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Whole-Genome Sequencing Reveals Mutational Signatures Related to Radiation-Induced Sarcomas and DNA-Damage-Repair Pathways. Mod Pathol 2023; 36:100004. [PMID: 36788076 DOI: 10.1016/j.modpat.2022.100004] [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: 02/22/2022] [Revised: 08/01/2022] [Accepted: 09/18/2022] [Indexed: 01/19/2023]
Abstract
Radiation-induced sarcoma (RIS) is a rare but serious late complication arising from radiotherapy. Despite unfavorable clinical outcomes, the genomic footprints of ionizing radiation in RIS development remain largely unknown. Hence, this study aimed to characterize RIS genomes and the genomic alterations in them. We analyzed whole-genome sequencing in 11 RIS genomes matched with normal genomes to identify somatic alterations potentially associated with RIS development. Furthermore, the abundance of mutations, mutation signatures, and structural variants in RIS were compared with those in radiation-naïve spontaneous sarcomas. The mutation abundance in RIS genomes, including one hypermutated genome, was variable. Cancer-related genes might show different types of genomic alterations. For instance, NF1, NF2, NOTCH1, NOTCH2, PIK3CA, RB1, and TP53 showed singleton somatic mutations; MYC, CDKN2A, RB1, and NF1 showed recurrent copy number alterations; and NF2, ARID1B, and RAD51B showed recurrent structural variations. The genomic footprints of nonhomologous end joining are prevalent at indels of RIS genomes compared with those in spontaneous sarcoma genomes, representing the genomic hallmark of RIS genomes. In addition, frequent chromothripsis was identified along with predisposing germline variants in the DNA-damage-repair pathways in RIS genomes. The characterization of RIS genomes on a whole-genome sequencing scale highlighted that the nonhomologous end joining pathway was associated with tumorigenesis, and it might pave the way for the development of advanced diagnostic and therapeutic strategies for RIS.
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Kunieda J, Yamashita K, Togashi Y, Baba S, Sakata S, Inamura K, Ae K, Matsumoto S, Machinami R, Kitagawa M, Takeuchi K. High prevalence of TERT aberrations in myxoid liposarcoma: TERT reactivation may play a crucial role in tumorigenesis. Cancer Sci 2021; 113:1078-1089. [PMID: 34971481 PMCID: PMC8898734 DOI: 10.1111/cas.15256] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 12/04/2021] [Accepted: 12/09/2021] [Indexed: 11/28/2022] Open
Abstract
Myxoid liposarcoma (MLPS) is genetically characterized by FUS‐DDIT3 or EWSR1‐DDIT3 gene fusion and the high frequency of hotspot mutations (C228T or C250T) in the promoter region of telomerase reverse transcriptase (TERT) that encodes the TERT protein. The latter leads to telomerase reactivation, a mechanism of telomere maintenance. Although the TERT promoter hotspot mutation is a poor prognostic factor in various tumors, its effect on MLPS has not been reported in detail. In the present study, we examined the clinicopathological characteristics, prognosis, and telomere maintenance mechanisms in 83 primary tumor samples of MLPS, which were resected surgically at the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan, from 2008 to 2020. TERT promoter hotspot mutations were observed in 77% (63/82) cases, and alternative lengthening of telomeres (ALT) was absent in all cases. Among the cases without TERT promoter hotspot mutations, TERT rearrangements, and minor point mutations in the TERT promoter region were found in 3 and 2 cases, respectively. TERT mRNA expression was observed consistently even in patients for whom no genomic TERT aberrations were detected, and the presence of TERT promoter hotspot mutation did not correlate significantly with either overall and metastasis‐free survival (P = .56, P = .83, respectively) or clinicopathological features. Therefore, patients with MLPS characteristically shows TERT expression and a high prevalence of TERT aberrations. Our findings suggest that TERT aberration is not prognostic factor, but might occur at an early stage and play a key role in tumorigenesis.
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Affiliation(s)
- Junko Kunieda
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kyoko Yamashita
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yuki Togashi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoko Baba
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiji Sakata
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kentaro Inamura
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Keisuke Ae
- Department of Orthopedic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiichi Matsumoto
- Department of Orthopedic Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Rikuo Machinami
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Kawakita General Hospital, Tokyo, Japan
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kengo Takeuchi
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.,Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
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Thway K. What’s new in adipocytic neoplasia? Histopathology 2021; 80:76-97. [DOI: 10.1111/his.14548] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/22/2022]
Affiliation(s)
- Khin Thway
- Sarcoma Unit Royal Marsden Hospital London UK
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Guo X, Chen T, Chen S, Song C, Shan D, Xu S, Xu S. Case Report: Identification of Multiple TERT and FGFR2 Gene Fusions in a Pineal Region Glioblastoma Case. Front Oncol 2021; 11:739309. [PMID: 34976798 PMCID: PMC8716851 DOI: 10.3389/fonc.2021.739309] [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: 07/10/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
As an oncogenic somatic variant, telomerase reverse transcriptase promoter (TERTp) mutations are frequently observed in adult glioblastoma (GBM). Alternatively, we report the first case of glioblastoma with TERT amplification accompanied by multiple TERT and FGFR2 gene fusions instead of TERTp mutation. A 55-year-old woman presented with dizziness, headache, and diplopia for three weeks. Magnetic resonance imaging (MRI) demonstrated a heterogeneously enhancing lobulated mass centered in the pineal region. Partial tumor resection and ventriculoperitoneal shunt were achieved, and the residual tumor was then treated with standard radiation. The tumor was diagnosed as GBM, IDH-wild type, WHO grade IV, and the Ki67 proliferation index was high (30–40%). Intriguingly, TERT amplification without TERTp mutation was identified via next generation sequencing (NGS). Further analysis revealed multiple TERT (TERT–NUBPL, MARCH6–TERT, and CJD4–TERT) and FGFR2 (CXCL17–FGFR2, SIPA1L3–FGFR2, FGFR2–SIPA1L3, and FGFR2–CEACAM1) gene fusions. After the surgery, the patient’s condition deteriorated rapidly due to the malignant nature of the tumor and she died with an overall survival of 3 months. Our report provides the molecular clue for a novel telomerase activation and maintenance mechanism in GBM.
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Affiliation(s)
- Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Teng Chen
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shiming Chen
- Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Dezhi Shan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shujun Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
| | - Shuo Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, China
- *Correspondence: Shuo Xu,
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Yoon JY, Jiang W, Orr CR, Rushton C, Gargano S, Song SJ, Modi M, Hozack B, Abraham J, Mallick AB, Brooks JSJ, Rosenbaum JN, Zhang PJ. TERT gene rearrangement in chordomas and comparison to other TERT-rearranged solid tumors. Cancer Genet 2021; 258-259:74-79. [PMID: 34583232 DOI: 10.1016/j.cancergen.2021.09.002] [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: 03/30/2021] [Revised: 08/25/2021] [Accepted: 09/16/2021] [Indexed: 11/27/2022]
Abstract
Chordomas are rare, slow-growing neoplasms thought to arise from the foetal notochord remnant. A limited number of studies that examined the mutational profiles in chordomas identified potential driver mutations, including duplication in the TBXT gene (encoding brachyury), mutations in the PI3K/AKT signaling pathway, and loss of the CDKN2A gene. Most chordomas remain without clear driver mutations, and no fusion genes have been identified thus far. We discovered a novel TERT in-frame fusion involving RPH3AL (exon 5) and TERT (exon 2) in the index chordoma case. We screened a discovery cohort of 18 additional chordoma cases for TERT gene rearrangement by FISH, in which TERT rearrangement was identified in one additional case. In our independent, validation cohort of 36 chordomas, no TERT rearrangement was observed by FISH. Immunohistochemistry optimized for nuclear TERT expression showed at least focal TERT expression in 40/55 (72.7%) chordomas. Selected cases underwent molecular genetic profiling, which showed low tumor mutational burdens (TMBs) without obvious driver oncogenic mutations. We next examined a cohort of 1,913 solid tumor patients for TERT rearrangements, and TERT fusions involving exon 2 were observed in 7/1,913 (0.4%) cases. The seven tumors comprised five glial tumors, and two poorly differentiated carcinomas. In contrast to chordomas, the other TERT-rearranged tumors were notable for higher TMBs, frequent TP53 mutations (6/7) and presence of other driver oncogenic mutations, including a concurrent fusion (TRIM24-MET). In conclusion, TERT gene rearrangements are seen in a small subset (2/55, 3.6%) of chordomas. In contrast to other TERT-rearranged tumors, where the TERT rearrangements are likely passenger events, the possibility that TERT protein overexpression representing a key event in chordoma tumorigenesis is left open.
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Affiliation(s)
- Ju-Yoon Yoon
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States; Department of Laboratory Medicine, St. Michael's Hospital/Unity Health Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Wei Jiang
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, United States
| | - Christopher R Orr
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Chase Rushton
- Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Stacey Gargano
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, United States
| | - Sharon J Song
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Mitul Modi
- Department of Pathology, Pennsylvania Hospital, Philadelphia, Pennsylvania, United States
| | - Bryan Hozack
- Rothman Orthopedic Institute, Philadelphia, Pennsylvania, United States
| | - John Abraham
- Rothman Orthopedic Institute, Philadelphia, Pennsylvania, United States; Division of Sarcoma and Bone Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
| | - Atrayee Basu Mallick
- Department of Medical Oncology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania, United States
| | - John S J Brooks
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States; Department of Pathology, Pennsylvania Hospital, Philadelphia, Pennsylvania, United States
| | - Jason N Rosenbaum
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States; Center for Personalized Diagnostics, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - Paul J Zhang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States.
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Zhang L, Chen L, Xiao M, Xie X, Wang F. Locally advanced undifferentiated sarcomatoid carcinoma of the right maxillary sinus with PDCD6-TERT fusion: A rare case report. Oral Oncol 2021; 124:105466. [PMID: 34348839 DOI: 10.1016/j.oraloncology.2021.105466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/16/2021] [Indexed: 02/05/2023]
Abstract
Sarcomatoid carcinoma of maxillary sinus tumor is extremely rare in head and neck tumors and has poor prognosis and frequently occurs to relapse locally after surgery. We first reported a case of locally advanced undifferentiated sarcomatoid carcinoma of right maxillary sinus with PDCD6-TERT fusion gene. The patient with a previous history of moderate alcohol drinking and smoking. The patient underwent surgical treatment. The tumor tissue using NGS analysis, no other driver gene mutations, and the PD-L1 IHC was negative. He received TPF regimen induction chemotherapy combined with anti-PD1 inhibitor and radiotherapy. The effect of treatment was good.
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Affiliation(s)
- Li Zhang
- Department of Medical Oncology, Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, China
| | - Lin Chen
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210002, China
| | - Mingzhe Xiao
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing Simcere Medical Laboratory Science Co., Ltd, The State Key Lab of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing 210002, China
| | - Xiaoqi Xie
- Department of Critical Care Medicine, West China Hospital, Sichuan University, Chendu, Sichuan Province, China
| | - Feng Wang
- Department of Medical Oncology, Cancer Center, West China Hospital, West China Medical School, Sichuan University, Sichuan, China.
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Chebib I, Taylor MS, Nardi V, Rivera MN, Lennerz JK, Cote GM, Choy E, Lozano Calderón SA, Raskin KA, Schwab JH, Mullen JT, Chen YLE, Hung YP, Nielsen GP, Deshpande V. Clinical Utility of Anchored Multiplex Solid Fusion Assay for Diagnosis of Bone and Soft Tissue Tumors. Am J Surg Pathol 2021; 45:1127-1137. [PMID: 34115673 DOI: 10.1097/pas.0000000000001745] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Sarcoma diagnosis has become increasingly complex, requiring a combination of morphology, immunohistochemistry, and molecular studies to derive specific diagnoses. We evaluated the role of anchored multiplex polymerase chain reaction-based gene fusion assay in sarcoma diagnostics. Between 2015 and 2018, bone and soft tissue sarcomas with fusion assay results were compared with the histologic diagnosis. Of 143 sarcomas tested for fusions, 43 (30%) had a detectable fusion. In review, they could be classified into 2 main categories: (1) 31 tumors with concordant morphologic and fusion data; and (2) 12 tumors where the fusion panel identified an unexpected rearrangement that played a significant role in classification. The overall concordance of the fusion assay results with morphology/immunohistochemistry or alternate confirmatory molecular studies was 83%. Collectively, anchored multiplex polymerase chain reaction-based solid fusion assay represents a robust means of detecting targeted fusions with known and novel partners. The predictive value of the panel is highest in tumors that show a monomorphic cell population, round cell tumors, as well as tumors rich in inflammatory cells. However, with an increased ability to discover fusions of uncertain significance, it remains essential to emphasize that the diagnosis of bone and soft tissue neoplasms requires the integration of morphology and immunohistochemical profile with these molecular methods, for accurate diagnosis and optimal clinical management of sarcomas.
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Affiliation(s)
| | | | | | | | | | - Gregory M Cote
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Edwin Choy
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | | | | | - Yen-Lin E Chen
- Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Yin P Hung
- James Homer Wright Pathology Laboratories
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