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Makise N, Lin J, Kageyama H, Kinoshita H, Kamoda H, Hagiwara Y, Oikawa M, Sugiyama T, Kawana H, Araki A, Yonemoto T, Kawazu M, Itami M. Nanopore DNA Sequencing Detected Chromothripsis-Induced PAFAH1B1::USP6 Rearrangement in Periosteal Solid Aneurysmal Bone Cyst Initially Diagnosed as Osteosarcoma. Genes Chromosomes Cancer 2024; 63:e23254. [PMID: 38979775 DOI: 10.1002/gcc.23254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 06/16/2024] [Accepted: 06/18/2024] [Indexed: 07/10/2024] Open
Abstract
An aneurysmal bone cyst (ABC) is a benign bone neoplasm that typically occurs during the first and second decades of life. ABC usually presents as a rapidly growing intramedullary expansile mass with multiple blood-filled cysts in the metaphysis of the long tubular bones. Here, we report a case of a periosteal solid ABC that was initially diagnosed as a high-grade surface osteosarcoma. A 10-year-old male was referred to our hospital for swelling and tenderness of the left upper arm. Radiography revealed periosteal mass without fluid-fluid levels. On performing open biopsy, the tumor showed hypercellular proliferation of uniform spindle to epithelioid cells with brisk mitotic activity (up to 12/2 mm2) and lace-like osteoid formation, which was diagnosed as a high-grade surface osteosarcoma. After one course of chemotherapy using adriamycin and cisplatin, peripheral sclerosis was conspicuous, which led to pathological review and revision of diagnosis as "possibly osteoblastoma." The patient was disease-free for 4 years after marginal resection and curettage. Retrospective nanopore DNA sequencing unexpectedly detected a PAFAH1B1::USP6 rearrangement. The fusion gene was further validated using reverse transcription-polymerase chain reaction and the diagnosis was revised to ABC. Chromothripsis involving chromosome 17 has also been identified. Methylation analysis classified the present tumor as an ABC or non-ossifying fibroma using t-distributed stochastic neighbor embedding and unsupervised hierarchical clustering. This case report highlights the utility of nanopore DNA sequencing for soft tissue and bone tumor diagnosis.
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Affiliation(s)
- Naohiro Makise
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
| | - Jason Lin
- Division of Cell Therapy, Chiba Cancer Center, Chiba, Japan
| | - Hajime Kageyama
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
| | | | - Hiroto Kamoda
- Department of Orthopedic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Yoko Hagiwara
- Department of Orthopedic Surgery, Chiba Cancer Center, Chiba, Japan
| | - Mariko Oikawa
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
| | | | - Hidetada Kawana
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
| | - Akinobu Araki
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
| | - Tsukasa Yonemoto
- Department of Orthopedic Surgery, Chiba Cancer Center, Chiba, Japan
| | | | - Makiko Itami
- Division of Surgical Pathology, Chiba Cancer Center, Chiba, Japan
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Torrence D, Dermawan JK, Zhang Y, Vanderbilt C, Hwang S, Mullaney K, Jungbluth A, Rao M, Gao K, Sukhadia P, Linos K, Agaram N, Hameed M. Detection of GRM1 gene rearrangements in chondromyxoid fibroma: a comparison of fluorescence in-situ hybridisation, RNA sequencing and immunohistochemical analysis. Histopathology 2024. [PMID: 38890779 DOI: 10.1111/his.15248] [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: 03/18/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/20/2024]
Abstract
AIMS Chondromyxoid fibroma (CMF) is a rare, benign bone tumour which arises primarily in young adults and is occasionally diagnostically challenging. Glutamate metabotropic receptor 1 (GRM1) gene encodes a metabotropic glutamate receptor and was recently shown to be up-regulated in chondromyxoid fibroma through gene fusion and promoter swapping. The aim of this study was to interrogate cases of CMF for the presence of GRM1 gene rearrangements, gene fusions and GRM1 protein overexpression. METHODS AND RESULTS Selected cases were subjected to testing by fluorescent in-situ hybridisation (FISH) with a GRM1 break-apart probe, a targeted RNA sequencing method and immunohistochemical study with an antibody to GRM1 protein. Two cases were subjected to whole transcriptomic sequencing. In 13 of 13 cases, GRM1 protein overexpression was detected by immunohistochemistry using the GRM1 antibody. Of the 12 cases successfully tested by FISH, nine of 12 showed GRM1 rearrangements by break-apart probe assay. Targeted RNA sequencing analysis did not detect gene fusions in any of the eight cases tested, but there was an increase in GRM1 mRNA expression in all eight cases. Two cases subjected to whole transcriptomic sequencing (WTS) showed elevated GRM1 expression and no gene fusions. CONCLUSION GRM1 gene rearrangements can be detected using FISH break-apart probes in approximately 75% of cases, and immunohistochemical detection of GRM1 protein over-expression is a sensitive diagnostic method. The gene fusion was not detected by targeted RNA sequencing, due most probably to the complexity of fusion mechanism, and is not yet a reliable method for confirming a diagnosis of CMF in the clinical setting.
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Affiliation(s)
- Dianne Torrence
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY, USA
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sinchun Hwang
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kerry Mullaney
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim Jungbluth
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mamta Rao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kate Gao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Purvil Sukhadia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konstantinos Linos
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Narasimhan Agaram
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Hameed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Li CX, Gong ZC. Chondromyxoid fibroma of the temporomandibular joint - a rare case. Cranio 2024:1-8. [PMID: 38884123 DOI: 10.1080/08869634.2024.2357988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
BACKGROUND Chondromyxoid fibroma (CMF) is a rare cartilaginous tumor, accounting for < 1% of benign bone tumors. We report a case of temporomandibular joint (TMJ)-CMF, involving the pterygopalatine space and skull base and discuss its epidemiology, clinical characteristics, and management. CASE PRESENTATION A 56-year-old woman presented with facial asymmetry and progressive mouth opening restriction due to a mass expanding upwardly to the auriculotemporal region. Using digital techniques to determine the lesion's boundary and reconstruct the normal glenoid fossa, the temporalis myofascial flap was transplanted between the titanium mesh and condyle to reconstruct the disc after tumor resection. CONCLUSION This case highlights the importance of identifying patients with TMJ-CMF.
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Affiliation(s)
- Chen-Xi Li
- Department of Oral and Maxillofacial Oncology & Surgery, School/Hospital of Stomatology, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Stomatological Research Institute of Xinjiang, Uygur Autonomous Region, Urumqi, China
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, School of Stomatology, Tongji Medical College, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Zhong-Cheng Gong
- Department of Oral and Maxillofacial Oncology & Surgery, School/Hospital of Stomatology, the First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- Stomatological Research Institute of Xinjiang, Uygur Autonomous Region, Urumqi, China
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Wani AK, Prakash A, Sena S, Akhtar N, Singh R, Chopra C, Ariyanti EE, Mudiana D, Yulia ND, Rahayu F. Unraveling molecular signatures in rare bone tumors and navigating the cancer pathway landscapes for targeted therapeutics. Crit Rev Oncol Hematol 2024; 196:104291. [PMID: 38346462 DOI: 10.1016/j.critrevonc.2024.104291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/23/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Rare cancers (RCs), which account for over 20% of cancer cases, face significant research and treatment challenges due to their limited prevalence. This results in suboptimal outcomes compared to more common malignancies. Rare bone tumors (RBTs) constitute 5-10% of rare cancer cases and pose unique diagnostic complexities. The therapeutic potential of anti-cancer drugs for RBTs remains largely unexplored. Identifying molecular alterations in cancer-related genes and their associated pathways is essential for precision medicine in RBTs. Small molecule inhibitors and monoclonal antibodies targeting specific RBT-associated proteins show promise. Ongoing clinical trials aim to define RBT biomarkers, subtypes, and optimal treatment contexts, including combination therapies and immunotherapeutic agents. This review addresses the challenges in diagnosing, treating, and studying RBTs, shedding light on the current state of RBT biomarkers, potential therapeutic targets, and promising inhibitors. Rare cancers demand attention and innovative solutions to improve clinical outcomes.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, India.
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Saikat Sena
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar 144411, India
| | - Esti Endah Ariyanti
- Research Center for Applied Botany, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Deden Mudiana
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Nina Dwi Yulia
- Research Center for Applied Botany, National Research and Innovation Agency, Bogor 16911, Indonesia
| | - Farida Rahayu
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor 16911, Indonesia
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Saba KH, Difilippo V, Kovac M, Cornmark L, Magnusson L, Nilsson J, van den Bos H, Spierings DC, Bidgoli M, Jonson T, Sumathi VP, Brosjö O, Staaf J, Foijer F, Styring E, Nathrath M, Baumhoer D, Nord KH. Disruption of the TP53 locus in osteosarcoma leads to TP53 promoter gene fusions and restoration of parts of the TP53 signalling pathway. J Pathol 2024; 262:147-160. [PMID: 38010733 DOI: 10.1002/path.6219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/24/2023] [Accepted: 09/19/2023] [Indexed: 11/29/2023]
Abstract
TP53 is the most frequently mutated gene in human cancer. This gene shows not only loss-of-function mutations but also recurrent missense mutations with gain-of-function activity. We have studied the primary bone malignancy osteosarcoma, which harbours one of the most rearranged genomes of all cancers. This is odd since it primarily affects children and adolescents who have not lived the long life thought necessary to accumulate massive numbers of mutations. In osteosarcoma, TP53 is often disrupted by structural variants. Here, we show through combined whole-genome and transcriptome analyses of 148 osteosarcomas that TP53 structural variants commonly result in loss of coding parts of the gene while simultaneously preserving and relocating the promoter region. The transferred TP53 promoter region is fused to genes previously implicated in cancer development. Paradoxically, these erroneously upregulated genes are significantly associated with the TP53 signalling pathway itself. This suggests that while the classical tumour suppressor activities of TP53 are lost, certain parts of the TP53 signalling pathway that are necessary for cancer cell survival and proliferation are retained. In line with this, our data suggest that transposition of the TP53 promoter is an early event that allows for a new normal state of genome-wide rearrangements in osteosarcoma. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Valeria Difilippo
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Michal Kovac
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
- Faculty of Informatics and Information Technologies, Slovak University of Technology, Bratislava, Slovakia
| | - Louise Cornmark
- 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
| | - Jenny Nilsson
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Diana Cj Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Mahtab Bidgoli
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Tord Jonson
- Department of Clinical Genetics and Pathology, Laboratory Medicine, Medical Services, Skåne University Hospital, Lund, Sweden
| | - Vaiyapuri P Sumathi
- Department of Musculoskeletal Pathology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Staaf
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Emelie Styring
- Department of Orthopedics, Lund University, Skåne University Hospital, Lund, Sweden
| | - Michaela Nathrath
- Children's Cancer Research Centre and Department of Pediatrics, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Pediatric Oncology, Klinikum Kassel, Kassel, Germany
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology, University Hospital and University of Basel, Basel, Switzerland
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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6
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Machado I, Zhang Y, Hameed M, Hwang S, Sharma AE, Bilsky MH, Linos K. GRM1-Rearranged Chondromyxoid Fibroma With FGF23 Expression: A Potential Pitfall in Small Biopsies. Int J Surg Pathol 2024:10668969241229345. [PMID: 38303543 DOI: 10.1177/10668969241229345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
The clinical, radiological, and histopathological features of chondromyxoid fibroma can sometimes resemble those of other benign or malignant tumors. Recently, recurrent GRM1 rearrangements have been identified in chondromyxoid fibroma, and GRM1 positivity by immunohistochemistry has emerged as a dependable surrogate marker for this molecular alteration. Phosphaturic mesenchymal tumor is a rare tumor that often exhibits overexpression of fibroblastic growth factor 23 (FGF23) through various mechanisms. In this report, we present a case of GRM1-rearranged chondromyxoid fibroma that also exhibited FGF23 expression via in situ hybridization, posing significant diagnostic challenges during workup of the initial core biopsy. We hope that this case can serve as an educational resource, shedding light on a rare diagnostic pitfall.
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Affiliation(s)
- Isidro Machado
- Department of Pathology, Instituto Valenciano de Oncología, Valencia, Spain
- Department of Pathology, Patologika Laboratory, Hospital Quiron-Salud, Valencia, Spain
- Pathology Department, University of Valencia and CIBERON Cancer, Madrid, Spain
| | - Yanming Zhang
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Hameed
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sinchun Hwang
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aarti E Sharma
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mark H Bilsky
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konstantinos Linos
- Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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7
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Watabe S, Kikuchi Y, Motoi T, Yamamoto A, Imanishi J, Tokizaki T, Sato K, Mukaiyama J, Minami S, Ishida T, Kawano H, Uozaki H. Cytopathology of Chondromyxoid Fibroma: Report of 2 Cases with Immunocytochemical Expression of GRM1. Acta Cytol 2024; 68:66-72. [PMID: 38281480 DOI: 10.1159/000536459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024]
Abstract
INTRODUCTION Chondromyxoid fibroma (CMF) is a rare, benign bone tumor that occurs predominantly in the second and third decades of life, more frequently in males. Overexpression of GRM1 as a consequence of tumor-specific gene rearrangement of GRM1 has recently been reported as a useful immunohistochemical marker for histopathological diagnosis of CMF. However, the usefulness of GRM1 staining of cytology specimens has not yet been evaluated. In this report, the cytological findings and GRM1 immunocytochemistry of two cases of CMF are described. CASE PRESENTATIONS Case 1 was a 15-year-old girl with a rib tumor. Imaging findings suggested a benign neurogenic tumor such as schwannoma. The tumor had increased in size over a 2-year period and was resected. Case 2 was a 14-year-old boy with a metatarsal tumor involving his left first toe. Imaging findings were suspicious of a benign neoplastic lesion. Biopsy findings suggested a benign tumor, and the patient underwent tumor resection. Cytologically, in both cases the tumor cells were predominantly spindle-shaped or stellate, with a myxoid to chondromyxoid background matrix and multinucleated giant cells, and these matrices were metachromatic with Giemsa staining. Cellular atypia was more accentuated in case 2 than in case 1. Immunocytochemical staining for GRM1 was positive in both cases. CONCLUSION Due to the overlap in cytological findings, it is often difficult to differentiate CMF from chondroblastoma and chondrosarcoma grade 2. Immunocytochemical staining for GRM1 may support the diagnosis of CMF, and the reuse of Papanicolaou-stained specimens is applicable. The present cases further demonstrated the difficulty of differentiating CMF from other mimicking tumors such as chondroblastoma and chondrosarcoma grade 2. In such instances, immunocytochemistry for GRM1 is applicable to the diagnostic process, the value of which is strengthened by reusing Papanicolaou-stained specimens.
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Affiliation(s)
- Shiori Watabe
- Department of Pathology, Teikyo University School of Medicine, Tokyo, Japan
| | - Yoshinao Kikuchi
- Department of Pathology, Teikyo University School of Medicine, Tokyo, Japan
| | - Toru Motoi
- Department of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Asako Yamamoto
- Department of Radiology, Teikyo University School of Medicine, Tokyo, Japan
| | - Jungo Imanishi
- Department of Orthopaedic Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Toru Tokizaki
- Department of Orthopaedic Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Kenji Sato
- Department of Orthopaedic Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Junji Mukaiyama
- Department of Pathology, Teikyo University Hospital, Tokyo, Japan
| | - Shuhei Minami
- Department of Pathology, Teikyo University Hospital, Tokyo, Japan
| | - Tsuyoshi Ishida
- Department of Diagnostic Pathology, National Hospital Organization Saitama Hospital, Saitama, Japan
| | - Hirotaka Kawano
- Department of Orthopaedic Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Hiroshi Uozaki
- Department of Pathology, Teikyo University School of Medicine, Tokyo, Japan
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Cordier F, Ferdinande L, Hoorens A, Van de Vijver K, Van Dorpe J, Creytens D. Soft Tissue and Bone Tumor Diagnostics: Harnessing the Power of Molecular Techniques. Genes (Basel) 2023; 14:2229. [PMID: 38137051 PMCID: PMC10742688 DOI: 10.3390/genes14122229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Since the introduction of new molecular techniques, the diagnostic landscape of soft tissue and bone tumors has expanded greatly over the past few years. The use of new molecular techniques has led to the identification of new genetic alterations and, therefore, to a better understanding of tumorigenesis, tumor detection and classification. Furthermore, methylation profiling has emerged as a classification tool for soft tissue and bone tumors. Molecular pathology also plays an important role in the determination of patient prognosis and in the identification of targets that can be used for targeted therapy. As a result, molecular pathology has gained a more prominent role in the daily practice of the surgical pathologist. This review delves into various molecular techniques applied in the surgical pathology of soft tissue and bone tumors. It highlights their applications through the analysis of five specific cases.
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Affiliation(s)
- Fleur Cordier
- Department of Pathology, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium; (F.C.); (L.F.); (A.H.); (K.V.d.V.); (J.V.D.)
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Liesbeth Ferdinande
- Department of Pathology, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium; (F.C.); (L.F.); (A.H.); (K.V.d.V.); (J.V.D.)
| | - Anne Hoorens
- Department of Pathology, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium; (F.C.); (L.F.); (A.H.); (K.V.d.V.); (J.V.D.)
| | - Koen Van de Vijver
- Department of Pathology, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium; (F.C.); (L.F.); (A.H.); (K.V.d.V.); (J.V.D.)
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium; (F.C.); (L.F.); (A.H.); (K.V.d.V.); (J.V.D.)
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium; (F.C.); (L.F.); (A.H.); (K.V.d.V.); (J.V.D.)
- CRIG, Cancer Research Institute Ghent, Ghent University Hospital, Ghent University, 9000 Ghent, Belgium
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9
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Kervarrec T, Lo Bello G, Pissaloux D, Tirode F, Poulalhon N, Samimi M, Houlier A, de la Fouchardière A. GRM1 Gene Fusions as an Alternative Molecular Driver in Blue Nevi and Related Melanomas. Mod Pathol 2023; 36:100264. [PMID: 37391170 DOI: 10.1016/j.modpat.2023.100264] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Activating mutations in GNAQ, GNA11, CYSLTR2, and PLCB4 genes are regarded as the main oncogenic drivers of blue nevi (BN) and blue malignant melanocytic tumors. Here we report 4 cases of blue melanocytic neoplasms devoid of these mutations but harboring GRM1 gene fusions. In this short series, there was no gender predominance (sex ratio, 1). The mean age at diagnosis was 40 years (range, 12-72). Tumors were located on the face (n = 2), forearm (n = 1), and dorsum of the foot (n = 1). Clinically, a plaque-like pre-existing BN was found in 2 cases, including a deep location; another case presented as an Ota nevus. Two cases were diagnosed as melanoma ex-BN, one as an atypical BN, and one as a plaque-like BN. Microscopic examination revealed a dermal proliferation of dendritic melanocytes in a sclerotic stroma. A dermal cellular nodule with atypia and mitotic activity was observed in 3 cases. Genetic investigation by whole exome RNA sequencing revealed MYO10::GRM1 (n = 2) and ZEB2::GRM1 (n = 1) fusions. A GRM1 rearrangement was identified by fluorescence in situ hybridization in the remaining case. SF3B1 comutations were present in the 2 melanomas, and both had a MYO10::GRM1 fusion. Array comparative genomic hybridization was feasible for 3 cases and displayed multiple copy number alterations in the 2 melanomas and limited copy number alterations in the atypical BN, all genomic profiles compatible with those of classical blue lesions. GRM1 was overexpressed in all cases compared with a control group of blue lesions with other typical mutations. Both melanomas rapidly developed visceral metastases following diagnosis, with a fatal outcome in one case and tumor progression under palliative care in the other. These data suggest that GRM1 gene fusions could represent an additional rare oncogenic driver in the setting of BN, mutually exclusive of classical canonical mutations, especially in plaque-type or Ota subtypes.
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Affiliation(s)
- Thibault Kervarrec
- Department of Pathology, Centre Hospitalier Universitaire de Tours, Tours, France; Biologie des infections à Polyomavirus, INRA UMR 1282 ISP, Université de Tours, Tours, France
| | | | - Daniel Pissaloux
- Department of Biopathology, Centre Léon Bérard, Lyon, France; INSERM U 1052 CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Franck Tirode
- INSERM U 1052 CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Nicolas Poulalhon
- Department of Dermatology, Hospices Civils de Lyon, Hôpital Lyon Sud, Pierre-Bénite, France
| | - Mahtab Samimi
- Department of Dermatology, Tours University Hospital, France
| | - Aurélie Houlier
- Department of Biopathology, Centre Léon Bérard, Lyon, France
| | - Arnaud de la Fouchardière
- Division of Pathology, St. Anna Hospital, ASST Lariana, Como, Italy; Department of Biopathology, Centre Léon Bérard, Lyon, France.
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10
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Huang SC, Lee JC, Hsu YC, Tsai JW, Kao YC, Hsieh TH, Chang YM, Chang KC, Wu PS, Chen PCH, Chen CH, Chang CD, Lee PH, Tai HC, Liu TT, Wen MC, Li WS, Yu SC, Wang JC, Huang HY. Extraskeletal Myxoid Chondrosarcomas: The Uncommon Clinicopathologic Manifestations and Significance of TAF15::NR4A3 Fusion. Mod Pathol 2023; 36:100161. [PMID: 36948401 DOI: 10.1016/j.modpat.2023.100161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/08/2023] [Accepted: 03/07/2023] [Indexed: 03/24/2023]
Abstract
Extraskeletal myxoid chondrosarcoma (EMC) is an ultrarare sarcoma typically exhibiting myxoid/reticular histology and NR4A3 translocation. However, morphologic variants and the relevance of non-EWSR1::NR4A3 fusions remain underexplored. Three challenging pan-Trk-expressing cases, featuring cellular to solid histology, were subjected to RNA exome sequencing (RES), unveiling different NR4A3-associated fusions. Alongside RES-analyzed cases, fluorescence in situ hybridization was performed to confirm 58 EMCs, with 48 available for pan-Trk immunostaining and KIT sequencing. Except for 1 (2%) NR4A3-rearranged EMC without identifiable partners, 46 (79%), 9 (16%), and 2 (3%) cases harbored EWSR1::NR4A3, TAF15::NR4A3, and TCF12::NR4A3 fusions, respectively. Five EWSR1::NR4A3-positive EMCs occurred in the subcutis (3) and bone (2). Besides 43 classical cases, there were 8 cellular, 4 rhabdoid/anaplastic, 2 solid, and 1 mixed tumor-like variants. Tumor cells were oval/spindle to pleomorphic and formed loose myxoid/reticular to compact sheet-like or fascicular patterns, imparting broad diagnostic considerations. RES showed upregulation of NTRK2/3, KIT, and INSM1. Moderate-to-strong immunoreactivities of pan-Trk, CD117, and INSM1 were present in 35.4%, 52.6%, and 54.6% of EMCs, respectively. KIT p. E554K mutation was detected in 2/48 cases. TAF15::NR4A3 was significantly associated with size >10 cm (78%, P = .025). Size >10 cm, moderate-to-severe nuclear pleomorphism, metastasis at presentation, TAF15::NR4A3 fusion, and the administration of chemotherapy portended shorter univariate disease-specific survival, whereas only size >10 cm (P = .004) and metastasis at presentation (P = .032) remained prognostically independent. Conclusively, EMC may manifest superficial or osseous lesions harboring EWSR1::NR4A3, underrecognized solid or anaplastic histology, and pan-Trk expression, posing tremendous challenges. Most TAF15::NR4A3-positive cases were >10 cm in size, ie, a crucial independent prognosticator, whereas pathogenic KIT mutation rarely occurred.
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Affiliation(s)
- Shih-Chiang Huang
- Department of Anatomic Pathology, Linkou Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Taoyuan, Taiwan; Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Jen-Chieh Lee
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yong-Chen Hsu
- Department of Pathology and Laboratory Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Jen-Wei Tsai
- Department of Pathology, E-DA Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Yu-Chien Kao
- Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Han Hsieh
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Yi-Ming Chang
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; Department of Pathology, Tri-service General Hospital, National Defense Medical Center, Taipei City, Taiwan; Institute of Medical Sciences, National Defense Medical Center, Taipei City, Taiwan
| | - Kung-Chao Chang
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pao-Shu Wu
- Department of Pathology, MacKay Memorial Hospital, Taipei, Taiwan; Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | | | - Chien-Heng Chen
- Department of Pathology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-Di Chang
- Department of Radiology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Pei-Hang Lee
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Hui-Chun Tai
- Department of Pathology, Changhua Christian Hospital, Changhua, Taiwan
| | - Ting-Ting Liu
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Mei-Chin Wen
- Division of Pathology, China Medical University Hsinchu Hospital, Hsinchu, Taiwan
| | - Wan-Shan Li
- Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan
| | - Shih-Chen Yu
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Jui-Chu Wang
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan
| | - Hsuan-Ying Huang
- Department of Anatomic Pathology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, College of Medicine, Kaohsiung, Taiwan.
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11
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Zupan A, Salapura V, Šekoranja D, Pižem J. Subcutaneous chondromyxoid fibroma with a novel PNISR::GRM1 fusion-report of a primary soft tissue tumour without connection to an underlying bone. Virchows Arch 2023; 482:917-921. [PMID: 36810795 PMCID: PMC10156755 DOI: 10.1007/s00428-023-03519-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/08/2023] [Accepted: 02/12/2023] [Indexed: 02/23/2023]
Abstract
Chondromyxoid fibroma (CMF) is a rare benign bone tumour. While CMF located entirely on the surface of a bone (i.e. juxtacortical CMF) has been well characterised, CMF has not so far been convincingly documented to arise in soft tissues without connection to an underlying bone.We report a subcutaneous CMF in a 34-year-old male, located on the distal medial aspect of the right thigh without any connection with the femur. The tumour measured 15 mm, it was well-circumscribed and displayed typical morphological features of a CMF. At the periphery, there was a small area of metaplastic bone. Immunohistochemically, the tumour cells were diffusely positive for smooth muscle actin and GRM1, and negative for S100 protein, desmin and cytokeratin AE1AE3. Whole transcriptome sequencing revealed a novel PNISR::GRM1 gene fusion.Our case indicates that CMF should be included in the differential diagnosis of soft tissue (including subcutaneous) tumours composed of spindle/ovoid cells, with a lobular architecture and chondromyxoid matrix. The diagnosis of CMF arising in soft tissues can be confirmed by identifying a GRM1 gene fusion or GRM1 expression by immunohistochemistry.
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Affiliation(s)
- Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Vladka Salapura
- Institute of Radiology, University Medical Centre Ljubljana, Zaloška 7, 1000, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, 1000, Ljubljana, Slovenia
| | - Daja Šekoranja
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia
| | - Jože Pižem
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, 1000, Ljubljana, Slovenia.
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12
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Xie L, Zhang L, Hu K, Hanyu M, Zhang Y, Fujinaga M, Minegishi K, Ohkubo T, Nagatsu K, Jiang C, Shimokawa T, Ashisuke K, Okonogi N, Yamada S, Wang F, Wang R, Zhang MR. A 211At-labelled mGluR1 inhibitor induces cancer senescence to elicit long-lasting anti-tumor efficacy. Cell Rep Med 2023; 4:100960. [PMID: 37003259 PMCID: PMC10140459 DOI: 10.1016/j.xcrm.2023.100960] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 02/09/2023] [Indexed: 04/03/2023]
Abstract
Metabotropic glutamate receptor 1 (mGluR1), a key mediator of glutamatergic signaling, is frequently overexpressed in tumor cells and is an attractive drug target for most cancers. Here, we present a targeted radiopharmaceutical therapy strategy that antagonistically recognizes mGluR1 and eradicates mGluR1+ human tumors by harnessing a small-molecule alpha (α)-emitting radiopharmaceutical, 211At-AITM. A single dose of 211At-AITM (2.96 MBq) in mGluR1+ cancers exhibits long-lasting in vivo antitumor efficacy across seven subtypes of four of the most common tumors, namely, breast cancer, pancreatic cancer, melanoma, and colon cancers, with little toxicity. Moreover, complete regression of mGluR1+ breast cancer and pancreatic cancer is observed in approximate 50% of tumor-bearing mice. Mechanistically, the functions of 211At-AITM are uncovered in downregulating mGluR1 oncoprotein and inducing senescence of tumor cells with a reprogrammed senescence-associated secretory phenotype. Our findings suggest α-radiopharmaceutical therapy with 211At-AITM can be a useful strategy for mGluR1+ pan-cancers, regardless of their tissue of origin.
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Affiliation(s)
- Lin Xie
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan.
| | - Lulu Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan; Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Kuan Hu
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan; State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Masayuki Hanyu
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Yiding Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Masayuki Fujinaga
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Katsuyuki Minegishi
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Takayuki Ohkubo
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kotaro Nagatsu
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Cuiping Jiang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan; Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Takashi Shimokawa
- Department of Charged Particle Therapy Research, Quantum Life and Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Kazuma Ashisuke
- Department of Charged Particle Therapy Research, Quantum Life and Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Noriyuki Okonogi
- Department of Charged Particle Therapy Research, Quantum Life and Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Shigeru Yamada
- Department of Charged Particle Therapy Research, Quantum Life and Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan
| | - Feng Wang
- Department of Nuclear Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 211166, China
| | - Rui Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Ming-Rong Zhang
- Department of Advanced Nuclear Medicine Sciences, Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba 263-8555, Japan.
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13
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Kao YC, Yoshida A, Hsieh TH, Nord KH, Saba KH, Ichikawa H, Tsai JW, Huang HY, Chih-Hsueh Chen P, Fletcher CDM, Lee JC. Identification of COL1A1/2 Mutations and Fusions With Noncoding RNA Genes in Bizarre Parosteal Osteochondromatous Proliferation (Nora Lesion). Mod Pathol 2023; 36:100011. [PMID: 36853784 DOI: 10.1016/j.modpat.2022.100011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/14/2022] [Accepted: 09/16/2022] [Indexed: 01/11/2023]
Abstract
Bizarre parosteal osteochondromatous proliferation (BPOP) (Nora lesion) is a benign bone surface lesion, which most commonly occurs in the digits of young patients and has a high rate of recurrence. Histologically, it is composed of a mixture of disorganized bone, cartilage, and spindle cells in variable proportions and characterized by amorphous "blue bone" mineralization. Recurrent chromosomal abnormalities, including t(1;17)(q32-42;q21-23) and inv(7)(q21.1-22q31.3-32), have been reported in BPOP. However, the exact genes involved in the rearrangements remain unknown. In this study, we analyzed 8 BPOP cases affecting the fingers, toe, ulna, radius, and fibula of 5 female and 3 male patients, aged 5 to 68 years. RNA sequencing of 5 cases identified genetic fusions between COL1A2 and LINC-PINT in 3 cases and COL1A1::MIR29B2CHG fusion in 1, both validated using fluorescence in situ hybridization and reverse transcription (RT)-PCR. The remaining fusion-negative case harbored 3 COL1A1 mutations as revealed by whole-exome sequencing and confirmed using Sanger sequencing. All these genetic alterations were predicted to cause frameshift and/or truncation of COL1A1/2. The chromosomal locations of COL1A2 (7q21.3), LINC-PINT (7q32.3), COL1A1 (17q21.33), and MIR29B2CHG (1q32.2) were consistent with the breakpoints identified in the previous cytogenetic studies. Subsequent screening of 3 BPOPs using fluorescence in situ hybridization identified 1 additional case each with COL1A1 or COL1A2 rearrangement. Our findings are consistent with reported chromosomal abnormalities and implicate the disruption of type I collagen, and perhaps of either noncoding RNA gene as a tumor suppressor, in the tumorigenesis of BPOP. The prevalence and tumorigenic mechanisms of these COL1A1/2 alterations in BPOP require further investigation.
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Affiliation(s)
- Yu-Chien Kao
- Department of Pathology, Taipei Medical University Hospital, Taipei, Taiwan; Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Akihiko Yoshida
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Tsung-Han Hsieh
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Hitoshi Ichikawa
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Jen-Wei Tsai
- Department of Pathology, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
| | - Hsuan-Ying Huang
- Department of Anatomical Pathology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | | | | | - Jen-Chieh Lee
- Department and Graduate Institute of Pathology, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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14
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Toland AMS, Lam SW, Varma S, Wang A, Howitt BE, Kunder CA, Kerr DA, Szuhai K, Bovée JVMG, Charville GW. GRM1 Immunohistochemistry Distinguishes Chondromyxoid Fibroma From its Histologic Mimics. Am J Surg Pathol 2022; 46:1407-1414. [PMID: 35650682 PMCID: PMC9481662 DOI: 10.1097/pas.0000000000001921] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Chondromyxoid fibroma (CMF) is a rare benign bone neoplasm that manifests histologically as a lobular proliferation of stellate to spindle-shaped cells in a myxoid background, exhibiting morphologic overlap with other cartilaginous and myxoid tumors of bone. CMF is characterized by recurrent genetic rearrangements that place the glutamate receptor gene GRM1 under the regulatory control of a constitutively active promoter, leading to increased gene expression. Here, we explore the diagnostic utility of GRM1 immunohistochemistry as a surrogate marker for GRM1 rearrangement using a commercially available monoclonal antibody in a study of 230 tumors, including 30 CMF cases represented by 35 specimens. GRM1 was positive by immunohistochemistry in 97% of CMF specimens (34/35), exhibiting moderate to strong staining in more than 50% of neoplastic cells; staining was diffuse (>95% of cells) in 25 specimens (71%). Among the 9 CMF specimens with documented exposure to acid decalcification, 4 (44%) exhibited diffuse immunoreactivity (>95%) for GRM1, whereas all 15 CMF specimens (100%) with lack of exposure to decalcification reagents were diffusely immunoreactive ( P =0.003). High GRM1 expression at the RNA level was previously observed by quantitative reverse transcription polymerase chain reaction in 9 CMF cases that were also positive by immunohistochemistry; low GRM1 expression was observed by quantitative reverse transcription polymerase chain reaction in the single case of CMF that was negative by immunohistochemistry. GRM1 immunohistochemistry was negative (<5%) in histologic mimics of CMF, including conventional chondrosarcoma, enchondroma, chondroblastoma, clear cell chondrosarcoma, giant cell tumor of the bone, fibrous dysplasia, chondroblastic osteosarcoma, myoepithelial tumor, primary aneurysmal bone cyst, brown tumor, phosphaturic mesenchymal tumor, CMF-like osteosarcoma, and extraskeletal myxoid chondrosarcoma. These results indicate that GRM1 immunohistochemistry may have utility in distinguishing CMF from its histologic mimics.
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Affiliation(s)
- Angus M. S. Toland
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Suk Wai Lam
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Aihui Wang
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Brooke E. Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Christian A. Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Darcy A. Kerr
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Gregory W. Charville
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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15
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Experimentally Deduced Criteria for Detection of Clinically Relevant Fusion 3′ Oncogenes from FFPE Bulk RNA Sequencing Data. Biomedicines 2022; 10:biomedicines10081866. [PMID: 36009413 PMCID: PMC9405289 DOI: 10.3390/biomedicines10081866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/15/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins demonstrate impressive anti-cancer activities. The fusion presence in the cancer is the respective drug prescription biomarker, but their identification is challenging as both the breakpoint and the exact fusion partners are unknown. RNAseq offers the advantage of finding both fusion parts by screening sequencing reads. Paraffin (FFPE) tissue blocks are the most common way of storing cancer biomaterials in biobanks. However, finding RTK fusions in FFPE samples is challenging as RNA fragments are short and their artifact ligation may appear in sequencing libraries. Here, we annotated RNAseq reads of 764 experimental FFPE solid cancer samples, 96 leukemia samples, and 2 cell lines, and identified 36 putative clinically relevant RTK fusions with junctions corresponding to exon borders of the fusion partners. Where possible, putative fusions were validated by RT-PCR (confirmed for 10/25 fusions tested). For the confirmed 3′RTK fusions, we observed the following distinguishing features. Both moieties were in-frame, and the tyrosine kinase domain was preserved. RTK exon coverage by RNAseq reads upstream of the junction site were lower than downstream. Finally, most of the true fusions were present by more than one RNAseq read. This provides the basis for automatic annotation of 3′RTK fusions using FFPE RNAseq profiles.
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16
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Xie X, Bian Y, Li H, Yin J, Tian L, Jiang R, Zeng Z, Shi X, Lei Z, Hou C, Qu Y, Wang L, Shen J. A Comprehensive Understanding of the Genomic Bone Tumor Landscape: A Multicenter Prospective Study. Front Oncol 2022; 12:835004. [PMID: 35756627 PMCID: PMC9213736 DOI: 10.3389/fonc.2022.835004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/09/2022] [Indexed: 11/25/2022] Open
Abstract
Complexity and heterogeneity increases the difficulty of diagnosis and treatment of bone tumors. We aimed to identify the mutational characterization and potential biomarkers of bone tumors. In this study, a total of 357 bone tumor patients were recruited and the next generation sequencing (NGS)-based YuanSu450 panel, that includes both DNA and RNA sequencing, was performed for genomic alteration identification. The most common mutated genes in bone tumors included TP53, NCOR1, VEGFA, RB1, CCND3, CDKN2A, GID4, CCNE1, TERT, and MAP2K4. The amplification of genes such as NCOR1, VEGFA, and CCND3 mainly occurred in osteosarcoma. Germline mutation analysis reveal a high frequency of HRD related mutations (46.4%, 13/28) in this cohort. With the assistance of RNA sequencing, 16.8% (19/113) gene fusions were independently detected in 20% (16/79) of patients. Nearly 34.2% of patients harbored actionable targeted mutations, of which the most common mutation is CDKN2A deletion. The different mutational characterizations between juvenile patients and adult patients indicated the potential effect of age in bone tumor treatment. According to the genomic alterations, the diagnosis of 26 (7.28%) bone tumors were corrected. The most easily misdiagnosed bone tumor included malignant giant cell tumors of bone (2.8%, 10/357) and fibrous dysplasia of bone (1.7%, 6/357). Meanwhile, we found that the mutations of MUC16 may be a potential biomarker for the diagnosis of mesenchymal chondrosarcomas. Our results indicated that RNA sequencing effectively complements DNA sequencing and increased the detection rate of gene fusions, supporting that NGS technology can effectively assist the diagnosis of bone tumors.
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Affiliation(s)
- Xianbiao Xie
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yiying Bian
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haomiao Li
- Department of Musculoskeletal Oncology, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Junqiang Yin
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lantian Tian
- Department of Hepatobiliary Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Renbing Jiang
- Department of Bone and Soft Tissue, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China
| | - Ziliang Zeng
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaoliang Shi
- Department of Medicine, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Zixiong Lei
- Department of Musculoskeletal Oncology, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Changhe Hou
- Department of Musculoskeletal Oncology, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Yueting Qu
- Department of Medicine, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Liwei Wang
- Department of Medicine, Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Jingnan Shen
- Department of Musculoskeletal Oncology Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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17
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Vered M, Wright JM. Update from the 5th Edition of the World Health Organization Classification of Head and Neck Tumors: Odontogenic and Maxillofacial Bone Tumours. Head Neck Pathol 2022; 16:63-75. [PMID: 35312978 PMCID: PMC9019005 DOI: 10.1007/s12105-021-01404-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
The 5th edition of the World Health Organization (WHO) Classification of Head and Neck Tumours (2022) comes out only five years after the previous edition, however it presents important updates that run in parallel with the rapid progression involving the increasingly sophisticated molecular investigation and its interpretation, some of which already have therapy-related impact. This manuscript provides an overview of the leading changes introduced in the classification of Odontogenic and Maxillofacial Bone Tumours that encompasses cysts of the jaws, odontogenic tumours, giant cell lesions and bone cysts, and bone and cartilage tumours. This is the first edition that Essential and Desirable Diagnostic Features were added for each entity, so that the most important clinical, microscopic and/or radiologic features were encapsulated and briefly highlighted. Surgical ciliated cyst was added to the group of odontogenic cysts, adenoid ameloblastoma was a newly recognized benign epithelial odontogenic tumour, and segmental odontomaxillary dysplasia was introduced in the group of fibro-osseous tumours and dysplasia. In addition, rhabdomyosarcoma with TFCP2 rearrangement, was introduced into the group of malignant jawbone tumours. The unique genetic aberrations distinguish it from other types of rhabdomyosarcomas. On the other hand, melanotic neuroectodermal tumour of infancy and osteoid osteoma were deleted from the benign bone and cartilageneous tumours, as was the hematolymphoid tumour of solitary plasmacytoma of bone. We systematically reviewed each entity in this chapter and provided important updated findings for selected topics that can further aid in the diagnostic process for challenging cases, broaden insights on the logic of the present classification, and finally, emphasize the potential that some of the molecular results may have in the near future to set new treatment approaches.
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Affiliation(s)
- Marilena Vered
- Department of Oral Pathology, Oral Medicine and Maxillofacial Imaging, School of Dental Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.
- Institute of Pathology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.
| | - John M Wright
- Department of Diagnostic Sciences, School of Dentistry, Texas A&M University, Dallas, TX, USA
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18
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Gomes CC. Recurrent driver mutations in benign tumors. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 789:108412. [PMID: 35690415 DOI: 10.1016/j.mrrev.2022.108412] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/02/2022] [Accepted: 02/09/2022] [Indexed: 06/15/2023]
Abstract
The understanding of the molecular pathogenesis of benign tumors may bring essential information to clarify the process of tumorigenesis, and ultimately improve the understanding of events such as malignant transformation. The definition of benign neoplasia is not always straightforward and herein the issues surrounding this concept are discussed. Benign neoplasms share all cancer hallmarks with malignancies, except for metastatic potential. Recently, next-generation sequencing has provided unprecedented opportunities to unravel the genetic basis of benign neoplasms and, so far, we have learned that benign neoplasms are indeed characterized by the presence of genetic mutations, including genes rearrangements. Driver mutations in advanced cancer are those that confer growth advantage, and which have been positively selected during cancer evolution. Herein, some discussion will be brought about this concept in the context of cancer prevention, involving precursor lesions and benign neoplasms. When considering early detection and cancer prevention, a driver mutation should not only be advantageous (i.e., confer survival advantage), but predisposing (i.e., promoting a cancer phenotype). By including the benign counterparts of malignant neoplasms in tumor biology studies, it is possible to evaluate the risk posed by a given mutation and to differentiate advantageous from predisposing mutations, further refining the concept of driver mutations. Therefore, the study of benign neoplasms should be encouraged because it provides valuable information on tumorigenesis central for understanding the progression from initiation to malignant transformation.
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Affiliation(s)
- Carolina Cavalieri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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19
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Wangsiricharoen S, Wakely PE, Siddiqui MT, Ali SZ. Cytopathology of chondromyxoid fibroma: a case series and review of the literature. J Am Soc Cytopathol 2021; 10:366-381. [PMID: 33958292 DOI: 10.1016/j.jasc.2021.04.001] [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: 02/03/2021] [Revised: 03/16/2021] [Accepted: 04/05/2021] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Chondromyxoid fibroma is a rare bone tumor characterized by immature myxoid mesenchymal tissue showing early primitive cartilaginous differentiation. There have been limited case reports describing the cytologic features of chondromyxoid fibroma. Herein, we reported cytologic features of chondromyxoid fibroma on fine-needle aspiration (FNA). MATERIALS AND METHODS We performed a retrospective search in our cytopathology and surgical pathology database for cases diagnosed as chondromyxoid fibroma that had corresponding cytology specimens from three medical institutions. All available cytopathology specimens were reviewed. RESULTS Eight cases were retrieved from patients aged 16-77 years (mean, 51 years), and M:F ratio of 1.7:1. Seven tumors (88%) were primary, and most (62%) occurred in flat bones. Cytologic diagnoses were made in 6 cases with cytologic slides not available to review in 1 case. All cases showed metachromatic matrix in the background, while hyaline cartilage fragments were absent. All cases had two cell populations comprising oval to round cells and stellate to spindle cells. The spindle to stellate cells were more commonly embedded in matrix material. Moderate atypia (hyperchromasia and moderate anisonucleosis) was present in 4 cases (80%), while no mitotic figure was present in all cases. CONCLUSIONS Our study highlights common cytologic features of chondromyxoid fibroma, including the presence of the spindle or stellate cells embedded in matrix material. Hyaline cartilage is uncommon and, if present, diagnostic considerations should include enchondroma or low-grade chondrosarcoma. A specific cytologic diagnosis primarily using FNA samples can be challenging but possible when evaluated in conjunction with clinical and radiologic data.
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Affiliation(s)
| | - Paul E Wakely
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Momin T Siddiqui
- Department of Pathology and Laboratory Medicine, Weil Cornell Medicine, New York Presbyterian Hospital, New York, New York
| | - Syed Z Ali
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Radiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
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20
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Anderson WJ, Doyle LA. Updates from the 2020 World Health Organization Classification of Soft Tissue and Bone Tumours. Histopathology 2021; 78:644-657. [PMID: 33438273 DOI: 10.1111/his.14265] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 12/16/2022]
Abstract
The fifth edition of the World Health Organization (WHO) classification of soft tissue and bone tumours was published in May 2020. This 'Blue Book', which is also available digitally for the first time, incorporates an array of new information on these tumours, amassed in the 7 years since the previous edition. Major advances in molecular characterisation have driven further refinements in classification and the development of ancillary diagnostic tests, and have improved our understanding of disease pathogenesis. Several new entities are also included. This review summarises the main changes introduced in the 2020 WHO classification for each subcategory of soft tissue and bone tumours.
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Affiliation(s)
- William J Anderson
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Leona A Doyle
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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21
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Grover A, Mannem RR, Hunt BC, Singh R. Chondromyxoid Fibroma of the Temporal Bone: Case Report and Literature Review. AJSP: REVIEWS AND REPORTS 2021; 26:68-72. [DOI: 10.1097/pcr.0000000000000421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
Abstract
Chondromyxoid fibroma (CMF) is a rare, benign, cartilaginous bone tumor that commonly affects the metaphysis of the lower-extremity long bones in young adults. Involvement of the craniofacial bones, especially the temporal bone, is exceedingly rare. We report a case of a 64-year-old man who presented with a left ear mass, but on subsequent imaging was found to have a more extensive mass centered in the temporal bone. Initial biopsy raised the concern for a low-grade chondrosarcoma. However, following surgical resection, a diagnosis of CMF was rendered. The clinical findings, radiographic features, histology, and differential diagnoses are discussed.
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Affiliation(s)
| | - Rajeev R. Mannem
- Radiology, Medical College of Wisconsin and Froedtert Hospital, Milwaukee, WI
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22
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Alaei-Mahabadi B, Elliott K, Larsson E. Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers. Sci Rep 2020; 10:18176. [PMID: 33097743 PMCID: PMC7584658 DOI: 10.1038/s41598-020-74420-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/10/2020] [Indexed: 11/21/2022] Open
Abstract
One of the ways in which genes can become activated in tumors is by somatic structural genomic rearrangements leading to promoter swapping events, typically in the context of gene fusions that cause a weak promoter to be substituted for a strong promoter. While identifiable by whole genome sequencing, limited availability of this type of data has prohibited comprehensive study of the phenomenon. Here, we leveraged the fact that copy number alterations (CNAs) arise as a result of structural alterations in DNA, and that they may therefore be informative of gene rearrangements, to pinpoint recurrent promoter swapping at a previously intractable scale. CNA data from nearly 9500 human tumors was combined with transcriptomic sequencing data to identify several cases of recurrent activating intrachromosomal promoter substitution events, either involving proper gene fusions or juxtaposition of strong promoters to gene upstream regions. Our computational screen demonstrates that a combination of CNA and expression data can be useful for identifying novel fusion events with potential driver roles in large cancer cohorts.
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Affiliation(s)
- Babak Alaei-Mahabadi
- Department Of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Kerryn Elliott
- Department Of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Erik Larsson
- Department Of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden.
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23
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Recurrent novel THBS1-ADGRF5 gene fusion in a new tumor subtype "Acral FibroChondroMyxoid Tumors". Mod Pathol 2020; 33:1360-1368. [PMID: 32047233 DOI: 10.1038/s41379-020-0493-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 11/08/2022]
Abstract
Acral soft tissue tumors are common neoplasms, a subset of which pose a diagnostic challenge. We report 10 cases of a previously unrecognized acral benign soft tissue tumor. These tumors arose on the fingers and toes and involved bone in half of cases. Histologically, the tumors were lobulated and displayed an abundant stroma made of variable fibrous, chondroid and myxoid material reminiscent of cartilaginous or myoepithelial differentiation. Tumor cells harbored small round to reniform nuclei with clear chromatin and inconspicuous nucleoli along with scant eosinophilic cytoplasm. The cells were mostly arranged haphazardly in the stroma but also in small clusters. No mitotic activity was detected. No specific feature was identified in recurrent cases. By immunohistochemistry, the cells consistently stained for CD34 (10/10), ERG (9/10), and SOX9 (7/10). Whole RNA sequencing identified a previously undescribed recurrent in frame THBS1-ADGRF5 gene fusion in all cases. The transcript was confirmed by RT-PCR and was not found in the control group of mimickers including soft tissue chondromas. We propose the name of Acral FibroChondroMyxoid Tumors for this new entity.
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24
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Suster D, Hung YP, Nielsen GP. Differential Diagnosis of Cartilaginous Lesions of Bone. Arch Pathol Lab Med 2020; 144:71-82. [PMID: 31877083 DOI: 10.5858/arpa.2019-0441-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Cartilaginous tumors represent one of the most common tumors of bone. Management of these tumors includes observation, curettage, and surgical excision or resection, depending on their locations and whether they are benign or malignant. They can be diagnostically challenging, particularly in small biopsies. In rare cases, benign tumors may undergo malignant transformation. OBJECTIVE.— To review common cartilaginous tumors, including in patients with multiple hereditary exostosis, Ollier disease, and Maffucci syndrome, and to discuss problems in the interpretation of well-differentiated cartilaginous neoplasms of bone. Additionally, the concept of atypical cartilaginous tumor/chondrosarcoma grade 1 will be discussed and its use clarified. DATA SOURCES.— PubMed (US National Library of Medicine, Bethesda, Maryland) literature review, case review of archival cases at the Massachusetts General Hospital, and personal experience of the authors. CONCLUSIONS.— This review has examined primary well-differentiated cartilaginous lesions of bone, including their differential diagnosis and approach to management. Because of the frequent overlap in histologic features, particularly between low-grade chondrosarcoma and enchondroma, evaluation of well-differentiated cartilaginous lesions should be undertaken in conjunction with thorough review of the imaging studies.
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Affiliation(s)
- David Suster
- From the Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Yin Pun Hung
- From the Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - G Petur Nielsen
- From the Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston
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25
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Baumhoer D, Höller S. [Molecular pathology in the diagnosis of bone tumors: current concepts]. DER PATHOLOGE 2020; 41:106-115. [PMID: 31993697 DOI: 10.1007/s00292-019-00746-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The integrative evaluation of histology and corresponding imaging is essential for the classification of bone tumors. Until a few years ago, there were hardly any molecular markers that could be used for diagnostic purposes. However, exome- and genome-wide sequencing analyses have since uncovered a number of tumor-specific aberrations that can be very helpful in ambiguous cases. In addition to characteristic gene mutations (e.g. H3F3A and H3F3B in giant-cell tumors and chondroblastomas), the detection of fusion transcripts (e.g. structural rearrangements in the AP‑1 transcription factors FOS and FOSB in osteoid osteomas and osteoblastomas) plays an increasing role. The article gives an overview of the current state of knowledge of the most important alterations in bone tumors.
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Affiliation(s)
- Daniel Baumhoer
- Knochentumor-Referenzzentrum, Institut für Pathologie, Universitätsspital Basel, Universität Basel, Schönbeinstrasse 40, Basel, 4031, Schweiz.
| | - Sylvia Höller
- Knochentumor-Referenzzentrum, Institut für Pathologie, Universitätsspital Basel, Universität Basel, Schönbeinstrasse 40, Basel, 4031, Schweiz
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26
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Hartmann W. [Challenges in the diagnosis of cartilage tumors : Morphological spectrum and molecular markers]. DER ORTHOPADE 2019; 48:735-743. [PMID: 31414142 DOI: 10.1007/s00132-019-03787-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The morphological and clinico-biological spectrum of chondrogenic tumours is wide. Given the diversity of therapeutic approaches, the correctness of the histological diagnosis is of major importance. The aim of this review is to provide insights into the challenges and limitations of diagnostic approaches restricted to morphology and to underscore the importance of an interdisciplinary dialogue between surgeons, radiologists and pathologists. Beyond this, the value of molecular analyses introduced in bone tumor diagnostics in recent years is discussed.
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Affiliation(s)
- Wolfgang Hartmann
- Sektion für Translationale Pathologie, Gerhard-Domagk-Institut für Pathologie, Universitätsklinikum Münster, Albert-Schweitzer-Campus 1, D17, 48149, Münster, Deutschland.
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27
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Saba KH, Cornmark L, Rissler M, Fioretos T, Åström K, Haglund F, Rosenberg AE, Brosjö O, Nord KH. Genetic profiling of a chondroblastoma-like osteosarcoma/malignant phosphaturic mesenchymal tumor of bone reveals a homozygous deletion of CDKN2A, intragenic deletion of DMD, and a targetable FN1-FGFR1 gene fusion. Genes Chromosomes Cancer 2019; 58:731-736. [PMID: 31066955 DOI: 10.1002/gcc.22764] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 12/22/2022] Open
Abstract
Conventional osteosarcoma is the most common primary malignancy of bone. This group of neoplasms is subclassified according to specific histological features, but hitherto there has been no correlation between subtype, treatment, and prognosis. By in-depth genetic analyses of a chondroblastoma-like osteosarcoma, we detect a genetic profile that is distinct from those previously reported in benign and malignant bone tumors. The overall genomic copy number profile was less complex than that typically associated with conventional osteosarcoma, and there was no activating point mutation in any of H3F3A, H3F3B, IDH1, IDH2, BRAF, or GNAS. Instead, we found a homozygous CDKN2A deletion, a DMD microdeletion and an FN1-FGFR1 gene fusion. The latter alteration has been described in phosphaturic mesenchymal tumor. This tumor type shares some morphological features with chondroblastoma-like osteosarcoma and we cannot rule out that the present case actually represents an FN1-FGFR1 positive malignant phosphaturic mesenchymal tumor of bone without osteomalacia.
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Affiliation(s)
- Karim H Saba
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Louise Cornmark
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Marianne Rissler
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Thoas Fioretos
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
| | - Kristina Åström
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Felix Haglund
- Department of Clinical Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.,Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
| | - Andrew E Rosenberg
- Department of Pathology, Miller School of Medicine, University of Miami, Miami, Florida
| | - Otte Brosjö
- Department of Orthopedics, Karolinska University Hospital, Stockholm, Sweden
| | - Karolin H Nord
- Department of Laboratory Medicine, Division of Clinical Genetics, Lund University, Lund, Sweden
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28
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Krzyzanowski PM, Sircoulomb F, Yousif F, Normand J, La Rose J, E Francis K, Suarez F, Beck T, McPherson JD, Stein LD, Rottapel RK. Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer. Sci Rep 2019; 9:3590. [PMID: 30837567 PMCID: PMC6401071 DOI: 10.1038/s41598-019-39878-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 01/30/2019] [Indexed: 01/10/2023] Open
Abstract
Genomic rearrangements are a hallmark of cancer biology and progression, allowing cells to rapidly transform through alterations in regulatory structures, changes in expression patterns, reprogramming of signaling pathways, and creation of novel transcripts via gene fusion events. Though functional gene fusions encoding oncogenic proteins are the most dramatic outcomes of genomic rearrangements, we investigated the relationship between rearrangements evidenced by fusion transcripts and local expression changes in cancer using transcriptome data alone. 9,953 gene fusion predictions from 418 primary serious ovarian cancer tumors were analyzed, identifying depletions of gene fusion breakpoints within coding regions of fused genes as well as an N-terminal enrichment of breakpoints within fused genes. We identified 48 genes with significant fusion-associated upregulation and furthermore demonstrate that significant regional overexpression of intact genes in patient transcriptomes occurs within 1 megabase of 78 novel gene fusions that function as central markers of these regions. We reveal that cancer transcriptomes select for gene fusions that preserve protein and protein domain coding potential. The association of gene fusion transcripts with neighboring gene overexpression supports rearrangements as mechanism through which cancer cells remodel their transcriptomes and identifies a new way to utilize gene fusions as indicators of regional expression changes in diseased cells with only transcriptomic data.
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Affiliation(s)
- Paul M Krzyzanowski
- Department of Medicine, University of Toronto, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.
| | - Fabrice Sircoulomb
- Department of Immunology, University of Toronto, Princess Margaret Cancer Center, MaRS Centre, Toronto, Ontario, Canada
| | - Fouad Yousif
- Department of Medicine, University of Toronto, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada
| | - Josee Normand
- Department of Immunology, University of Toronto, Princess Margaret Cancer Center, MaRS Centre, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jose La Rose
- Department of Immunology, University of Toronto, Princess Margaret Cancer Center, MaRS Centre, Toronto, Ontario, Canada
| | - Kyle E Francis
- Department of Immunology, University of Toronto, Princess Margaret Cancer Center, MaRS Centre, Toronto, Ontario, Canada
| | - Fernando Suarez
- Department of Immunology, University of Toronto, Princess Margaret Cancer Center, MaRS Centre, Toronto, Ontario, Canada
| | - Tim Beck
- Human Longevity Inc., San Diego, California, USA
| | - John D McPherson
- Department of Medicine, University of Toronto, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada.,University of California, Davis Medical Center, Sacramento, California, USA
| | - Lincoln D Stein
- Department of Medicine, University of Toronto, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Robert K Rottapel
- Department of Medicine, University of Toronto, Ontario Institute for Cancer Research, MaRS Centre, Toronto, Ontario, Canada. .,Department of Immunology, University of Toronto, Princess Margaret Cancer Center, MaRS Centre, Toronto, Ontario, Canada.
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29
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Lam SW, van IJzendoorn DG, Cleton-Jansen AM, Szuhai K, Bovée JV. Molecular Pathology of Bone Tumors. J Mol Diagn 2019; 21:171-182. [DOI: 10.1016/j.jmoldx.2018.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/04/2018] [Accepted: 11/16/2018] [Indexed: 12/23/2022] Open
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30
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Baumhoer D, Amary F, Flanagan AM. An update of molecular pathology of bone tumors. Lessons learned from investigating samples by next generation sequencing. Genes Chromosomes Cancer 2018; 58:88-99. [PMID: 30582658 DOI: 10.1002/gcc.22699] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/25/2018] [Accepted: 10/25/2018] [Indexed: 12/27/2022] Open
Abstract
The last decade has seen the majority of primary bone tumor subtypes become defined by molecular genetic alteration. Examples include giant cell tumour of bone (H3F3A p.G34W), chondroblastoma (H3F3B p.K36M), mesenchymal chondrosarcoma (HEY1-NCOA2), chondromyxoid fibroma (GRM1 rearrangements), aneurysmal bone cyst (USP6 rearrangements), osteoblastoma/osteoid osteoma (FOS/FOSB rearrangements), and synovial chondromatosis (FN1-ACVR2A and ACVR2A-FN1). All such alterations are mutually exclusive. Many of these have been translated into clinical service using immunohistochemistry or FISH. 60% of central chondrosarcoma is characterised by either isocitrate dehydrogenase (IDH) 1 or IDH2 mutations distinguishing them from other cartilaginous tumours. In contrast, recurrent alterations which are clinically helpful have not been found in high grade osteosarcoma. High throughput next generation sequencing has also proved valuable in identifying germ line alterations in a significant proportion of young patients with primary malignant bone tumors. These findings will play an increasing role in reaching a diagnosis and in patient management.
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Affiliation(s)
- Daniel Baumhoer
- Bone Tumour Reference Centre, Institute of Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Fernanda Amary
- Department of Pathology, The Royal National Orthopaedic Hospital, Stanmore, Middlesex, United Kingdom.,Department of Pathology, Cancer Institute, University College London, London, United Kingdom
| | - Adrienne M Flanagan
- Department of Pathology, The Royal National Orthopaedic Hospital, Stanmore, Middlesex, United Kingdom.,Department of Pathology, Cancer Institute, University College London, London, United Kingdom
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31
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Sono T, Ware AD, McCarthy EF, James AW. Chondromyxoid Fibroma of the Pelvis: Institutional Case Series With a Focus on Distinctive Features. Int J Surg Pathol 2018; 27:352-359. [PMID: 30580642 DOI: 10.1177/1066896918820446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chondromyxoid fibroma (CMF) is a relatively uncommon benign bone tumor of cartilaginous differentiation. The primary pitfall in the histopathologic diagnosis of CMF is confusion with a high-grade chondrosarcoma, owing to the atypical stellate and spindled cells set within a chondromyxoid background. CMF is particularly challenging to diagnose within the pelvis, where clinical suspicion for chondrosarcoma is high and benign lesions may grow to a large size to occupy the pelvic bones. In our practice, we noted this difficulty in several consecutive cases, especially when older patients presented with CMF within the pelvis. This prompted an institutional retrospective case review of all CMF within the pelvis. In 10 cases, we found overall that CMF of pelvis occurred in an older age range (mean age = 48.6 years), was larger in size (mean size = 6.0 cm), and showed a higher rate of soft tissue extension (50%) as compared with prior reports of nonpelvic CMF. Typical histologic features of CMF were seen in all cases; however, a high frequency of dystrophic calcification (50%) and necrosis (30%) was observed. Of interest, these aggregate demographic, radiologic, and histologic findings are all consistent with a benign neoplasm that has grown undetected within the pelvis over a long period of time. Recognition of these differences between pelvic CMF and tumors involving other sites will aid in avoiding misdiagnosis of this uncommon entity.
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32
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He K, Jiang S, Zhang X, Mao Y, Zhu W, Wang Y, Song J, Chen L. Preliminary Exploration of the Diagnosis and Treatment of Skull-Based Chondromyxoid Fibromas. Oper Neurosurg (Hagerstown) 2018; 15:270-277. [PMID: 29165705 DOI: 10.1093/ons/opx233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Accepted: 10/10/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Chondromyxoid fibromas (CMFs) are benign tumors that occur rarely in the skull base. OBJECTIVE To conduct a preliminary exploration of the diagnosis and treatment of cranial CMFs. METHODS A retrospective analysis of 19 cases of CMFs in the base of the skull between 2009 and 2014 in our hospital was conducted. The clinical manifestations, imaging characteristics, pathology, treatment strategies, and outcomes were examined. RESULTS The study cohort included 7 women (36.8%) and 12 men (63.2%), and symptom duration ranged from 1 mo to 5 yr. Of the 19 intracranial CMF cases examined, 15 (78.9%) conformed with the diagnostic criteria for extracranial CMF. Resection operations yielded subtotal removal of 13 tumors (68.4%) and partial removal of 6 tumors (31.6%). Postoperative pathological analysis demonstrated that the tumors were characterized by spindle-shaped or stellate cells arranged in a myxoid matrix without mitoses or permeation. Follow-up (range 2-7.3 yr; mean, 4.4 ± 1.7 yr) revealed that symptoms improved postoperatively in 15 cases (78.9%), were maintained in 2 cases (10.5%), and worsened in 2 cases (10.5%). Imaging follow-up revealed that residual tumors were stable in 18 cases (94.7%) and enlarged in 1 case (5.3%). CONCLUSION An accurate diagnosis should involve comprehensive consideration of clinical, radiological, and pathological features. The treatment strategy for CMFs consists of maximizing tumor removal while protecting adjacent key structures. Postoperative stereotactic radiotherapy is appropriate for residual tumors.
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Affiliation(s)
- Kangmin He
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Shize Jiang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xin Zhang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Wei Zhu
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yin Wang
- Department of Pathology, Hua-shan Hospital, Fudan University, Shan-ghai, China
| | - Jianping Song
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Liang Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
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33
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Anderson ND, de Borja R, Young MD, Fuligni F, Rosic A, Roberts ND, Hajjar S, Layeghifard M, Novokmet A, Kowalski PE, Anaka M, Davidson S, Zarrei M, Id Said B, Schreiner LC, Marchand R, Sitter J, Gokgoz N, Brunga L, Graham GT, Fullam A, Pillay N, Toretsky JA, Yoshida A, Shibata T, Metzler M, Somers GR, Scherer SW, Flanagan AM, Campbell PJ, Schiffman JD, Shago M, Alexandrov LB, Wunder JS, Andrulis IL, Malkin D, Behjati S, Shlien A. Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors. Science 2018; 361:eaam8419. [PMID: 30166462 PMCID: PMC6176908 DOI: 10.1126/science.aam8419] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 03/19/2018] [Accepted: 07/13/2018] [Indexed: 12/25/2022]
Abstract
Sarcomas are cancers of the bone and soft tissue often defined by gene fusions. Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors. We explored how and when EWSR1-ETS fusions arise by studying the whole genomes of Ewing sarcomas. In 52 of 124 (42%) of tumors, the fusion gene arises by a sudden burst of complex, loop-like rearrangements, a process called chromoplexy, rather than by simple reciprocal translocations. These loops always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions. Similar loops forming canonical fusions were found in three other sarcoma types. Chromoplexy-generated fusions appear to be associated with an aggressive form of Ewing sarcoma. These loops arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.
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Affiliation(s)
- Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Richard de Borja
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Fabio Fuligni
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrej Rosic
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicola D Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Simon Hajjar
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Layeghifard
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ana Novokmet
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul E Kowalski
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew Anaka
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Davidson
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Badr Id Said
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - L Christine Schreiner
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Remi Marchand
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Sitter
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Garrett T Graham
- Department of Oncology and Pediatrics, Georgetown University, Washington, DC, USA
| | - Anthony Fullam
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nischalan Pillay
- University College London Cancer Institute, Huntley Street, London, UK
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Jeffrey A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, Washington, DC, USA
| | - Akihiko Yoshida
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Sciences, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Gino R Somers
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adrienne M Flanagan
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Peter J Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joshua D Schiffman
- Departments of Pediatrics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Mary Shago
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA
| | - Jay S Wunder
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Orthopaedic Surgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Division of Hematology-Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Ontario, Canada
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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Tran AN, Taylan F, Zachariadis V, Ivanov Öfverholm I, Lindstrand A, Vezzi F, Lötstedt B, Nordenskjöld M, Nordgren A, Nilsson D, Barbany G. High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing. PLoS One 2018. [PMID: 29529047 PMCID: PMC5846771 DOI: 10.1371/journal.pone.0193928] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The detection of recurrent somatic chromosomal rearrangements is standard of care for most leukemia types. Even though karyotype analysis-a low-resolution genome-wide chromosome analysis-is still the gold standard, it often needs to be complemented with other methods to increase resolution. To evaluate the feasibility and applicability of mate pair whole genome sequencing (MP-WGS) to detect structural chromosomal rearrangements in the diagnostic setting, we sequenced ten bone marrow samples from leukemia patients with recurrent rearrangements. Samples were selected based on cytogenetic and FISH results at leukemia diagnosis to include common rearrangements of prognostic relevance. Using MP-WGS and in-house bioinformatic analysis all sought rearrangements were successfully detected. In addition, unexpected complexity or additional, previously undetected rearrangements was unraveled in three samples. Finally, the MP-WGS analysis pinpointed the location of chromosome junctions at high resolution and we were able to identify the exact exons involved in the resulting fusion genes in all samples and the specific junction at the nucleotide level in half of the samples. The results show that our approach combines the screening character from karyotype analysis with the specificity and resolution of cytogenetic and molecular methods. As a result of the straightforward analysis and high-resolution detection of clinically relevant rearrangements, we conclude that MP-WGS is a feasible method for routine leukemia diagnostics of structural chromosomal rearrangements.
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Affiliation(s)
- Anh Nhi Tran
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ingegerd Ivanov Öfverholm
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Britta Lötstedt
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Gisela Barbany
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Laboratory Division Karolinska University Hospital, Clinical Genetics, Stockholm, Sweden
- * E-mail:
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36
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Flanagan AM, Lindsay D. A diagnostic approach to bone tumours. Pathology 2017; 49:675-687. [PMID: 29110879 DOI: 10.1016/j.pathol.2017.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/03/2017] [Accepted: 08/07/2017] [Indexed: 12/21/2022]
Abstract
In this review we discuss an approach to diagnosing primary bone tumours, namely the cartilaginous, bone-forming, giant cell-rich, fibro-osseous and round cell neoplasms. Less common lesions including chordoma are also discussed. The value of integrating clinical, histopathological and relevant radiological features is emphasised with a view to providing the general histopathologist with a methodical approach to reaching an accurate diagnosis.
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Affiliation(s)
- Adrienne M Flanagan
- Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, United Kingdom; UCL - Cancer Institute, London, United Kingdom.
| | - Daniel Lindsay
- Royal National Orthopaedic Hospital, Brockley Hill, Stanmore, United Kingdom
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Abstract
Giant cell-containing tumors of bone are characterized morphologically by the presence of numerous osteoclastic giant cells. Correlation of clinical, radiologic, and laboratory findings is required for accurate histopathologic diagnosis and treatment of a giant cell-containing tumor of bone. In differential diagnosis, it is particularly important to note the age of the patient and the skeletal location of the lesion. This article considers the range of neoplastic and nonneoplastic lesions, which histologically contain numerous osteoclastic giant cells, and focuses on several lesions that frequently enter into the differential diagnosis.
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Affiliation(s)
- Zsolt Orosz
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal and Sciences, Nuffield Orthopaedic Centre, Windmill Road, University of Oxford, Oxford OX3 7HE, UK
| | - Nicholas A Athanasou
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal and Sciences, Nuffield Orthopaedic Centre, Windmill Road, University of Oxford, Oxford OX3 7HE, UK.
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38
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Mariño-Enríquez A, Bovée JVMG. Molecular Pathogenesis and Diagnostic, Prognostic and Predictive Molecular Markers in Sarcoma. Surg Pathol Clin 2017; 9:457-73. [PMID: 27523972 DOI: 10.1016/j.path.2016.04.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sarcomas are infrequent mesenchymal neoplasms characterized by notable morphological and molecular heterogeneity. Molecular studies in sarcoma provide refinements to morphologic classification, and contribute diagnostic information (frequently), prognostic stratification (rarely) and predict therapeutic response (occasionally). Herein, we summarize the major molecular mechanisms underlying sarcoma pathogenesis and present clinically useful diagnostic, prognostic and predictive molecular markers for sarcoma. Five major molecular alterations are discussed, illustrated with representative sarcoma types, including 1. the presence of chimeric transcription factors, in vascular tumors; 2. abnormal kinase signaling, in gastrointestinal stromal tumor; 3. epigenetic deregulation, in chondrosarcoma, chondroblastoma, and other tumors; 4. deregulated cell survival and proliferation, due to focal copy number alterations, in dedifferentiated liposarcoma; 5. extreme genomic instability, in conventional osteosarcoma as a representative example of sarcomas with highly complex karyotype.
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Affiliation(s)
- Adrián Mariño-Enríquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
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39
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Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res 2017; 6:664. [PMID: 28781756 DOI: 10.12688/f1000research.11168.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2017] [Indexed: 01/07/2023] Open
Abstract
Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - Pall Olason
- Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-752 37, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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40
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Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res 2017; 6:664. [PMID: 28781756 PMCID: PMC5521161 DOI: 10.12688/f1000research.11168.2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2017] [Indexed: 01/25/2023] Open
Abstract
Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - Pall Olason
- Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-752 37, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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41
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Nilsson D, Pettersson M, Gustavsson P, Förster A, Hofmeister W, Wincent J, Zachariadis V, Anderlid BM, Nordgren A, Mäkitie O, Wirta V, Käller M, Vezzi F, Lupski JR, Nordenskjöld M, Lundberg ES, Carvalho CMB, Lindstrand A. Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation. Hum Mutat 2017; 38:180-192. [PMID: 27862604 PMCID: PMC5225243 DOI: 10.1002/humu.23146] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/01/2016] [Indexed: 11/07/2022]
Abstract
Most balanced translocations are thought to result mechanistically from nonhomologous end joining or, in rare cases of recurrent events, by nonallelic homologous recombination. Here, we use low-coverage mate pair whole-genome sequencing to fine map rearrangement breakpoint junctions in both phenotypically normal and affected translocation carriers. In total, 46 junctions from 22 carriers of balanced translocations were characterized. Genes were disrupted in 48% of the breakpoints; recessive genes in four normal carriers and known dominant intellectual disability genes in three affected carriers. Finally, seven candidate disease genes were disrupted in five carriers with neurocognitive disabilities (SVOPL, SUSD1, TOX, NCALD, SLC4A10) and one XX-male carrier with Tourette syndrome (LYPD6, GPC5). Breakpoint junction analyses revealed microhomology and small templated insertions in a substantive fraction of the analyzed translocations (17.4%; n = 4); an observation that was substantiated by reanalysis of 37 previously published translocation junctions. Microhomology associated with templated insertions is a characteristic seen in the breakpoint junctions of rearrangements mediated by error-prone replication-based repair mechanisms. Our data implicate that a mechanism involving template switching might contribute to the formation of at least 15% of the interchromosomal translocation events.
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Affiliation(s)
- Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Alisa Förster
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Vasilios Zachariadis
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
- Children's Hospital, Helsinki University Central Hospital and University of Helsinki, 00290 Helsinki, Finland
- Folkhälsan Institute of Genetics, 00290 Helsinki, Finland
| | - Valtteri Wirta
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Max Käller
- SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, 171 71 Stockholm, Sweden
| | - Francesco Vezzi
- SciLifeLab, Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
- Texas Children’s Hospital, 77030 Houston TX, USA
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Elisabeth Syk Lundberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Claudia M. B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, 77030 Houston TX, USA
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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42
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Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. Proc Natl Acad Sci U S A 2016; 113:13768-13773. [PMID: 27856756 DOI: 10.1073/pnas.1606220113] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tumor genomes are mosaics of somatic structural variants (SVs) that may contribute to the activation of oncogenes or inactivation of tumor suppressors, for example, by altering gene copy number amplitude. However, there are multiple other ways in which SVs can modulate transcription, but the general impact of such events on tumor transcriptional output has not been systematically determined. Here we use whole-genome sequencing data to map SVs across 600 tumors and 18 cancers, and investigate the relationship between SVs, copy number alterations (CNAs), and mRNA expression. We find that 34% of CNA breakpoints can be clarified structurally and that most amplifications are due to tandem duplications. We observe frequent swapping of strong and weak promoters in the context of gene fusions, and find that this has a measurable global impact on mRNA levels. Interestingly, several long noncoding RNAs were strongly activated by this mechanism. Additionally, SVs were confirmed in telomere reverse transcriptase (TERT) upstream regions in several cancers, associated with elevated TERT mRNA levels. We also highlight high-confidence gene fusions supported by both genomic and transcriptomic evidence, including a previously undescribed paired box 8 (PAX8)-nuclear factor, erythroid 2 like 2 (NFE2L2) fusion in thyroid carcinoma. In summary, we combine SV, CNA, and expression data to provide insights into the structural basis of CNAs as well as the impact of SVs on gene expression in tumors.
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43
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Kjeldsen E. Data on affected cancer-related genes in pediatric t(12;21)-positive acute lymphoblastic leukemia patients harboring unbalanced der(6)t(X;6) translocations. Data Brief 2016; 8:894-903. [PMID: 27508240 PMCID: PMC4961797 DOI: 10.1016/j.dib.2016.06.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 11/17/2022] Open
Abstract
The t(12;21)(p13;q22), leading to ETV6/RUNX1 fusion, is of importance for leukemogenesis in acute lymphoblastic leukemia but is not sufficient for the leukemic transformation. Acquired secondary chromosomal aberrations are necessary for overt leukemia but their complete nature and genes involved are still elusive. In our recent publication, “Oligo-based aCGH analysis reveals cryptic unbalanced der(6)t(X;6) in pediatric t(12;21)-positive acute lymphoblastic leukemia”, we identified acquired common concurrent regions with 6q deletion and Xq duplication E. Kjeldsen (2016) [1]. The present article provides data on genes that are associated with hematological malignancy and other cancers located in these common regions of chromosomal aberrations.
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Marino-Enriquez A. Advances in the Molecular Analysis of Soft Tissue Tumors and Clinical Implications. Surg Pathol Clin 2016; 8:525-37. [PMID: 26297069 DOI: 10.1016/j.path.2015.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The emergence of high-throughput molecular technologies has accelerated the discovery of novel diagnostic, prognostic and predictive molecular markers. Clinical implementation of these technologies is expected to transform the practice of surgical pathology. In soft tissue tumor pathology, accurate interpretation of comprehensive genomic data provides useful diagnostic and prognostic information, and informs therapeutic decisions. This article reviews recently developed molecular technologies, focusing on their application to the study of soft tissue tumors. Emphasis is made on practical issues relevant to the surgical pathologist. The concept of genomically-informed therapies is presented as an essential motivation to identify targetable molecular alterations in sarcoma.
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Affiliation(s)
- Adrian Marino-Enriquez
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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Shiba E, Matsuyama A, Shibuya R, Yabuki K, Harada H, Nakamoto M, Kasai T, Hisaoka M. Immunohistochemical and molecular detection of the expression of FGF23 in phosphaturic mesenchymal tumors including the non-phosphaturic variant. Diagn Pathol 2016; 11:26. [PMID: 26956379 PMCID: PMC4784377 DOI: 10.1186/s13000-016-0477-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 03/03/2016] [Indexed: 01/12/2023] Open
Abstract
Background Phosphaturic mesenchymal tumors (PMTs) are rare neoplasms that are often associated with tumor-induced osteomalacia (TIO) due to excessive serum levels of fibroblast growth factor 23 (FGF23). PMTs share overlapping histologic features with other types of tumors; thus, accurate pathological diagnosis may be challenging. We performed an immunohistochemical examination of FGF23 expression in PMTs and other types of tumors, together with pertinent molecular analyses. Methods Seven PMTs (5 with TIO and 2 without TIO) and 46 other types of bone and soft tissue tumors were retrieved, and immunohistochemistry was performed using a commercially available anti-FGF23 antibody. In addition, FGF23 mRNA expression was detected by reverse transcription-polymerase chain reaction (RT-PCR), using RNA extracted from formalin-fixed, paraffin-embedded tissues. Results Immunohistochemical analysis of FGF23 expression showed distinct, punctate staining in the cytoplasm in 5 PMTs with TIO, whereas FGF23 expression was negative in the 2 PMTs without TIO and the other 46 tumors. FGF23 mRNA expression was detected in all 4 PMTs examined, as well as in 1 chondromyxoid fibroma and 1 myxoid liposarcoma. The real-time RT-PCR data showed that the relative expression levels of the FGF23 mRNA tended to be higher in PMTs with TIO than in PMTs without TIO, or in the chondromyxoid fibroma specimen. Conclusions Our data suggested that the feasibility of immunohistochemical detection of FGF23 may depend on the level of secreted FGF23 from tumor cells. Thus, immunohistochemistry for FGF23 is an useful diagnostic adjunct for PMT, although its utility appears to be limited in cases without TIO.
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Affiliation(s)
- Eisuke Shiba
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
| | - Atsuji Matsuyama
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
| | - Ryo Shibuya
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
| | - Kei Yabuki
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
| | - Hiroshi Harada
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
| | - Mitsuhiro Nakamoto
- Kagoshima Occupational and Environmental Health Center, 4-96 Tokaicho, Kagoshima, 891-0115, Japan.
| | - Takahiko Kasai
- National Hospital Organization Kinki-Chuo Chest Medical Center, 1180 Nagasonecho, Kita-ku, Sakai, Osaka, 591-8025, Japan.
| | - Masanori Hisaoka
- Department of Pathology and Oncology, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan.
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Mutation Analysis of H3F3A and H3F3B as a Diagnostic Tool for Giant Cell Tumor of Bone and Chondroblastoma. Am J Surg Pathol 2016; 39:1576-83. [PMID: 26457357 DOI: 10.1097/pas.0000000000000512] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Specific H3F3A driver mutations and IDH2 mutations were recently described in giant cell tumor of bone (GCTB) and H3F3B driver mutations in chondroblastoma; these may be helpful as a diagnostic tool for giant cell-containing tumors of the bone. Using Sanger sequencing, we determined the frequency of H3F3A, H3F3B, IDH1, and IDH2 mutations in GCTBs (n=60), chondroblastomas (n=12), and other giant cell-containing tumors (n=24), including aneurysmal bone cyst, chondromyxoid fibroma, and telangiectatic osteosarcoma. To find an easy applicable marker for H3F3A mutation status, H3K36 trimethylation and ATRX expression were correlated with H3F3A mutations. In total, 69% of all GCTBs harbored an H3F3A (G34W/V) mutation compared with 0% of all other giant cell-containing tumors (P<0.001), whereas 70% of chondroblastomas showed an H3F3B (K36M) mutation compared with 0% of other giant cell-containing tumors (P<0.001). Diffuse H3K36 trimethylation positivity was more often seen in mutated H3F3A GCTBs compared with other giant cell-containing tumors (P=0.005). ATRX protein expression was not correlated with H3F3A mutation status. Hotspot mutations in IDH1 or IDH2 were absent. Our results show that H3F3A and H3F3B mutation analysis appears to be a highly specific, although less sensitive, diagnostic tool for the distinction of GCTB and chondroblastoma from other giant cell-containing tumors. Although H3K36 trimethylation and ATRX immunohistochemistry cannot be used as surrogate markers for H3F3A mutation status, mutations in H3F3A are associated with increased H3K36 trimethylation, suggesting that methylation at this residue may play a role in the etiology of the disease.
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Cleven AHG, Briaire-de Bruijn I, Szuhai K, Bovée JVMG. DOG1 expression in giant-cell-containing bone tumours. Histopathology 2015; 68:942-5. [DOI: 10.1111/his.12873] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arjen H G Cleven
- Department of Pathology; Leiden University Medical Centre; Leiden The Netherlands
| | | | - Károly Szuhai
- Department of Pathology; Leiden University Medical Centre; Leiden The Netherlands
| | - Judith V M G Bovée
- Department of Pathology; Leiden University Medical Centre; Leiden The Netherlands
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de Graaff MA, de Jong D, Briaire-de Bruijn IH, Hogendoorn PC, Bovée JV, Szuhai K. A translocation t(6;14) in two cases of leiomyosarcoma: Molecular cytogenetic and array-based comparative genomic hybridization characterization. Cancer Genet 2015; 208:537-44. [DOI: 10.1016/j.cancergen.2015.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/29/2015] [Accepted: 07/27/2015] [Indexed: 11/17/2022]
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Abstract
Spontaneously occurring mutations accumulate in somatic cells throughout a person’s lifetime. The majority of these mutations do not have a noticeable effect, but some can alter key cellular functions. Early somatic mutations can cause developmental disorders, whereas the progressive accumulation of mutations throughout life can lead to cancer and contribute to aging. Genome sequencing has revolutionized our understanding of somatic mutation in cancer, providing a detailed view of the mutational processes and genes that drive cancer. Yet, fundamental gaps remain in our knowledge of how normal cells evolve into cancer cells. We briefly summarize a number of the lessons learned over 5 years of cancer genome sequencing and discuss their implications for our understanding of cancer progression and aging.
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Affiliation(s)
| | - Peter J. Campbell
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
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Presneau N, Baumhoer D, Behjati S, Pillay N, Tarpey P, Campbell PJ, Jundt G, Hamoudi R, Wedge DC, Loo PV, Hassan AB, Khatri B, Ye H, Tirabosco R, Amary MF, Flanagan AM. Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2015; 1:113-23. [PMID: 27499898 PMCID: PMC4858131 DOI: 10.1002/cjp2.13] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/24/2014] [Indexed: 12/11/2022]
Abstract
Driver mutations in the two histone 3.3 (H3.3) genes, H3F3A and H3F3B, were recently identified by whole genome sequencing in 95% of chondroblastoma (CB) and by targeted gene sequencing in 92% of giant cell tumour of bone (GCT). Given the high prevalence of these driver mutations, it may be possible to utilise these alterations as diagnostic adjuncts in clinical practice. Here, we explored the spectrum of H3.3 mutations in a wide range and large number of bone tumours (n = 412) to determine if these alterations could be used to distinguish GCT from other osteoclast-rich tumours such as aneurysmal bone cyst, nonossifying fibroma, giant cell granuloma, and osteoclast-rich malignant bone tumours and others. In addition, we explored the driver landscape of GCT through whole genome, exome and targeted sequencing (14 gene panel). We found that H3.3 mutations, namely mutations of glycine 34 in H3F3A, occur in 96% of GCT. We did not find additional driver mutations in GCT, including mutations in IDH1, IDH2, USP6, TP53. The genomes of GCT exhibited few somatic mutations, akin to the picture seen in CB. Overall our observations suggest that the presence of H3F3A p.Gly34 mutations does not entirely exclude malignancy in osteoclast-rich tumours. However, H3F3A p.Gly34 mutations appear to be an almost essential feature of GCT that will aid pathological evaluation of bone tumours, especially when confronted with small needle core biopsies. In the absence of H3F3A p.Gly34 mutations, a diagnosis of GCT should be made with caution.
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Affiliation(s)
- Nadège Presneau
- UCL Cancer Institute, University College LondonHuntley StreetLondonUK; Sarah Cannon-University College London Advanced Diagnostics Molecular Profiling Research LaboratoriesUCL Cancer Institute, UCLLondonUK; Present address: Department of Biomedical SciencesFaculty of Science and TechnologyUniversity of WestminsterW1W 6UWUK
| | - Daniel Baumhoer
- Bone Tumour Reference Centre at the Institute of Pathology University Hospital Basel Basel Switzerland
| | - Sam Behjati
- Cancer Genome Project Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridgeshire UK
| | - Nischalan Pillay
- Department of Histopathology Royal National Orthopaedic Hospital NHS Trust Middlesex UK
| | - Patrick Tarpey
- Cancer Genome Project Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridgeshire UK
| | - Peter J Campbell
- Cancer Genome Project Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridgeshire UK
| | - Gernot Jundt
- Bone Tumour Reference Centre at the Institute of Pathology University Hospital Basel Basel Switzerland
| | - Rifat Hamoudi
- UCL Cancer Institute, University College LondonHuntley StreetLondonUK; Sarah Cannon-University College London Advanced Diagnostics Molecular Profiling Research LaboratoriesUCL Cancer Institute, UCLLondonUK; Present address: Division of Surgery and Interventional ScienceUniversity College LondonW1W 7EJUK
| | - David C Wedge
- Cancer Genome Project Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridgeshire UK
| | - Peter Van Loo
- Cancer Genome ProjectWellcome Trust Sanger InstituteWellcome Trust Genome CampusCambridgeshireUK; Department of Human GeneticsUniversity of LeuvenLeuvenBelgium
| | - A Bassim Hassan
- CR-UK Tumour Growth Group Oxford Molecular Pathology Institute Sir William Dunn School of Pathology University of Oxford Oxford UK
| | - Bhavisha Khatri
- Department of Histopathology Royal National Orthopaedic Hospital NHS Trust Middlesex UK
| | - Hongtao Ye
- Department of Histopathology Royal National Orthopaedic Hospital NHS Trust Middlesex UK
| | - Roberto Tirabosco
- Department of Histopathology Royal National Orthopaedic Hospital NHS Trust Middlesex UK
| | - M Fernanda Amary
- Department of Histopathology Royal National Orthopaedic Hospital NHS Trust Middlesex UK
| | - Adrienne M Flanagan
- UCL Cancer Institute, University College LondonHuntley StreetLondonUK; Sarah Cannon-University College London Advanced Diagnostics Molecular Profiling Research LaboratoriesUCL Cancer Institute, UCLLondonUK; Department of HistopathologyRoyal National Orthopaedic Hospital NHS TrustMiddlesexUK
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