferation (NES = 2.31; p < 0.0001) and cell cycling (NES = 2.27; p < 0.0001). We found a greater similarity between accessibility patterns of non-responders to hematopoietic progenitors, including hematopoietic stem cells (p = 0.037) and common myeloid progenitors (p = 0.047). These findings were supported by an increased frequency of cell subpopulations expressing a multi-lineage phenotype (CD19, CD20, CD33, CD34; p = 0.009). Moreover, we find decreased expression of antigen presentation and processing pathways across all leukemic cells relative to responders (p = 0.0001).
Conclusions: This study, one of the most comprehensive multi-omic analyses of samples from patients treated with CAR T-cells, identified resistance mechanisms that can be detected prior to treatment. We report the novel association of a stem cell phenotype, lineage plasticity, and decreased antigen presentation with resistance. These results support further refinement of eligibility for CART19 for children with leukemia and highlights the need for alternative of complimentary approaches for these patients.
Citation Format: Katherine E. Masih, Rebecca Gardner, Hsien-Chao Chou, Abdalla Abdelmaksoud, Young K. Song, Luca Mariani, Vineela Gangalapudi, Berkley E. Gryder, Ashley Wilson, Serifat O. Adebola, Benjamin Z. Stanton, Chaoyu Wang, Xinyu Wen, Gregoire Altan-Bonnet, Michael C. Kelly, Jun S. Wei, Martha L. Bulyk, Michael C. Jensen, Rimas J. Orentas, Javed Khan. Multi-omic analysis identifies mechanisms of resistance to CD19 CAR T-cell therapy in children with acute lymphoblastic leukemia [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 3581.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Xinyu Wen
- 1National Cancer Institute, Bethesda, MD
| | | | | | - Jun S. Wei
- 1National Cancer Institute, Bethesda, MD
| | | | | | | | - Javed Khan
- 1National Cancer Institute, Bethesda, MD
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6
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Brohl AS, Sindiri S, Wei JS, Milewski D, Chou HC, Song YK, Wen X, Kumar J, Reardon HV, Mudunuri US, Collins JR, Nagaraj S, Gangalapudi V, Tyagi M, Zhu YJ, Masih KE, Yohe ME, Shern JF, Qi Y, Guha U, Catchpoole D, Orentas RJ, Kuznetsov IB, Llosa NJ, Ligon JA, Turpin BK, Leino DG, Iwata S, Andrulis IL, Wunder JS, Toledo SRC, Meltzer PS, Lau C, Teicher BA, Magnan H, Ladanyi M, Khan J. Immuno-transcriptomic profiling of extracranial pediatric solid malignancies. Cell Rep 2021; 37:110047. [PMID: 34818552 PMCID: PMC8642810 DOI: 10.1016/j.celrep.2021.110047] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
We perform an immunogenomics analysis utilizing whole-transcriptome sequencing of 657 pediatric extracranial solid cancer samples representing 14 diagnoses, and additionally utilize transcriptomes of 131 pediatric cancer cell lines and 147 normal tissue samples for comparison. We describe patterns of infiltrating immune cells, T cell receptor (TCR) clonal expansion, and translationally relevant immune checkpoints. We find that tumor-infiltrating lymphocytes and TCR counts vary widely across cancer types and within each diagnosis, and notably are significantly predictive of survival in osteosarcoma patients. We identify potential cancer-specific immunotherapeutic targets for adoptive cell therapies including cell-surface proteins, tumor germline antigens, and lineage-specific transcription factors. Using an orthogonal immunopeptidomics approach, we find several potential immunotherapeutic targets in osteosarcoma and Ewing sarcoma and validated PRAME as a bona fide multi-pediatric cancer target. Importantly, this work provides a critical framework for immune targeting of extracranial solid tumors using parallel immuno-transcriptomic and -peptidomic approaches.
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Affiliation(s)
- Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | | | - Jun S Wei
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Young K Song
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Xinyu Wen
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Hue V Reardon
- Advanced Biomedical Computational Science, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, MD 21702, USA
| | - Uma S Mudunuri
- Advanced Biomedical Computational Science, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, MD 21702, USA
| | - Jack R Collins
- Advanced Biomedical Computational Science, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, MD 21702, USA
| | - Sushma Nagaraj
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Manoj Tyagi
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Yuelin J Zhu
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Katherine E Masih
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Marielle E Yohe
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Jack F Shern
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Yue Qi
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Daniel Catchpoole
- The Tumour Bank, Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Rimas J Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Igor B Kuznetsov
- Cancer Research Center and Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY 12144, USA
| | - Nicolas J Llosa
- Pediatric Oncology, John Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - John A Ligon
- Pediatric Oncology, John Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Brian K Turpin
- Division of Oncology, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA
| | - Daniel G Leino
- Division of Oncology, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA
| | | | - Irene L Andrulis
- Lunenfelf-Tanenbaum Research Institute, Sinai Health System; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jay S Wunder
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System; Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Silvia R C Toledo
- Support Group for Children and Adolescents with Cancer (GRAACC), Pediatric Oncology Institute (IOP), Universidade Federal de Sao Paulo, Sao Paulo, Brail
| | | | - Ching Lau
- The Jackson Laboratory, Farmington, CT 06032, USA
| | - Beverly A Teicher
- Molecular Pharmacology Branch, DCTD, NCI, NIH, Bethesda, MD 20892, USA
| | - Heather Magnan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Javed Khan
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA.
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7
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Masih KE, Ligon JA, Yates B, Shalabi H, Little L, Islam Z, Ombrello AK, Inglefield J, Nussenblatt V, Manion M, Khan J, Shah NN. Consequences of hemophagocytic lymphohistiocytosis-like cytokine release syndrome toxicities and concurrent bacteremia. Pediatr Blood Cancer 2021; 68:e29247. [PMID: 34309174 PMCID: PMC9410765 DOI: 10.1002/pbc.29247] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/18/2022]
Abstract
Serious bacterial infections (SBI) can lead to devastating complications with CD19 CAR T cells and cytokine release syndrome (CRS). Little is known about consequences of and risk factors for SBI with novel CAR T-cell constructs or with CRS complicated by HLH-like toxicities. We report on three patients with B-cell acute lymphoblastic leukemia treated with CD22 CAR T cells who developed SBI and CRS-associated HLH. Serum cytokine profiling revealed sustained elevations well beyond CRS resolution, suggesting ongoing systemic inflammation. Heightened inflammatory states converging with SBI contribute to poor outcomes, and recognition and prevention of extended inflammation may be needed to improve outcomes.
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Affiliation(s)
- Katherine E. Masih
- Oncogenomics Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA,Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - John A. Ligon
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Bonnie Yates
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Haneen Shalabi
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Lauren Little
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Zahin Islam
- Oncogenomics Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Amanda K. Ombrello
- Inflammatory Disease Section, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Jon Inglefield
- Applied Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Veronique Nussenblatt
- Infectious Disease Consult Service, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Maura Manion
- Infectious Disease Consult Service, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Nirali N. Shah
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, Maryland, USA
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8
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Kupp R, Ruff L, Terranova S, Nathan E, Ballereau S, Stark R, Sekhar Reddy Chilamakuri C, Hoffmann N, Wickham-Rahrmann K, Widdess M, Arabzade A, Zhao Y, Varadharajan S, Zheng T, Murugesan M, Pfister SM, Kawauchi D, Pajtler KW, Deneen B, Mack SC, Masih KE, Gryder BE, Khan J, Gilbertson RJ. ZFTA Translocations Constitute Ependymoma Chromatin Remodeling and Transcription Factors. Cancer Discov 2021; 11:2216-2229. [PMID: 33741711 PMCID: PMC8918067 DOI: 10.1158/2159-8290.cd-20-1052] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 07/16/2020] [Revised: 01/06/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
ZFTA (C11orf95)-a gene of unknown function-partners with a variety of transcriptional coactivators in translocations that drive supratentorial ependymoma, a frequently lethal brain tumor. Understanding the function of ZFTA is key to developing therapies that inhibit these fusion proteins. Here, using a combination of transcriptomics, chromatin immunoprecipitation sequencing, and proteomics, we interrogated a series of deletion-mutant genes to identify a tripartite transformation mechanism of ZFTA-containing fusions, including: spontaneous nuclear translocation, extensive chromatin binding, and SWI/SNF, SAGA, and NuA4/Tip60 HAT chromatin modifier complex recruitment. Thereby, ZFTA tethers fusion proteins across the genome, modifying chromatin to an active state and enabling its partner transcriptional coactivators to promote promiscuous expression of a transforming transcriptome. Using mouse models, we validate further those elements of ZFTA-fusion proteins that are critical for transformation-including ZFTA zinc fingers and partner gene transactivation domains-thereby unmasking vulnerabilities for therapeutic targeting. SIGNIFICANCE: Ependymomas are hard-to-treat brain tumors driven by translocations between ZFTA and a variety of transcriptional coactivators. We dissect the transforming mechanism of these fusion proteins and identify protein domains indispensable for tumorigenesis, thereby providing insights into the molecular basis of ependymoma tumorigenesis and vulnerabilities for therapeutic targeting.This article is highlighted in the In This Issue feature, p. 2113.
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Affiliation(s)
- Robert Kupp
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Lisa Ruff
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Sabrina Terranova
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Erica Nathan
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Stephane Ballereau
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Rory Stark
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | | | - Nadin Hoffmann
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | | | - Marcus Widdess
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England
| | - Amir Arabzade
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Yanhua Zhao
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Srinidhi Varadharajan
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Tuyu Zheng
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mohankumar Murugesan
- Centre for Stem Cell Research, Christian Medical College Campus, Bagayam, Vellore, Tamil Nadu, India
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daisuke Kawauchi
- Department of Biochemistry and Cellular Biology, National Center of Neurology and Psychiatry (NCNP), Tokyo, Japan
| | - Kristian W Pajtler
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benjamin Deneen
- Cancer and Cell Biology Program, Baylor College of Medicine, Dan L. Duncan Cancer Center, Houston, Texas
| | - Stephen C Mack
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Katherine E Masih
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Berkley E Gryder
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, NCI, Bethesda, Maryland
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, England.
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, England
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9
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Masih KE, Gardner R, Gryder BE, Abdelmaksoud A, Wilson A, Adebola S, Stanton BZ, Song YK, Lack J, Wang C, Wen X, Rae Z, Cheuk A, Altan-Bonnet G, Kelly M, Wei JS, Jensen MC, Orentas RJ, Khan J. Abstract A11: A comprehensive and integrative omic analysis of multiply relapsed refractory pediatric pre-B cell acute lymphoblastic leukemia predicts response to CD19 CAR T-cell therapy. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-a11] [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
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer with a peak incidence at 3-5 years of age. Despite the improved survival rate of 90% for newly diagnosed children with ALL, the outcome for patients with relapsed disease is poor with a less than 30% overall survival. CD19 CAR T-cell therapy has shown remarkable response rates in relapsed/refractory disease. Long-term survival analysis has shown that initial response rates exceed 80%. However, durable response rates at one year are closer to 40%. Little is known about factors predicting durable response to CAR T therapy. We hypothesize that patients with CD19 CAR T-cell resistant ALL have a distinct disease compared to responders to therapy that can be identified in pretreatment leukemia. Utilizing advanced genomic, epigenetic, proteomic, and single-cell (sc) techniques, we characterized patient bone marrow aspirates (BMA) to identify mechanisms of resistance. Patients enrolled in PLAT-02 at Seattle Children’s Hospital were categorized according to the durability of their response to CD19 CAR T therapy. To characterize the molecular and genomic alterations specific to the therapy-resistant ALLs, we performed comprehensive analyses on pre-treatment therapy-resistant and sensitive BMAs using whole-exome sequencing, RNA- BMAs seq, scRNA-seq, sc B cell receptor (BCR)-seq, methylation array, H3K27ac ChIP-seq, ATAC-seq, and CyTOF. Additionally, we developed murine patient-derived xenografts (PDXs) for future studies. Initial mutation analyses revealed 5 hotspot mutations (ABL1, 2 x KRAS, IKZF1, and EP300) and actionable fusion (2 ABL1, 2 ETV6, 2 ETV5, KMT2A). Interestingly, we identified a KMT2A-AFF1 fusion in a sensitive leukemia, which has been demonstrated to predispose patients to CD19 CAR T resistance through lineage switching. Additionally, we identified a novel CREBBP-fusion in leukemias resistant to CD19 CAR T-induced B-cell aplasia. Alterations of CREBBP have previously been associated with ALL that is refractory to conventional therapies. Integrated gene expression and epigenetic analyses are ongoing to identify genes or pathways associated with resistant disease. scRNA- and scBCR-seq data are being analyzed and integrated with CyTOF analyses to detect mixed lineage and gene expression-based heterogeneity that may predict clonal selection by CAR T pressure. Finally, we developed and genetically analyzed murine PDXs for 64% of the patient samples, establishing a valuable resource for future studies and developing novel therapies for resistant leukemias. This study is one of the most integrative and comprehensive genomic profiling approaches to identify the molecular traits of therapy-resistant ALL in patient samples. We hope to identify and develop crucial biomarkers predicting responsiveness to CAR T-cell therapy.
Citation Format: Katherine E. Masih, Rebecca Gardner, Berkley E. Gryder, Abdalla Abdelmaksoud, Ashley Wilson, Serifat Adebola, Benjamin Z. Stanton, Young K. Song, Justin Lack, Chaoyu Wang, Xinyu Wen, Zachary Rae, Adam Cheuk, Gregoire Altan-Bonnet, Michael Kelly, Jun S. Wei, Michael C. Jensen, Rimas J. Orentas, Javed Khan. A comprehensive and integrative omic analysis of multiply relapsed refractory pediatric pre-B cell acute lymphoblastic leukemia predicts response to CD19 CAR T-cell therapy [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A11.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Justin Lack
- 1National Institutes of Health, Bethesda, MD,
| | - Chaoyu Wang
- 1National Institutes of Health, Bethesda, MD,
| | - Xinyu Wen
- 1National Institutes of Health, Bethesda, MD,
| | - Zachary Rae
- 1National Institutes of Health, Bethesda, MD,
| | - Adam Cheuk
- 1National Institutes of Health, Bethesda, MD,
| | | | | | - Jun S. Wei
- 1National Institutes of Health, Bethesda, MD,
| | | | | | - Javed Khan
- 1National Institutes of Health, Bethesda, MD,
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10
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Masih KE, Gardner R, Gryder BE, Lack J, Stanton BZ, Wilson A, Finney O, Sindiri S, Song Y, Rae Z, Kelly M, Wang C, Wen X, Cheuk A, Wei JS, Jensen M, Orentas R, Khan J. Abstract LB-056: An integrated genomic, epigenetic, proteomic, and single cell analysis of pediatric B cell acute lymphoblastic leukemia to elucidate resistance mechanisms to CD19 CAR T cell therapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-056] [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
Background
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer with a peak incidence at 3-5 years of age. Despite the improved survival rate of 90% for newly diagnosed children with ALL, the outcome for patients with relapsed disease is poor with a less than 30% overall survival. CD19 CAR T cell therapy has shown impressive response rates in relapsed/refractory disease. However, long-term survival analysis has shown that despite initial response rates exceeding 80%, durable response rates at one year are closer to 40%. Currently, little is known about molecular factors predicting durable response to CAR T therapy. We hypothesized that patients with CD19 CAR T therapy resistant ALL have a molecularly distinct disease compared to patients who respond to therapy, which can be identified in pre-treatment leukemia samples. Utilizing advanced genomic, epigenetic, proteomic, and single-cell techniques, we characterized the bone marrow of patients that were resistant or sensitive to therapy to identify mechanisms of resistance.
Methods
Patients enrolled in a phase I clinical trial at Seattle Children’s Hospital (PLAT-02) were categorized according to the durability of their response to CD19 CAR T therapy. Bone marrow aspirates from patients with leukemias resistant to therapy (4 pre-treatment with 2 paired post-treatment) were analyzed and compared to patients with therapy sensitive leukemias (5 pre-treatment). We performed bulk whole-exome sequencing and RNA-seq, single cell (sc) RNA-seq, scB cell receptor (BCR)-seq, methylation array, H3K27ac ChIP-seq, and ATAC-seq.
Results
Initial genomic analysis revealed a total of 5 previously reported recurrent hotspot mutations in ABL1, 2 x KRAS (Q61H), IKZF1, and EP300. RNA-seq analyses identified actionable fusions in 2 x ABL1, 2 x ETV6, 2 x ETV5, and 1x KMT2A with variable partners. Interestingly, a therapy-sensitive leukemia harbored a KMT2A-AFF1fusion that was previously shown to predispose patients treated with blinatumomab to leukemic plasticity and lineage switching. Additionally, we identified in-frame CREBBP-fusions in all leukemias that failed to achieve CD19 CAR T cell induced B cell aplasia. CREBBP perturbations have previously been associated with relapsed and refractory ALL. Integrated gene expression and epigenetic analyses identified several pathways associated with resistant disease. ATAC-seq and methylation data are being analyzed for lineage specification. Similarly, scRNA- and scBCR-seq data are being analyzed for the existence of mixed lineage and gene expression-based heterogeneity that may predict clonal selection under CAR T pressure.
Conclusions
This study establishes one of the most comprehensive approaches to genomic profiling for leukemia patient samples. Although our analysis is preliminary and sample number is small, in-depth analyses are highlighting crucial differences in leukemia that will allow improved prediction of responsiveness to CAR T therapy.
Citation Format: Katherine E. Masih, Rebecca Gardner, Berkley E. Gryder, Justin Lack, Benjamin Z. Stanton, Ashley Wilson, Olivia Finney, Sivasish Sindiri, Young Song, Zachary Rae, Michael Kelly, Chaoyu Wang, Xinyu Wen, Adam Cheuk, Jun S. Wei, Michael Jensen, Rimas Orentas, Javed Khan. An integrated genomic, epigenetic, proteomic, and single cell analysis of pediatric B cell acute lymphoblastic leukemia to elucidate resistance mechanisms to CD19 CAR T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-056.
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Affiliation(s)
| | | | | | - Justin Lack
- 1National Institutes of Health, Bethesda, MD
| | | | | | | | | | - Young Song
- 1National Institutes of Health, Bethesda, MD
| | - Zachary Rae
- 1National Institutes of Health, Bethesda, MD
| | | | - Chaoyu Wang
- 1National Institutes of Health, Bethesda, MD
| | - Xinyu Wen
- 1National Institutes of Health, Bethesda, MD
| | - Adam Cheuk
- 1National Institutes of Health, Bethesda, MD
| | - Jun S. Wei
- 1National Institutes of Health, Bethesda, MD
| | | | | | - Javed Khan
- 1National Institutes of Health, Bethesda, MD
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11
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Iacobucci I, Wen J, Meggendorfer M, Choi JK, Shi L, Pounds SB, Carmichael CL, Masih KE, Morris SM, Lindsley RC, Janke LJ, Alexander TB, Song G, Qu C, Li Y, Payne-Turner D, Tomizawa D, Kiyokawa N, Valentine M, Valentine V, Basso G, Locatelli F, Enemark EJ, Kham SKY, Yeoh AEJ, Ma X, Zhou X, Sioson E, Rusch M, Ries RE, Stieglitz E, Hunger SP, Wei AH, To LB, Lewis ID, D'Andrea RJ, Kile BT, Brown AL, Scott HS, Hahn CN, Marlton P, Pei D, Cheng C, Loh ML, Ebert BL, Meshinchi S, Haferlach T, Mullighan CG. Genomic subtyping and therapeutic targeting of acute erythroleukemia. Nat Genet 2019; 51:694-704. [PMID: 30926971 PMCID: PMC6828160 DOI: 10.1038/s41588-019-0375-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [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: 07/19/2018] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Acute erythroid leukemia (AEL) is a high-risk leukemia of poorly understood genetic basis, with controversy regarding diagnosis in the spectrum of myelodysplasia and myeloid leukemia. We compared genomic features of 159 childhood and adult AEL cases with non-AEL myeloid disorders and defined five age-related subgroups with distinct transcriptional profiles: adult, TP53 mutated; NPM1 mutated; KMT2A mutated/rearranged; adult, DDX41 mutated; and pediatric, NUP98 rearranged. Genomic features influenced outcome, with NPM1 mutations and HOXB9 overexpression being associated with a favorable prognosis and TP53, FLT3 or RB1 alterations associated with poor survival. Targetable signaling mutations were present in 45% of cases and included recurrent mutations of ALK and NTRK1, the latter of which drives erythroid leukemogenesis sensitive to TRK inhibition. This genomic landscape of AEL provides the framework for accurate diagnosis and risk stratification of this disease, and the rationale for testing targeted therapies in this high-risk leukemia.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - John K Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lei Shi
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stanley B Pounds
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Catherine L Carmichael
- The Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Katherine E Masih
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sarah M Morris
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Laura J Janke
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guangchun Song
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Chunxu Qu
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yongjin Li
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Debbie Payne-Turner
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Marcus Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Virginia Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Giuseppe Basso
- Clinic of Paediatric Haematology and Oncology, Department for Children's and Women's Health, University of Padua, Padua, Italy
- Italian Institute for Genomic Medicine, Turin, Italy
| | - Franco Locatelli
- Department of Gynecology/Obstetrics and Pediatrics, Sapienza University of Rome, Rome, Italy
- Department of Pediatric Hematology and Oncology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Eric J Enemark
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shirley K Y Kham
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Allen E J Yeoh
- Centre for Translational Research in Acute Leukaemia, Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Edgar Sioson
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rhonda E Ries
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elliot Stieglitz
- Department of Pediatrics, Benioff Children's Hospital, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew H Wei
- The Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
- Department of Clinical Haematology, The Alfred Hospital, Melbourne, Victoria, Australia
- Department of Pathology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - L Bik To
- Departments of Haematology, SA Pathology and Royal Adelaide Hospital, Adelaide, South Australia, Australia
- Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ian D Lewis
- Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Richard J D'Andrea
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Benjamin T Kile
- The Walter & Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anna L Brown
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Hamish S Scott
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Christopher N Hahn
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Paula Marlton
- Princess Alexandra Hospital and University of Queensland School of Clinical Medicine, Brisbane, Queensland, Australia
| | - Deqing Pei
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cheng Cheng
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital, and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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