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      Oncogenic and immunological targets for matched therapy of pediatric blood cancer patients: Dutch iTHER study experience

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          Abstract

          Over the past 10 years, institutional and national molecular tumor boards have been implemented for relapsed or refractory pediatric cancer to prioritize targeted drugs for individualized treatment based on actionable oncogenic lesions, including the Dutch iTHER platform. Hematological malignancies form a minority in precision medicine studies. Here, we report on 56 iTHER leukemia/lymphoma patients for which we considered cell surface markers and oncogenic aberrations as actionable events, supplemented with ex vivo drug sensitivity for six patients. Prior to iTHER registration, 34% of the patients had received allogeneic hematopoietic cell transplantation (HCT) and 18% CAR‐T therapy. For 51 patients (91%), a sample with sufficient tumor percentage (≥20%) required for comprehensive diagnostic testing was obtained. Up to 10 oncogenic actionable events were prioritized in 49/51 patients, and immunotherapy targets were identified in all profiled patients. Targeted treatment(s) based on the iTHER advice was given to 24 of 51 patients (47%), including immunotherapy in 17 patients, a targeted drug matching an oncogenic aberration in 12 patients, and a drug based on ex vivo drug sensitivity in one patient, resulting in objective responses and a bridge to HCT in the majority of the patients. In conclusion, comprehensive profiling of relapsed/refractory hematological malignancies showed multiple oncogenic and immunotherapy targets for a precision medicine approach, which requires multidisciplinary expertise to prioritize the best treatment options for this rare, heavily pretreated pediatric population.

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          Most cited references37

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          ClinVar: improvements to accessing data

          ClinVar is a freely available, public archive of human genetic variants and interpretations of their relationships to diseases and other conditions, maintained at the National Institutes of Health (NIH). Submitted interpretations of variants are aggregated and made available on the ClinVar website (https://www.ncbi.nlm.nih.gov/clinvar/), and as downloadable files via FTP and through programmatic tools such as NCBI’s E-utilities. The default view on the ClinVar website, the Variation page, was recently redesigned. The new layout includes several new sections that make it easier to find submitted data as well as summary data such as all diseases and citations reported for the variant. The new design also better represents more complex data such as haplotypes and genotypes, as well as variants that are in ClinVar as part of a haplotype or genotype but have no interpretation for the single variant. ClinVar's variant-centric XML had its production release in April 2019. The ClinVar website and E-utilities both have been updated to support the VCV (variation in ClinVar) accession numbers found in the variant-centric XML file. ClinVar's search engine has been fine-tuned for improved retrieval of search results.
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            EuroFlow standardization of flow cytometer instrument settings and immunophenotyping protocols

            The EU-supported EuroFlow Consortium aimed at innovation and standardization of immunophenotyping for diagnosis and classification of hematological malignancies by introducing 8-color flow cytometry with fully standardized laboratory procedures and antibody panels in order to achieve maximally comparable results among different laboratories. This required the selection of optimal combinations of compatible fluorochromes and the design and evaluation of adequate standard operating procedures (SOPs) for instrument setup, fluorescence compensation and sample preparation. Additionally, we developed software tools for the evaluation of individual antibody reagents and antibody panels. Each section describes what has been evaluated experimentally versus adopted based on existing data and experience. Multicentric evaluation demonstrated high levels of reproducibility based on strict implementation of the EuroFlow SOPs and antibody panels. Overall, the 6 years of extensive collaborative experiments and the analysis of hundreds of cell samples of patients and healthy controls in the EuroFlow centers have provided for the first time laboratory protocols and software tools for fully standardized 8-color flow cytometric immunophenotyping of normal and malignant leukocytes in bone marrow and blood; this has yielded highly comparable data sets, which can be integrated in a single database.
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              Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies

              We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. Mathematical model estimation and continuous interpolation makes the scoring approach robust against sources of technical variability and widely applicable to various experimental settings, both in cancer cell line models and primary patient-derived cells. Here, we demonstrate its improved performance over other response parameters especially in a leukemia patient case study, where differential DSS between patient and control cells enabled identification of both cancer-selective drugs and drug-sensitive patient sub-groups, as well as dynamic monitoring of the response patterns and oncogenic driver signals during cancer progression and relapse in individual patient cells ex vivo. An open-source and easily extendable implementation of the DSS calculation is made freely available to support its tailored application to translating drug sensitivity testing results into clinically actionable treatment options.
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                Author and article information

                Contributors
                j.m.boer-20@prinsesmaximacentrum.nl
                Journal
                Hemasphere
                Hemasphere
                10.1002/(ISSN)2572-9241
                HEM3
                HemaSphere
                John Wiley and Sons Inc. (Hoboken )
                2572-9241
                15 July 2024
                July 2024
                : 8
                : 7 ( doiID: 10.1002/hem3.v8.7 )
                : e122
                Affiliations
                [ 1 ] Princess Máxima Center for Pediatric Oncology Utrecht The Netherlands
                [ 2 ] Amsterdam UMC University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory of Experimental Oncology and Radiobiology Amsterdam The Netherlands
                [ 3 ] Center for Translational Immunology UMC Utrecht Utrecht The Netherlands
                [ 4 ] Department of Pediatric Oncology, Hematology, and Immunology Heidelberg University Hospital Heidelberg Germany
                [ 5 ] Department of Pediatric Oncology and Hematology Erasmus Medical Center ‐ Sophia Children's Hospital Rotterdam The Netherlands
                Author notes
                [*] [* ] Correspondence: Judith M. Boer ( j.m.boer-20@ 123456prinsesmaximacentrum.nl )

                [^]

                Judith M. Boer and Uri Ilan contributed equally to this work. Bianca F. Goemans, Monique L. den Boer, and C. Michel Zwaan shared senior authors.

                Author information
                https://orcid.org/0000-0003-4848-7789
                Article
                HEM3122
                10.1002/hem3.122
                11247331
                39011126
                a360ea03-1784-428d-9df1-33055603913f
                © 2024 The Author(s). HemaSphere published by John Wiley & Sons Ltd on behalf of European Hematology Association.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 15 April 2024
                : 23 February 2024
                : 04 June 2024
                Page count
                Figures: 5, Tables: 2, Pages: 13, Words: 6787
                Funding
                Funded by: Pediatric Cancer Foundation Rotterdam
                Funded by: Stichting Kinderen Kankervrij , doi 10.13039/501100006244;
                Funded by: Oncode Institute
                Funded by: ZonMw , doi 10.13039/501100001826;
                Award ID: 848101004
                Categories
                Lymphoid Malignancies
                Article
                Article
                Custom metadata
                2.0
                July 2024
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.4.5 mode:remove_FC converted:15.07.2024

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