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Gelineau NU, van Barneveld A, Samim A, Van Zogchel L, Lak N, Tas ML, Matser Y, Mavinkurve-Groothuis AMC, van Grotel M, Zsiros J, van Eijkelenburg NKA, Knops RRG, van Ewijk R, Langenberg KPS, Krijger RD, Hiemcke-Jiwa LS, Van Paemel R, Cornelli L, De Preter K, De Wilde B, Van Der Schoot E, Tytgat G. Case series on clinical applications of liquid biopsy in pediatric solid tumors: towards improved diagnostics and disease monitoring. Front Oncol 2023; 13:1209150. [PMID: 37664065 PMCID: PMC10473251 DOI: 10.3389/fonc.2023.1209150] [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: 04/20/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Background and aims Solid tumors account for about 30% of all pediatric cancers. The diagnosis is typically based on histological and molecular analysis of a primary tumor biopsy. Liquid biopsies carry several advantages over conventional tissue biopsy. However, their use for genomic analysis and response monitoring of pediatric solid tumors is still in experimental stages and mostly performed retrospectively without direct impact on patient management. In this case series we discuss six clinical cases of children with a solid tumor for whom a liquid biopsy assay was performed and demonstrate the potential of liquid biopsy for future clinical decision making. Methods We performed quantitative real-time PCR (RT-qPCR), droplet digital PCR (ddPCR) or reduced representation bisulphite sequencing of cell-free DNA (cfRRBS) on liquid biopsies collected from six pediatric patients with a solid tumor treated between 2017 and 2023 at the Princess Máxima Center for Pediatric Oncology in the Netherlands. Results were used to aid in clinical decision making by contribution to establish a diagnosis, by prognostication and response to therapy monitoring. Results In three patients cfRRBS helped to establish the diagnosis of a rhabdomyosarcoma, an Ewing sarcoma and a neuroblastoma (case 1-3). In two patients, liquid biopsies were used for prognostication, by MYCN ddPCR in a patient with neuroblastoma and by RT-qPCR testing rhabdomyosarcoma-specific mRNA in bone marrow of a patient with a rhabdomyosarcoma (case 4 and 5). In case 6, mRNA testing demonstrated disease progression and assisted clinical decision making. Conclusion This case series illustrates the value of liquid biopsy. We further demonstrate and recommend the use of liquid biopsies to be used in conjunction with conventional methods for the determination of metastatic status, prognostication and monitoring of treatment response in patients with pediatric solid tumors.
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Affiliation(s)
- Nina U. Gelineau
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | | | - Atia Samim
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Lieke Van Zogchel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | - Nathalie Lak
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | - Michelle L. Tas
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Yvette Matser
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Martine van Grotel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Jószef Zsiros
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Rutger R. G. Knops
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Roelof van Ewijk
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Ronald De Krijger
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Laura S. Hiemcke-Jiwa
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ruben Van Paemel
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University, Ghent, Belgium
- Research Institute, Ghent University, Ghent, East Flanders, Belgium
| | - Lotte Cornelli
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Katleen De Preter
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Research Institute, Ghent University, Ghent, East Flanders, Belgium
- VIB-UGent Center for Medical Biotechnology, Gent, Belgium
| | - Bram De Wilde
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University, Ghent, Belgium
- Research Institute, Ghent University, Ghent, East Flanders, Belgium
| | - Ellen Van Der Schoot
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
| | - Godelieve Tytgat
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Department of Experimental Immunohematology, Sanquin Research, Amsterdam, Netherlands
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Dehner CA, Geiersbach K, Rowsey R, Murugan P, Broski SM, Meis JM, Rosenberg AE, Folpe AL. Rhabdomyosarcoma Arising in Inflammatory Rhabdomyoblastic Tumor: A Genetically Distinctive Subtype of Rhabdomyosarcoma. Mod Pathol 2023; 36:100131. [PMID: 36966552 DOI: 10.1016/j.modpat.2023.100131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/05/2023] [Indexed: 03/03/2023]
Abstract
"Inflammatory rhabdomyoblastic tumor" (IRMT) is a recently coined name for a distinctive soft tissue neoplasm characterized by slow growth, a dense histiocytic infiltrate, scattered, bizarre-appearing tumor cells with morphologic and immunohistochemical evidence of skeletal muscle differentiation, a near-haploid karyotype with retained biparental disomy of chromosomes 5 and 22, and usually indolent behavior. There are 2 reports of rhabdomyosarcoma (RMS) arising in IRMT. We studied the clinicopathologic and cytogenomic features of 6 cases of IRMT with progression to RMS. Tumors occurred in the extremities of 5 men and 1 woman (median patient age, 50 years; median tumor size, 6.5 cm). Clinical follow-up (6 patients: median, 11 months; range 4-163 months) documented local recurrence and distant metastases in 1 and 5 of 6 patients, respectively. Therapy included complete surgical resection (4 patients) and adjuvant/neoadjuvant chemo/radiotherapy (6 patients). One patient died of disease, 4 were alive with metastatic disease, and one was without evidence of disease. All primary tumors contained conventional IRMT. Progression to RMS appeared as follows: (1) overgrowth of monomorphic rhabdomyoblasts with diminished histiocytes, (2) monomorphic spindle cell morphology with variably pleomorphic rhabdomyoblasts and low mitotic activity, or (3) morphologically undifferentiated spindle cell and epithelioid sarcoma. All but one were diffusely desmin-positive, with more limited MyoD1/myogenin expression. All RMS arising in IRMT, either primary or metastatic, demonstrated widespread loss of heterozygosity with retained heterozygosity of chromosomes 5 and 20, and all but one displayed additional gains and losses involving loci containing oncogenes/ tumor suppressor genes, most often CDKN2A and CDKN2B. RMS arising in IRMT have unique clinicopathologic and cytogenomic features, warranting classification as a distinct, potentially aggressive RMS subtype. It should be distinguished from other RMSs, particularly fusion-driven spindle cell RMS and pleomorphic RMS.
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Affiliation(s)
- Carina A Dehner
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Katherine Geiersbach
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ross Rowsey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota
| | | | - Jeanne M Meis
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew E Rosenberg
- Department of Pathology, Miller School of Medicine, University of Miami, Miami Florida
| | - Andrew L Folpe
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
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Zhang P, Huang L, Li X, Hu F, Niu X, Sun Y, Yao W, Tian W. NF1-Related MicroRNA Gene Polymorphisms and the Susceptibility to Soft Tissue Sarcomas: A Case-Control Study. DNA Cell Biol 2023; 42:229-238. [PMID: 36989515 DOI: 10.1089/dna.2022.0552] [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: 03/31/2023] Open
Abstract
Soft tissue sarcomas (STS) are rare malignant tumors of mesenchymal origin, which are easy to metastasize and relapse and are a great threat to human health. In our previous study, the abnormal expression of neurofibromin 1 (NF1) is observed in tumor tissue of STS, and the NF1 gene is regulated by miRNAs. The study aimed to assess the association between NF1-related miRNA gene polymorphisms and the risk of STS. In this case-control study, the information and peripheral blood were collected from 169 patients with STS and 170 healthy controls. Six single-nucleotide polymorphisms of the NF1-related miRNAs were investigated and genotyped using a Sequenom MassARRAY® matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. The association between the polymorphisms and the risk of STS was estimated using unconditional logistic regression analysis. There was a significant statistical difference on genotype distribution of miR-199a2 rs12139213 between the case group and the control group (p = 0.026). Comparing with individuals with wild-type AA, individuals with the AT/TT genotype had a 1.753-fold (odds ratio [OR] = 1.753, 95% confidence interval [CI] = 1.090-2.819, p = 0.021) increased risk of STS and 1.907-fold (OR = 1.907, 95% CI = 1.173-3.102, p = 0.009) increased risk of STS adjusted for age and smoking status. Individuals with the AG/GG genotype for miR24-3p rs4743988 displayed a significantly reduced risk of STS compared with individuals with homozygous mutations AA (OR = 0.605, 95% CI = 0.376-0.973, p = 0.038). Individuals carrying the AT/TT genotype for miR-199a2 rs12139213 or the AA genotype for miR24-3p rs4743988 may be susceptible to STS, which could be potential biomarkers for the diagnosis of STS.
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Affiliation(s)
- Peng Zhang
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
| | - Lingling Huang
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
| | - Xinling Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Fulan Hu
- Department of Biostatistics and Epidemiology, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Xiaoying Niu
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
| | - Yang Sun
- Department of Orthopaedic Oncology Surgery, Beijing Jishuitan Hospital, Peking University, Beijing, China
| | - Weitao Yao
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
| | - Wen Tian
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
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Li Y, Li D, Wang J, Tang J. Epithelioid and spindle rhabdomyosarcoma with TFCP2 rearrangement in abdominal wall: a distinctive entity with poor prognosis. Diagn Pathol 2023; 18:41. [PMID: 36998041 PMCID: PMC10061849 DOI: 10.1186/s13000-023-01330-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 03/21/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Epithelioid and spindle rhabdomyosarcoma (ES-RMS) with TFCP2 rearrangement is a recently discovered rare variant of rhabdomyosarcoma composed of epithelioid and spindle cells, because it shows extraordinarily adverse prognosis and is easily misdiagnosed as other epithelioid or spindle cell tumors. METHODS A rare case of ES-RMS with TFCP2 rearrangement was presented and English literatures in Pubmed online up to 01 July 2022 were gathered by two authors for a systematic review according to the inclusion and exclusion criteria. CASE PRESENTATION/RESULTS We report a case of ES-RMS in an early 30s-years-old female, the neoplastic cells are remarkably immunoreactive with CK(AE1/AE3), and partially with ALK protein. Unexpectedly, the tumor shows TFCP2 rearrangement with coexistence of increased copy numbers of EWSR1 and ROS1 gene and MET gene mutation. Besides, Next-generation sequencing for genetic mutational profiling revealed frequent MET exon14 mutations in chromosome 7, most of which are C > T nonsynonymous SNV, and exon42 of ROS1 in chromosome 6 showed frequent G > T mutation up to 57.54%. In addition, neither MyoD1 mutation nor gene fusions were detected. Moreover, the patient shows high tumor mutational burden (TMB) up to 14.11 counts/Mb. Finally, as many cases of ES-RMS including our case had local progression or metastasis, we find, similar to epithelioid rhabdomyosarcoma (median survival time is 10 month), ES-RMS shows a more aggressive behavior and adverse prognosis (median survival time is 17 month) than spindle cell/sclerosing rhabdomyosarcoma (median survival time is 65 month) according previous studies. CONCLUSIONS ES-RMS with TFCP2 rearrangement is a rare malignant tumor and easily confused with other epithelioid or spindle cell tumors, it may harbor additional gene alteration in addition to TFCP2 rearrangement, such as MET mutation, increased copy numbers of EWSR1 and ROS1 gene, high TMB. Most importantly, it may show very poor outcome with extensive metastasis.
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Affiliation(s)
- Yuan Li
- Department of Pediatrics, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310000, Hangzhou, Zhejiang, China.
| | - Dan Li
- Department of Pediatrics, the Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, 310000, Hangzhou, Zhejiang, China
| | - Jingyu Wang
- Department of Pathology, Ministry of scientific research and discipline construction, Affiliated Hospital of Jiaxing University, The First Hospital of Jiaxing, 314001, Jiaxing, Zhejiang, China
| | - Jinlong Tang
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009, Hangzhou, Zhejiang, China
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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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Affiliation(s)
- Sietse M Aukema
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Mari F C M van den Hout
- Department of Pathology, Research Institute GROW, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sonja Dahlum
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
| | - Morten Hillmer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Julia Kolarova
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Raf Sciot
- Department of Pathology, University Hospital, University of Leuven, 3000, Louvain, Belgium
| | - Dina A Schott
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands
- Department of Pediatrics, Zuyderland Medical Center, Heerlen, The Netherlands
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Constance T R M Stumpel
- Department of Clinical Genetics, Maastricht University Medical Centre (MUMC+), PO Box 5800, 6202 AZ, Maastricht, The Netherlands.
- Department of Clinical Genetics and GROW-School for Oncology & Developmental Biology, Maastricht University Medical Center+, Maastricht, The Netherlands.
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Ciceri S, Carenzo A, Iannó MF, Bertolotti A, Morosi C, Luksch R, Spreafico F, Collini P, Radice P, Massimino M, De Cecco L, Perotti D. Gene expression-based dissection of inter-histotypes, intra-histotype and intra-tumor heterogeneity in pediatric tumors. Sci Rep 2022; 12:17837. [PMID: 36284197 PMCID: PMC9596396 DOI: 10.1038/s41598-022-20536-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/14/2022] [Indexed: 02/07/2023] Open
Abstract
Intra-tumor heterogeneity (ITH) fosters tumor evolution, resistance to therapy, and relapse. Recently, many evidence have been accumulated on the occurrence of genetic ITH in pediatric cancers. With this study we aimed to address the downstream effects that genetic and epigenetic ITH, and tumor-microenvironment interactions may produce within a tumor mass. To this aim, we investigated by high-throughput gene expression multiple samples of 5 hepatoblastomas, 5 neuroblastomas, 5 rhabdomyosarcomas, and 5 Wilms tumors. Principal component analysis, single sample hallmark gene sets analysis, and weighted gene co-expression network analysis were performed on gene expression data. We observed that the different tumors clustered by histotype, and then by case, and in addition, a variable degree of ITH was visible in all the investigated cases. The ITH highlighted in this study can represent a challenge in tumor treatment since we demonstrated that different druggable hallmarks and targets may be heterogeneously present within the same tumor mass, and this can potentially lead to therapeutic failure. Despite this heterogeneity, we could highlight some commonalities among the different histotypes investigated, supporting the feasibility to move in the clinic from a histotype-driven to a target-driven, sometimes agnostic, approach at least in some cases.
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Affiliation(s)
- Sara Ciceri
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Andrea Carenzo
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Maria Federica Iannó
- grid.417893.00000 0001 0807 2568Integrated Biology Platform, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Alessia Bertolotti
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Carlo Morosi
- grid.417893.00000 0001 0807 2568Department of Radiology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Roberto Luksch
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Filippo Spreafico
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paola Collini
- grid.417893.00000 0001 0807 2568Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Paolo Radice
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Maura Massimino
- grid.417893.00000 0001 0807 2568Pediatric Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Loris De Cecco
- grid.417893.00000 0001 0807 2568Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
| | - Daniela Perotti
- grid.417893.00000 0001 0807 2568Molecular Bases of Genetic Risk and Genetic Testing Unit, Department of Research, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, 20133 Milano, Italy
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Zhang P, Huang L, Ma P, Niu X. Altered Expressions of NF1 and NF1-Related microRNAs as Biomarkers in the Diagnosis of Undifferentiated Pleomorphic Sarcoma. Front Genet 2022; 13:870191. [PMID: 35559021 PMCID: PMC9086456 DOI: 10.3389/fgene.2022.870191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/11/2022] [Indexed: 11/29/2022] Open
Abstract
Objective: Undifferentiated pleomorphic sarcoma (UPS) is a highly malignant, aggressive, and pleomorphic subtype of soft tissue sarcoma in adults. However, UPS is difficult to be diagnosed due to the lack of specific morphological and immunophenotypic features. Here, we aimed to identify new biomarkers for the diagnosis of UPS. Methods: The mRNA and protein expression of neurofibromin 1 (NF1) in 68 pairs of UPS and adjacent normal tissues were detected by qRT-PCR and immunohistochemistry, and the correlation between the NF1 protein expression and clinicopathological characteristics was analyzed. Then, differentially expressed microRNAs (DE miRNAs) were identified between the UPS tumor tissue and matched adjacent normal tissue using Hisep sequencing, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). The DE miRNAs of the regulating NF1 gene were also identified using the TargetScan and miRanda databases and validated by qRT-PCR. Results: Compared with the adjacent normal tissue, both mRNA and protein expressions of NF1 in the UPS tumor tissue were significantly decreased, and the positive rate of NF1 protein was associated with the tumor size, metastasis, and recurrence. A total of 125 known DE miRNAs were identified from the screened miRNAs based on | log2(Fold Change) ≥5 and p-value < 0.05 (A total of 82 upregulated and 43 downregulated DE miRNAs in the UPS tissue). Target genes regulated by the DE miRNAs were enriched in pathways of metabolisms, RNA degradation, PI3K-Akt, and Rap1 pathway. In total, 11 miRNAs which were predicted to regulate the NF1 gene were screened. After verification, the relative expressions of hsa-miR-199a-3p and hsa-miR-34a-5p were increased and decreased in the UPS tumor tissue compared with those in the adjacent normal tissue, respectively. Conclusion: NF1 and NF1-related microRNAs including hsa-miR-199a-3p and hsa-miR-34a-5p may be novel biomarkers in the diagnosis of undifferentiated pleomorphic sarcoma (UPS).
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Affiliation(s)
- Peng Zhang
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
| | - Lingling Huang
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
| | - Pengwei Ma
- Department of Toxicology, College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xiaoying Niu
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, China
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8
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Panagopoulos I, Gorunova L, Andersen K, Lund-Iversen M, Tafjord S, Micci F, Heim S. Fusion of the Paired Box 3 ( PAX3) and Myocardin ( MYOCD) Genes in Pediatric Rhabdomyosarcoma. Cancer Genomics Proteomics 2021; 18:723-734. [PMID: 34697065 DOI: 10.21873/cgp.20293] [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: 07/05/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Fusions of the paired box 3 gene (PAX3 in 2q36) with different partners have been reported in rhabdomyosarcomas and biphenotypic sinonasal sarcomas. We herein report the myocardin (MYOCD on 17p12) gene as a novel PAX3-fusion partner in a pediatric tumor with adverse clinical outcome. MATERIALS AND METHODS A rhabdomyo-sarcoma found in a 10-year-old girl was studied using a range of genetic methodologies. RESULTS The karyotype of the tumor cells was 48,XX,add(2)(q11),+del(2)(q35),add(3)(q?25),-7, del(8)(p 21),-15, add(17)(p 11), + 20, +der(?) t(?; 15) (?;q15),+mar[8]/46,XX[2]. Fluorescence in situ hybridization detected PAX3 rearrangement whereas array comparative genomic hybridization revealed genomic imbalances affecting hundreds of genes, including MYCN, MYC, FOXO3, and the tumor suppressor gene TP53. A PAX3-MYOCD fusion transcript was found by RNA sequencing and confirmed by Sanger sequencing. CONCLUSION The investigated rhabdomyosarcoma carried a novel PAX3-MYOCD fusion gene and extensive additional aberrations affecting the allelic balance of many genes, among them TP53 and members of MYC and FOXO families of transcription factors.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Marius Lund-Iversen
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Svetlana Tafjord
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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9
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Mitra S, Sydow S, Magnusson L, Piccinelli P, Törnudd L, Øra I, Ljungman G, Sandgren J, Gisselsson D, Mertens F. Amplification of ERBB2 (HER2) in embryonal rhabdomyosarcoma: A potential treatment target in rare cases? Genes Chromosomes Cancer 2021; 61:5-9. [PMID: 34418214 DOI: 10.1002/gcc.22996] [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: 07/20/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 11/11/2022] Open
Abstract
The ERBB2 gene encodes a receptor tyrosine kinase also known as HER2. The gene is amplified and overexpressed in one-fifth of breast carcinomas; patients with such tumors benefit from targeted treatment with trastuzumab or other drugs blocking the receptor. In addition, ERBB2 has been shown to be amplified and/or overexpressed in a variety of other malignancies. Notably, both alveolar and embryonal rhabdomyosarcoma (RMS), especially in children, often show increased expression of ERBB2. Although high-level amplification of the gene has not been described in RMS, its frequent expression at the cell surface of RMS cells has been exploited for chimeric antigen receptor T-cell (CAR T)-based treatment strategies. We here describe two cases of pediatric, fusion-negative embryonal RMS with high-level amplification of the ERBB2 gene. One patient is currently treated with conventional chemotherapy for a recently detected standard risk RMS, whereas the other patient died from metastatic disease. Both tumors displayed focal amplicons (210 and 274 Kb, respectively) in chromosome band 17q12, with proximal and distal borders corresponding to those typically seen in breast cancer. In both tumors, the ERBB2 amplicon correlated with high expression at the RNA and protein levels. Thus, breast cancer-like ERBB2 amplification is a very rare, but recurrent feature of pediatric RMS, and should be exploited as an alternative treatment target.
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Affiliation(s)
- Shamik Mitra
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Saskia Sydow
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Linda Magnusson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Paul Piccinelli
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Lisa Törnudd
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Ingrid Øra
- Department of Pediatric Oncology, Skåne University Hospital, Lund, Sweden
| | - Gustaf Ljungman
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Johanna Sandgren
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - David Gisselsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
| | - Fredrik Mertens
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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10
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HER Tyrosine Kinase Family and Rhabdomyosarcoma: Role in Onset and Targeted Therapy. Cells 2021; 10:cells10071808. [PMID: 34359977 PMCID: PMC8305095 DOI: 10.3390/cells10071808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 12/29/2022] Open
Abstract
Rhabdomyosarcomas (RMS) are tumors of the skeletal muscle lineage. Two main features allow for distinction between subtypes: morphology and presence/absence of a translocation between the PAX3 (or PAX7) and FOXO1 genes. The two main subtypes are fusion-positive alveolar RMS (ARMS) and fusion-negative embryonal RMS (ERMS). This review will focus on the role of receptor tyrosine kinases of the human epidermal growth factor receptor (EGFR) family that is comprised EGFR itself, HER2, HER3 and HER4 in RMS onset and the potential therapeutic targeting of receptor tyrosine kinases. EGFR is highly expressed by ERMS tumors and cell lines, in some cases contributing to tumor growth. If not mutated, HER2 is not directly involved in control of RMS cell growth but can be expressed at significant levels. A minority of ERMS carries a HER2 mutation with driving activity on tumor growth. HER3 is frequently overexpressed by RMS and can play a role in the residual myogenic differentiation ability and in resistance to signaling-directed therapy. HER family members could be exploited for therapeutic approaches in two ways: blocking the HER member (playing a driving role for tumor growth with antibodies or inhibitors) and targeting expressed HER members to vehiculate toxins or immune effectors.
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11
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Tsuchiya R, Yoshimatsu Y, Noguchi R, Sin Y, Ono T, Sei A, Takeshita F, Sugaya J, Nakatani F, Yoshida A, Ohtori S, Kawai A, Kondo T. Establishment and characterization of NCC-ssRMS2-C1: a novel patient-derived cell line of spindle cell/sclerosing rhabdomyosarcoma. Hum Cell 2021; 34:1569-1578. [PMID: 34164773 DOI: 10.1007/s13577-021-00569-1] [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: 05/09/2021] [Accepted: 06/15/2021] [Indexed: 11/24/2022]
Abstract
Spindle cell/sclerosing rhabdomyosarcoma (ssRMS) is a rare subtype of rhabdomyosarcoma (RMS) that has fascicular spindle cell and/or sclerosing morphology. SsRMS has a diverse molecular background and is categorized into three groups: congenital/infantile ssRMS with a gene fusion involving the NCOA2 and VGLL2, ssRMS with the MYOD1 mutation, and ssRMS with no recurrent identifiable genetic alterations. Because ssRMS is a newly defined disease concept of RMS, the optimal treatment methods have not been determined. This results in unfavorable prognosis and consequently signals the urgent need for continuous research. Patient-derived cell lines are essential tools in basic and translational research. However, only two ssRMS cell lines with the MYOD1 mutation have been reported to date. Thus, we established a novel ssRMS cell line named NCC-ssRMS2-C1 using a surgically resected tumor tissue from an adult ssRMS patient. NCC-ssRMS2-C1 cells retained the copy number alterations corresponding to the original tumor and are categorized into the group with no recurrent identifiable genetic alterations. NCC-ssRMS2-C1 cells demonstrated constant proliferation, spheroid formation, and capability for invasion in vitro, reflecting the malignant features of the original tumor tissue. In a drug screening test, ssRMS demonstrated remarkable sensitivity to romidepsin, trabectedin, actinomycin D, and bortezomib. Hence, we conclude that the NCC-ssRMS2-C1 cell line is the first ssRMS cell line which belongs to the group with no recurrent identifiable genetic alterations, and it will be a useful resource in both basic and translational studies for ssRMS.
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Affiliation(s)
- Ryuto Tsuchiya
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.,Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Yuki Yoshimatsu
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Rei Noguchi
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yooksil Sin
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Takuya Ono
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akane Sei
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Fumitaka Takeshita
- Department of Translational Oncology, Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Jun Sugaya
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Fumihiko Nakatani
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Seiji Ohtori
- Department of Orthopaedic Surgery, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Akira Kawai
- Department of Musculoskeletal Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tadashi Kondo
- Division of Rare Cancer Research, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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12
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Gorunova L, Bjerkehagen B, Micci F, Heim S, Panagopoulos I. Cytogenetic and Molecular Study of an Adult Sclerosing Rhabdomyosarcoma of the Extremity: MYOD1-mutation and Clonal Evolution. Cancer Genomics Proteomics 2021; 17:563-569. [PMID: 32859634 DOI: 10.21873/cgp.20212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Spindle cell/sclerosing rhabdomyosarcoma is a genomically heterogeneous, uncommon subtype of rhabdomyosarcoma, particularly rare in adults. Its MYOD1-mutant variant is aggressive irrespective of age. Cytogenetic data on spindle cell/sclerosing rhabdomyosarcoma are sparse and disparate. MATERIALS AND METHODS Cytogenetic and molecular analyses were performed on an adult sclerosing rhabdomyosarcoma. RESULTS The karyotype of the sclerosing rhabdomyosarcoma displayed clonal evolution corresponding to two hyperdiploid clones: 48,XY,+i(19)(p10),+22/48,idem,der(9)t(2;9)(q21~22;p21). The changes were gain of chromosome 19 with the overrepresentation of 19p arm, gain of chromosome 22, gain of the 2q arm, and loss of 9p21. Mutation analysis revealed a homozygous c.T365G (p.L122R) mutation of the MYOD1 gene, but none of PIK3CA. CONCLUSION To our knowledge, this is the first adult MYOD1-mutant sclerosing rhabdomyosarcoma studied cytogenetically. The only other reported sclerosing rhabdomyosarcoma with MYOD1 mutation and abnormal karyotype was pediatric. Since these tumors are highly aggressive, further studies unravelling their cytogenetic and molecular characteristics are warranted.
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Affiliation(s)
- Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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13
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"Inflammatory Leiomyosarcoma" and "Histiocyte-rich Rhabdomyoblastic Tumor": a clinicopathological, immunohistochemical and genetic study of 13 cases, with a proposal for reclassification as "Inflammatory Rhabdomyoblastic Tumor". Mod Pathol 2021; 34:758-769. [PMID: 33318583 DOI: 10.1038/s41379-020-00703-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/08/2022]
Abstract
Inflammatory leiomyosarcoma (ILMS), defined as "a malignant neoplasm showing smooth muscle differentiation, a prominent inflammatory infiltrate, and near-haploidization", is a very rare soft tissue tumor with a generally favorable prognosis. The morphologic features of "histiocyte-rich rhabdomyoblastic tumor" (HRRMT) are similar to those of ILMS, although this lesion shows by definition a skeletal muscle phenotype. Recent gene expression profiling and immunohistochemical studies have also suggested that ILMS and HRRMT may be related. We studied the clinicopathologic, immunohistochemical and genetic features of four cases previously classified as ILMS and nine classified as HRRMT. Tumors from both groups tended to occur in the deep soft tissues of the extremities of young to middle-aged males and exhibited indolent behavior. Morphologically, all were well-circumscribed, often encapsulated, and showed a striking histiocyte-rich inflammatory infiltrate admixed with variably pleomorphic tumor cells showing spindled and epithelioid to rhabdoid morphology, eosinophilic cytoplasm, and prominent nucleoli, but few, if any, mitotic figures. Immunohistochemically, the tumor cells expressed desmin, alpha-smooth muscle actin, and the rhabdomyoblastic markers PAX7, MyoD1, and myogenin. H-caldesmon expression was absent in all cases, using the specific h-CD antibody. Karyotypic study (1 HRRMT) and genome-wide copy number analysis (7 HRRMT, OncoScan SNP assay), revealed near-haploidization in four cases, with subsequent genome doubling in one, an identical phenotype to that seen in ILMS. We propose reclassification of ILMS and HRRMT as "inflammatory rhabdomyoblastic tumor", a name which accurately describes the salient morphologic and immunohistochemical features of this distinctive tumor, as well as its intermediate (rarely metastasizing) clinical behavior.
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14
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Feng J, Ouyang Y, Xu D, He Q, Liu D, Fan X, Xu P, Mo Y. Genetic variants in MIR17HG affect the susceptibility and prognosis of glioma in a Chinese Han population. BMC Cancer 2020; 20:976. [PMID: 33036577 PMCID: PMC7547478 DOI: 10.1186/s12885-020-07417-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 09/15/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND lncRNA MIR17HG was upregulated in glioma, and participated in promoting proliferation, migration and invasion of glioma. However, the role of MIR17HG polymorphisms in the occurrence and prognosis of glioma is still unclear. METHODS In the study, 592 glioma patients and 502 control subjects were recruited. Agena MassARRAY platform was used to detect the genotype of MIR17HG polymorphisms. Logistic regression analysis was used to evaluate the relationship between MIR17HG single nucleotide polymorphisms (SNPs) and glioma risk by odds ratio (OR) and 95% confidence intervals (CIs). Kaplan-Meier curves, Cox hazards models were performed for assessing the role of these SNPs in glioma prognosis by hazard ratios (HR) and 95% CIs. RESULTS We found that rs7318578 (OR = 2.25, p = 3.18 × 10- 5) was significantly associated with glioma susceptibility in the overall participants. In the subgroup with age < 40 years, rs17735387 (OR = 1.53, p = 9.05 × 10- 3) and rs7336610 (OR = 1.35, p = 0.016) were related to the higher glioma susceptibility. More importantly, rs17735387 (HR = 0.82, log-rank p = 0.026) were associated with the longer survival of glioma patients. The GA genotype of rs17735387 had a better overall survival (HR = 0.75, log-rank p = 0.013) and progression free survival (HR = 0.73, log-rank p = 0.032) in patients with I-II glioma. We also found that rs72640334 was related to the poor prognosis (HR = 1.49, Log-rank p = 0.035) in female patients. In the subgroup of patients with age ≥ 40 years, rs17735387 was associated with a better prognosis (HR = 0.036, Log-rank p = 0.002). CONCLUSION Our study firstly reported that MIR17HG rs7318578 was a risk factor for glioma susceptibility and rs17735387 was associated with the longer survival of glioma among Chinese Han population, which might help to enhance the understanding of MIR17HG gene in gliomagenesis. In subsequent studies, we will continue to collect samples and follow up to further validate our findings and further explore the function of these MIR17HG SNPs in glioma in a larger sample size.
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Affiliation(s)
- Jigao Feng
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Yibin Ouyang
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Dedong Xu
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Qinglong He
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Dayuan Liu
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Xudong Fan
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Pengxiang Xu
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China
| | - Yehe Mo
- Department of Neurosurgery, the Second Affiliated Hospital of Hainan Medical University, #48 Baishuitang Road, Haikou, 570311, Hainan, China.
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15
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Gleditsch K, Peñas J, Mercer D, Umrigar A, Briscoe J, Stark M, Tsien F, Hollenbach AD. Intratumoral Translocation Positive Heterogeneity in Pediatric Alveolar Rhabdomyosarcoma Tumors Correlates to Patient Survival Prognosis. Front Cell Dev Biol 2020; 8:564136. [PMID: 33072748 PMCID: PMC7530338 DOI: 10.3389/fcell.2020.564136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/01/2020] [Indexed: 11/17/2022] Open
Abstract
Alveolar rhabdomyosarcoma (ARMS) is characterized by one of three translocation states: t(2;13) (q35;q14) producing PAX3-FOXO1, t(1;13) (p36;q14) producing PAX7-FOXO1, or translocation-negative. Tumors with t(2;13) are associated with greater disease severity and mortality than t(1;13) positive or translocation negative patients. Consistent with this fact, previous work concluded that a molecular analysis of RMS translocation status is essential for the accurate determination of prognosis and diagnosis. However, despite this knowledge, most diagnoses rely on histology and in some cases utilize fluorescence in situ hybridization (FISH) probes unable to differentiate between translocation products. Along these same lines, diagnostic RT-PCR analysis, which can differentiate translocation status, is unable to determine intratumoral translocation heterogeneity, making it difficult to determine if heterogeneity exists and whether correlations exist between this heterogeneity and patient outcomes. Using newly developed FISH probes, we demonstrate that intratumoral heterogeneity exists in ARMS tumors with respect to the presence or absence of the translocation product. We found between 3 and 98% of cells within individual tumor samples contained a translocation event with a significant inverse correlation (R2 = 0.66, p = 0.001) between the extent of intratumoral translocation heterogeneity and failure-free survival of patients. Taken together, these results provide additional support for the inclusion of the molecular analysis of these tumors and expand on this idea to support determining the extent of intratumoral translocation heterogeneity in the diagnosis of ARMS to improve diagnostic and prognostic indicators for patients with these tumors.
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Affiliation(s)
- Katrina Gleditsch
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States.,Division of Pediatric Hematology/Oncology, Children's Hospital of New Orleans, New Orleans, LA, United States
| | - Jorge Peñas
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Danielle Mercer
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Ayesha Umrigar
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - James Briscoe
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Matthew Stark
- Department of Pathology, Children's Hospital of New Orleans, New Orleans, LA, United States
| | - Fern Tsien
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Andrew D Hollenbach
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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16
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Tolomeo D, Agostini A, Macchia G, L'Abbate A, Severgnini M, Cifola I, Frassanito MA, Racanelli V, Solimando AG, Haglund F, Mertens F, Storlazzi CT. BL1391: an established cell line from a human malignant peripheral nerve sheath tumor with unique genomic features. Hum Cell 2020; 34:238-245. [PMID: 32856169 DOI: 10.1007/s13577-020-00418-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive tumors, accounting for around 5% of all soft tissue sarcomas. A better understanding of the pathogenesis of these tumors and the development of effective treatments are needed. In this context, established tumor cell lines can be very informative, as they may be used for in-depth molecular analyses and improvement of treatment strategies. Here, we present the genomic and transcriptomic profiling analysis of a MPNST cell line (BL1391) that was spontaneously established in our laboratory from a primary tumor that had not been exposed to genotoxic treatment. This cell line shows peculiar genetic features, such as a large marker chromosome composed of high-copy number amplifications of regions from chromosomes 1 and 11 with an embedded neocentromere. Moreover, the transcriptome profiling revealed the presence of several fusion transcripts involving the CACHD1, TNMA4, MDM4, and YAP1 genes, all of which map to the amplified regions of the marker. BL1391 could be a useful tool to study genomic amplifications and neocentromere seeding in MPNSTs and to develop new therapeutic strategies.
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Affiliation(s)
- Doron Tolomeo
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy
| | - Antonio Agostini
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Gemma Macchia
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy
| | - Alberto L'Abbate
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy.,Institute of Biomembranes, Bioenergetics, and Molecular Biotechnologies, National Research Council (IBIOM-CNR), 70125, Bari, Italy
| | - Marco Severgnini
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, 20090, Milan, Italy
| | - Ingrid Cifola
- Institute for Biomedical Technologies, National Research Council (ITB-CNR), Segrate, 20090, Milan, Italy
| | - Maria Antonia Frassanito
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy
| | - Antonio Giovanni Solimando
- Department of Biomedical Sciences and Human Oncology, Unit of Internal Medicine "Guido Baccelli", University of Bari Medical School, Piazza Giulio Cesare 11, 70124, Bari, Italy.,IRCCS Istituto Tumori "Giovanni Paolo II", 70124, Bari, Italy
| | - Felix Haglund
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics, Lund University and Skåne University Hospital, 221 85, Lund, Sweden
| | - Clelia Tiziana Storlazzi
- Department of Biology, University of Bari "Aldo Moro", Via G. Orabona no. 4, 70125, Bari, Italy.
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17
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Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma. Am J Surg Pathol 2020; 44:594-606. [PMID: 31913156 DOI: 10.1097/pas.0000000000001423] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Sclerosing epithelioid fibrosarcoma (SEF) is an aggressive soft tissue sarcoma. In the majority of cases, there is overexpression of MUC4, and most cases show EWSR1-CREB3L1 gene fusions. A subset of SEF displays composite histologic features of SEF and low-grade fibromyxoid sarcoma (LGFMS). These "hybrid" tumors are more likely to harbor the FUS-CREB3L2 fusion, which is also seen in most LGFMS. We, here, characterize a series of 8 soft tissue neoplasms with morphologic features highly overlapping with LGFMS and SEF but lacking MUC4 expression and EWSR1/FUS-CREB3L gene fusions. Seven tumors showed fusions of the YAP1 and KMT2A genes, and 1 had a fusion of PRRX1 and KMT2D; all but 1 case displayed reciprocal gene fusions. At gene expression profiling, YAP1 and KMT2A/PRRX1 and KMT2D tumors were distinct from LGFMS/SEF. The patients were 4 female individuals and 4 male individuals aged 11 to 91 years. Tumors with known locations were in the lower extremity (5), trunk (2), and upper extremity (1); 3 originated in acral locations. Tumor size ranged from 2.5 to 13 cm. Proportions of SEF-like and LGFMS-like areas varied considerably among tumors. All tumors that showed infiltrative growth and mitotic figures per 10 HPFs ranged from 0 to 18. Tumor necrosis was present in 1 case. Follow-up was available for 5 patients (11 to 321 mo), 2 of whom developed local recurrences, and 1 died of metastatic disease. The clinical behavior of these soft tissue sarcomas remains to be further delineated in larger series with extended follow-up; however, our limited clinical data indicate that they are potentially aggressive.
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18
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Dawson LE, D'Agostino L, Hakim AA, Lackman RD, Brown SA, Sensenig RB, Antonello ZA, Kuzin II. Induction of Myogenic Differentiation Improves Chemosensitivity of Chemoresistant Cells in Soft-Tissue Sarcoma Cell Lines. Sarcoma 2020; 2020:8647981. [PMID: 32300280 PMCID: PMC7136814 DOI: 10.1155/2020/8647981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/30/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Rhabdomyosarcoma (RMS) and rhabdoid tumors (RT) are rare soft-tissue malignancies with the highest incidence in infants, children, and adolescents. Advanced, recurrent, and/or metastatic RMS and RT exhibit poor response to treatment. One of the main mechanisms behind resistance to treatment is believed to be intratumoral heterogeneity. In this study, we investigated the myogenic determination factor 1 (MYOD1) and Noggin (NOG) markers in an embryonal RMS (ERMS) cell line and an RT cell line and the differential response of the MYOD1 and NOG expressing subpopulations to chemotherapy. Importantly, we found that these markers together identify a subpopulation of cells (MYOD1+ NOG+ cells) with primary resistance to Vincristine and Doxorubicin, two commonly used chemotherapies for ERMS and RT. The chemoresistant MYOD1+ NOG+ cells express markers of undifferentiated cells such as myogenin and ID1. Combination of Vincristine with TPA/GSK126, a drug combination shown to induce differentiation of RMS cell lines, is able to partially overcome MYOD1/NOG cells chemoresistance.
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Affiliation(s)
| | | | | | - Richard D. Lackman
- Cooper University Hospital, Camden, NJ, USA
- MD Anderson Cancer Center at Cooper, Camden, NJ, USA
| | | | | | - Zeus A. Antonello
- Cooper University Hospital, Camden, NJ, USA
- Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Igor I. Kuzin
- Cooper University Hospital, Camden, NJ, USA
- Cooper Medical School of Rowan University, Camden, NJ, USA
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19
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Arbajian E, Hofvander J, Magnusson L, Mertens F. Deep sequencing of myxoinflammatory fibroblastic sarcoma. Genes Chromosomes Cancer 2020; 59:309-317. [PMID: 31898851 DOI: 10.1002/gcc.22832] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/30/2019] [Accepted: 12/30/2019] [Indexed: 12/20/2022] Open
Abstract
Myxoinflammatory fibroblastic sarcoma (MIFS) has recurrent genetic features in the form of a translocation t(1;10)(p22-31;q24-25), BRAF gene fusions, and/or an amplicon in 3p11-12 including the VGLL3 gene. The breakpoints on chromosomes 1 and 10 in the t(1;10) cluster in or near the TGFBR3 and OGA genes, respectively. We here used a combination of deep sequencing of the genome (WGS), captured sequences (Cap-seq), and transcriptome (RNA-seq) and genomic arrays to investigate the molecular outcome of the t(1;10) and the VGLL3 amplicon, as well as to assess the spectrum of other recurrent genomic features in MIFS. Apart from a ROBO1-BRAF chimera in a t(1;10)-negative MIFS-like tumor, no fusion gene was found at RNA-seq. This was in line with WGS and Cap-seq results, revealing variable breakpoints in chromosomes 1 and 10 and genomic breakpoints that should not yield functional fusion transcripts. The most common genomic rearrangements were breakpoints in or around the OGA, NPM3, and FGF8 genes in chromosome band 10q24, and loss of 1p11-p21 and 10q26-qter (all simultaneously present in 6/7 MIFS); a breakpoint in or near TGFBR3 in chromosome 1 was found in four of these tumors. Amplification and overexpression of VGLL3 was a consistent feature in MIFS and MIFS-like tumors with amplicons in 3p11-12. The significant molecular genetic outcome of the recurrent t(1;10) could be loss of genetic material from 1p and 10q. Other recurrent genomic imbalances in MIFS, such as homozygous loss of CDKN2A and 3p- and 13q-deletions, are shared with other sarcomas, suggesting overlapping pathogenetic pathways.
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Affiliation(s)
- Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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20
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Köster J, Arbajian E, Viklund B, Isaksson A, Hofvander J, Haglund F, Bauer H, Magnusson L, Mandahl N, Mertens F. Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development. Cancer Genet 2019; 241:34-41. [PMID: 31870844 DOI: 10.1016/j.cancergen.2019.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 11/06/2019] [Accepted: 12/06/2019] [Indexed: 12/11/2022]
Abstract
The dermatofibrosarcoma protuberans family of tumors (DPFT) comprises cutaneous soft tissue neoplasms associated with aberrant PDGFBR signaling, typically through a COL1A1-PDGFB fusion. The aim of the present study was to obtain a better understanding of the chromosomal origin of this fusion and to assess the spectrum of secondary mutations at the chromosome and nucleotide levels. We thus investigated 42 tumor samples from 35 patients using chromosome banding, fluorescence in situ hybridization, single nucleotide polymorphism arrays, and/or massively parallel sequencing (gene panel, whole exome and transcriptome sequencing) methods. We confirmed the age-associated differences in the origin of the COL1A1-PDGFB fusion and could show that it in most cases must arise after DNA synthesis, i.e., in the S or G2 phase of the cell cycle. Whereas there was a non-random pattern of secondary chromosomal rearrangements, single nucleotide variants seem to have little impact on tumor progression. No clear genomic differences between low-grade and high-grade DPFT were found, but the number of chromosomes and chromosomal imbalances as well as the frequency of 9p deletions all tended to be greater among the latter. Gene expression profiling of tumors with COL1A1-PDGFB fusions associated with unbalanced translocations or ring chromosomes identified several transcriptionally up-regulated genes in the amplified regions of chromosomes 17 and 22, including TBX2, PRKCA, MSI2, SOX9, SOX10, and PRAME.
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Affiliation(s)
- Jan Köster
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden.
| | - Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Björn Viklund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Felix Haglund
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Bauer
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden; Department of Clinical Genetics and Pathology, Division of Laboratory Medicine, Lund, Sweden
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21
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Hofvander J, Puls F, Pillay N, Steele CD, Flanagan AM, Magnusson L, Nilsson J, Mertens F. Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile. J Pathol 2019; 249:425-434. [PMID: 31313299 DOI: 10.1002/path.5326] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022]
Abstract
Undifferentiated pleomorphic sarcoma (UPS) is a highly aggressive soft tissue tumor. A subset of UPS is characterized by a CITED2-PRDM10 or a MED12-PRDM10 gene fusion. Preliminary data suggest that these so-called PRDM10-rearranged tumors (PRT) are clinically more indolent than classical high-grade UPS, and hence important to recognize. Here, we assessed the spectrum of accompanying mutations and the gene expression profile in PRT using genomic arrays and sequencing of the genome (WGS) and transcriptome (RNA-seq). The fusion protein's function was further investigated by conditional expression of the CITED2-PRDM10 fusion in a fibroblast cell line, followed by RNA-seq and an assay for transposase-accessible chromatin (ATAC-seq). The CADM3 gene was found to be differentially up-regulated in PRT and cell lines and was also evaluated for expression at the protein level using immunohistochemistry (IHC). The genomic analyses identified few and nonrecurrent mutations in addition to the structural variants giving rise to the gene fusions, strongly indicating that the PRDM10-fusions represent the critical driver mutations. RNA-seq of tumors showed a distinct gene expression profile, separating PRT from high-grade UPS and other soft tissue tumors. CADM3 was among the genes that was consistently and highly expressed in both PRT and fibroblasts expressing CITED2-PRDM10, suggesting that it is a direct target of the PRDM10 transcription factor. This conclusion is in line with sequencing data from ATAC-seq, showing enrichment of PRDM10 binding sites, suggesting that the amino-terminal fusion partner contributes by making the DNA more accessible to PRDM10 binding. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Florian Puls
- Department of Pathology and Clinical Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Nischalan Pillay
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
| | | | - Adrienne M Flanagan
- Department of Histopathology, Royal National Orthopaedic Hospital, Stanmore, UK
- UCL Cancer Institute, London, UK
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund University, Lund, Sweden
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22
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Baskaran S, Mayrhofer M, Kultima HG, Bergström T, Elfineh L, Cavelier L, Isaksson A, Nelander S. Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages. Neuro Oncol 2019; 20:1080-1091. [PMID: 29462414 PMCID: PMC6280139 DOI: 10.1093/neuonc/noy024] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Background Primary glioblastoma cell (GC) cultures have emerged as a key model in brain tumor research, with the potential to uncover patient-specific differences in therapy response. However, there is limited quantitative information about the stability of such cells during the initial 20–30 passages of culture. Methods We interrogated 3 patient-derived GC cultures at dense time intervals during the first 30 passages of culture. Combining state-of-the-art signal processing methods with a mathematical model of growth, we estimated clonal composition, rates of change, affected pathways, and correlations between altered gene dosage and transcription. Results We demonstrate that GC cultures undergo sequential clonal takeovers, observed through variable proportions of specific subchromosomal lesions, variations in aneuploid cell content, and variations in subpopulation cell cycling times. The GC cultures also show significant transcriptional drift in several metabolic and signaling pathways, including ribosomal synthesis, telomere packaging and signaling via the mammalian target of rapamycin, Wnt, and interferon pathways, to a high degree explained by changes in gene dosage. In addition to these adaptations, the cultured GCs showed signs of shifting transcriptional subtype. Compared with chromosomal aberrations and gene expression, DNA methylations remained comparatively stable during passaging, and may be favorable as a biomarker. Conclusion Taken together, GC cultures undergo significant genomic and transcriptional changes that need to be considered in functional experiments and biomarker studies that involve primary glioblastoma cells.
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Affiliation(s)
- Sathishkumar Baskaran
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Markus Mayrhofer
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | | | - Tobias Bergström
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Lioudmila Elfineh
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Sweden
| | - Sven Nelander
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Sweden
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23
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Rebolledo-Jaramillo B, Ziegler A. Teneurins: An Integrative Molecular, Functional, and Biomedical Overview of Their Role in Cancer. Front Neurosci 2018; 12:937. [PMID: 30618566 PMCID: PMC6297388 DOI: 10.3389/fnins.2018.00937] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/28/2018] [Indexed: 12/16/2022] Open
Abstract
Teneurins are large transmembrane proteins originally identified in Drosophila. Their essential role in development of the central nervous system is conserved throughout species, and evidence supports their involvement in organogenesis of additional tissues. Homophilic and heterophilic interactions between Teneurin paralogues mediate cellular adhesion in crucial processes such as neuronal pathfinding and synaptic organization. At the molecular level, Teneurins are proteolytically processed into distinct subdomains that have been implicated in extracellular and intracellular signaling, and in transcriptional regulation. Phylogenetic studies have shown a high degree of intra- and interspecies conservation of Teneurin genes. Accordingly, the occurrence of genetic variants has been associated with functional and phenotypic alterations in experimental systems, and with some inherited or sporadic conditions. Recently, tumor-related variations in Teneurin gene expression have been associated with patient survival in different cancers. Although these findings were incidental and molecular mechanisms were not addressed, they suggested a potential utility of Teneurin transcript levels as biomarkers for disease prognosis. Mutations and chromosomal alterations affecting Teneurin genes have been found occasionally in tumors, but literature remains scarce. The analysis of open-access molecular and clinical datasets derived from large oncologic cohorts provides an invaluable resource for the identification of additional somatic mutations. However, Teneurin variants have not been classified in terms of pathogenic risk and their phenotypic impact remains unknown. On this basis, is it plausible to hypothesize that Teneurins play a role in carcinogenesis? Does current evidence support a tumor suppressive or rather oncogenic function for these proteins? Here, we comprehensively discuss available literature with integration of molecular evidence retrieved from open-access databases. We show that Teneurins undergo somatic changes comparable to those of well-established cancer genes, and discuss their involvement in cancer-related signaling pathways. Current data strongly suggest a functional contribution of Teneurins to human carcinogenesis.
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Affiliation(s)
| | - Annemarie Ziegler
- Center for Genetics and Genomics, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
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24
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Gui H, Lhospital E, Staddon AP, Nagda SN, Zager EL, Zhang PJL, Brooks JS. Combined Sclerosing and Spindle Cell Rhabdomyosarcoma in Previous Craniotomy Site: A Case Report and a Review of the Literature. Int J Surg Pathol 2018; 27:328-335. [PMID: 30270691 DOI: 10.1177/1066896918802030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Sclerosing rhabdomyosarcoma (RMS) is a rare subtype of RMS with unique prominent stromal hyalinization and a pseudovascular architecture. It overlaps morphologically with spindle cell RMS and poses both diagnostic and therapeutic challenges because of its rarity and aggressive clinical course. In this article, we report a case of sclerosing RMS arising from a prior craniotomy site, which demonstrated both sclerosing and spindle cell components. A literature review of RMS with sclerosing morphology identified 122 cases. Our review documents the following: sclerosing RMS occurs in both childhood and adult populations, has a predilection for the head and neck areas, and has a worse prognosis in adults. Sclerosing RMS harbors a high frequency of MYOD1 mutations, conferring a poor clinical outcome. Sclerosing RMS and spindle RMS likely represent a morphologic spectrum of one entity.
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Affiliation(s)
- Hongxing Gui
- 1 Department of Pathology and Laboratory Medicine, Pennsylvania Hospital of the University of Pennsylvania Health System, Philadelphia, PA, USA
| | - Elliott Lhospital
- 1 Department of Pathology and Laboratory Medicine, Pennsylvania Hospital of the University of Pennsylvania Health System, Philadelphia, PA, USA
| | - Arthur P Staddon
- 2 Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Suneel N Nagda
- 3 Department of Radiation Oncology, Perelman Center for Advanced Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Eric L Zager
- 4 Department of Neurosurgery, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul J L Zhang
- 5 Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, PA, USA
| | - John S Brooks
- 1 Department of Pathology and Laboratory Medicine, Pennsylvania Hospital of the University of Pennsylvania Health System, Philadelphia, PA, USA.,6 Professor of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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25
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Hofvander J, Viklund B, Isaksson A, Brosjö O, Vult von Steyern F, Rissler P, Mandahl N, Mertens F. Different patterns of clonal evolution among different sarcoma subtypes followed for up to 25 years. Nat Commun 2018; 9:3662. [PMID: 30201954 PMCID: PMC6131146 DOI: 10.1038/s41467-018-06098-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/14/2018] [Indexed: 02/08/2023] Open
Abstract
To compare clonal evolution in tumors arising through different mechanisms, we selected three types of sarcoma-amplicon-driven well-differentiated liposarcoma (WDLS), gene fusion-driven myxoid liposarcoma (MLS), and sarcomas with complex genomes (CXS)-and assessed the dynamics of chromosome and nucleotide level mutations by cytogenetics, SNP array analysis and whole-exome sequencing. Here we show that the extensive single-cell variation in WDLS has minor impact on clonal key amplicons in chromosome 12. In addition, only a few of the single nucleotide variants in WDLS were present in more than one lesion, suggesting that such mutations are of little significance in tumor development. MLS displays few mutations other than the FUS-DDIT3 fusion, and the primary tumor is genetically sometimes much more complex than its relapses, whereas CXS in general shows a gradual increase of both nucleotide- and chromosome-level mutations, similar to what has been described in carcinomas.
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Affiliation(s)
- Jakob Hofvander
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.
| | - Björn Viklund
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Anders Isaksson
- Science for Life Laboratory, Department of Medical Sciences, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Otte Brosjö
- Department of Orthopedics, Karolinska Hospital, SE-171 76, Stockholm, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics, Clinical Sciences, Lund University and Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Pehr Rissler
- Department of Clinical Genetics and Pathology, University and Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
| | - Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84, Lund, Sweden.,Department of Clinical Genetics and Pathology, University and Regional Laboratories Region Skåne, SE-221 85, Lund, Sweden
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26
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Arbajian E, Köster J, Vult von Steyern F, Mertens F. Inflammatory leiomyosarcoma is a distinct tumor characterized by near-haploidization, few somatic mutations, and a primitive myogenic gene expression signature. Mod Pathol 2018; 31:93-100. [PMID: 28884746 DOI: 10.1038/modpathol.2017.113] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/30/2017] [Accepted: 06/30/2017] [Indexed: 12/28/2022]
Abstract
Inflammatory leiomyosarcoma is a soft-tissue tumor resembling conventional leiomyosarcoma, but with a prominent intrinsic inflammatory component. Previous studies have suggested that inflammatory leiomyosarcoma differs genetically from leiomyosarcoma, but in-depth analyses are lacking. Here we provide a comprehensive picture of the genome and transcriptome of inflammatory leiomyosarcoma by combining cytogenetic, single-nucleotide polymorphism array, mRNA-sequencing, and whole-exome sequencing data. The results show that inflammatory leiomyosarcoma has a specific genetic profile characterized by near-haploidization with or without subsequent whole-genome doubling. Consistently, both parental copies of chromosomes 5 and 22 are preserved. Apart from recurrent mutation of the NF1 gene, additional somatic events that could serve as driver mutations were not found at either the nucleotide or the genome level. Furthermore, no fusion transcripts were identified. Global gene expression profiling revealed particularly prominent differential expression of genes, including ITGA7, MYF5, MYF6, MYOD1, MYOG, and PAX7, involved in muscle development and function, providing strong argument for grouping inflammatory leiomyosarcoma with myogenic sarcomas, rather than with myofibroblastic lesions. Combined with previously published data, there are now 10 cases of inflammatory leiomyosarcoma with confirmed near-haploid genotype. These patients differ from leiomyosarcoma patients in being younger (median 41 years), showing a male predominance (9:1), and few relapses (1 of 8 informative patients). Thus, the clinical, morphological, and genetic data provide compelling support for inflammatory leiomyosarcoma being a distinct subtype of myogenic tumors.
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Affiliation(s)
- Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Jan Köster
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics and Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
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27
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Arbajian E, Puls F, Antonescu CR, Amary F, Sciot R, Debiec-Rychter M, Sumathi VP, Järås M, Magnusson L, Nilsson J, Hofvander J, Mertens F. In-depth Genetic Analysis of Sclerosing Epithelioid Fibrosarcoma Reveals Recurrent Genomic Alterations and Potential Treatment Targets. Clin Cancer Res 2017; 23:7426-7434. [DOI: 10.1158/1078-0432.ccr-17-1856] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/01/2017] [Accepted: 09/15/2017] [Indexed: 11/16/2022]
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28
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Mandahl N, Magnusson L, Nilsson J, Viklund B, Arbajian E, von Steyern FV, Isaksson A, Mertens F. Scattered genomic amplification in dedifferentiated liposarcoma. Mol Cytogenet 2017; 10:25. [PMID: 28652867 PMCID: PMC5483303 DOI: 10.1186/s13039-017-0325-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/08/2017] [Indexed: 01/07/2023] Open
Abstract
Background Atypical lipomatous tumor (ALT), well differentiated liposarcoma (WDLS) and dedifferentiated liposarcoma (DDLS) are cytogenetically characterized by near-diploid karyotypes with no or few other aberrations than supernumerary ring or giant marker chromosomes, although DDLS tend to have somewhat more complex rearrangements. In contrast, pleomorphic liposarcomas (PLS) have highly aberrant and heterogeneous karyotypes. The ring and giant marker chromosomes contain discontinuous amplicons, in particular including multiple copies of the target genes CDK4, HMGA2 and MDM2 from 12q, but often also sequences from other chromosomes. Results The present study presents a DDLS with an atypical hypertriploid karyotype without any ring or giant marker chromosomes. SNP array analyses revealed amplification of almost the entire 5p and discontinuous amplicons of 12q including the classical target genes, in particular CDK4. In addition, amplicons from 1q, 3q, 7p, 9p, 11q and 20q, covering from 2 to 14 Mb, were present. FISH analyses showed that sequences from 5p and 12q were scattered, separately or together, over more than 10 chromosomes of varying size. At RNA sequencing, significantly elevated expression, compared to myxoid liposarcomas, was seen for TRIO and AMACR in 5p and of CDK4, HMGA2 and MDM2 in 12q. Conclusions The observed pattern of scattered amplification does not show the characteristics of chromothripsis, but is novel and differs from the well known cytogenetic manifestations of amplification, i.e., double minutes, homogeneously staining regions and ring chromosomes. Possible explanations for this unusual distribution of amplified sequences might be the mechanism of alternative lengthening of telomeres that is frequently active in DDLS and events associated with telomere crisis. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0325-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nils Mandahl
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Linda Magnusson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Jenny Nilsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Björn Viklund
- Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Elsa Arbajian
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
| | - Fredrik Vult von Steyern
- Department of Orthopedics, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden
| | - Anders Isaksson
- Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Fredrik Mertens
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, SE-221 84 Lund, Sweden
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29
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Balogh P, Bánusz R, Csóka M, Váradi Z, Varga E, Sápi Z. Primary alveolar rhabdomyosarcoma of the bone: two cases and review of the literature. Diagn Pathol 2016; 11:99. [PMID: 27756397 PMCID: PMC5069778 DOI: 10.1186/s13000-016-0552-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 10/08/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rhabdomyosarcoma (RMS) is a malignant tumor of mesenchymal origin and comprises the largest category of soft-tissue sarcomas both in children and adolescents. From a pediatric oncology point of view, RMS has traditionally been classified into alveolar (ARMS) and embryonal (ERMS) subtypes. The anatomical localization of the tumor may vary, but commonly involve the head/neck regions, male and female urogenital tract or the trunk and extremities. CASE PRESENTATION Here, we report two challenging cases involving 17- and 9-years-olds males where diffuse and multiplex bone lesions suggested either a hematological disease or a primary bone tumor (mesenchymal chondrosarcoma). Biopsies, proved a massive infiltration of the bone marrow cavity with rhabdomyosarcoma. In both cases, the ARMS subtype was confirmed using FOXO1 break-apart probes (FISH). Radiological examination could not identify primary soft tissue component in any localization at the time of diagnosis in either cases. CONCLUSIONS Primary alveolar rhabdomyosarcoma of the bone as a subtype of ARMS, seems to be a distinct clinico-pathological entity with challenging diagnostic difficulties and different, yet better, biological behavior in comparison to soft tissue ARMS. However, it is difficult to be characterized or predict its prognosis and long-term survival as only sporadic cases (four) were reported so far.
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Affiliation(s)
- Petra Balogh
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, H-1085, Hungary
| | - Rita Bánusz
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó utca 7-9, Budapest, H-1094, Hungary
| | - Monika Csóka
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó utca 7-9, Budapest, H-1094, Hungary
| | - Zsófia Váradi
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó utca 7-9, Budapest, H-1094, Hungary
| | - Edit Varga
- 2nd Department of Pediatrics, Semmelweis University, Tűzoltó utca 7-9, Budapest, H-1094, Hungary.,Magnetic Resonance Research Center, Semmelweis University, Tűzoltó utca 7-9, Budapest, H-1094, Hungary
| | - Zoltán Sápi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, Budapest, H-1085, Hungary.
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30
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Hofvander J, Jo VY, Ghanei I, Gisselsson D, Mårtensson E, Mertens F. Comprehensive genetic analysis of a paediatric pleomorphic myxoid liposarcoma reveals near-haploidization and loss of theRB1gene. Histopathology 2016; 69:141-147. [DOI: 10.1111/his.12913] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Jakob Hofvander
- Department of Clinical Genetics; University and Regional Laboratories; Skåne University Hospital; Lund University; Lund Sweden
| | - Vickie Y Jo
- Department of Pathology; Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Iman Ghanei
- Department of Orthopedics; Skåne University Hospital; Lund University; Lund Sweden
| | - David Gisselsson
- Department of Clinical Genetics; University and Regional Laboratories; Skåne University Hospital; Lund University; Lund Sweden
| | - Emma Mårtensson
- Department of Clinical Genetics; University and Regional Laboratories; Skåne University Hospital; Lund University; Lund Sweden
| | - Fredrik Mertens
- Department of Clinical Genetics; University and Regional Laboratories; Skåne University Hospital; Lund University; Lund Sweden
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