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Seiboldt T, Zeiser C, Nguyen D, Celikyürekli S, Herter S, Najafi S, Stroh-Dege A, Meulenbroeks C, Mack N, Salem-Altintas R, Westermann F, Schlesner M, Milde T, Kool M, Holland-Letz T, Vogler M, Peterziel H, Witt O, Oehme I. Synergy of retinoic acid and BH3 mimetics in MYC(N)-driven embryonal nervous system tumours. Br J Cancer 2024; 131:763-777. [PMID: 38942989 PMCID: PMC11333474 DOI: 10.1038/s41416-024-02740-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Certain paediatric nervous system malignancies have dismal prognoses. Retinoic acid (RA) is used in neuroblastoma treatment, and preclinical data indicate potential benefit in selected paediatric brain tumour entities. However, limited single-agent efficacy necessitates combination treatment approaches. METHODS We performed drug sensitivity profiling of 76 clinically relevant drugs in combination with RA in 16 models (including patient-derived tumouroids) of the most common paediatric nervous system tumours. Drug responses were assessed by viability assays, high-content imaging, and apoptosis assays and RA relevant pathways by RNAseq from treated models and patient samples obtained through the precision oncology programme INFORM (n = 2288). Immunoprecipitation detected BCL-2 family interactions, and zebrafish embryo xenografts were used for in vivo efficacy testing. RESULTS Group 3 medulloblastoma (MBG3) and neuroblastoma models were highly sensitive to RA treatment. RA induced differentiation and regulated apoptotic genes. RNAseq analysis revealed high expression of BCL2L1 in MBG3 and BCL2 in neuroblastomas. Co-treatments with RA and BCL-2/XL inhibitor navitoclax synergistically decreased viability at clinically achievable concentrations. The combination of RA with navitoclax disrupted the binding of BIM to BCL-XL in MBG3 and to BCL-2 in neuroblastoma, inducing apoptosis in vitro and in vivo. CONCLUSIONS RA treatment primes MBG3 and NB cells for apoptosis, triggered by navitoclax cotreatment.
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Affiliation(s)
- Till Seiboldt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Constantia Zeiser
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Duy Nguyen
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simay Celikyürekli
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sonja Herter
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Sara Najafi
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Alexandra Stroh-Dege
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | | | - Norman Mack
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Rabia Salem-Altintas
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Frank Westermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Division of Neuroblastoma Genomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Schlesner
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tim Holland-Letz
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Meike Vogler
- Institute for Experimental Pediatric Hematology and Oncology, Goethe-University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz, a partnership between DKFZ and University Hospital Frankfurt, Frankfurt, Germany
- University Cancer Center Frankfurt (UCT), University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany
| | - Heike Peterziel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology (B310), German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany.
- National Center for Tumor Diseases Heidelberg, Heidelberg, Germany.
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Zeuner S, Vollmer J, Sigaud R, Oppermann S, Peterziel H, ElHarouni D, Oehme I, Witt O, Milde T, Ecker J. Combination drug screen identifies synergistic drug interaction of BCL-XL and class I histone deacetylase inhibitors in MYC-amplified medulloblastoma cells. J Neurooncol 2024; 166:99-112. [PMID: 38184819 PMCID: PMC10824805 DOI: 10.1007/s11060-023-04526-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 11/27/2023] [Indexed: 01/08/2024]
Abstract
PURPOSE Patients with MYC-amplified Group 3 medulloblastoma (MB) (subtype II) show poor progression-free survival rates. Class I histone deacetylase inhibitors (HDACi) are highly effective for the treatment of MYC-amplified MB in vitro and in vivo. Drug combination regimens including class I HDACi may represent an urgently needed novel treatment approach for this high risk disease. METHODS A medium-throughput in vitro combination drug screen was performed in three MYC-amplified and one non-MYC-amplified MB cell line testing 75 clinically relevant drugs alone and in combination with entinostat. The drug sensitivity score (DSS) was calculated based on metabolic inhibition quantified by CellTiter-Glo. The six top synergistic combination hits were evaluated in a 5 × 5 combination matrix and a seven-ray design. Synergy was validated and characterized by cell counts, caspase-3-like-activity and poly-(ADP-ribose)-polymerase-(PARP)-cleavage. On-target activity of drugs was validated by immunoprecipitation and western blot. BCL-XL dependency of the observed effect was explored with siRNA mediated knockdown of BCL2L1, and selective inhibition with targeted compounds (A-1331852, A-1155463). RESULTS 20/75 drugs effectively reduced metabolic activity in combination with entinostat in all three MYC-amplified cell lines (DSS ≥ 10). The combination entinostat and navitoclax showed the strongest synergistic interaction across all MYC-amplified cell lines. siRNA mediated knockdown of BCL2L1, as well as targeted inhibition with selective inhibitors showed BCL-XL dependency of the observed effect. Increased cell death was associated with increased caspase-3-like-activity. CONCLUSION Our study identifies the combination of class I HDACi and BCL-XL inhibitors as a potential new approach for the treatment of MYC-amplified MB cells.
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Affiliation(s)
- Simon Zeuner
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Johanna Vollmer
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Romain Sigaud
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Sina Oppermann
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Heike Peterziel
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Dina ElHarouni
- Department of Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ina Oehme
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Jonas Ecker
- Hopp Children's Cancer Center Heidelberg (KiTZ), Im Neuenheimer Feld 430, 69120, Heidelberg, Germany.
- National Center for Tumor Diseases (NCT), NCT Heidelberg, a partnership between DKFZ and Heidelberg University Hospital, Im Neuenheimer Feld 460, 69120, Heidelberg, Germany.
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany.
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Wolf Á, Romeder-Finger S, Széll K, Galambos P. WITHDRAWN: Towards robotic laboratory automation Plug & play: Survey and concept proposal on teaching-free robot integration with the LAPP digital twin. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 29:132. [PMID: 38101573 DOI: 10.1016/j.slasd.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 12/19/2022] [Accepted: 01/10/2023] [Indexed: 12/17/2023]
Affiliation(s)
- Ádám Wolf
- Takeda Manufacturing Austria AG, Industriestraße 67, Wien, A-1221, Austria; Doctoral School of Applied Informatics and Applied Mathematics, Óbuda University, Baxalta Innovations GmbH, a Takeda Company, Austria.
| | | | - Károly Széll
- Alba Regia Technical Faculty, Óbuda University, H-8000, Székesfehérvár, Hungary
| | - Péter Galambos
- Antal Bejczy Center for Intelligent Robotics, Óbuda University, Hungary
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Feodoroff M, Mikkonen P, Turunen L, Hassinen A, Paasonen L, Paavolainen L, Potdar S, Murumägi A, Kallioniemi O, Pietiäinen V. Comparison of two supporting matrices for patient-derived cancer cells in 3D drug sensitivity and resistance testing assay (3D-DSRT). SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023:S2472-5552(23)00025-4. [PMID: 36934951 DOI: 10.1016/j.slasd.2023.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/12/2023] [Accepted: 03/13/2023] [Indexed: 03/21/2023]
Abstract
Central to the success of functional precision medicine of solid tumors is to perform drug testing of patient-derived cancer cells (PDCs) in tumor-mimicking ex vivo conditions. While high throughput (HT) drug screening methods have been well-established for cells cultured in two-dimensional (2D) format, this approach may have limited value in predicting clinical responses. Here, we describe the results of the optimization of drug sensitivity and resistance testing (DSRT) in three-dimensional (3D) growth supporting matrices in a HT mode (3D-DSRT) using the hepatocyte cell line (HepG2) as an example. Supporting matrices included widely used animal-derived Matrigel and cellulose-based hydrogel, GrowDex, which has earlier been shown to support 3D growth of cell lines and stem cells. Further, the sensitivity of ovarian cancer PDCs, from two patients included in the functional precision medicine study, was tested for 52 drugs in 5 different concentrations using 3D-DSRT. Shortly, in the optimized protocol, the PDCs are embedded with matrices and seeded to 384-well plates to allow the formation of the spheroids prior to the addition of drugs in nanoliter volumes with acoustic dispenser. The sensitivity of spheroids to drug treatments is measured with cell viability readout (here, 72 h after addition of drugs). The quality control and data analysis are performed with openly available Breeze software. We show the usability of both matrices in established 3D-DSRT, and report 2D vs 3D growth condition dependent differences in sensitivities of ovarian cancer PDCs to MEK-inhibitors and cytotoxic drugs. This study provides a proof-of-concept for robust and fast screening of drug sensitivities of PDCs in 3D-DSRT, which is important not only for drug discovery but also for personalized ex vivo drug testing in functional precision medicine studies. These findings suggest that comparing results of 2D- and 3D-DSRT is essential for understanding drug mechanisms and for selecting the most effective treatment for the patient.
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Affiliation(s)
- Michaela Feodoroff
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; Laboratory of Immunovirotherapy, Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; TRIMM, Translational Immunology Research Program, University of Helsinki, Helsinki, Uusimaa, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Piia Mikkonen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; UPM-Kymmene Oyj, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | - Antti Hassinen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | | | - Lassi Paavolainen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland; Science for Life Laboratory and Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland-FIMM, Helsinki Institute for Life Sciences -HiLIFE, University of Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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Feodoroff M, Mikkonen P, Arjama M, Murumägi A, Kallioniemi O, Potdar S, Turunen L, Pietiäinen V. Protocol for 3D drug sensitivity and resistance testing of patient-derived cancer cells in 384-well plates. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:36-41. [PMID: 36464160 DOI: 10.1016/j.slasd.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/01/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022]
Abstract
Establishment of drug testing of patient-derived cancer cells (PDCs) in physiologically relevant 3-dimensional (3D) culture is central for drug discovery and cancer research, as well as for functional precision medicine. Here, we describe the detailed protocol allowing the 3D drug testing of PDCs - or any type of cells of interest - in Matrigel in 384-well plate format using automation. We also provide an alternative protocol, which does not require supporting matrices. The cancer tissue is obtained directly from clinics (after surgery or biopsy) and processed into single cell suspension. Systematic drug sensitivity and resistance testing (DSRT) is carried out on the PDCs directly after cancer cell isolation from tissue or on cells expanded for a few passages. In the 3D-DSRT assay, the PDCs are plated in 384-well plates in Matrigel, grown as spheroids, and treated with compounds of interest for 72 h. The cell viability is directly measured using a luminescence-based assay. Alternatively, prior to the cell viability measurement, drug-treated cells can be directly subjected to automated high-content bright field imaging or stained for fluorescence (live) cell microscopy for further image analysis. This is followed by the quality control and data analysis. The 3D-DSRT can be performed within a 1-3-week timeframe of the clinical sampling of cancer tissue, depending on the amount of the obtained tissue, growth rate of cancer cells, and the number of drugs being tested. The 3D-DSRT method can be flexibly modified, e.g., to be carried out with or without supporting matrices with U-bottom 384-well plates when appropriate for the PDCs or other cell models used.
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Affiliation(s)
- Michaela Feodoroff
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; Laboratory of Immunovirotherapy, Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland; Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Piia Mikkonen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; UPM-Kymmene Corporation, UPM Biomedicals, Helsinki, Finland
| | - Mariliina Arjama
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Astrid Murumägi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Olli Kallioniemi
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Solna, Sweden
| | - Swapnil Potdar
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Laura Turunen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Vilja Pietiäinen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute for Life Sciences (HiLIFE), University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland.
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Prabhakar H, Kerr WL, Bock CH, Kong F. Effect of relative humidity, storage days, and packaging on pecan kernel texture: Analyses and modeling. J Texture Stud 2023; 54:115-126. [PMID: 36146907 PMCID: PMC10092868 DOI: 10.1111/jtxs.12723] [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: 05/19/2022] [Revised: 09/08/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]
Abstract
The studies expounding on the effects of storage conditions on texture changes are limited. The researchers have been proposing methods to measure pecan texture instrumentally. But current protocols and/or attributes fail to address huge variability during experimentation. Additionally, there are no predictive models to estimate changes in pecan texture during storage. This study addresses all the above concerns and investigates the effects of different relative humidity (RH, 30-90%) and packaging material (Polyethylene-Nylon [PEN], polypropylene [PP], low density polyethylene [LDPE], and metallic laminates [ML]) on pecan texture, introducing a rift ratio (F/H or fracturability to hardness ratio) to address variability in the data and predictive model to estimate changes in the textural attribute of pecans during storage. The textural analysis was conducted on pecan cores and intact pecans to measure the area under curve, fracturability, hardness, cohesiveness, chewiness, springiness, and rift ratio. It was observed that values for the rift ratio obtained using the intact pecan method had high R2 (0.72) as compared to the rest of the textural attributes. A three-parameter logistic model was employed to predict pecan texture during storage. The pecans stored at 75, 80, and 90% reached the rift ratio (F/H) of 0.5 at approx. 115, 3, and 0.15 days (~ 4 hr), respectively. Similarly, pecans stored in LDPE, PP, and PEN packs at 80% reached rift ratio (F/H) of 0.5 at approx. 26, 57, and 78 days, respectively. The presence of any kind of package delayed fracturability loss by at least eight folds at 80% RH. The pecans stored in ML did not experience a significant change in textural attributes.
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Affiliation(s)
- Himanshu Prabhakar
- Department of Food Science & Technology, University of Georgia, Athens, Georgia, USA
| | - William L Kerr
- Department of Food Science & Technology, University of Georgia, Athens, Georgia, USA
| | - Clive H Bock
- Fruit and Tree Nut Research, USDA-ARS-SEFNTRL, Byron, Georgia, USA
| | - Fanbin Kong
- Department of Food Science & Technology, University of Georgia, Athens, Georgia, USA
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Aaltonen K, Radke K, Adamska A, Seger A, Mañas A, Bexell D. Patient-derived models: Advanced tools for precision medicine in neuroblastoma. Front Oncol 2023; 12:1085270. [PMID: 36776363 PMCID: PMC9910084 DOI: 10.3389/fonc.2022.1085270] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/21/2022] [Indexed: 01/27/2023] Open
Abstract
Neuroblastoma is a childhood cancer derived from the sympathetic nervous system. High-risk neuroblastoma patients have a poor overall survival and account for ~15% of childhood cancer deaths. There is thus a need for clinically relevant and authentic models of neuroblastoma that closely resemble the human disease to further interrogate underlying mechanisms and to develop novel therapeutic strategies. Here we review recent developments in patient-derived neuroblastoma xenograft models and in vitro cultures. These models can be used to decipher mechanisms of metastasis and treatment resistance, for drug screening, and preclinical drug testing. Patient-derived neuroblastoma models may also provide useful information about clonal evolution, phenotypic plasticity, and cell states in relation to neuroblastoma progression. We summarize current opportunities for, but also barriers to, future model development and application. Integration of patient-derived models with patient data holds promise for the development of precision medicine treatment strategies for children with high-risk neuroblastoma.
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Peterziel H, Jamaladdin N, ElHarouni D, Gerloff XF, Herter S, Fiesel P, Berker Y, Blattner-Johnson M, Schramm K, Jones BC, Reuss D, Turunen L, Friedenauer A, Holland-Letz T, Sill M, Weiser L, Previti C, Balasubramanian G, Gerber NU, Gojo J, Hutter C, Øra I, Lohi O, Kattamis A, de Wilde B, Westermann F, Tippelt S, Graf N, Nathrath M, Sparber-Sauer M, Sehested A, Kramm CM, Dirksen U, Kallioniemi O, Pfister SM, van Tilburg CM, Jones DTW, Saarela J, Pietiäinen V, Jäger N, Schlesner M, Kopp-Schneider A, Oppermann S, Milde T, Witt O, Oehme I. Drug sensitivity profiling of 3D tumor tissue cultures in the pediatric precision oncology program INFORM. NPJ Precis Oncol 2022; 6:94. [PMID: 36575299 PMCID: PMC9794727 DOI: 10.1038/s41698-022-00335-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/29/2022] [Indexed: 12/28/2022] Open
Abstract
The international precision oncology program INFORM enrolls relapsed/refractory pediatric cancer patients for comprehensive molecular analysis. We report a two-year pilot study implementing ex vivo drug sensitivity profiling (DSP) using a library of 75-78 clinically relevant drugs. We included 132 viable tumor samples from 35 pediatric oncology centers in seven countries. DSP was conducted on multicellular fresh tumor tissue spheroid cultures in 384-well plates with an overall mean processing time of three weeks. In 89 cases (67%), sufficient viable tissue was received; 69 (78%) passed internal quality controls. The DSP results matched the identified molecular targets, including BRAF, ALK, MET, and TP53 status. Drug vulnerabilities were identified in 80% of cases lacking actionable (very) high-evidence molecular events, adding value to the molecular data. Striking parallels between clinical courses and the DSP results were observed in selected patients. Overall, DSP in clinical real-time is feasible in international multicenter precision oncology programs.
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Affiliation(s)
- Heike Peterziel
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Nora Jamaladdin
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Dina ElHarouni
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Xenia F. Gerloff
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Mathematics and Computer Science, Heidelberg University, 69120 Heidelberg, Germany
| | - Sonja Herter
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Petra Fiesel
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
| | - Yannick Berker
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Mirjam Blattner-Johnson
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Kathrin Schramm
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Barbara C. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David Reuss
- grid.5253.10000 0001 0328 4908Department Neuropathology at Institute of Pathology, Heidelberg University Hospital, 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Present Address: Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), German Consortium for Translational Cancer Research (DKTK), 69120 Heidelberg, Germany
| | - Laura Turunen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Aileen Friedenauer
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Tim Holland-Letz
- grid.7497.d0000 0004 0492 0584Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Sill
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Lena Weiser
- grid.7497.d0000 0004 0492 0584Core Facility Omics IT and Data Management (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christopher Previti
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Core Facility Omics IT and Data Management (ODCF), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gnanaprakash Balasubramanian
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Nicolas U. Gerber
- grid.412341.10000 0001 0726 4330Department of Oncology, University Children’s Hospital Zürich, CH-8032 Zürich, Switzerland
| | - Johannes Gojo
- grid.22937.3d0000 0000 9259 8492Department of Pediatrics and Adolescent Medicine, Comprehensive Cancer Center and Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Caroline Hutter
- grid.22937.3d0000 0000 9259 8492St. Anna Children’s Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria ,grid.416346.2St. Anna Children’s Cancer Research Institute (CCRI), Vienna, Austria
| | - Ingrid Øra
- grid.411843.b0000 0004 0623 9987Children’s Hospital, Pediatric Oncology, Skåne University Hospital, Lund & Karolinska University Hospital, Stockholm, Sweden
| | - Olli Lohi
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, Tampere Center for Child Health Research, Tampere University, Tampere, Finland, and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Antonis Kattamis
- grid.5216.00000 0001 2155 0800First Department of Pediatrics, National and Kapodistrian University of Athens, Athens, Greece
| | - Bram de Wilde
- grid.5342.00000 0001 2069 7798Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frank Westermann
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Neuroblastoma Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Stephan Tippelt
- grid.410718.b0000 0001 0262 7331Pediatrics III Pediatric Hematology, Oncology, Immunology, Cardiology, Pulmonology, West German Cancer Center; German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Norbert Graf
- grid.411937.9Department of Pediatric Oncology, Saarland University Medical Center, 66421 Homburg, Germany
| | - Michaela Nathrath
- grid.419824.20000 0004 0625 3279Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany ,grid.6936.a0000000123222966Department of Pediatrics and Children’s Cancer Research Center, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Monika Sparber-Sauer
- grid.459687.10000 0004 0493 3975Klinikum der Landeshauptstadt Stuttgart gKAöR, Olgahospital, Stuttgart Cancer Center, Zentrum für Kinder-, Jugend- und Frauenmedizin, Pädiatrie 5 (Pädiatrische Onkologie, Hämatologie, Immunologie), Stuttgart, Germany ,University of Medicine Tübingen, Tübingen, Germany
| | - Astrid Sehested
- grid.475435.4Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen Denmark
| | - Christof M. Kramm
- grid.411984.10000 0001 0482 5331Division of Pediatric Hematology and Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Uta Dirksen
- grid.410718.b0000 0001 0262 7331Pediatrics III Pediatric Hematology, Oncology, Immunology, Cardiology, Pulmonology, West German Cancer Center; German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Olli Kallioniemi
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, FI-00014 Finland
| | - Stefan M. Pfister
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Cornelis M. van Tilburg
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David T. W. Jones
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Jani Saarela
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Vilja Pietiäinen
- grid.7737.40000 0004 0410 2071Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, 00014 Helsinki, Finland ,grid.7737.40000 0004 0410 2071iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, FI-00014 Finland
| | - Natalie Jäger
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Matthias Schlesner
- grid.7497.d0000 0004 0492 0584Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany ,grid.7307.30000 0001 2108 9006Biomedical Informatics, Data Mining and Data Analytics, Faculty of Applied Computer Science and Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Annette Kopp-Schneider
- grid.7497.d0000 0004 0492 0584Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sina Oppermann
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Till Milde
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Olaf Witt
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Ina Oehme
- grid.510964.fHopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany ,grid.461742.20000 0000 8855 0365National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
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Berker Y, ElHarouni D, Peterziel H, Fiesel P, Witt O, Oehme I, Schlesner M, Oppermann S. Patient-by-Patient Deep Transfer Learning for Drug-Response Profiling Using Confocal Fluorescence Microscopy of Pediatric Patient-Derived Tumor-Cell Spheroids. IEEE TRANSACTIONS ON MEDICAL IMAGING 2022; 41:3981-3999. [PMID: 36099221 DOI: 10.1109/tmi.2022.3205554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Image-based phenotypic drug profiling is receiving increasing attention in drug discovery and precision medicine. Compared to classical end-point measurements quantifying drug response, image-based profiling enables both the quantification of drug response and characterization of disease entities and drug-induced cell-death phenotypes. Here, we aim to quantify image-based drug responses in patient-derived 3D spheroid tumor cell cultures, tackling the challenges of a lack of single-cell-segmentation methods and limited patient-derived material. Therefore, we investigate deep transfer learning with patient-by-patient fine-tuning for cell-viability quantification. We fine-tune a convolutional neural network (pre-trained on ImageNet) with 210 control images specific to a single training cell line and 54 additional screen -specific assay control images. This method of image-based drug profiling is validated on 6 cell lines with known drug sensitivities, and further tested with primary patient-derived samples in a medium-throughput setting. Network outputs at different drug concentrations are used for drug-sensitivity scoring, and dense-layer activations are used in t-distributed stochastic neighbor embeddings of drugs to visualize groups of drugs with similar cell-death phenotypes. Image-based cell-line experiments show strong correlation to metabolic results ( R ≈ 0.7 ) and confirm expected hits, indicating the predictive power of deep learning to identify drug-hit candidates for individual patients. In patient-derived samples, combining drug sensitivity scoring with phenotypic analysis may provide opportunities for complementary combination treatments. Deep transfer learning with patient-by-patient fine-tuning is a promising, segmentation-free image-analysis approach for precision medicine and drug discovery.
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Functional Therapeutic Target Validation Using Pediatric Zebrafish Xenograft Models. Cancers (Basel) 2022; 14:cancers14030849. [PMID: 35159116 PMCID: PMC8834194 DOI: 10.3390/cancers14030849] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Despite the major progress of precision and personalized oncology, a significant therapeutic benefit is only achieved in cases with directly druggable genetic alterations. This highlights the need for additional methods that reliably predict each individual patient’s response in a clinically meaningful time, e.g., through ex vivo functional drug screen profiling. Moreover, patient-derived xenograft (PDX) models are more predictive than cell culture studies, as they reconstruct cell–cell and cell–extracellular matrix (ECM) interactions and consider the tumor microenvironment, drug metabolism and toxicities. Zebrafish PDXs (zPDX) are nowadays emerging as a fast model allowing for multiple drugs to be tested at the same time in a clinically relevant time window. Here, we show that functional drug response profiling of zPDX from primary material obtained through the INdividualized Therapy FOr Relapsed Malignancies in Childhood (INFORM) pediatric precision oncology pipeline provides additional key information for personalized precision oncology. Abstract The survival rate among children with relapsed tumors remains poor, due to tumor heterogeneity, lack of directly actionable tumor drivers and multidrug resistance. Novel personalized medicine approaches tailored to each tumor are urgently needed to improve cancer treatment. Current pediatric precision oncology platforms, such as the INFORM (INdividualized Therapy FOr Relapsed Malignancies in Childhood) study, reveal that molecular profiling of tumor tissue identifies targets associated with clinical benefit in a subgroup of patients only and should be complemented with functional drug testing. In such an approach, patient-derived tumor cells are exposed to a library of approved oncological drugs in a physiological setting, e.g., in the form of animal avatars injected with patient tumor cells. We used molecularly fully characterized tumor samples from the INFORM study to compare drug screen results of individual patient-derived cell models in functional assays: (i) patient-derived spheroid cultures within a few days after tumor dissociation; (ii) tumor cells reisolated from the corresponding mouse PDX; (iii) corresponding long-term organoid-like cultures and (iv) drug evaluation with the corresponding zebrafish PDX (zPDX) model. Each model had its advantage and complemented the others for drug hit and drug combination selection. Our results provide evidence that in vivo zPDX drug screening is a promising add-on to current functional drug screening in precision medicine platforms.
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