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Decraene B, Coppens G, Spans L, Solie L, Sciot R, Vanden Bempt I, De Smet F, De Vleeschouwer S. A novel methylation signature predicts extreme long-term survival in glioblastoma. J Neurooncol 2024; 169:341-347. [PMID: 38898218 PMCID: PMC11341684 DOI: 10.1007/s11060-024-04741-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
PURPOSE Glioblastoma (GBM) is the most common malignant primary brain tumor with a dismal prognosis of less than 2 years under maximal therapy. Despite the poor prognosis, small fractions of GBM patients seem to have a markedly longer survival than the vast majority of patients. Recently discovered intertumoral heterogeneity is thought to be responsible for this peculiarity, although the exact underlying mechanisms remain largely unknown. Here, we investigated the epigenetic contribution to survival. METHODS GBM treatment-naïve samples from 53 patients, consisting of 12 extremely long-term survivors (eLTS) patients and 41 median-term survivors (MTS) patients, were collected for DNA methylation analysis. 865 859 CpG sites were examined and processed for detection of differentially methylated CpG positions (DMP) and regions (DMR) between both survival groups. Gene Ontology (GO) and pathway functional annotations were used to identify associated biological processes. Verification of these findings was done using The Cancer Genome Atlas (TCGA) database. RESULTS We identified 67 DMPs and 5 DMRs that were associated with genes and pathways - namely reduced interferon beta signaling, in MAPK signaling and in NTRK signaling - which play a role in survival in GBM. CONCLUSION In conclusion, baseline DNA methylation differences already present in treatment-naïve GBM samples are part of genes and pathways that play a role in the survival of these tumor types and therefore may explain part of the intrinsic heterogeneity that determines prognosis in GBM patients.
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Vanhauwaert D, Silversmit G, Vanschoenbeek K, Coucke G, Di Perri D, Clement PM, Sciot R, De Vleeschouwer S, Boterberg T, De Gendt C. Association of hospital volume with survival but not with postoperative mortality in glioblastoma patients in Belgium. J Neurooncol 2024:10.1007/s11060-024-04776-2. [PMID: 39093532 DOI: 10.1007/s11060-024-04776-2] [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: 06/15/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
OBJECTIVES Standard of care treatment for glioblastoma (GBM) involves surgical resection followed by chemoradiotherapy. However, variations in treatment decisions and outcomes exist across hospitals and physicians. In Belgium, where oncological care is dispersed, the impact of hospital volume on GBM outcomes remains unexplored. This nationwide study aims to analyse interhospital variability in 30-day postoperative mortality and 1-/2-year survival for GBM patients. METHODS Data collected from the Belgian Cancer Registry, identified GBM patients diagnosed between 2016 and 2019. Surgical resection and biopsy cases were identified, and hospital case load was determined. Associations between hospital volume and mortality and survival probabilities were analysed, considering patient characteristics. Statistical analysis included logistic regression for mortality and Cox proportional hazard models for survival. RESULTS A total of 2269 GBM patients were identified (1665 underwent resection, 662 underwent only biopsy). Thirty-day mortality rates post-resection/post-biopsy were 5.1%/11.9% (target < 3%/<5%). Rates were higher in elderly patients and those with worse WHO-performance scores. No significant difference was found based on hospital case load. Survival probabilities at 1/2 years were 48.6% and 21.3% post-resection; 22.4% and 8.3% post-biopsy. Hazard ratio for all-cause death for low vs. high volume centres was 1.618 in first 0.7 year post-resection (p < 0.0001) and 1.411 in first 0.8 year post-biopsy (p = 0.0046). CONCLUSION While 30-day postoperative mortality rates were above predefined targets, no association between hospital volume and mortality was found. However, survival probabilities demonstrated benefits from treatment in higher volume centres, particularly in the initial months post-surgery. These variations highlight the need for continuous improvement in neuro-oncological practice and should stimulate reflection on the neuro-oncological care organisation in Belgium.
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De Cock L, Paternostro F, Vanleeuw U, Wyns K, Laenen A, Lee CJ, Sciot R, Wozniak A, Schöffski P. Potentially actionable targets in synovial sarcoma: A tissue microarray study. Transl Oncol 2024; 48:102057. [PMID: 39029378 PMCID: PMC11305002 DOI: 10.1016/j.tranon.2024.102057] [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: 05/03/2024] [Revised: 06/23/2024] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND Synovial sarcoma (SynSa) is one of the most common translocation-related soft tissue sarcomas. Patients with metastatic SynSa have limited treatment options and a very poor prognosis. Several novel experimental therapies are currently being explored in clinical trials, including T cell-based therapies targeting cancer testis antigens such as New York esophageal squamous cell carcinoma 1 (NY-ESO-1) or melanoma-associated antigen A4 (MAGE-A4), and degraders targeting bromodomain-containing protein 9 (BRD9). Preclinical studies investigate inhibitors of Yes associated protein 1 (YAP1), transcriptional co-activator with PDZ-binding motif (TAZ) and inhibitors of chemokine receptor 4 (CXCR4). METHODS We explored the immunohistochemical expression of these targets using a tissue microarray (TMA) constructed from 91 clinical SynSa samples and correlated these findings with corresponding clinicopathological data. RESULTS Expression of MAGE-A4 and NY-ESO-1 was found in 69 % and 56 % of the samples, respectively. NY-ESO-1 was statistically higher expressed in samples from metastatic lesions as compared to samples from primary tumors. Nuclear expression of YAP1 and TAZ was observed in 92 % and 51 % of the samples, respectively. CXCR4 was expressed in the majority of the samples (82 %). BRD9 was highly expressed in all specimens. No prognostic role could be identified for any of the investigated proteins. CONCLUSION This study is a comprehensive study providing real-world data on the expression of several actionable proteins in a large proportion of SynSa samples. All evaluated markers were expressed in a clinically meaningful proportion of cases represented in our TMA, supporting the relevance of ongoing preclinical and clinical research with novel agents directed against these targets.
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Smeijers S, Brems H, Verhaeghe A, van Paesschen W, van Loon J, Van der Auweraer S, Sciot R, Thal DR, Lagae L, Legius E, Theys T. Encephalocraniocutaneous lipomatosis phenotype associated with mosaic biallelic pathogenic variants in the NF1 gene. J Med Genet 2024:jmg-2023-109785. [PMID: 38825366 DOI: 10.1136/jmg-2023-109785] [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: 11/27/2023] [Accepted: 05/21/2024] [Indexed: 06/04/2024]
Abstract
Encephalocraniocutaneous lipomatosis (ECCL) is a sporadic congenital condition characterised by ocular, cutaneous and central nervous system involvement. Mosaic activating variants in FGFR1 and KRAS have been reported in several individuals with this syndrome. We report on a patient with neurofibromatosis type 1 (NF1) with a germline pathogenic variant in the NF1 gene and an ECCL phenotype, suggesting ECCL to be part of a spectrum of malformations associated with NF1 pathogenic variants. An anatomical hemispherectomy was performed for intractable epilepsy. Through genetic analysis of blood, cerebral tissue and giant cell lesions in both jaws, we identified the germline NF1 pathogenic variant in all samples and a second-hit pathogenic NF1 variant in cerebral tissue and both giant cell lesions. Both NF1 variants were located on different alleles resulting in somatic mosaicism for a biallelic NF1 inactivation originating in early embryogenesis (second-hit mosaicism or Happle type 2 mosaicism). The biallelic deficit in NF1 in the left hemicranium explains the severe localised, congenital abnormality in this patient. Identical first and second-hit variants in a giant cell lesion of both upper and lower jaws provide confirmatory evidence for an early embryonic second hit involving at least the neural crest. We suggest that the ECCL phenotype may be part of a spectrum of congenital problems associated with mosaic NF1 nullisomy originating during early embryogenesis. The biallelic NF1 inactivation during early embryogenesis mimics the severe activation of the RAS-MAPK pathway seen in ECCL caused by embryonic mosaic activating FGFR1 and KRAS variants in the cranial region. We propose that distinct mechanisms of mosaicism can cause the ECCL phenotype through convergence on the RAS-MAPK pathway.
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Nikoghosyan A, Sciot R, Jacobs SA, Verhaaren BFJ. Is Neuroradiology Complementary to Histopathology in Central Nervous System Tumors with an Alteration of the BCOR Gene? Clin Neuroradiol 2024; 34:507-509. [PMID: 38129591 DOI: 10.1007/s00062-023-01367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/12/2023] [Indexed: 12/23/2023]
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Schepens J, Van Havenbergh F, Dejaegher J, Demaerel P, Sciot R, De Vleeschouwer S. Tension Pneumocephalus With Acute Cerebellar Symptoms Due to an Intradiploic Epidermoid Cyst Eroding the Mastoid Bone. Cureus 2024; 16:e60427. [PMID: 38882976 PMCID: PMC11179587 DOI: 10.7759/cureus.60427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2024] [Indexed: 06/18/2024] Open
Abstract
This case report presents a unique presentation of an intradiploic epidermoid cyst (IDEC) in a 55-year-old female. She presented with acute cerebellar symptoms triggered by a Valsalva maneuver. IDECs are a rare type of intracranial epidermoid cysts. They are benign and have a slow growth pattern that translates into progressively developing symptoms instead of acute symptoms. Symptoms include local deformities, focal neurologic deficits, and pain. This patient developed acute cerebellar symptoms due to erosion of the mastoid bone that created a pathway between the eustachian tube and the intracranial space via the mastoid air cells. Consequently, tension pneumocephalus emerged via a ball-valve effect that caused a significant mass effect in the posterior fossa. Surgical resection of the IDEC and closing of the mastoid air cells resulted in symptom relief by restoring the integrity of the intracranial-extracranial barrier. This case highlights that a higher level of vigilance is warranted for an IDEC in the proximity of aerated bone structures, such as the mastoid air cells and the paranasal sinuses, and that a more proactive approach is advocated.
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Vandaele T, Van Slambrouck J, Schöffski P, Dumez H, Weynand B, Sciot R, Barbarossa A, Provoost AL, Van de Voorde K, Debaveye Y, Bouneb S, Nafteux P, Ceulemans LJ. Extensive surgical resections for rare pleural neoplasms: a single-center experience with a yolk sac tumor and synovial sarcoma. World J Surg Oncol 2024; 22:96. [PMID: 38622623 PMCID: PMC11021014 DOI: 10.1186/s12957-024-03367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/28/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Pleural neoplasms are rare and can be subdivided into pleural metastasis and primary pleural neoplasms. Non-mesothelioma primary pleural neoplasms are a diverse group of extremely rare pathologies. CASE PRESENTATION In this case series, we describe the presentation and management of two rare primary pleural neoplasms. A first case describes a primary pleural yolk sac tumor treated with neoadjuvant chemotherapy, extended pleurectomy decortication, and hyperthermic intrathoracic chemotherapy. In a second case we describe the management of a primary pleural synovial sarcoma by neoadjuvant chemotherapy and extrapleural pneumonectomy. A complete resection was obtained in both cases and the post-operative course was uncomplicated. No signs of tumor recurrence were noted during follow-up in the first patient. In the second patient a local recurrence was diagnosed 6 months after surgery. CONCLUSION Neo-adjuvant chemotherapy followed by extensive thoracic surgery, including hyperthermic intrathoracic chemotherapy, is a feasible treatment strategy for non-mesothelioma primary pleural neoplasms, but careful follow-up is required.
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Herrtwich A, Sciot R, Ernst C. Myopericytoma in an Infant-Imaging Characteristics of a Rare but Benign Entity. J Belg Soc Radiol 2024; 108:3. [PMID: 38312148 PMCID: PMC10836187 DOI: 10.5334/jbsr.3441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/19/2023] [Indexed: 02/06/2024] Open
Abstract
Teaching point: Myopericytoma is a rare soft tissue tumor but should be considered in the differential diagnosis of infants with a fast-growing perivascular tumor.
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Koshyk O, Dehner CA, van den Hout MFCM, Bempt IV, Sciot R, Huang HY, Agaimy A, Din NU, Klubíčková N, Mosaieby E, Skálová A, Michalová K, Schöffski P, Oliveira AM, Halling KC, Gupta S, Gross JM, Nin JWM, Michal M, Folpe AL, Kosemehmetoglu K, Torres-Mora J, Michal M. EWSR1::POU2AF3(COLCA2) Sarcoma: An Aggressive, Polyphenotypic Sarcoma With a Head and Neck Predilection. Mod Pathol 2023; 36:100337. [PMID: 37742928 DOI: 10.1016/j.modpat.2023.100337] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/25/2023] [Accepted: 09/15/2023] [Indexed: 09/26/2023]
Abstract
EWSR1::POU2AF3 (COLCA2) sarcomas are a recently identified group of undifferentiated round/spindle cell neoplasms with a predilection for the head and neck region. Herein, we report our experience with 8 cases, occurring in 5 men and 3 women (age range, 37-74 years; median, 60 years). Tumors involved the head/neck (4 cases), and one each the thigh, thoracic wall, fibula, and lung. Seven patients received multimodal therapy; 1 patient was treated only with surgery. Clinical follow-up (8 patients; range, 4-122 months; median, 32 months) showed 5 patients with metastases (often multifocal, with a latency ranging from 7 to 119 months), and 3 of them also with local recurrence. The median local recurrence-free and metastasis-free survival rates were 24 months and 29 months, respectively. Of the 8 patients, 1 died of an unknown cause, 4 were alive with metastatic disease, 1 was alive with unresectable local disease, and 2 were without disease. The tumors were composed of 2 morphologic subgroups: (1) relatively bland tumors consisting of spindled to stellate cells with varying cellularity and fibromyxoid stroma (2 cases) and (2) overtly malignant tumors composed of nests of "neuroendocrine-appearing" round cells surrounded by spindled cells (6 cases). Individual cases in the second group showed glandular, osteogenic, or rhabdomyoblastic differentiation. Immunohistochemical results included CD56 (4/4 cases), GFAP (5/8), SATB2 (4/6), keratin (AE1/AE3) (5/8), and S100 protein (4/7). RNA sequencing identified EWSR1::POU2AF3 gene fusion in all cases. EWSR1 gene rearrangement was confirmed by fluorescence in situ hybridization in 5 cases. Our findings confirm the head/neck predilection and aggressive clinical behavior of EWSR1::POU2AF3 sarcomas and widen the morphologic spectrum of these rare lesions to include relatively bland spindle cell tumors and tumors with divergent differentiation.
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Cornelis S, Sciot R, Degreef I. Flexor carpi radialis tendon tear due to scaphoid osteoid osteoma: A case report. HAND SURGERY & REHABILITATION 2023; 42:459-461. [PMID: 37499796 DOI: 10.1016/j.hansur.2023.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
Osteoid osteoma is a benign osteoblastic tumor with a low incidence. Due to its uncommon and often confusing clinical presentation, accurate diagnosis is frequently significantly delayed. We report a case of a 56-year old right-handed woman with a history of increasing pain in her right scaphotrapeziotrapezoidal (STT) joint and distal flexor carpi radialis (FCR). Due to its confusing clinical presentation, the diagnosis of a parosteal osteoid osteoma in the scaphoid and a rupture of the FCR, presenting as a Mannerfelt like lesion, was delayed for 1 year. The patient was treated with surgical exploration and excision. At follow-up, the patient recovered with complete resolution of pain and resumed daily life activities after 2 weeks. A high index of suspicion remains the key point in the diagnosis of osteoid osteoma, certainly in cases of unusual clinical presentation and anatomic localization as presented in this case.
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Verbeek S, Sciot R, Debiec-Rychter M, Labarque V, Meyns B, Cools B. Case report: Cardiac intimal sarcoma in a young child. Front Pediatr 2023; 11:1238847. [PMID: 37818167 PMCID: PMC10560764 DOI: 10.3389/fped.2023.1238847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023] Open
Abstract
Undifferentiated mesenchymal tumors from the intimal layer (intimal sarcomas) are rare within the ventricles and exceptional in children. A rare case of an intimal sarcoma located in the right ventricle in a young child is presented with need for urgent surgical resection due to mechanical flow obstruction. Tumor cells showed amplification of MDM2 gene and a homozygous loss of CDKN2A on 9p21. A review of the literature regarding primary cardiac malignancies and intimal sarcoma in children is provided.
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De Sutter L, Wozniak A, Verreet J, Vanleeuw U, De Cock L, Linde N, Drechsler C, Esdar C, Sciot R, Schöffski P. Antitumor Efficacy of the Novel KIT Inhibitor IDRX-42 (Formerly M4205) in Patient- and Cell Line-Derived Xenograft Models of Gastrointestinal Stromal Tumor (GIST). Clin Cancer Res 2023; 29:2859-2868. [PMID: 37223931 DOI: 10.1158/1078-0432.ccr-22-3822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/17/2023] [Accepted: 05/19/2023] [Indexed: 05/25/2023]
Abstract
PURPOSE The majority of gastrointestinal stromal tumors (GIST) are driven by constitutively activated KIT/PDGFRA kinases and are susceptible to treatment with tyrosine kinase inhibitors. During treatment, most of these tumors will develop secondary mutations in KIT or PDGFRA inducing drug resistance, so there is an unmet need for novel therapies. We tested the efficacy of IDRX-42, a novel selective KIT inhibitor with high activity toward the most relevant KIT mutations, in 4 GIST xenograft models. EXPERIMENTAL DESIGN NMRI nu/nu mice were transplanted with patient-derived GIST xenograft models UZLX-GIST9 (KIT:p.P577del;W557LfsX5;D820G), UZLX-GIST2B (KIT:p.A502_Y503dup), UZLX-GIST25 (KIT:p.K642E), and the cell line-derived model GIST882 (KIT:p.K642E). Mice were treated daily with vehicle (control), imatinib (100 mg/kg), sunitinib (20 mg/kg), avapritinib (5 mg/kg), or IDRX-42 (10 mg/kg, 25 mg/kg). Efficacy was assessed by tumor volume evolution, histopathology, grading of histologic response, and IHC. The Kruskal-Wallis and Wilcoxon matched-pairs tests were used for statistical analysis, with P < 0.05 considered as significant. RESULTS IDRX-42 (25 mg/kg) caused tumor volume shrinkage in UZLX-GIST25, GIST882, and UZLX-GIST2B, with a relative decrease to 45.6%, 57.3%, and 35.1% on the last day as compared with baseline, and tumor growth delay (160.9%) compared with control in UZLX-GIST9. Compared with controls, IDRX-42 (25 mg/kg) induced a significant decrease in mitosis. In UZLX-GIST25 and GIST882 grade 2-4 histologic response with myxoid degeneration was observed in all IDRX-42 (25 mg/kg)-treated tumors. CONCLUSIONS IDRX-42 showed significant antitumor activity in patient- and cell line-derived GIST xenograft models. The novel kinase inhibitor induced volumetric responses, decreased mitotic activity, and had antiproliferative effects. In models with KIT exon 13 mutation IDRX-42 induced characteristic myxoid degeneration.
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Panovska D, Nazari P, Cole B, Creemers PJ, Derweduwe M, Solie L, Van Gassen S, Claeys A, Verbeke T, Cohen EF, Tolstorukov MY, Saeys Y, Van der Planken D, Bosisio FM, Put E, Bamps S, Clement PM, Verfaillie M, Sciot R, Ligon KL, De Vleeschouwer S, Antoranz A, De Smet F. Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma. Cell Mol Life Sci 2023; 80:147. [PMID: 37171617 PMCID: PMC11071868 DOI: 10.1007/s00018-023-04772-1] [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: 12/01/2022] [Revised: 03/06/2023] [Accepted: 03/29/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Functional profiling of freshly isolated glioblastoma (GBM) cells is being evaluated as a next-generation method for precision oncology. While promising, its success largely depends on the method to evaluate treatment activity which requires sufficient resolution and specificity. METHODS Here, we describe the 'precision oncology by single-cell profiling using ex vivo readouts of functionality' (PROSPERO) assay to evaluate the intrinsic susceptibility of high-grade brain tumor cells to respond to therapy. Different from other assays, PROSPERO extends beyond life/death screening by rapidly evaluating acute molecular drug responses at single-cell resolution. RESULTS The PROSPERO assay was developed by correlating short-term single-cell molecular signatures using mass cytometry by time-of-flight (CyTOF) to long-term cytotoxicity readouts in representative patient-derived glioblastoma cell cultures (n = 14) that were exposed to radiotherapy and the small-molecule p53/MDM2 inhibitor AMG232. The predictive model was subsequently projected to evaluate drug activity in freshly resected GBM samples from patients (n = 34). Here, PROSPERO revealed an overall limited capacity of tumor cells to respond to therapy, as reflected by the inability to induce key molecular markers upon ex vivo treatment exposure, while retaining proliferative capacity, insights that were validated in patient-derived xenograft (PDX) models. This approach also allowed the investigation of cellular plasticity, which in PDCLs highlighted therapy-induced proneural-to-mesenchymal (PMT) transitions, while in patients' samples this was more heterogeneous. CONCLUSION PROSPERO provides a precise way to evaluate therapy efficacy by measuring molecular drug responses using specific biomarker changes in freshly resected brain tumor samples, in addition to providing key functional insights in cellular behavior, which may ultimately complement standard, clinical biomarker evaluations.
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De Langhe E, Van Loo S, Malengier-Devlies B, Metzemaekers M, Staels F, Vandenhaute J, Berghen N, Sciot R, Corveleyn A, Tšuiko O, Gouwy M, Lenaerts J, Verschueren P, Wouters CH, Proost P, Matthys P, Legius E, Schrijvers R. TET2-Driver and NLRC4-Passenger Variants in Adult-Onset Autoinflammation. N Engl J Med 2023; 388:1626-1629. [PMID: 37099347 DOI: 10.1056/nejmc2212928] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
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Decraene B, Vanmechelen M, Clement P, Daisne JF, Vanden Bempt I, Sciot R, Garg AD, Agostinis P, De Smet F, De Vleeschouwer S. Cellular and molecular features related to exceptional therapy response and extreme long-term survival in glioblastoma. Cancer Med 2023. [PMID: 36776000 DOI: 10.1002/cam4.5681] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/17/2023] [Accepted: 01/31/2023] [Indexed: 02/14/2023] Open
Abstract
Glioblastoma Multiforme (GBM) remains the most common malignant primary brain tumor with a dismal prognosis that rarely exceeds beyond 2 years despite extensive therapy, which consists of maximal safe surgical resection, radiotherapy, and/or chemotherapy. Recently, it has become clear that GBM is not one homogeneous entity and that both intra-and intertumoral heterogeneity contributes significantly to differences in tumoral behavior which may consequently be responsible for differences in survival. Strikingly and in spite of its dismal prognosis, small fractions of GBM patients seem to display extremely long survival, defined as surviving over 10 years after diagnosis, compared to the large majority of patients. Although the underlying mechanisms for this peculiarity remain largely unknown, emerging data suggest that still poorly characterized both cellular and molecular factors of the tumor microenvironment and their interplay probably play an important role. We hereby give an extensive overview of what is yet known about these cellular and molecular features shaping extreme long survival in GBM.
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Aukema SM, Glaser S, van den Hout MFCM, Dahlum S, Blok MJ, Hillmer M, Kolarova J, Sciot R, Schott DA, Siebert R, Stumpel CTRM. Molecular characterization of an embryonal rhabdomyosarcoma occurring in a patient with Kabuki syndrome: report and literature review in the light of tumor predisposition syndromes. Fam Cancer 2023; 22:103-118. [PMID: 35856126 PMCID: PMC9829644 DOI: 10.1007/s10689-022-00306-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 01/13/2023]
Abstract
Kabuki syndrome is a well-recognized syndrome characterized by facial dysmorphism and developmental delay/intellectual disability and in the majority of patients a germline variant in KMT2D is found. As somatic KMT2D variants can be found in 5-10% of tumors a tumor predisposition in Kabuki syndrome is discussed. So far less than 20 patients with Kabuki syndrome and a concomitant malignancy have been published. Here we report on a female patient with Kabuki syndrome and a c.2558_2559delCT germline variant in KMT2D who developed an embryonal rhabdomyosarcoma (ERMS) at 10 years. On tumor tissue we performed DNA-methylation profiling and exome sequencing (ES). Copy number analyses revealed aneuploidies typical for ERMS including (partial) gains of chromosomes 2, 3, 7, 8, 12, 15, and 20 and 3 focal deletions of chromosome 11p. DNA methylation profiling mapped the case to ERMS by a DNA methylation-based sarcoma classifier. Sequencing suggested gain of the wild-type KMT2D allele in the trisomy 12. Including our patient literature review identified 18 patients with Kabuki syndrome and a malignancy. Overall, the landscape of malignancies in patients with Kabuki syndrome was reminiscent of that of the pediatric population in general. Histopathological and molecular data were only infrequently reported and no report included next generation sequencing and/or DNA-methylation profiling. Although we found no strong arguments pointing towards KS as a tumor predisposition syndrome, based on the small numbers any relation cannot be fully excluded. Further planned studies including profiling of additional tumors and long term follow-up of KS-patients into adulthood could provide further insights.
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Verheggen K, Bhattacharya N, Verhaert M, Goossens B, Sciot R, Verhaert P. HistoSnap: A Novel Software Tool to Extract m/z-Specific Images from Large MSHC Datasets. Methods Mol Biol 2023; 2688:15-26. [PMID: 37410280 DOI: 10.1007/978-1-0716-3319-9_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
We describe an informatics tool for comfortable browsing through highly complex, multi-gigabyte mass spectrometry histochemistry (MSHC) datasets, via clever ion-specific image extraction.The package is developed particularly for the untargeted localization/discovery of biomolecules such as endogenous (neuro)secretory peptides on histological sections of biobanked formaldehyde-fixed paraffin-embedded (FFPE) samples straight from tissue banks.Atmospheric pressure-MALDI-Orbitrap MSHC data of sections through human pituitary adenomas in which two well-known human neuropeptides are detected are used as an example to demonstrate the key features of the novel software, named HistoSnap.
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Bhattacharya N, Nagornov K, Verheggen K, Verhaert M, Sciot R, Verhaert P. MS1-Based Data Analysis Approaches for FFPE Tissue Imaging of Endogenous Peptide Ions by Mass Spectrometry Histochemistry (MSHC). Methods Mol Biol 2023; 2688:187-202. [PMID: 37410294 DOI: 10.1007/978-1-0716-3319-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Ambiguous reports in the literature exist regarding the use and usefulness of formalin-fixed paraffin-embedded (FFPE) tissues in mass spectrometry imaging (MSI). Especially for the study of endogenous (non-tryptic) peptides, several studies have concluded that MSI on archived FFPE tissue bank samples is virtually impossible. We here illustrate that by employing a variant of MSI, called mass spectrometry histochemistry (MSHC), biomolecular tissue localization data are obtained that unequivocally comprise endogenous peptides. We here discuss different informatics steps in a data analysis workflow to help filter peptide-related features out of large and complex datasets generated by atmospheric pressure matrix-assisted laser desorption/ionization high-resolution (Orbitrap mass analyzer) MSHC. These include, in addition to accurate mass measurements, Kendrick mass defect filtering and isotopic distribution scrutiny.
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Mennens F, Van Herck Y, Sciot R, Vanden Bempt I, Boecxstaens V, Garmyn M, Bechter O. Melanoma cell plasticity poses diagnostic challenges: a case series. Melanoma Res 2022; 32:428-439. [PMID: 36125893 DOI: 10.1097/cmr.0000000000000852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Phenotype switching is an emerging concept in melanoma research and deals with the cancer cell plasticity. In this paper, we present five cases of patients with metastatic malignant melanoma where the tumor underwent dramatic morphological and immunohistochemical changes thereby mimicking other types of malignancies. The diagnosis of melanoma in all these cases was based on the mutational profile of the tumor assessed by next-generation sequencing compared to the primary lesion or local regional lymph nodes. These cases highlight the importance of thorough diagnostic measures in patients with metastatic melanoma who show progressive disease and where basic pathological assessment shows a diagnostic discrepancy.
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Decraene B, Antoranz A, Verbeke T, Vanmechelen M, Nazari P, Solie L, Dubroja N, Derweduwe M, Spans L, Bempt IV, Sciot R, De Smet F, De Vleeschouwer S. TMIC-37. SINGLE-CELL CHARACTERIZATION OF THE IMMUNE LANDSCAPE OF EXTREME LONG-TERM SURVIVORS WITH MALIGNANT GLIOMA. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.1081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Glioblastoma Multiforme (GBM) remains the most common malignant primary brain tumor with a dismal prognosis that rarely exceeds beyond two years despite extensive therapy, which consists of maximal safe surgical resection, radiotherapy and/or chemotherapy. Recently, it has become clear that GBM is not one homogeneous entity and that both intra-and intertumoral heterogeneity contribute significantly to differences in tumoral behavior which may consequently be responsible for differences in survival. Strikingly and despite its dismal prognosis, small fractions of GBM patients seem to display extreme extended survival compared to the large majority of patients. The underlying mechanisms for this peculiarity remain largely unknown however, even though emerging data suggest that both cancer cell-autonomous and microenvironmental factors and their interplay probably play an important role. We used high-dimensional, multiplexed immunohistochemistry to spatially, and cytometry by time-of-flight to quantitively, characterize the cell constitution and interactions within the tumor microenvironment (TME) in 21 extreme long-term survivors (living over 10 year) and 42 deeply matched controls and therefore short-term survivors (living under 1.5 year) on a single cell level. For all tumors (epi)genetic data was also collected. We identified a high level of both inter-and intrapatient heterogeneity defined by several distinct tumoral niches, as well as described interactions within these niches and with the surrounding infiltrating immune cells of the TME in GBM. Finally, by linking patient characteristics with the heterogeneous immune composition we are able to create an immune stratification that can be linked to patient survival in GBM. Therefore, this study is an essential initial step towards strategies to alter the TME in a favorable way with a personalized modulation strategy.
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De Visser Y, Panovska D, Cole B, Hermans L, Martinez AA, Nazari P, Van Trimpont M, Derweduwe M, Claeys A, De Vleeschouwer S, Solie L, Clement P, Sciot R, Verfaillie M, Daenekindt T, Bamps S, Van Vlierberghe P, De Smet F. BIOM-16. A MULTI-OMIC, FUNCTIONAL PRECISION ONCOLOGY METHOD TO IDENTIFY RESPONSIVE GLIOBLASTOMA TUMOR CELLS AT SINGLE CELL RESOLUTION. Neuro Oncol 2022. [PMCID: PMC9661181 DOI: 10.1093/neuonc/noac209.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Glioblastoma remains a highly malignant and intrinsically resistant brain tumor. Despite intensive research through which numerous potential druggable targets were identified, virtually all clinical trials of the past 20 years failed to improve the outcome for the vast majority of GBM patients. However, the identification of small subgroups of patients that showed an exceptional response across several trials, implies that, when selected more carefully, some GBM patients could probably still benefit from these therapies. Identifying these patients requires that suitable biomarkers are identified. In this project, we reassessed the molecular mechanisms of ten actionable compounds (selected from previously failed trials but for which exceptional responders had been observed) in a set of carefully selected patient-derived cell lines that were sensitive/resistant to the selected therapies. Moreover, to deal with tumor heterogeneity, we used a multi-omic functional precision oncology approach, combining scRNA-seq and CyTOF, to identify drug-specific biomarkers by comparing control and treated samples at single-cell resolution. By subsequently correlating the molecular signatures to eventual cytotoxicity profiles, we could identify intrinsically responsive tumor cells at the single-cell level within hours following drug exposure. Overall, this work lays the foundation for an actionable functional diagnostic assay that could help to identify eligible GBM patients in future clinical trials.
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Georgiesh T, Aggerholm-Pedersen N, Schöffski P, Zhang Y, Napolitano A, Bovée JVMG, Hjelle Å, Tang G, Spalek M, Nannini M, Swanson D, Baad-Hansen T, Sciot R, Hesla AC, Huang P, Dorleijn D, Haugland HK, Lacambra M, Skoczylas J, Pantaleo MA, Haas RL, Meza-Zepeda LA, Haller F, Czarnecka AM, Loong H, Jebsen NL, van de Sande M, Jones RL, Haglund F, Timmermans I, Safwat A, Bjerkehagen B, Boye K. Validation of a novel risk score to predict early and late recurrence in solitary fibrous tumour. Br J Cancer 2022; 127:1793-1798. [PMID: 36030294 PMCID: PMC9643389 DOI: 10.1038/s41416-022-01959-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Current risk models in solitary fibrous tumour (SFT) were developed using cohorts with short follow-up and cannot reliably identify low-risk patients. We recently developed a novel risk model (G-score) to account for both early and late recurrences. Here, we aimed to validate the G-score in a large international cohort with long-term follow-up. METHODS Data were collected from nine sarcoma referral centres worldwide. Recurrence-free interval (RFi) was the primary endpoint. RESULTS The cohort comprised 318 patients with localised extrameningeal SFTs. Disease recurrence occurred in 96 patients (33%). The estimated 5-year RFi rate was 72%, and the 10-year RFi rate was 52%. G-score precisely predicted recurrence risk with estimated 10-year RFi rate of 84% in low risk, 54% in intermediate risk and 36% in high risk (p < 0.001; C-index 0.691). The mDemicco (p < 0.001; C-index 0.749) and SalasOS (p < 0.001; C-index 0.674) models also predicted RFi but identified low-risk patients less accurate with 10-year RFi rates of 72% and 70%, respectively. CONCLUSIONS G-score is a highly significant predictor of early and late recurrence in SFT and is superior to other models to predict patients at low risk of relapse. A less intensive follow-up schedule could be considered for patients at low recurrence risk according to G-score.
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Parik S, Fernández-García J, Lodi F, De Vlaminck K, Derweduwe M, De Vleeschouwer S, Sciot R, Geens W, Weng L, Bosisio FM, Bergers G, Duerinck J, De Smet F, Lambrechts D, Van Ginderachter JA, Fendt SM. GBM tumors are heterogeneous in their fatty acid metabolism and modulating fatty acid metabolism sensitizes cancer cells derived from recurring GBM tumors to temozolomide. Front Oncol 2022; 12:988872. [PMID: 36338708 PMCID: PMC9635944 DOI: 10.3389/fonc.2022.988872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/16/2022] [Indexed: 07/30/2023] Open
Abstract
Glioblastoma is a highly lethal grade of astrocytoma with very low median survival. Despite extensive efforts, there is still a lack of alternatives that might improve these prospects. We uncovered that the chemotherapeutic agent temozolomide impinges on fatty acid synthesis and desaturation in newly diagnosed glioblastoma. This response is, however, blunted in recurring glioblastoma from the same patient. Further, we describe that disrupting cellular fatty acid homeostasis in favor of accumulation of saturated fatty acids such as palmitate synergizes with temozolomide treatment. Pharmacological inhibition of SCD and/or FADS2 allows palmitate accumulation and thus greatly augments temozolomide efficacy. This effect was independent of common GBM prognostic factors and was effective against cancer cells from recurring glioblastoma. In summary, we provide evidence that intracellular accumulation of saturated fatty acids in conjunction with temozolomide based chemotherapy induces death in glioblastoma cells derived from patients.
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De Sutter L, Wozniak A, Verreet J, Vanleeuw U, De Cock L, Linde N, Drechsler C, Esdar C, Sciot R, Schoeffski P. 1514P Anti-tumor effects of the novel KIT mutant inhibitor M4205 in gastrointestinal stromal tumor (GIST) xenograft models. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Van Renterghem B, Wozniak A, Castro PG, Franken P, Pencheva N, Sciot R, Schöffski P. Enapotamab Vedotin, an AXL-Specific Antibody-Drug Conjugate, Demonstrates Antitumor Efficacy in Patient-Derived Xenograft Models of Soft Tissue Sarcoma. Int J Mol Sci 2022; 23:7493. [PMID: 35886842 PMCID: PMC9322120 DOI: 10.3390/ijms23147493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/16/2022] Open
Abstract
Doxorubicin (doxo) remains the standard of care for patients with advanced soft tissue sarcoma (STS), even though response rates to doxo are only around 14% to 18%. We evaluated enapotamab vedotin (EnaV), an AXL-specific antibody-drug conjugate (ADC), in a panel of STS patient-derived xenografts (PDX). Eight models representing multiple STS subtypes were selected from our STS PDX platform (n = 45) by AXL immunostaining on archived passages. Models were expanded by unilateral transplantation of tumor tissue into the left flank of 20 NMRI nu/nu mice. Once tumors were established, mice were randomized into an EnaV treatment group, or a group treated with isotype control ADC. Treatment efficacy was assessed by tumor volume evaluation, survival analysis, and histological evaluation of tumors, and associated with AXL expression. EnaV demonstrated significant tumor growth delay, regression, and/or prolonged survival compared to isotype control ADC in 5/8 STS PDX models investigated. Experimental passages of responding models were all found positive for AXL at varying levels, but no linear relationship could be identified between the level of expression and level of response to EnaV. One model was found negative for AXL on experimental passage and did not respond to EnaV. This study provides a preclinical rationale for the evaluation of AXL-targeting ADCs in the treatment of AXL-expressing sarcomas.
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