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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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Tian M, Cheuk ATC, Song Y, Sindiri S, Li N, Dower CM, Ho M, Croix BS, Khan J. Abstract 5871: Immunogenomic approaches to optimize immunotherapeutic targeting of neuroblastoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5871] [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 most common extra-cranial solid cancer in children. Although multimodal therapies with differentiating agents and immunotherapy with anti-GD2 antibody and GM-CSF have shown promising results, it remains deadly in approximately 50% of patients with high-risk disease. Chimeric antigen receptor T-cell therapies (CAR-T) have been found to be effective in treating refractory and relapsed leukemia and lymphoma, and two of them have been recently approved by the FDA. However, current CARs frequently lose efficacy due to T cell exhaustion and CARs against solid tumor antigens often lack enough specificity due to a low incidence of somatic mutations resulting in a paucity of tumor neoantigens. There have not been effective CAR-T therapies against other solid cancers to date although many clinical trials are underway. We previously identified 2 cell surface cancer-associated antigens, GPC2 (Glypican-2) and CD276 (B7-H3), both highly expressed in NB tumor cells but expressed at low or undetectable levels in normal organs. Here we attempt to develop a high throughput way of identifying optimal CART cell binders that show activation and expansion in the presence of GPC2 and CD276 but lack of exhaustion.
Methods: Binders targeting GPC2 or CD276 were cloned into CAR lentiviral constructs and then were separately transduced into T cells to develop CAR-T cells. Then we analyzed cytotoxicity of these CART cells individually. To identify the most effective GPC2 or CD276-specific targeting CAR-T cells, we utilized a combined proteomics and transcriptomics method for every single CAR-T cell to quantify RNA and protein at the same. All CAR-T cells were pooled and co-cultured with CD276/GPC2-expressing NB cancer cells (target cells) for 24 hr. Co-cultured CAR-T cells were examined for their activation, exhaustion, cytotoxicity state and distinguished different cell types by staining with CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) antibodies, and then molecularly barcoded using 10X Genomics platform for single cell RNA-sequencing (scRNA-seq).
Results: We attempted to test the efficacy of CAR-T cells using 14 established and novel binders against GPC2 or CD276. According to cytotoxicity assay of these 14 CART cells, we found CT3 was the most effective GPC2 targeting CART cells but majority of CD276 CART cells showed high cytolytic activity in vitro.
Conclusions and Future Directions: Using the CITE-seq and RNAseq analyses, we can identify which of the CARs are enriched and have an activated T cell signature, but lack exhaustion markers. Top candidate binders for each antigen are currently being developed into “AND” or “OR” CARs that are being tested in in-vitro and in-vivo models of NB. Thus, we have developed a high throughput method to identify high affinity functional binders against tumor cell surface antigens and provide a novel immunogenomics methods of CARs optimization for development of highly effective immunotherapies against NB and other cancers.
Citation Format: Meijie Tian, Adam Tai-Chi Cheuk, Yong Song, Sivasish Sindiri, Nan Li, Christopher M. Dower, Mitchell Ho, Bradley St Croix, Javed Khan. Immunogenomic approaches to optimize immunotherapeutic targeting of neuroblastoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5871.
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Affiliation(s)
| | | | - Yong Song
- 1National Cancer Institute, Bethesda, MD
| | | | - Nan Li
- 1National Cancer Institute, Bethesda, MD
| | | | | | | | - Javed Khan
- 1National Cancer Institute, Bethesda, MD
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Tian M, Cheuk ATC, Kumar J, Song YK, Sindiri S, Li N, Dower CM, Ho M, St. Croix B, Khan J. Abstract A13: Immunogenomic approaches to optimize immunotherapeutic targeting of neuroblastoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.pedca19-a13] [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
Neuroblastoma (NB) is the most common extracranial solid cancer in children. Although multimodal therapies with differentiating agents and immunotherapy with anti-GD2 antibody and GM-CSF have shown promising results, it remains deadly in approximately 50% of patients with high-risk disease. Chimeric antigen receptor T-cell therapies (CAR-T) have been found to be effective in treating refractory and relapsed leukemia and lymphoma, and two of them have been recently approved by the FDA. However, current CARs frequently lose efficacy due to T-cell exhaustion, and CARs against solid tumor antigens often lack enough specificity due to a low incidence of somatic mutations resulting in a paucity of tumor neoantigens. There have not been effective CAR-T therapies against other solid cancers to date, although many clinical trials are under way. Therefore, we attempted to develop a high-throughput way of identifying optimal CART cell binders that show activation and expansion in the presence of targets but lack of exhaustion. We previously identified two cell surface cancer-associated antigens, GPC2 (Glypican-2) and CD276 (B7-H3), both highly expressed in NB tumor cells but expressed at low or undetectable levels in normal organs. 14 established binders as well as novel binders targeting these two antigens were cloned into CAR lentiviral constructs and then were separately transduced into T cells to develop 14 CAR-T cells using a 2nd-generation design. All 14 CAR-T cells were pooled and cocultured with CD276/GPC2-expressing NB cancer cells (target cells) for 24 hr. To identify the effective GPC2 or CD276-specific targeting CAR-T cells, we utilized a combined proteomics and transcriptomics method for every single CAR-T cell to quantify RNA and protein at the same. Cocultured CAR-T cells were examined for their activation, exhaustion, cytotoxicity state and distinguished different cell types by staining with CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) antibodies, and then molecularly barcoded using 10X Genomics platform for single-cell RNA-sequencing (scRNA-seq). The data are currently being analyzed and will be presented. Using this method, we will be able to identify which of the CARs are enriched and have an activated T-cell signature, and lack exhaustion marks as determined by the CITE-seq and RNAseq analyses. Finally, top candidate binders for each antigen will be developed into “AND” or “OR” CARs and will be tested in in vitro and in vivo models of NB. Thus, we will develop a high-throughput way to identify high-affinity functional binders against tumor cell surface antigens. This study also will provide novel immunogenomics methods of CARs optimization for development of highly effective immunotherapies against NB and other cancers.
Citation Format: Meijie Tian, Adam Tai-Chi Cheuk, Jeetendra Kumar, Young K. Song, Sivasish Sindiri, Nan Li, Christopher M. Dower, Mitchell Ho, Brad St. Croix, Javed Khan. Immunogenomic approaches to optimize immunotherapeutic targeting of neuroblastoma [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 A13.
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Affiliation(s)
| | | | | | | | | | - Nan Li
- National Cancer Institute, Bethesda, MD
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