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Cinar M, Martinez-Medina L, Puvvula PK, Arakelyan A, Vardarajan BN, Anthony N, Nagaraju GP, Park D, Feng L, Sheff F, Mosunjac M, Saxe D, Flygare S, Alese OB, Kaufman JL, Lonial S, Sarmiento JM, Lossos IS, Vertino PM, Lopez JA, El-Rayes B, Bernal-Mizrachi L. Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells. Nucleic Acids Res 2024:gkae427. [PMID: 38783375 DOI: 10.1093/nar/gkae427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The exchange of genes between cells is known to play an important physiological and pathological role in many organisms. We show that circulating tumor DNA (ctDNA) facilitates cell-specific gene transfer between human cancer cells and explain part of the mechanisms behind this phenomenon. As ctDNA migrates into the nucleus, genetic information is transferred. Cell targeting and ctDNA integration require ERVL, SINE or LINE DNA sequences. Chemically manufactured AluSp and MER11C sequences replicated multiple myeloma (MM) ctDNA cell targeting and integration. Additionally, we found that ctDNA may alter the treatment response of MM and pancreatic cancer models. This study shows that retrotransposon DNA sequences promote cancer gene transfer. However, because cell-free DNA has been detected in physiological and other pathological conditions, our findings have a broader impact than just cancer. Furthermore, the discovery that transposon DNA sequences mediate tissue-specific targeting will open up a new avenue for the delivery of genes and therapies.
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Affiliation(s)
- Munevver Cinar
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | | | - Arsen Arakelyan
- Bioinformatics group, Institute of Molecular Biology NAS RA, Yerevan, Armenia
| | | | - Neil Anthony
- Integrated Cellular Imaging Core, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ganji P Nagaraju
- Division of hematology and oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongkyoo Park
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Lei Feng
- Kodikaz Therapeutic Solutions, Inc, New York, NY, USA
| | - Faith Sheff
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Marina Mosunjac
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Debra Saxe
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Steven Flygare
- Department of Computational Biology/ Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Olatunji B Alese
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Jonathan L Kaufman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Juan M Sarmiento
- Department of Surgery, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Izidore S Lossos
- Department of Medicine, Division of Hematology-Oncology and Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Paula M Vertino
- Department of Biomedical Genetics and the Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Jose A Lopez
- Bloodworks Northwest Research Institute, Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
| | - Bassel El-Rayes
- Division of hematology and oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leon Bernal-Mizrachi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
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Chu F, Cao J, Liu J, Yang H, Davis TJ, Kuang SQ, Cheng X, Zhang Z, Karri S, Vien LT, Bover L, Sun R, Vega F, Green M, Davis RE, Neelapu SS. Chimeric antigen receptor T cells to target CD79b in B-cell lymphomas. J Immunother Cancer 2023; 11:e007515. [PMID: 38007239 PMCID: PMC10680003 DOI: 10.1136/jitc-2023-007515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T cells targeting CD19 mediate potent and durable effects in B-cell malignancies. However, antigen loss or downregulation is a frequent cause of resistance. Here, we report development of a novel CAR T-cell therapy product to target CD79b, a pan B-cell antigen, widely expressed in most B-cell lymphomas. METHODS We generated a novel anti-CD79b monoclonal antibody by hybridoma method. The specificity of the antibody was determined by testing against isogenic cell lines with human CD79b knock-in or knock-out. A single-chain variable fragment derived from the monoclonal antibody was used to make a panel of CD79b-targeting CAR molecules containing various hinge, transmembrane, and co-stimulatory domains. These were lentivirally transduced into primary T cells and tested for antitumor activity in in vitro and in vivo B-cell lymphoma models. RESULTS We found that the novel anti-CD79b monoclonal antibody was highly specific and bound only to human CD79b and no other cell surface protein. In testing the various CD79b-targeting CAR molecules, superior antitumor efficacy in vitro and in vivo was found for a CAR consisting CD8α hinge and transmembrane domains, an OX40 co-stimulatory domain, and a CD3ζ signaling domain. This CD79b CAR specifically recognized human CD79b-expressing lymphoma cell lines but not CD79b knock-out cell lines. CD79b CAR T cells, generated from T cells from either healthy donors or patients with lymphoma, proliferated, produced cytokines, degranulated, and exhibited robust cytotoxic activity in vitro against CD19+ and CD19- lymphoma cell lines and patient-derived lymphoma tumors relapsing after prior CD19 CAR T-cell therapy. Furthermore, CD79b CAR T cells were highly efficient at eradicating pre-established lymphoma tumors in vivo in three aggressive lymphoma xenograft models, including two cell line-derived xenografts and one patient-derived xenograft. Notably, these CAR T cells did not demonstrate any significant tonic signaling activity or markers of exhaustion. CONCLUSION Our results indicated that this novel CD79b CAR T-cell therapy product has robust antitumor activity against B-cell lymphomas. These results supported initiation of a phase 1 clinical trial to evaluate this product in patients with relapsed or refractory B-cell lymphomas.
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Affiliation(s)
- Fuliang Chu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jingjing Cao
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jingwei Liu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Haopeng Yang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Timothy J Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shao-Qing Kuang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaoyun Cheng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zheng Zhang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Swathi Karri
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Long T Vien
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura Bover
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sattva S Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Tang JP, Peters CW, Quiros C, Wang X, Klomhaus AM, Yamada RE, Timmerman JM, Moore TB, Nowicki TS. Hypophosphatemia Due to Increased Effector Cell Metabolic Activity Is Associated with Neurotoxicity Symptoms in CD19-Targeted CAR T-cell Therapy. Cancer Immunol Res 2022; 10:1433-1440. [PMID: 36259217 PMCID: PMC9722515 DOI: 10.1158/2326-6066.cir-22-0418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 09/15/2022] [Indexed: 01/10/2023]
Abstract
A major complication of chimeric antigen receptor (CAR) T-cell therapy is immune effector cell-associated neurotoxicity syndrome (ICANS), which presents as aphasia, confusion, weakness, somnolence, seizures, and coma. This is similar to the neurologic manifestations of hypophosphatemia, which can result from sudden increases in metabolic demand for phosphorylated intermediates (e.g., refeeding syndrome and sepsis). Given these similarities, we investigated whether CAR T-cell effector metabolic activity is associated with increased extracellular phosphate consumption and a possible association between hypophosphatemia and ICANS. In vitro 4-1BB and CD28 CD19-targeted CAR T-cell effector activity was found to be associated with increased consumption of media phosphorus, which was temporally associated with increased single-cell effector secretomic activity and increased phosphorus-dependent metabolic demand of the CAR T cells. A clinical cohort of 77 patients treated with CD19-targeted CAR T-cell therapy demonstrated a significant anticorrelation between serum phosphorus and ICANS incidence and severity, with earlier onset of hypophosphatemia after CAR T-cell infusion more likely to result in neurotoxicity. These results imply phosphorous level monitoring could alert to the development of ICANS in clinical scenarios. See related Spotlight by Tobin et al., p. 1422.
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Affiliation(s)
- Jack Pengfei Tang
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Cole W. Peters
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Crystal Quiros
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, University of California, Los Angeles, California
| | - Alexandra M. Klomhaus
- Department of General Internal Medicine and Health Services Research, University of California, Los Angeles, California
| | - Reiko E. Yamada
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, California
| | - John M. Timmerman
- Division of Hematology-Oncology, Department of Medicine, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California
| | - Theodore B. Moore
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Theodore S. Nowicki
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, California
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California
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Magistri M, Happ LE, Ramdial J, Lu X, Stathias V, Kunkalla K, Agarwal N, Jiang X, Schürer SC, Dubovy SR, Chapman JR, Vega F, Dave S, Lossos IS. The Genetic Landscape of Ocular Adnexa MALT Lymphoma Reveals Frequent Aberrations in NFAT and MEF2B Signaling Pathways. Cancer Res Commun 2021; 1:1-16. [PMID: 35528192 PMCID: PMC9075502 DOI: 10.1158/2767-9764.crc-21-0022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/03/2021] [Indexed: 12/31/2022]
Abstract
A comprehensive constellation of somatic non-silent mutations and copy number (CN) variations in ocular adnexa marginal zone lymphoma (OAMZL) is unknown. By utilizing whole-exome sequencing in 69 tumors we define the genetic landscape of OAMZL. Mutations and CN changes in CABIN1 (30%), RHOA (26%), TBL1XR1 (22%), and CREBBP (17%) and inactivation of TNFAIP3 (26%) were among the most common aberrations. Candidate cancer driver genes cluster in the B-cell receptor (BCR), NFkB, NOTCH and NFAT signaling pathways. One of the most commonly altered genes is CABIN1, a calcineurin inhibitor acting as a negative regulator of the NFAT and MEF2B transcriptional activity. CABIN1 deletions enhance BCR-stimulated NFAT and MEF2B transcriptional activity, while CABIN1 mutations enhance only MEF2B transcriptional activity by impairing binding of mSin3a to CABIN1. Our data provide an unbiased identification of genetically altered genes that may play a role in the molecular pathogenesis of OAMZL and serve as therapeutic targets.
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Affiliation(s)
- Marco Magistri
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Lanie E. Happ
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Jeremy Ramdial
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - XiaoQing Lu
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
- Center for Computational Science, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Kranthi Kunkalla
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Nitin Agarwal
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Xiaoyu Jiang
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Stephan C. Schürer
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
- Center for Computational Science, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Sander R. Dubovy
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Jennifer R. Chapman
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Francisco Vega
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, University of Miami, Miami, Florida
| | - Sandeep Dave
- Center for Genomic and Computational Biology and Department of Medicine, Duke University, Durham, North Carolina
| | - Izidore S. Lossos
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
- Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida
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