1
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Fieuws C, Van der Meulen J, Proesmans K, De Jaeghere EA, Loontiens S, Van Dorpe J, Tummers P, Denys H, Van de Vijver K, Claes KBM. Identification of potentially actionable genetic variants in epithelial ovarian cancer: a retrospective cohort study. NPJ Precis Oncol 2024; 8:71. [PMID: 38519644 PMCID: PMC10959961 DOI: 10.1038/s41698-024-00565-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
Ovarian cancer is the most lethal gynecologic malignancy, mainly due to late-stage diagnosis, frequent recurrences, and eventually therapy resistance. To identify potentially actionable genetic variants, sequencing data of 351 Belgian ovarian cancer patients were retrospectively captured from electronic health records. The cohort included 286 (81%) patients with high-grade serous ovarian cancer, 17 (5%) with low-grade serous ovarian cancer, and 48 (14%) with other histotypes. Firstly, an overview of the prevalence and spectrum of the BRCA1/2 variants highlighted germline variants in 4% (11/250) and somatic variants in 11% (37/348) of patients. Secondly, application of a multi-gene panel in 168 tumors revealed a total of 214 variants in 28 genes beyond BRCA1/2 with a median of 1 (IQR, 1-2) genetic variant per patient. The ten most often altered genes were (in descending order): TP53, BRCA1, PIK3CA, BRCA2, KRAS, ERBB2 (HER2), TERT promotor, RB1, PIK3R1 and PTEN. Of note, the genetic landscape vastly differed between the studied histotypes. Finally, using ESCAT the clinical evidence of utility for every genetic variant was scored. Only BRCA1/2 pathogenic variants were classified as tier-I. Nearly all patients (151/168; 90%) had an ESCAT tier-II variant, most frequently in TP53 (74%), PIK3CA (9%) and KRAS (7%). In conclusion, our findings imply that although only a small proportion of genetic variants currently have direct impact on ovarian cancer treatment decisions, other variants could help to identify novel (personalized) treatment options to address the poor prognosis of ovarian cancer, particularly in rare histotypes.
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Affiliation(s)
- Charlotte Fieuws
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Joni Van der Meulen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | | | - Emiel A De Jaeghere
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | - Siebe Loontiens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Jo Van Dorpe
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | - Philippe Tummers
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | - Hannelore Denys
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Medical Oncology, Ghent University Hospital, Ghent, Belgium
| | - Koen Van de Vijver
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Kathleen B M Claes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
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2
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Cordier F, Loontiens S, Van der Meulen J, Lapeire L, van Ramshorst GH, Sys G, Van Dorpe J, Creytens D. RAF1-rearranged Spindle Cell Mesenchymal Tumor With Calcification and Heterotopic Ossification: A Case Report and Review of Literature. Int J Surg Pathol 2024; 32:133-139. [PMID: 37141633 DOI: 10.1177/10668969231167493] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report an exceptional case of a spindle cell mesenchymal tumor with S100 and CD34 co-reactivity, which harbored a SLMAP::RAF1 fusion. To the best of our knowledge, this is the second case of a spindle cell mesenchymal tumor with S100 and CD34 co-reactivity with this specific fusion. Remarkable is the presence of calcification and heterotopic ossification in the center of our lesion, a feature that, to our knowledge, has not been described yet in RAF1-rearranged spindle cell mesenchymal tumors.
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Affiliation(s)
- Fleur Cordier
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Siebe Loontiens
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Joni Van der Meulen
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lore Lapeire
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Medical Oncology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Gabrielle H van Ramshorst
- Department of Gastrointestinal Surgery, Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Gwen Sys
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Traumatology and Orthopaedics, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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3
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Deolet E, Cordier F, Ferdinande L, Loontiens S, Van der Meulen J, Van Dorpe J, Creytens D. A case of a lipoblastoma with EEF1A1::PLAG1 fusion and metaplastic ossification. Genes Chromosomes Cancer 2024; 63:e23225. [PMID: 38470300 DOI: 10.1002/gcc.23225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Ellen Deolet
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Fleur Cordier
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | | | - Siebe Loontiens
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Joni Van der Meulen
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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4
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Cordier F, Fadaei S, Ferdinande L, Dochy F, Vanwalleghem L, Van Den Bossche K, Loontiens S, Van der Meulen J, Van Roy N, Van Dorpe J, Creytens D. Revealing RB1 loss in an emerging entity: report of two cases of PRRX1-rearranged mesenchymal tumours. J Clin Pathol 2023:jcp-2023-209267. [PMID: 38154915 DOI: 10.1136/jcp-2023-209267] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/07/2023] [Indexed: 12/30/2023]
Abstract
AIMS PRRX1-rearranged mesenchymal tumours are a recently identified and rare subgroup of soft tissue neoplasms with distinct morphological features and genetic alterations. This study aims to further investigate the immunohistochemical profile and underlying genetic alterations in these tumours in order to get more insight on their underlying biology and the unique profile of these tumours. METHODS Two new molecular confirmed cases of PRRX1-rearranged mesenchymal tumours were thoroughly studied with immunohistochemical stainings (RB1, CD34, ALK and pan-TRK), fluorescence in situ hybridisation (FISH) RB1/13q12 and RNA-based next-generation sequencing. RESULTS Both cases exhibited typical morphological and molecular features, confirming the diagnosis of PRRX1-rearranged mesenchymal tumours. Immunohistochemistry revealed RB1 loss in both cases, which was subsequently confirmed through FISH analysis. Additionally, one case showed focal positivity for CD34, ALK and pan-TRK on immunohistochemistry. CONCLUSIONS We identified loss of RB1 in two cases of PRRX1-rearranged mesenchymal tumours. This could suggest a potential association with RB1-deficient soft tissue tumours, although further research is necessary. Furthermore, the finding of focal positivity for CD34, ALK and pan-TRK on immunohistochemistry enriches the immunohistochemical profile of these tumours.
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Affiliation(s)
- Fleur Cordier
- Department of Pathology, Ghent University Hospital,Ghent University, Ghent, Belgium
| | - Sharareh Fadaei
- Department of Pathology, Ghent University Hospital,Ghent University, Ghent, Belgium
- Department of Pathology, AZ Sint-Jan Bruges-Ostend, Bruges, Belgium
| | - Liesbeth Ferdinande
- Department of Pathology, Ghent University Hospital,Ghent University, Ghent, Belgium
| | - Frederick Dochy
- Department of Otorhinolaryngology, head and neck surgery, AZ Sint-Jan Bruges-Ostend AV, Bruges, Belgium
| | | | | | - Siebe Loontiens
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Joni Van der Meulen
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Molecular Diagnostics Ghent University Hospital (MDG), Ghent University Hospital, Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital,Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital,Ghent University, Ghent, Belgium
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
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5
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Donati M, Nosek D, Olivares S, Lemahieu J, Loontiens S, Mansour B, Gerami P, Kazakov DV. Spitz tumor with RAF1 fusion: A report of 3 cases. Ann Diagn Pathol 2023; 67:152215. [PMID: 37856952 DOI: 10.1016/j.anndiagpath.2023.152215] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023]
Abstract
Spitz tumors are melanocytic neoplasms morphologically characterized by spindled and/or epithelioid cells and specific stromal and epidermal changes associated with mutually exclusive fusion kinases involving ALK, ROS1, NTRK1, NTRK2, NTRK3, MET and RET, BRAF and MAP3K8 genes or, less commonly, HRAS mutation. RAF1 fusions have been recently detected in cutaneous melanocytic neoplasms, including conventional melanoma, congenital nevus and BAP-1 inactivated tumors. We report herewith three Spitz neoplasms with a RAF1 fusion, including a previously reported CTDSPL::RAF1 fusion and two novel PPAP2B::RAF1 and ATP2B4::RAF1 fusions. Two cases were classified as Spitz nevus, while the remaining neoplasm was classified as Spitz melanoma at the time of the diagnosis, given 9p21 homozygous deletion and positive sentinel lymph node biopsy. We suggest that RAF1 fused melanocytic neoplasms can represent a novel subgroup of Spitz tumors, with a RAF1 fusion representing an oncogenic driver.
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Affiliation(s)
- Michele Donati
- Department of Pathology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy.
| | - Daniel Nosek
- Department of Pathology, Umeå University, Umeå, Sweden
| | - Shantel Olivares
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Siebe Loontiens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Molecular Diagnostics Ghent University Hospital (MDG), Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent, Belgium
| | - Boulos Mansour
- Department of Pathology, Ospedale Israelitico di Roma, Rome, Italy
| | - Pedram Gerami
- Department of Dermatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Dmitry V Kazakov
- IDP Institut für Dermatohistopathologie, Pathologie Institut Enge, Zürich, Switzerland
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6
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Decaesteker B, Louwagie A, Loontiens S, De Vloed F, Bekaert SL, Roels J, Vanhauwaert S, De Brouwer S, Sanders E, Berezovskaya A, Denecker G, D'haene E, Van Haver S, Van Loocke W, Van Dorpe J, Creytens D, Van Roy N, Pieters T, Van Neste C, Fischer M, Van Vlierberghe P, Roberts SS, Schulte J, Ek S, Versteeg R, Koster J, van Nes J, Zimmerman M, De Preter K, Speleman F. SOX11 regulates SWI/SNF complex components as member of the adrenergic neuroblastoma core regulatory circuitry. Nat Commun 2023; 14:1267. [PMID: 36882421 PMCID: PMC9992472 DOI: 10.1038/s41467-023-36735-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
The pediatric extra-cranial tumor neuroblastoma displays a low mutational burden while recurrent copy number alterations are present in most high-risk cases. Here, we identify SOX11 as a dependency transcription factor in adrenergic neuroblastoma based on recurrent chromosome 2p focal gains and amplifications, specific expression in the normal sympatho-adrenal lineage and adrenergic neuroblastoma, regulation by multiple adrenergic specific (super-)enhancers and strong dependency on high SOX11 expression in adrenergic neuroblastomas. SOX11 regulated direct targets include genes implicated in epigenetic control, cytoskeleton and neurodevelopment. Most notably, SOX11 controls chromatin regulatory complexes, including 10 SWI/SNF core components among which SMARCC1, SMARCA4/BRG1 and ARID1A. Additionally, the histone deacetylase HDAC2, PRC1 complex component CBX2, chromatin-modifying enzyme KDM1A/LSD1 and pioneer factor c-MYB are regulated by SOX11. Finally, SOX11 is identified as a core transcription factor of the core regulatory circuitry (CRC) in adrenergic high-risk neuroblastoma with a potential role as epigenetic master regulator upstream of the CRC.
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Affiliation(s)
- Bieke Decaesteker
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.
| | - Amber Louwagie
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Siebe Loontiens
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Fanny De Vloed
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Sarah-Lee Bekaert
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Juliette Roels
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Suzanne Vanhauwaert
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Sara De Brouwer
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Ellen Sanders
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Alla Berezovskaya
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Geertrui Denecker
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Eva D'haene
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Stéphane Van Haver
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Wouter Van Loocke
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Jo Van Dorpe
- Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.,Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - David Creytens
- Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.,Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Nadine Van Roy
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Tim Pieters
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Christophe Van Neste
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Matthias Fischer
- Department for Experimental Pediatric Oncology, and Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
| | - Pieter Van Vlierberghe
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Stephen S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Johannes Schulte
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, 13353, Germany
| | - Sara Ek
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Rogier Versteeg
- Department of Oncogenomics, Academic Medical Center, Amsterdam, 1105, AZ, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, Academic Medical Center, Amsterdam, 1105, AZ, The Netherlands
| | - Johan van Nes
- Department of Oncogenomics, Academic Medical Center, Amsterdam, 1105, AZ, The Netherlands
| | - Mark Zimmerman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Katleen De Preter
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium
| | - Frank Speleman
- Department of Biomolecular medicine, Ghent University, Ghent, 9000, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent, 9000, Belgium.
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7
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Cordier F, Van der Meulen J, Loontiens S, Van Roy N, Lapeire L, Willaert W, Ferdinande L, Van de Vijver K, Van Dorpe J, Creytens D. High-grade endometrial stromal sarcoma-like' sarcoma in male: Does it exist? A case report and review of the literature. Pathol Res Pract 2023; 241:154228. [PMID: 36455366 DOI: 10.1016/j.prp.2022.154228] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
We report an exceptional case of an undifferentiated round and spindle cell sarcoma, occurring in the periprostatic region of a 54-year-old male, with a 'high-grade endometrial stromal sarcoma-like' (HG-ESS) morphology and harboring a ZC3H7B::BCOR gene fusion identified by RNA-based next-generation sequencing. In this report, we describe the striking overlap of morphologic, immunohistochemical and molecular features of this current case and previously reported similar cases with ZC3H7B::BCOR fusion-positive HG-ESS, and discuss the differential diagnosis and possible pathogenesis of this unusual entity.
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Affiliation(s)
- Fleur Cordier
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Joni Van der Meulen
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium; Centre for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Siebe Loontiens
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium; Centre for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium; Centre for Medical Genetics, Ghent University Hospital, Ghent University, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lore Lapeire
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium; Department of Medical Oncology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Wouter Willaert
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium; Department of GI Surgery, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Liesbeth Ferdinande
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Koen Van de Vijver
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent University, Ghent, Belgium; CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, Ghent, Belgium.
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8
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Laukkanen S, Veloso A, Yan C, Oksa L, Alpert EJ, Do D, Hyvärinen N, McCarthy K, Adhikari A, Yang Q, Iyer S, Garcia SP, Pello A, Ruokoranta T, Moisio S, Adhikari S, Yoder JA, Gallagher K, Whelton L, Allen JR, Jin AH, Loontiens S, Heinäniemi M, Kelliher M, Heckman CA, Lohi O, Langenau DM. Therapeutic targeting of LCK tyrosine kinase and mTOR signaling in T-cell acute lymphoblastic leukemia. Blood 2022; 140:1891-1906. [PMID: 35544598 PMCID: PMC10082361 DOI: 10.1182/blood.2021015106] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Relapse and refractory T-cell acute lymphoblastic leukemia (T-ALL) has a poor prognosis, and new combination therapies are sorely needed. Here, we used an ex vivo high-throughput screening platform to identify drug combinations that kill zebrafish T-ALL and then validated top drug combinations for preclinical efficacy in human disease. This work uncovered potent drug synergies between AKT/mTORC1 (mammalian target of rapamycin complex 1) inhibitors and the general tyrosine kinase inhibitor dasatinib. Importantly, these same drug combinations effectively killed a subset of relapse and dexamethasone-resistant zebrafish T-ALL. Clinical trials are currently underway using the combination of mTORC1 inhibitor temsirolimus and dasatinib in other pediatric cancer indications, leading us to prioritize this therapy for preclinical testing. This combination effectively curbed T-ALL growth in human cell lines and primary human T-ALL and was well tolerated and effective in suppressing leukemia growth in patient-derived xenografts (PDX) grown in mice. Mechanistically, dasatinib inhibited phosphorylation and activation of the lymphocyte-specific protein tyrosine kinase (LCK) to blunt the T-cell receptor (TCR) signaling pathway, and when complexed with mTORC1 inhibition, induced potent T-ALL cell killing through reducing MCL-1 protein expression. In total, our work uncovered unexpected roles for the LCK kinase and its regulation of downstream TCR signaling in suppressing apoptosis and driving continued leukemia growth. Analysis of a wide array of primary human T-ALLs and PDXs grown in mice suggest that combination of temsirolimus and dasatinib treatment will be efficacious for a large fraction of human T-ALLs.
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Affiliation(s)
- Saara Laukkanen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Alexandra Veloso
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Chuan Yan
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Laura Oksa
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Eric J. Alpert
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Daniel Do
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Noora Hyvärinen
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Karin McCarthy
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Abhinav Adhikari
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Qiqi Yang
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Sowmya Iyer
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Sara P. Garcia
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Annukka Pello
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Sanni Moisio
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Sadiksha Adhikari
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jeffrey A. Yoder
- Department of Molecular Biomedical Sciences, Comparative Medicine Institute, and Center for Human Health and the Environment, North Carolina State University, Raleigh, NC
| | - Kayleigh Gallagher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Lauren Whelton
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - James R. Allen
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Alex H. Jin
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Siebe Loontiens
- Cancer Research Institute Ghent and Center for Medical Genetics, Ghent, Belgium
| | - Merja Heinäniemi
- The Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Michelle Kelliher
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Caroline A. Heckman
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Olli Lohi
- Tampere Center for Child, Adolescent, and Maternal Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tampere University Hospital, Tays Cancer Center, Tampere, Finland
| | - David M. Langenau
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA
- Harvard Stem Cell Institute, Boston, MA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
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9
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Nunes C, Depestel L, Mus L, Keller KM, Delhaye L, Louwagie A, Rishfi M, Whale A, Kara N, Andrews SR, Dela Cruz F, You D, Siddiquee A, Cologna CT, De Craemer S, Dolman E, Bartenhagen C, De Vloed F, Sanders E, Eggermont A, Bekaert SL, Van Loocke W, Bek JW, Dewyn G, Loontiens S, Van Isterdael G, Decaesteker B, Tilleman L, Van Nieuwerburgh F, Vermeirssen V, Van Neste C, Ghesquiere B, Goossens S, Eyckerman S, De Preter K, Fischer M, Houseley J, Molenaar J, De Wilde B, Roberts SS, Durinck K, Speleman F. RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition. Sci Adv 2022; 8:eabn1382. [PMID: 35857500 PMCID: PMC9278860 DOI: 10.1126/sciadv.abn1382] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/26/2022] [Indexed: 05/06/2023]
Abstract
High-risk neuroblastoma, a pediatric tumor originating from the sympathetic nervous system, has a low mutation load but highly recurrent somatic DNA copy number variants. Previously, segmental gains and/or amplifications allowed identification of drivers for neuroblastoma development. Using this approach, combined with gene dosage impact on expression and survival, we identified ribonucleotide reductase subunit M2 (RRM2) as a candidate dependency factor further supported by growth inhibition upon in vitro knockdown and accelerated tumor formation in a neuroblastoma zebrafish model coexpressing human RRM2 with MYCN. Forced RRM2 induction alleviates excessive replicative stress induced by CHK1 inhibition, while high RRM2 expression in human neuroblastomas correlates with high CHK1 activity. MYCN-driven zebrafish tumors with RRM2 co-overexpression exhibit differentially expressed DNA repair genes in keeping with enhanced ATR-CHK1 signaling activity. In vitro, RRM2 inhibition enhances intrinsic replication stress checkpoint addiction. Last, combinatorial RRM2-CHK1 inhibition acts synergistic in high-risk neuroblastoma cell lines and patient-derived xenograft models, illustrating the therapeutic potential.
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Affiliation(s)
- Carolina Nunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Depestel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Liselot Mus
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Louis Delhaye
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Amber Louwagie
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Muhammad Rishfi
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Alex Whale
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Neesha Kara
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | - Filemon Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daoqi You
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Armaan Siddiquee
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Camila Takeno Cologna
- Metabolomics Expertise Center, Center for Cancer Biology (CCB), VIB, Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Sam De Craemer
- Metabolomics Expertise Center, Center for Cancer Biology (CCB), VIB, Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Emmy Dolman
- Princess Maxima Center, Utrecht, Netherlands
| | - Christoph Bartenhagen
- Center for Molecular Medicine Cologne, Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, Cologne, Germany
| | - Fanny De Vloed
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Ellen Sanders
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Aline Eggermont
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Sarah-Lee Bekaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jan Willem Bek
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Givani Dewyn
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Siebe Loontiens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Bieke Decaesteker
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Laurentijn Tilleman
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | | | - Vanessa Vermeirssen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Christophe Van Neste
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Bart Ghesquiere
- Metabolomics Expertise Center, Center for Cancer Biology (CCB), VIB, Leuven, Belgium
- Metabolomics Expertise Center, Department of Oncology, KU Leuven, Leuven, Belgium
| | - Steven Goossens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent University, Ghent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Matthias Fischer
- Center for Molecular Medicine Cologne, Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, Cologne, Germany
| | - Jon Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Stephen S. Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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10
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Loontiens S, Vanhauwaert S, Depestel L, Dewyn G, Van Loocke W, Moore FE, Garcia EG, Batchelor L, Borga C, Squiban B, Malone-Perez M, Volders PJ, Olexiouk V, Van Vlierberghe P, Langenau DM, Frazer JK, Durinck K, Speleman F. A novel TLX1-driven T-ALL zebrafish model: comparative genomic analysis with other leukemia models. Leukemia 2020; 34:3398-3403. [PMID: 32591643 PMCID: PMC7906429 DOI: 10.1038/s41375-020-0938-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Siebe Loontiens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Suzanne Vanhauwaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Depestel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Givani Dewyn
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Finola E Moore
- Department of Pathology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
- Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Harvard Stem Cell Institute, Boston, MA, 02114, USA
- Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Elaine G Garcia
- Department of Pathology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
- Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Harvard Stem Cell Institute, Boston, MA, 02114, USA
- Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Lance Batchelor
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Chiara Borga
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Barbara Squiban
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Megan Malone-Perez
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Pieter-Jan Volders
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Volodimir Olexiouk
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David M Langenau
- Department of Pathology, Massachusetts General Hospital Research Institute, Boston, MA, 02114, USA
- Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Harvard Stem Cell Institute, Boston, MA, 02114, USA
- Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - J Kimble Frazer
- Section of Pediatric Hematology-Oncology, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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11
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Loontiens S, Dolens AC, Strubbe S, Van de Walle I, Moore FE, Depestel L, Vanhauwaert S, Matthijssens F, Langenau DM, Speleman F, Van Vlierberghe P, Durinck K, Taghon T. PHF6 Expression Levels Impact Human Hematopoietic Stem Cell Differentiation. Front Cell Dev Biol 2020; 8:599472. [PMID: 33251223 PMCID: PMC7672048 DOI: 10.3389/fcell.2020.599472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 01/10/2023] Open
Abstract
Transcriptional control of hematopoiesis involves complex regulatory networks and functional perturbations in one of these components often results in malignancies. Loss-of-function mutations in PHF6, encoding a presumed epigenetic regulator, have been primarily described in T cell acute lymphoblastic leukemia (T-ALL) and the first insights into its function in normal hematopoiesis only recently emerged from mouse modeling experiments. Here, we investigated the role of PHF6 in human blood cell development by performing knockdown studies in cord blood and thymus-derived hematopoietic precursors to evaluate the impact on lineage differentiation in well-established in vitro models. Our findings reveal that PHF6 levels differentially impact the differentiation of human hematopoietic progenitor cells into various blood cell lineages, with prominent effects on lymphoid and erythroid differentiation. We show that loss of PHF6 results in accelerated human T cell development through reduced expression of NOTCH1 and its downstream target genes. This functional interaction in developing thymocytes was confirmed in vivo using a phf6-deficient zebrafish model that also displayed accelerated developmental kinetics upon reduced phf6 or notch1 activation. In summary, our work reveals that appropriate control of PHF6 expression is important for normal human hematopoiesis and provides clues towards the role of PHF6 in T-ALL development.
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Affiliation(s)
- Siebe Loontiens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Finola E. Moore
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, United States
| | - Lisa Depestel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Filip Matthijssens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - David M. Langenau
- Molecular Pathology and Cancer Center, Massachusetts General Hospital, Boston, MA, United States
- Harvard Stem Cell Institute, Cambridge, MA, United States
| | - Frank Speleman
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Van Vlierberghe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kaat Durinck
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
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12
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Garcia EG, Veloso A, Oliveira ML, Allen JR, Loontiens S, Brunson D, Do D, Yan C, Morris R, Iyer S, Garcia SP, Iftimia N, Van Loocke W, Matthijssens F, McCarthy K, Barata JT, Speleman F, Taghon T, Gutierrez A, Van Vlierberghe P, Haas W, Blackburn JS, Langenau DM. PRL3 enhances T-cell acute lymphoblastic leukemia growth through suppressing T-cell signaling pathways and apoptosis. Leukemia 2020; 35:679-690. [PMID: 32606318 PMCID: PMC8009053 DOI: 10.1038/s41375-020-0937-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 01/06/2023]
Abstract
T cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy of thymocytes and is largely driven by the NOTCH/MYC pathway. Yet, additional oncogenic drivers are required for transformation. Here, we identify protein tyrosine phosphatase type 4 A3 (PRL3) as a collaborating oncogenic driver in T-ALL. PRL3 is expressed in a large fraction of primary human T-ALLs and is commonly co-amplified with MYC. PRL3 also synergized with MYC to initiate early-onset ALL in transgenic zebrafish and was required for human T-ALL growth and maintenance. Mass spectrometry phosphoproteomic analysis and mechanistic studies uncovered that PRL3 suppresses downstream T cell phosphorylation signaling pathways, including those modulated by VAV1, and subsequently suppresses apoptosis in leukemia cells. Taken together, our studies have identified new roles for PRL3 as a collaborating oncogenic driver in human T-ALL and suggest that therapeutic targeting of the PRL3 phosphatase will likely be a useful treatment strategy for T-ALL.
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Affiliation(s)
- E G Garcia
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - A Veloso
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - M L Oliveira
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - J R Allen
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - S Loontiens
- Cancer Research Institute Ghent, Ghent, Belgium
| | - D Brunson
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - D Do
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - C Yan
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - R Morris
- Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - S Iyer
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - S P Garcia
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - N Iftimia
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - W Van Loocke
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - F Matthijssens
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - K McCarthy
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - J T Barata
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - F Speleman
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - T Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - A Gutierrez
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Boston, USA
| | - P Van Vlierberghe
- Cancer Research Institute Ghent, Ghent, Belgium.,Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - W Haas
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA.,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA.,Harvard Stem Cell Institute, Boston, MA, 02114, USA.,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - J S Blackburn
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, 40536, USA
| | - D M Langenau
- Department of Pathology, Massachusetts General Research Institute, Boston, MA, 02114, USA. .,Center of Cancer Research, Massachusetts General Hospital, Charlestown, MA, 02129, USA. .,Harvard Stem Cell Institute, Boston, MA, 02114, USA. .,Center of Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
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13
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Loontiens S, Durinck K, Vanhauwaert S, Depestel L, Oliveira ML, Dewyn G, Bock CD, Barata JT, Langenau D, Cools J, Taghon T, Vlierberghe PV, Speleman F. Abstract 3696: PHF6loss drives IL7R oncogene addiction in TLX1 driven T-ALL. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease. The PHF6 gene is frequently targeted by loss-of-function mutations or deletions, with the highest prevalence in TLX1 or TLX3 rearranged T-ALLs. To gain insights into the putative function of PHF6 as a tumor suppressor in the T-cell lineage, we investigated the effects of PHF6 knock down during normal and malignant thymocytes. Notably, we observed broad effects on the investigated transcriptomes suggesting an important role for PHF6 in gene regulation. Furthermore, IL7R was identified as a common transcriptional target that was significantly upregulated upon PHF6 knockdown in both normal and malignant T cells. IL7R encodes a cytokine receptor critically involved in normal thymic development and which also acts as a bona fide oncogene in subset of primary T-ALLs. Thus, loss of PHF6 might further boost oncogenic addiction of leukemic T-cell lymphoblast to IL7-induced JAK-STAT signaling.
To further explore the role of PHF6 inactivation in TLX1 driven leukemogenesis in vivo, we performed zebrafish modeling. For this, we generated a stable tg(rag2:TLX1, rag2:GFP) overexpressing as well as a phf6 knock out zebrafish line. These lines were crossed and offspring was monitored for T-ALL formation. Interestingly, three fish out of a cohort of 80 animals developed leukemia between 10 to 18 months of age. These leukemias originated from the thymus, spreaded throughout the whole body and were transplantable. Thus far, no leukemia was detected in PHF6 mutated or TLX1 overexpressing only zebrafish. Leukemic cells obtained from tumors that developed in the PHF6null TLX1rag2-TLX1/GFP animals were subjected to RNA-, ATAC- and H3K27ac ChIP-sequencing to assess the epigenetic status of the IL7R locus. In addition, exome-, and CNV-sequencing was performed to identify somatic lesions that cooperated loss of Phf6 during TLX1 driven T-cell transformation in zebrafish. Furthermore, additional injections of TLX1 in combination with an activating IL7R mutant into phf6 mutant zebrafish are currently ongoing to monitor additional effects on accelerated tumor formation. In conclusion, our data suggest that loss of PHF6 drives TLX1 mediated leukemogenesis, at least in part, by increasing surface IL7R expression. Therefore, we believe that increased addiction to oncogenic JAK-STAT signaling may render PHF6 mutant leukemic cells more sensitive to JAK inhibitors, a notion that we are currently investigating in our TLX1/PHF6 and TLX1/PHF6/IL7R zebrafish models.
Citation Format: Siebe Loontiens, Kaat Durinck, Suzanne Vanhauwaert, Lisa Depestel, Mariana L. Oliveira, Givani Dewyn, Charles De Bock, João T. Barata, David Langenau, Jan Cools, Tom Taghon, Pieter Van Vlierberghe, Frank Speleman. PHF6loss drives IL7R oncogene addiction in TLX1 driven T-ALL [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3696.
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Loontiens S, Depestel L, Vanhauwaert S, Dewyn G, Gistelinck C, Verboom K, Van Loocke W, Matthijssens F, Willaert A, Vandesompele J, Speleman F, Durinck K. Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes. BMC Genomics 2019; 20:228. [PMID: 30894119 PMCID: PMC6425699 DOI: 10.1186/s12864-019-5608-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/14/2019] [Indexed: 11/30/2022] Open
Abstract
Background Transgenic zebrafish lines with the expression of a fluorescent reporter under the control of a cell-type specific promoter, enable transcriptome analysis of FACS sorted cell populations. RNA quality and yield are key determinant factors for accurate expression profiling. Limited cell number and FACS induced cellular stress make RNA isolation of sorted zebrafish cells a delicate process. We aimed to optimize a workflow to extract sufficient amounts of high-quality RNA from a limited number of FACS sorted cells from Tg(fli1a:GFP) zebrafish embryos, which can be used for accurate gene expression analysis. Results We evaluated two suitable RNA isolation kits (the RNAqueous micro and the RNeasy plus micro kit) and determined that sorting cells directly into lysis buffer is a critical step for success. For low cell numbers, this ensures direct cell lysis, protects RNA from degradation and results in a higher RNA quality and yield. We showed that this works well up to 0.5× dilution of the lysis buffer with sorted cells. In our sort settings, this corresponded to 30,000 and 75,000 cells for the RNAqueous micro kit and RNeasy plus micro kit respectively. Sorting more cells dilutes the lysis buffer too much and requires the use of a collection buffer. We also demonstrated that an additional genomic DNA removal step after RNA isolation is required to completely clear the RNA from any contaminating genomic DNA. For cDNA synthesis and library preparation, we combined SmartSeq v4 full length cDNA library amplification, Nextera XT tagmentation and sample barcoding. Using this workflow, we were able to generate highly reproducible RNA sequencing results. Conclusions The presented optimized workflow enables to generate high quality RNA and allows accurate transcriptome profiling of small populations of sorted zebrafish cells. Electronic supplementary material The online version of this article (10.1186/s12864-019-5608-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Siebe Loontiens
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Lisa Depestel
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Suzanne Vanhauwaert
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Givani Dewyn
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Charlotte Gistelinck
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Department of Orthopedics and Sports Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Karen Verboom
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Wouter Van Loocke
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Filip Matthijssens
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine & Center for Medical Genetics, Ghent University, 9000, Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), 9000, Ghent, Belgium.
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