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Mocking TR, Duetz C, van Kuijk BJ, Westers TM, Cloos J, Bachas C. Merging and imputation of flow cytometry data: A critical assessment. Cytometry A 2023; 103:818-829. [PMID: 37338802 DOI: 10.1002/cyto.a.24774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/16/2023] [Accepted: 06/17/2023] [Indexed: 06/21/2023]
Abstract
Although most modern techniques and analysis methods in multiparameter flow cytometry (MFC) allow for increased dimensionality for the characterization and quantification of cell populations, most MFC applications depend on flow cytometers measuring relatively small (<16) numbers of parameters. When more markers than the available parameters need to be acquired, these are commonly distributed over multiple independent measurements that include a backbone of common markers. Several methods have been proposed to impute values for combinations of markers that were not measured simultaneously. These imputation methods are frequently used without proper validation and knowledge of their effects on data analysis. We evaluated the performance of existing imputation software (Infinicyt, CyTOFmerge, CytoBackBone, and cyCombine) in approximating known measured expression data in terms of similarity in visual appearance, cell expression, and gating in different datasets by splitting MFC samples into separate measurements with partially overlapping markers and re-calculating missing marker expression. Out of the assessed packages, CyTOFmerge showed the most accurate approximation of the known expression in terms of similar expression values and concordance with manual gating, with a mean F-score between 0.53 and 0.87 when retrieving cell populations in different datasets. Performance remained inadequate for all methods, with only limited similarity at the cell level. In conclusion, the use of imputed MFC data should take such limitations into account and include independent validation of results to justify conclusions.
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Affiliation(s)
- T R Mocking
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - C Duetz
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - B J van Kuijk
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - T M Westers
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - J Cloos
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - C Bachas
- Department of Hematology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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Pelosi E, Castelli G, Testa U. CD123 a Therapeutic Target for Acute Myeloid Leukemia and Blastic Plasmocytoid Dendritic Neoplasm. Int J Mol Sci 2023; 24:ijms24032718. [PMID: 36769040 PMCID: PMC9917129 DOI: 10.3390/ijms24032718] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
In spite of consistent progress at the level of basic research and of clinical treatment, acute myeloid leukemia (AML) still represents an unmet clinical need for adult and pediatric patients. To improve the outcomes of these patients, it is necessary to identify new therapeutic targets. IL3RA (CD123, alpha subunit of the interleukin 3 receptor) is a cell membrane protein overexpressed in several hematologic malignancies, including AML blastic plasmocytoid dendritic cell neoplasms (BPDCN). Given the higher expression of CD123 on leukemic cells compared to normal hematopoietic cells and its low/absent expression on normal hematopoietic stem cells, it appears as a suitable and attractive target for therapy. Various drugs targeting CD123 have been developed and evaluated at clinical level: interleukin-3 conjugated with diphtheria toxin; naked neutralizing anti-CD123 antibodies; drug-antibody conjugates; bispecific antibodies targeting both CD123 and CD3; and chimeric antigen receptor (CAR) T cells engineered to target CD123. Some of these agents have shown promising results at the clinical level, including tagraxofusp (CD123 conjugated with diphtheria toxin) for the treatment of BPDCN and IMGN632 (anti-CD123 drug-conjugate), and flotetuzumab (bispecific anti-CD123 and anti-CD3 monoclonal antibody) for the treatment of AML. However, the therapeutic efficacy of CD123-targeting treatments is still unsatisfactory and must be improved through new therapeutic strategies and combined treatments with other antileukemic drugs.
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Trad R, Warda W, Alcazer V, Neto da Rocha M, Berceanu A, Nicod C, Haderbache R, Roussel X, Desbrosses Y, Daguindau E, Renosi F, Roumier C, Bouquet L, Biichle S, Guiot M, Seffar E, Caillot D, Depil S, Robinet E, Salma Y, Deconinck E, Deschamps M, Ferrand C. Chimeric antigen receptor T-cells targeting IL-1RAP: a promising new cellular immunotherapy to treat acute myeloid leukemia. J Immunother Cancer 2022; 10:jitc-2021-004222. [PMID: 35803613 PMCID: PMC9272123 DOI: 10.1136/jitc-2021-004222] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background Acute myeloid leukemia (AML) remains a very difficult disease to cure due to the persistence of leukemic stem cells (LSCs), which are resistant to different lines of chemotherapy and are the basis of refractory/relapsed (R/R) disease in 80% of patients with AML not receiving allogeneic transplantation. Methods In this study, we showed that the interleukin-1 receptor accessory protein (IL-1RAP) protein is overexpressed on the cell surface of LSCs in all subtypes of AML and confirmed it as an interesting and promising target in AML compared with the most common potential AML targets, since it is not expressed by the normal hematopoietic stem cell. After establishing the proof of concept for the efficacy of chimeric antigen receptor (CAR) T-cells targeting IL-1RAP in chronic myeloid leukemia, we hypothesized that third-generation IL-1RAP CAR T-cells could eliminate AML LSCs, where the medical need is not covered. Results We first demonstrated that IL-1RAP CAR T-cells can be produced from AML T-cells at the time of diagnosis and at relapse. In vitro and in vivo, we showed the effectiveness of IL-1RAP CAR T-cells against AML cell lines expressing different levels of IL-1RAP and the cytotoxicity of autologous IL-1RAP CAR T-cells against primary cells from patients with AML at diagnosis or at relapse. In patient-derived relapsed AML xenograft models, we confirmed that IL-1RAP CAR T-cells are able to circulate in peripheral blood and to migrate in the bone marrow and spleen, are cytotoxic against primary AML cells and increased overall survival. Conclusion In conclusion, our preclinical results suggest that IL-1RAP CAR T-based adoptive therapy could be a promising strategy in AML treatment and it warrants the clinical investigation of this CAR T-cell therapy.
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Affiliation(s)
- Rim Trad
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France
| | - Walid Warda
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France.,CanCell Therapeutics, Besancon, France
| | | | - Mathieu Neto da Rocha
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France.,CanCell Therapeutics, Besancon, France
| | - Ana Berceanu
- Clinical Hematology, C.H. Univ Jean Minjoz, Besancon, France
| | | | | | - Xavier Roussel
- Clinical Hematology, C.H. Univ Jean Minjoz, Besancon, France
| | | | | | - Florain Renosi
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France
| | | | - Lucie Bouquet
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France
| | - Sabeha Biichle
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France
| | - Melanie Guiot
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France
| | - Evan Seffar
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France
| | - Denis Caillot
- Clinical Hematology, CHU François Mitterrand, Dijon, France
| | | | | | - Yahya Salma
- Laboratory of Applied Biotechnology (LBA3B), Lebanese University, Tripoli, Lebanon
| | - Eric Deconinck
- Clinical Hematology, C.H. Univ Jean Minjoz, Besancon, France
| | - Marina Deschamps
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France.,CanCell Therapeutics, Besancon, France
| | - Christophe Ferrand
- TIMC, EFSBFC, INSERM UMR1098 RIGHT,UFC, Besancon, France .,CanCell Therapeutics, Besancon, France
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Aust G, Zheng L, Quaas M. To Detach, Migrate, Adhere, and Metastasize: CD97/ADGRE5 in Cancer. Cells 2022; 11:cells11091538. [PMID: 35563846 PMCID: PMC9101421 DOI: 10.3390/cells11091538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Tumorigenesis is a multistep process, during which cells acquire a series of mutations that lead to unrestrained cell growth and proliferation, inhibition of cell differentiation, and evasion of cell death. Growing tumors stimulate angiogenesis, providing them with nutrients and oxygen. Ultimately, tumor cells invade the surrounding tissue and metastasize; a process responsible for about 90% of cancer-related deaths. Adhesion G protein-coupled receptors (aGPCRs) modulate the cellular processes closely related to tumor cell biology, such as adhesion and detachment, migration, polarity, and guidance. Soon after first being described, individual human aGPCRs were found to be involved in tumorigenesis. Twenty-five years ago, CD97/ADGRE5 was discovered to be induced in one of the most severe tumors, dedifferentiated anaplastic thyroid carcinoma. After decades of research, the time has come to review our knowledge of the presence and function of CD97 in cancer. In summary, CD97 is obviously induced or altered in many tumor entities; this has been shown consistently in nearly one hundred published studies. However, its high expression at circulating and tumor-infiltrating immune cells renders the systemic targeting of CD97 in tumors difficult.
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Affiliation(s)
- Gabriela Aust
- Research Laboratories of the Clinic of Visceral, Transplantation, Thoracic, and Vascular Surgery, Medical School, University Hospital Leipzig, Leipzig University, 04103 Leipzig, Germany;
- Research Laboratories of the Clinic of Orthopedics, Traumatology and Plastic Surgery, Medical School, University Hospital Leipzig, Leipzig University, 04103 Leipzig, Germany;
| | - Leyu Zheng
- Research Laboratories of the Clinic of Orthopedics, Traumatology and Plastic Surgery, Medical School, University Hospital Leipzig, Leipzig University, 04103 Leipzig, Germany;
| | - Marianne Quaas
- Research Laboratories of the Clinic of Visceral, Transplantation, Thoracic, and Vascular Surgery, Medical School, University Hospital Leipzig, Leipzig University, 04103 Leipzig, Germany;
- Correspondence:
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