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Yao Q, Bai Q, Zhang X, Ji G, Chang H, Cai X, Yu L, Wang J, Zhu X, Zhou X. Assessment of ALK Fusions in Uncommon Inflammatory Myofibroblastic Tumors With ALK IHC Positivity but FISH-Equivocal Findings by Targeted RNA Sequencing. Arch Pathol Lab Med 2022; 146:1234-1242. [PMID: 35041745 DOI: 10.5858/arpa.2021-0230-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) are common methods to detect ALK status in inflammatory myofibroblastic tumors (IMTs). However, equivocal ALK FISH signals and inconsistency between FISH and IHC are occasionally observed. OBJECTIVE.— To study the inconsistency between FISH and IHC, and clarify ALK status in IMT by targeted RNA sequencing (RNAseq). DESIGN.— In this study, 12 consultation cases preliminarily diagnosed as uncommon IMTs with ALK IHC positivity but FISH negativity, plus 3 ALK-positive and 3 ALK-negative IMTs, were re-analyzed by IHC, FISH, and RNAseq. RESULTS.— As a result, 1 case with FUS-TFCP2 fusion was detected by RNAseq, which was previously misdiagnosed as IMT. In the other 11 uncommon IMTs, 90.9% (10 of 11) showed equivocal ALK FISH signals, and all were confirmed to harbor ALK fusion by RNAseq, except for 1 failure, suggesting that a low threshold for ALK FISH might be proposed in IMT. Furthermore, RNAseq also identified IGFBP5-ALK in 1 case with ALK IHC positivity but typical FISH negativity, suggesting the possibility of false negatives for ALK FISH. For the typical IMTs, ALK fusion was identified by RNAseq in all 3 ALK-positive IMTs as expected, and additionally FN1-ROS1 fusions were identified in 2 of 3 ALK-negative IMTs. CONCLUSIONS.— These findings indicated that RNAseq can simultaneously detect multiple gene fusions and provide fusion forms and breakpoints, which is of great value for differential diagnosis, especially for those uncommon IMTs with equivocal FISH findings, or inconsistency between IHC and FISH.
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Affiliation(s)
- Qianlan Yao
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Qianming Bai
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Xin Zhang
- Department of Pathology, Fudan University, Zhongshan Hospital, Shanghai, China (Zhang)
| | - Gang Ji
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Heng Chang
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Xu Cai
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Lin Yu
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Jian Wang
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Xiaoli Zhu
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
| | - Xiaoyan Zhou
- From the Department of Pathology, Shanghai Cancer Center, the Department of Oncology, Shanghai Medical College, and the Institute of Pathology, Fudan University, Shanghai, China (Yao, Bai, Ji, Chang, Cai, Yu, Wang, Zhu, Zhou)
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Cerrone M, Cantile M, Collina F, Marra L, Liguori G, Franco R, De Chiara A, Botti G. Molecular strategies for detecting chromosomal translocations in soft tissue tumors (review). Int J Mol Med 2014; 33:1379-91. [PMID: 24714847 PMCID: PMC4055444 DOI: 10.3892/ijmm.2014.1726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/29/2014] [Indexed: 02/07/2023] Open
Abstract
Approximately one third of soft tissue tumors are characterized by chromosomal aberrations, in particular, translocations and amplifications, which appear to be highly specific. The identification of fusion transcripts not only supports the diagnosis, but provides the basis for the development of novel therapeutic strategies aimed at blocking the aberrant activity of chimeric proteins. Molecular biology, and in particular, cytogenetic and qualitative and quantitative polymerase chain reaction technologies, allow with high efficiency and specificity, the determination of specific fusion transcripts resulting from chromosomal translocations, as well as the analysis of gene amplifications. In this review, various molecular techniques that allow the identification of translocations and consequent fusion transcripts generated are discussed in the broad spectrum of soft tissue tumors.
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Affiliation(s)
| | - Monica Cantile
- Pathology Unit, INT Pascale Foundation, I-80131 Naples, Italy
| | | | - Laura Marra
- Pathology Unit, INT Pascale Foundation, I-80131 Naples, Italy
| | | | - Renato Franco
- Pathology Unit, INT Pascale Foundation, I-80131 Naples, Italy
| | | | - Gerardo Botti
- Pathology Unit, INT Pascale Foundation, I-80131 Naples, Italy
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