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Argani P, Gross JM, Baraban E, Rooper LM, Chen S, Lin MT, Gocke C, Agaimy A, Lotan T, Suurmeijer AJH, Antonescu CR. TFE3 -Rearranged PEComa/PEComa-like Neoplasms : Report of 25 New Cases Expanding the Clinicopathologic Spectrum and Highlighting its Association With Prior Exposure to Chemotherapy. Am J Surg Pathol 2024; 48:777-789. [PMID: 38597260 PMCID: PMC11189753 DOI: 10.1097/pas.0000000000002218] [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] [Indexed: 04/11/2024]
Abstract
Since their original description as a distinctive neoplastic entity, ~50 TFE3 -rearranged perivascular epithelioid cell tumors (PEComas) have been reported. We herein report 25 new TFE3 -rearranged PEComas and review the published literature to further investigate their clinicopathologic spectrum. Notably, 5 of the 25 cases were associated with a prior history of chemotherapy treatment for cancer. This is in keeping with prior reports, based mainly on small case series, with overall 11% of TFE3 -rearranged PEComas being diagnosed postchemotherapy. The median age of our cohort was 38 years. Most neoplasms demonstrated characteristic features such as nested architecture, epithelioid cytology, HMB45 positive, and muscle marker negative immunophenotype. SFPQ was the most common TFE3 fusion partner present in half of the cases, followed by ASPSCR1 and NONO genes. Four of 7 cases in our cohort with meaningful follow-up presented with or developed systemic metastasis, while over half of the reported cases either recurred locally, metastasized, or caused patient death. Follow-up for the remaining cases was limited (median 18.5 months), suggesting that the prognosis may be worse. Size, mitotic activity, and necrosis were correlated with aggressive behavior. There is little evidence that treatment with MTOR inhibitors, which are beneficial against TSC -mutated PEComas, is effective against TFE3 -rearranged PEComas: only one of 6 reported cases demonstrated disease stabilization. As co-expression of melanocytic and muscle markers, a hallmark of conventional TSC -mutated PEComa is uncommon in the spectrum of TFE3 -rearranged PEComa, an alternative terminology may be more appropriate, such as " TFE3 -rearranged PEComa-like neoplasms," highlighting their distinctive morphologic features and therapeutic implications.
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Affiliation(s)
- Pedram Argani
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - John M. Gross
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Ezra Baraban
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Departments of Urology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Lisa M. Rooper
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Suping Chen
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Christopher Gocke
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Abbas Agaimy
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Tamara Lotan
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Departments of Urology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Albert J. H. Suurmeijer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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Chen Y, Lu Y, Yang L, Ma W, Dong Y, Zhou S, Liu N, Gan W, Li D. LncRNA like NMRK2 mRNA functions as a key molecular scaffold to enhance mitochondrial respiration of NONO-TFE3 rearranged renal cell carcinoma in an NAD + kinase-independent manner. J Exp Clin Cancer Res 2023; 42:252. [PMID: 37770905 PMCID: PMC10537463 DOI: 10.1186/s13046-023-02837-4] [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: 06/05/2023] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND NONO-TFE3 rearranged renal cell carcinoma (NONO-TFE3 rRCC) is one of a subtype of TFE3 rRCCs with high malignancy and poor prognosis. Compared with clear cell RCC, NONO-TFE3 rRCC shows a preference for mitochondrial respiration. We recently identified that the upregulation of nicotinamide ribokinase 2 (NMRK2) was associated with enhanced mitochondrial respiration and tumor progression in TFE3 rRCC. METHODS A tumor-bearing mouse model was established to verify the pro-oncogenic effect of NMRK2 on NONO-TFE3 rRCC. Then the expression of NMRK2 RNA and protein was detected in cell lines and patient specimens. The NMRK2 transcripts were Sanger-sequenced and blasted at NCBI website. We constructed dCas13b-HA system to investigate the factors binding with NMRK2 RNA. We also used molecular experiments like RIP-seq, IP-MS, FISH and fluorescence techniques to explore the mechanisms that long non-coding RNA (lncRNA) like NMRK2 mRNA promoted the mitochondrial respiration of NONO-TFE3 rRCC. The efficacy of the combination of shRNA (NMRK2)-lentivirus and metformin on NONO-TFE3 rRCC was assessed by CCK-8 assay. RESULTS In this study, we confirmed that NMRK2 showed transcriptional-translational conflict and functioned as lncRNA like mRNA in the NONO-TFE3 rRCC. Furthermore, we revealed the molecular mechanism that NONO-TFE3 fusion suppressed the translation of NMRK2 mRNA. Most importantly, three major pathways were shown to explain the facilitation effects of lncRNA like NMRK2 mRNA on the mitochondrial respiration of NONO-TFE3 rRCC in an NAD+ kinase-independent manner. Finally, the efficacy of combination of shRNA (NMRK2)-lentivirus and metformin on NONO-TFE3 rRCC was demonstrated to be superior than either agent alone. CONCLUSIONS Overall, our data comprehensively demonstrated the mechanisms for the enhanced mitochondrial respiration in NONO-TFE3 rRCC and proposed lncRNA like NMRK2 mRNA as a therapy target for NONO-TFE3 rRCC.
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Affiliation(s)
- Yi Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Yanwen Lu
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Lei Yang
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226000, China
| | - Wenliang Ma
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Yuhan Dong
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Shuoming Zhou
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China
| | - Ning Liu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, 210001, China.
| | - Weidong Gan
- Department of Urology, Affiliated Drum Tower Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, 210008, China.
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, 210093, China.
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, 210093, China.
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Lu Y, Zhu Y, Ma W, Liu N, Dong X, Shi Q, Yu F, Guo H, Li D, Gan W. Estrogen associates with female predominance in Xp11.2 translocation renal cell carcinoma. Sci Rep 2023; 13:6141. [PMID: 37061606 PMCID: PMC10105720 DOI: 10.1038/s41598-023-33363-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/12/2023] [Indexed: 04/17/2023] Open
Abstract
Based on the epidemiological characteristics of susceptibility and age selectivity for women in Xp11.2 translocation renal cell carcinoma (Xp11.2 tRCC), we inferred that estrogen was to be blamed. Rad54 like 2 (Rad54l2) which might be one of key effector proteins of DNA damage mediated by estrogen was downregulated in numerous cancers, however, its role in epidemiological characteristics of Xp11.2 tRCC was needed to further study. We reviewed 1005 Xp11.2 tRCC cases and collected estrogen data and then compared the onset time of Xp11.2 tRCC cases in female with estrogen changing trend. An RNA-sequencing was performed in estrogen treated HK-2 cells and subsequently bioinformatic analysis was applied based on the Cancer Genome Atlas (TCGA) and GEO database. The male-to-female ratio of Xp11.2 tRCC was 1:1.4 and the median age of onset was 29.7 years old. The onset trend of female was similar to estrogen physiological rhythm (r = 0.67, p < 0.01). In Xp11.2 tRCC and HK-2 cells after estrogen treatment, Rad54l2 was downregulated, and GSEA showed that pathways significantly enriched in DNA damage repair and cancer related clusters after estrogen treated, as well as GO and KEGG analysis. Downregulation of Rad54l2 was in numerous cancers, including renal cell carcinoma (RCC), in which Rad54l2 expression was significantly decreased in male, age over 60 years old, T2&T3&T4 stages, pathologic SII&SIII&SIV stages as well as histologic G3&G4 grades, and cox regression analysis proved that Rad54l2 expression was a risk factor for overall survival, disease-specific survival and progression-free interval in univariate analysis. There existed female predominance in Xp11.2 tRCC and Rad54l2 might play vital role in estrogen mediating female predominance in Xp11.2 tRCC.
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Affiliation(s)
- Yanwen Lu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Yiqi Zhu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Wenliang Ma
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Ning Liu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Xiang Dong
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Qiancheng Shi
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Fei Yu
- Department of Laboratory Medicine, Nanjing Children's Hospital, The Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory and State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, People's Republic of China
- Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, People's Republic of China
| | - Weidong Gan
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008, Jiangsu, People's Republic of China.
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Guo W, Zhu Y, Pu X, Guo H, Gan W. Clinical and pathological heterogeneity of four common fusion subtypes in Xp11.2 translocation renal cell carcinoma. Front Oncol 2023; 13:1116648. [PMID: 36816933 PMCID: PMC9935599 DOI: 10.3389/fonc.2023.1116648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background Xp11.2 translocation renal cell carcinoma (Xp11.2 tRCC) is a group of rare and highly heterogeneous renal cell carcinoma (RCC). The translocation involving TFE3 and different fusion partners lead to overexpression of the chimeric protein. The purpose of this study is to explore the clinicopathological features of Xp11.2 tRCC with four common fusion subtypes. Methods We screened out 40 Xp11.2 tRCC patients from January 2007 to August 2021 in our institution. The diagnosis was initially confirmed by TFE3 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) assay and their fusion partners were verified by RNA sequencing. Then the 40 cases were divided into two groups (DBHS family and non-DBHS family group) and a clinical comparison among the four common fusion subtypes was performed. Results Among the 40 cases, 11 cases with SFPQ-TFE3 gene fusion and 7 cases with NONO-TFE3 gene fusion were classified in DBHS group, the remaining cases with ASPL-TFE3 (11 cases) or PRCC-TFE3 (11 cases) gene fusion were classified in non-DBHS group. Lymph node (LN) metastasis (P=0.027) and distant metastasis (P=0.009) were more common seen in non-DBHS family group than DBHS family group and cases in DBHS family group have better progressive-free survival (PFS) (P=0.02). In addition, ASPL-TFE3 fusion was associated with worse outcome (P=0.03) while NONO-TFE3 fusion (P=0.04) predicted a better prognosis. Conclusions Different fusion partner genes may play a functional role in various morphology, molecular and biological features of Xp11.2 tRCCs. The impact of fusion partners on clinical characteristics of Xp11.2 tRCCs deserves further exploration.
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Affiliation(s)
- Wei Guo
- Department of Urology, Drum Tower Clinical Medical School of Nanjing Medical University, Nanjing, Jiangsu, China,Department of Urology, Taizhou People’s Hospital Affiliated to Nanjing Medical University, Taizhou, Jiangsu, China
| | - Yiqi Zhu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Xiaohong Pu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Weidong Gan
- Department of Urology, Drum Tower Clinical Medical School of Nanjing Medical University, Nanjing, Jiangsu, China,Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China,*Correspondence: Weidong Gan,
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Tang J, Baba M. MiT/TFE Family Renal Cell Carcinoma. Genes (Basel) 2023; 14:genes14010151. [PMID: 36672892 PMCID: PMC9859458 DOI: 10.3390/genes14010151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The microphthalmia-associated transcription factor/transcription factor E (MiT/TFE) family of transcription factors are evolutionarily conserved, basic helix-loop-helix leucine zipper (bHLH-Zip) transcription factors, consisting of MITF, TFEB, TFE3, and TFEC. MiT/TFE proteins, with the exception of TFEC, are involved in the development of renal cell carcinoma (RCC). Most of the MiT/TFE transcription factor alterations seen in sporadic RCC cases of MiT family translocation renal cell carcinoma (tRCC) are chimeric proteins generated by chromosomal rearrangements. These chimeric MiT/TFE proteins retain the bHLH-Zip structures and act as oncogenic transcription factors. The germline variant of MITF p.E318K has been reported as a risk factor for RCC. E 318 is present at the SUMOylation consensus site of MITF. The p.E318K variant abrogates SUMOylation on K 316, which results in alteration of MITF transcriptional activity. Only a few cases of MITF p.E318K RCC have been reported, and their clinical features have not yet been fully described. It would be important for clinicians to recognize MITF p.E318K RCC and consider MITF germline testing for undiagnosed familial RCC cases. This review outlines the involvement of the MiT/TFE transcription factors in RCC, both in sporadic and hereditary cases. Further elucidation of the molecular function of the MiT/TFE family is necessary for better diagnosis and treatment of these rare diseases.
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Nardone C, Palanski BA, Scott DC, Timms RT, Barber KW, Gu X, Mao A, Leng Y, Watson EV, Schulman BA, Cole PA, Elledge SJ. A central role for regulated protein stability in the control of TFE3 and MITF by nutrients. Mol Cell 2023; 83:57-73.e9. [PMID: 36608670 PMCID: PMC9908011 DOI: 10.1016/j.molcel.2022.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/24/2022] [Accepted: 12/13/2022] [Indexed: 01/07/2023]
Abstract
The TFE3 and MITF master transcription factors maintain metabolic homeostasis by regulating lysosomal, melanocytic, and autophagy genes. Previous studies posited that their cytosolic retention by 14-3-3, mediated by the Rag GTPases-mTORC1, was key for suppressing transcriptional activity in the presence of nutrients. Here, we demonstrate using mammalian cells that regulated protein stability plays a fundamental role in their control. Amino acids promote the recruitment of TFE3 and MITF to the lysosomal surface via the Rag GTPases, activating an evolutionarily conserved phospho-degron and leading to ubiquitination by CUL1β-TrCP and degradation. Elucidation of the minimal functional degron revealed a conserved alpha-helix required for interaction with RagA, illuminating the molecular basis for a severe neurodevelopmental syndrome caused by missense mutations in TFE3 within the RagA-TFE3 interface. Additionally, the phospho-degron is recurrently lost in TFE3 genomic translocations that cause kidney cancer. Therefore, two divergent pathologies converge on the loss of protein stability regulation by nutrients.
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Affiliation(s)
- Christopher Nardone
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brad A Palanski
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge, Cambridgeshire CB2 0AW, UK
| | - Karl W Barber
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Xin Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Aoyue Mao
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Emma V Watson
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Argani P, Wobker SE, Gross JM, Matoso A, Fletcher CD, Antonescu CR. PEComa-like Neoplasms Characterized by ASPSCR1-TFE3 Fusion: Another Face of TFE3-related Mesenchymal Neoplasia. Am J Surg Pathol 2022; 46:1153-1159. [PMID: 35848761 PMCID: PMC9298479 DOI: 10.1097/pas.0000000000001894] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Identical TFE3-related gene fusions may be found in renal cell carcinoma and mesenchymal neoplasms such as alveolar soft part sarcoma and TFE3-rearranged perivascular epithelioid cell tumor (PEComa). Among mesenchymal neoplasms, the ASPSCR1-TFE3 gene fusion has previously been described only in alveolar soft part sarcoma. We report 3 unusual mesenchymal neoplasms harboring the ASPSCR1-TFE3 gene fusion, the morphologic phenotype of which more closely matches PEComa rather than alveolar soft part sarcoma. All 3 neoplasms occurred in females ranging in age from 18 to 34 years and were located in the viscera (kidney, bladder, and uterus). All 3 contained nests of epithelioid cells bounded by fibrovascular septa. However, all were associated with hyalinized stroma, tight nested architecture, mixed spindle cell and epithelioid pattern, clear cytoplasm, and lacked significant discohesion. Overall, morphologic features closely resembled PEComa, being distinct from the typical alveolar soft part sarcoma phenotype. While none of the neoplasms labeled for HMB45, cytokeratin, or PAX8 all showed positivity for TFE3 and cathepsin K, and all except 1 were positive for smooth muscle actin. One patient developed a liver metastasis 7 years after nephrectomy. These cases bridge the gap between 2 TFE3-rearranged neoplasms, specifically alveolar soft part sarcoma and Xp11 translocation PEComa, highlighting the relatedness and overlap among Xp11 translocation neoplasms. While most TFE3-rearranged neoplasms can be confidently placed into a specific diagnostic category such as alveolar soft part sarcoma, PEComa, or Xp11 translocation renal cell carcinoma, occasional cases have overlapping features, highlighting the potential role that the cell of origin and the specific gene fusion play in the phenotype of these neoplasms.
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Affiliation(s)
- Pedram Argani
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Sara E. Wobker
- Departments of Pathology and Laboratory Medicine and Urology, University of North Carolina, Chapel Hill, NC, USA
| | - John M. Gross
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Andres Matoso
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
- Department of Urology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
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Simonaggio A, Ambrosetti D, Verkarre V, Auvray M, Oudard S, Vano YA. MiTF/TFE Translocation Renal Cell Carcinomas: From Clinical Entities to Molecular Insights. Int J Mol Sci 2022; 23:ijms23147649. [PMID: 35886994 PMCID: PMC9324307 DOI: 10.3390/ijms23147649] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 12/30/2022] Open
Abstract
MiTF/TFE translocation renal cell carcinoma (tRCC) is a rare and aggressive subtype of RCC representing the most prevalent RCC in the pediatric population (up to 40%) and making up 4% of all RCCs in adults. It is characterized by translocations involving either TFE3 (TFE3-tRCC), TFEB (TFEB-tRCC) or MITF, all members of the MIT family (microphthalmia-associated transcriptional factor). TFE3-tRCC was first recognized in the World Health Organization (WHO) classification of kidney cancers in 2004. In contrast to TFEB-tRCC, TFE3-tRCC is associated with many partners that can be detected by RNA or exome sequencing. Both diagnoses of TFE3 and TFEB-tRCC are performed on morphological and immunohistochemical features, but, to date, TFE break-apart fluorescent in situ hybridization (FISH) remains the gold standard for diagnosis. The clinical behavior of tRCC is heterogeneous and more aggressive in adults. Management of metastatic tRCC is challenging, especially in the younger population, and data are scarce. Efficacy of the standard of care-targeted therapies and immune checkpoint inhibitors remains low. Recent integrative exome and RNA sequencing analyses have provided a better understanding of the biological heterogeneity, which can contribute to a better therapeutic approach. We describe the clinico-pathological entities, the response to systemic therapy and the molecular features and techniques used to diagnose tRCC.
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Affiliation(s)
- Audrey Simonaggio
- Department of Medical Oncology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP. Centre—Université Paris-Cité, F-75015 Paris, France; (A.S.); (M.A.); (S.O.)
| | - Damien Ambrosetti
- Department of Pathology, CHU Nice, Université Côte d’Azur, F-06107 Nice, France;
- Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University Côte d’Azur, F-06107 Nice, France
| | - Virginie Verkarre
- Department of Pathology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP. Centre—Université Paris-Cité, F-75015 Paris, France;
- INSERM UMR-970, PARCC, Université Paris-Cité, F-75015 Paris, France
| | - Marie Auvray
- Department of Medical Oncology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP. Centre—Université Paris-Cité, F-75015 Paris, France; (A.S.); (M.A.); (S.O.)
| | - Stéphane Oudard
- Department of Medical Oncology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP. Centre—Université Paris-Cité, F-75015 Paris, France; (A.S.); (M.A.); (S.O.)
- INSERM UMR-970, PARCC, Université Paris-Cité, F-75015 Paris, France
| | - Yann-Alexandre Vano
- Department of Medical Oncology, Hôpital Européen Georges Pompidou, Institut du Cancer Paris CARPEM, AP-HP. Centre—Université Paris-Cité, F-75015 Paris, France; (A.S.); (M.A.); (S.O.)
- INSERM UMR-970, PARCC, Université Paris-Cité, F-75015 Paris, France
- Centre de Recherche des Cordeliers, INSERM, Université Paris-Cité, Sorbonne Université, F-75006 Paris, France
- Correspondence: ; Tel.: +33-624281311
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Tretiakova MS. Chameleon TFE3-translocation RCC and How Gene Partners Can Change Morphology: Accurate Diagnosis Using Contemporary Modalities. Adv Anat Pathol 2022; 29:131-140. [PMID: 35180736 DOI: 10.1097/pap.0000000000000332] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translocation renal cell carcinoma (tRCC) with TFE3 gene rearrangements has been born as a distinct entity 20 years ago. These relatively rare tumors were notable among other RCC subtypes because of their disproportionally high incidence among children and young adults. Initial reports were focused on describing unifying morphologic criteria and typical clinical presentation. Follow-up studies of ancillary immunohistochemical and hybridization techniques provided additional diagnostic tools allowing recognition of tRCC tumors in practice. However, a growing body of literature also expanded the clinicomorphologic spectrum of tRCCs, to include a significant morphologic overlap with other RCC variants thus blurring the diagnostic clarity of this entity. More recent molecular studies utilizing next-generation sequencing technology accelerated recognition of numerous novel gene partners fusing at different breakpoints with the TFE3 gene. Accumulating data indicates that morphologic and clinical heterogeneity of tRCC could be explained by fusion subtypes, and knowledge of TFE3 partnering genes may be important in predicting tumor behavior. Herein we provided a comprehensive analysis of ∼400 tRCC cases with known TFE3 fusion partners, estimated their relative incidence and summarized clinicomorphologic features associated with most common fusion subtypes. Our data was based on an extensive literature review and had a special focus on comparing immunohistochemistry, fluorescent in situ hybridization and contemporary molecular studies for the accurate diagnosis of tRCC.
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Affiliation(s)
- Maria S Tretiakova
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
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10
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Ge Y, Lin X, Zhang Q, Lin D, Luo L, Wang H, Li Z. Xp11.2 Translocation Renal Cell Carcinoma With TFE3 Rearrangement: Distinct Morphological Features and Prognosis With Different Fusion Partners. Front Oncol 2021; 11:784993. [PMID: 34917511 PMCID: PMC8668609 DOI: 10.3389/fonc.2021.784993] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 01/20/2023] Open
Abstract
BackgroundRenal cell carcinoma (RCC) associated with Xp11.2 translocation/TFE3 gene fusion is a rare and new subtype of RCC and was classified by the WHO in 2004. Since then, multiple 5′ fusion partners for TFE3 have been reported; however, the impact of individual fusion variant on specific clinicopathologic features of Xp11.2 RCCs has not been well defined.MethodsFour Xp11.2 translocation RCCs were identified by morphological, immunostaining, and fluorescence in situ hybridization (FISH) assays from 200 patients who attended Guangdong General Hospital between January 2017 and January 2020. All these four cases were further analyzed by RNA sequencing to explore their TFE3 gene fusion partners. The clinicopathologic features, including clinical manifestations, pathological findings, treatment strategies, clinical outcomes, and follow-up information on Xp11.2 translocation RCCs, were recorded and evaluated.ResultsThese four cases affected one male and three females. The median age was 13 years at the time of diagnosis (range = 4–20 years). All the examined tumors were unilateral and unifocal. The largest diameter of these tumors ranged from 2.0 to 10.0 cm, and the average was 5.55 cm. Regional lymph node or distant metastasis developed in two patients. Three cases demonstrated known fusions: ASPCR1–TFE3 (two cases) and PRCC–TFE3 (one case). However, one case showed an unreported VCP–TFE3 fusion gene in Xp11.2 translocation RCCs. Immunohistochemistry results revealed tumor cells diffusely positive for TFE3, but have no consistency in other markers. Moreover, there were different clinical prognoses among the different variant TFE3 rearrangements; RCC patients with VCP–TFE3 translocation had worse prognosis compared to those with other fusion types. Follow-up were available for all the patients and ranged from 3 to 36 months. Three patients were without evidence of disease progression, while that with VCP–TFE3 fusion died of the disease 3 months after the diagnosis.ConclusionIn conclusion, our data expand the list of TFE3 gene fusion partners and the clinicopathologic features of Xp11.2 RCCs with specific TFE3 gene fusions. We identified a novel VCP–TFE3 fusion in Xp11.2 translocation RCCs for the first time, which has unique morphology and worse prognosis than those with other variant TFE3 rearrangements. Integration of morphological, immunohistochemical, and molecular methods is often necessary for the precise diagnosis and optimal clinical management of malignant tumors.
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Affiliation(s)
- Yan Ge
- Department of Pathology, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xingtao Lin
- Department of Pathology, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qingling Zhang
- Department of Pathology, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Danyi Lin
- Department of Pathology, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Luqiao Luo
- Department of Pathology, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Huiling Wang
- Department of General Surgery, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Huiling Wang, ; Zhi Li,
| | - Zhi Li
- Department of Pathology, Guangdong Provincial People’s Hospital/Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Huiling Wang, ; Zhi Li,
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11
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Argani P. Translocation carcinomas of the kidney. Genes Chromosomes Cancer 2021; 61:219-227. [PMID: 34704642 DOI: 10.1002/gcc.23007] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/24/2021] [Indexed: 01/19/2023] Open
Abstract
The MiT subfamily of transcription factors includes TFE3, TFEB, TFEC, and MITF. Gene fusions involving two of these transcription factors have been well-characterized in renal cell carcinoma (RCC). The TFE3-rearranged RCC (also known as Xp11 translocation RCC) was first officially recognized in the 2004 World Health Organization (WHO) renal tumor classification. The TFEB-rearranged RCC, which typically harbor a t(6;11)(p21;q12) translocation which results in a MALAT1-TFEB gene fusion, were first officially recognized in the 2016 WHO renal tumor classification. These two subtypes of translocation RCC have many similarities. Both disproportionately involve young patients, although adult translocation RCC overall outnumber pediatric cases. Both often have unusual and distinctive morphologies; the TFE3-rearranged RCCs frequently have clear cells with papillary architecture and abundant psammoma bodies, while the TFEB-rearranged RCCs frequently have a biphasic appearance with both small and large epithelioid cells and nodules of basement membrane material. However, the morphology of these two neoplasms can overlap, with one mimicking the other or other more common renal neoplasms. Both of these RCC underexpress epithelial immunohistochemical markers, such as cytokeratin and epithelial membrane antigen, relative to most other RCC. Unlike other RCC, both frequently express the cysteine protease cathepsin k and often express melanocytic markers like HMB45 and Melan A. Finally, TFE3 and TFEB have overlapping functional activity as these two transcription factors frequently heterodimerize and bind to the same targets. Therefore, these two neoplasms are now grouped together under the heading of "MiT family translocation RCC." Approximately 50 renal cell carcinomas with gene fusions involving the anaplastic lymphoma kinase (ALK) gene have now been reported. While those with a Vinculin-ALK fusion have distinctive features (predilection to affect children with sickle cell trait and to show solid architecture with striking cytoplasmic vacuolization), other ALK-fusion RCCs have more varied clinical presentations and pathologic features. This review summarizes our current knowledge of these recently described RCC.
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Affiliation(s)
- Pedram Argani
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Jang JS, Holicky E, Lau J, McDonough S, Mutawe M, Koster MJ, Warrington KJ, Cuninngham JM. Application of the 3' mRNA-Seq using unique molecular identifiers in highly degraded RNA derived from formalin-fixed, paraffin-embedded tissue. BMC Genomics 2021; 22:759. [PMID: 34689749 PMCID: PMC8543821 DOI: 10.1186/s12864-021-08068-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/10/2021] [Indexed: 11/11/2022] Open
Abstract
Background Archival formalin-fixed, paraffin-embedded (FFPE) tissue samples with clinical and histological data are a singularly valuable resource for developing new molecular biomarkers. However, transcriptome analysis remains challenging with standard mRNA-seq methods as FFPE derived-RNA samples are often highly modified and fragmented. The recently developed 3′ mRNA-seq method sequences the 3′ region of mRNA using unique molecular identifiers (UMI), thus generating gene expression data with minimal PCR bias. In this study, we evaluated the performance of 3′ mRNA-Seq using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD with UMI, comparing with TruSeq Stranded mRNA-Seq and RNA Exome Capture kit. The fresh-frozen (FF) and FFPE tissues yielded nucleotide sizes range from 13 to > 70% of DV200 values; input amounts ranged from 1 ng to 100 ng for validation. Results The total mapped reads of QuantSeq 3′ mRNA-Seq to the reference genome ranged from 99 to 74% across all samples. After PCR bias correction, 3 to 56% of total sequenced reads were retained. QuantSeq 3′ mRNA-Seq data showed highly reproducible data across replicates in Universal Human Reference RNA (UHR, R > 0.94) at input amounts from 1 ng to 100 ng, and FF and FFPE paired samples (R = 0.92) at 10 ng. Severely degraded FFPE RNA with ≤30% of DV200 value showed good concordance (R > 0.87) with 100 ng input. A moderate correlation was observed when directly comparing QuantSeq 3′ mRNA-Seq data with TruSeq Stranded mRNA-Seq (R = 0.78) and RNA Exome Capture data (R > 0.67). Conclusion In this study, QuantSeq 3′ mRNA-Seq with PCR bias correction using UMI is shown to be a suitable method for gene quantification in both FF and FFPE RNAs. 3′ mRNA-Seq with UMI may be applied to severely degraded RNA from FFPE tissues generating high-quality sequencing data. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08068-1.
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Affiliation(s)
- Jin Sung Jang
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - Eileen Holicky
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA
| | - Julie Lau
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA
| | - Samantha McDonough
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA
| | - Mark Mutawe
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA
| | - Matthew J Koster
- Department of Internal Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Kenneth J Warrington
- Department of Internal Medicine, Division of Rheumatology, Mayo Clinic, Rochester, MN, USA
| | - Julie M Cuninngham
- Genome Analysis Core, Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Stabile Research Building, 200 First Street SW, Rochester, MN, 55905, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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13
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Di Mauro I, Dadone-Montaudie B, Sibony M, Ambrosetti D, Molinie V, Decaussin-Petrucci M, Bland V, Arbaud C, Cenciu B, Arbib F, Just PA, Derman J, Rioux-Leclercq N, Pedeutour F. RBM10-TFE3 fusions: A FISH-concealed anomaly in adult renal cell carcinomas displaying a variety of morphological and genomic features: Comprehensive study of six novel cases. Genes Chromosomes Cancer 2021; 60:772-784. [PMID: 34358382 DOI: 10.1002/gcc.22985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/05/2021] [Accepted: 07/16/2021] [Indexed: 11/07/2022] Open
Abstract
The accurate diagnosis of Xp11-translocation renal cell carcinoma (RCC) in adults is challenging. TFE3 (located on chromosome X) fuses with a partner gene generally located on another chromosome. In rare cases TFE3 may fuse with a neighboring gene: RBM10. Because TFE3 false-positive immunostaining is a common pitfall in many laboratories, demonstration of the chromosomal rearrangement is required in order to ascertain the diagnosis. Fluorescence in situ hybridization (FISH)-that has been considered as the gold standard method-reaches its limits for detecting small Xp11 paracentric inversions. We performed a comprehensive clinical, histological and genomic study of six novel cases of RCC with RBM10-TFE3 fusion. Using FISH, TFE3 rearrangement was equivocal in one case and negative in others. RBM10-TFE3 fusion was discovered using targeted RNA sequencing (RNASeq). As all the previously reported cases (mean age: 50), the six patients were adults (mean age: 42), suggesting an epidemiologic difference between RBM10-TFE3 RCC and tumors harboring some other partner genes, such as ASPSCR1 that rather occur in children. Array-comparative genomic hybridization showed several alterations, notably a gain of 17q in four cases with papillary features and loss of 3p in one case with clear cells. Our study demonstrates that, though rare among adult cases of RCC, RBM10-TFE3 fusion is not exceptional and warrants appropriate molecular detection. Notably, it would be worthy to systemically investigate by RNASeq challenging RCC with type-2 papillary features and 17q gain.
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Affiliation(s)
- Ilaria Di Mauro
- Laboratory of Solid Tumor Genetics, University Hospital of Nice-Côte d'Azur University, Nice, France.,Laboratory of Solid Tumor Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Nice, France
| | - Bérengère Dadone-Montaudie
- Laboratory of Solid Tumor Genetics, University Hospital of Nice-Côte d'Azur University, Nice, France.,Laboratory of Solid Tumor Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Nice, France
| | - Mathilde Sibony
- Department of Pathology, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris-Centre, Hôpital Cochin, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Damien Ambrosetti
- Central Laboratory of Pathology, University Hospital of Nice-Côte d'Azur University, Nice, France
| | - Vincent Molinie
- Pathology Department, Aix en Provence Hospital, Aix en Provence, France
| | | | | | - Claire Arbaud
- Pathology Department, Métropole Savoie Hospital, Chambéry, France
| | - Béatrice Cenciu
- Oncology Department, Andrée Rosemon Hospital, Cayenne, France
| | | | - Pierre-Alexandre Just
- Department of Pathology, Assistance Publique - Hôpitaux de Paris (AP-HP), Hôpitaux Universitaires Paris-Centre, Hôpital Cochin, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Jonathan Derman
- Department of Pathology, Henri-Mondor Hospital, Créteil, France
| | | | - Florence Pedeutour
- Laboratory of Solid Tumor Genetics, University Hospital of Nice-Côte d'Azur University, Nice, France.,Laboratory of Solid Tumor Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Nice, France
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- CARARE French Network (CAncers RAres du Rein: Rare Renal Cancers Network of the National Institute of Cancer, INCa), France
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14
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New developments in existing WHO entities and evolving molecular concepts: The Genitourinary Pathology Society (GUPS) update on renal neoplasia. Mod Pathol 2021; 34:1392-1424. [PMID: 33664427 DOI: 10.1038/s41379-021-00779-w] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 12/28/2022]
Abstract
The Genitourinary Pathology Society (GUPS) reviewed recent advances in renal neoplasia, particularly post-2016 World Health Organization (WHO) classification, to provide an update on existing entities, including diagnostic criteria, molecular correlates, and updated nomenclature. Key prognostic features for clear cell renal cell carcinoma (RCC) remain WHO/ISUP grade, AJCC/pTNM stage, coagulative necrosis, and rhabdoid and sarcomatoid differentiation. Accrual of subclonal genetic alterations in clear cell RCC including SETD2, PBRM1, BAP1, loss of chromosome 14q and 9p are associated with variable prognosis, patterns of metastasis, and vulnerability to therapies. Recent National Comprehensive Cancer Network (NCCN) guidelines increasingly adopt immunotherapeutic agents in advanced RCC, including RCC with rhabdoid and sarcomatoid changes. Papillary RCC subtyping is no longer recommended, as WHO/ISUP grade and tumor architecture better predict outcome. New papillary RCC variants/patterns include biphasic, solid, Warthin-like, and papillary renal neoplasm with reverse polarity. For tumors with 'borderline' features between oncocytoma and chromophobe RCC, a term "oncocytic renal neoplasm of low malignant potential, not further classified" is proposed. Clear cell papillary RCC may warrant reclassification as a tumor of low malignant potential. Tubulocystic RCC should only be diagnosed when morphologically pure. MiTF family translocation RCCs exhibit varied morphologic patterns and fusion partners. TFEB-amplified RCC occurs in older patients and is associated with more aggressive behavior. Acquired cystic disease (ACD) RCC-like cysts are likely precursors of ACD-RCC. The diagnosis of renal medullary carcinoma requires a negative SMARCB1 (INI-1) expression and sickle cell trait/disease. Mucinous tubular and spindle cell carcinoma (MTSCC) can be distinguished from papillary RCC with overlapping morphology by losses of chromosomes 1, 4, 6, 8, 9, 13, 14, 15, and 22. MTSCC with adverse histologic features shows frequent CDKN2A/2B (9p) deletions. BRAF mutations unify the metanephric family of tumors. The term "fumarate hydratase deficient RCC" ("FH-deficient RCC") is preferred over "hereditary leiomyomatosis and RCC syndrome-associated RCC". A low threshold for FH, 2SC, and SDHB immunohistochemistry is recommended in difficult to classify RCCs, particularly those with eosinophilic morphology, occurring in younger patients. Current evidence does not support existence of a unique tumor subtype occurring after chemotherapy/radiation in early childhood.
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15
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Wang Y, Wang Y, Feng M, Lian X, Lei Y, Zhou H. Renal cell carcinoma associated with Xp11.2 translocation/transcription factor E3 gene fusion: an adult case report and literature review. J Int Med Res 2021; 48:300060520942095. [PMID: 33026261 PMCID: PMC7545772 DOI: 10.1177/0300060520942095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Renal cell carcinoma (RCC) associated with Xp11.2 translocation/transcription factor E3 (TFE3) gene fusion is a rare and independent subtype of RCC included in the classification of MiT (microphthalmia-associated transcriptional factor) family translocation RCC. Herein, we report an adult case of Xp11.2 translocation RCC, and review the relevant literature to improve our understanding of the pathogenesis, epidemiology, clinical manifestations, diagnosis, differential diagnosis, treatment, and other aspects of the disease.
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Affiliation(s)
- Yuxiong Wang
- The Second Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yuantao Wang
- The Second Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Mingliang Feng
- The Second Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xin Lian
- The Second Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yongsheng Lei
- The Second Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Honglan Zhou
- The Second Department of Urology, The First Hospital of Jilin University, Changchun, Jilin, China
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16
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Chen Y, Yang L, Liu N, Shi Q, Yin X, Han X, Gan W, Li D. NONO-TFE3 fusion promotes aerobic glycolysis and angiogenesis by targeting HIF1A in NONO-TFE3 translocation renal cell carcinoma. Curr Cancer Drug Targets 2021; 21:713-723. [PMID: 33845743 DOI: 10.2174/1568009621666210412115026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/17/2021] [Accepted: 03/20/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND NONO-TFE3 translocation renal cell carcinoma (tRCC), one of RCCs associated with Xp11.2 translocation/TFE3 gene fusion (Xp11.2 tRCCs), involves an X chromosome inversion between NONO and TFE3 with the characteristics of endonuclear aggregation of NONO-TFE3 fusion protein. Nowadays, the oncogenic mechanisms of NONO-TFE3 fusion have not been fully elucidated. OBJECTIVE This study aimed at investigating the mechanism of NONO-TFE3 fusion regulating HIF1A as well as the role of HIF-1α in the progression of NONO-TFE3 tRCC under hypoxia. METHODS Immunohistochemistry and Western Blotting assays were performed to profile HIF-1α expression in renal clear cell carcinoma (ccRCC) or in Xp11.2 tRCC. Chromatin immunoprecipitation (ChIP), luciferase reporter assay and real-time quantitative PCR (RT-qPCR) were used to evaluate the regulation of HIF1A expression by NONO-TFE3 fusion. Then, flow cytometry analysis, tube formation assays and cell migration assays were used as well as glucose or lactic acid levels were measured to establish the impact of HIF-1α on the progression of NONO-TFE3 tRCC. Besides, the effect of HIF-1α inhibitor (PX-478) on UOK109 cells was analyzed. RESULTS We found that HIF1A was targeting gene of NONO-TFE3 fusion. In UOK109 cells, which were isolated from NONO-TFE3 tRCC samples, NONO-TFE3 fusion promoted aerobic glycolysis and angiogenesis by up-regulating the expression of HIF-1α under hypoxia. Furthermore, inhibition of HIF-1α mediated by PX-478 suppressed the development of NONO-TFE3 tRCC under hypoxia. CONCLUSION HIF-1α is a potential target for therapy of NONO-TFE3 tRCC under hypoxia.
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Affiliation(s)
- Yi Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| | - Lei Yang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| | - Ning Liu
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu 210008. China
| | - Qiancheng Shi
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu 210008. China
| | - Xiaoqin Yin
- Department of Endocrinology, Shanghai Children's Hospital, Shanghai 200000. China
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
| | - Weidong Gan
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, Jiangsu 210008. China
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Sciences, Medical School, Nanjing University, Nanjing, Jiangsu 210093. China
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17
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Yang L, Chen Y, Liu N, Shi Q, Han X, Gan W, Li D. Low expression of TRAF3IP2-AS1 promotes progression of NONO-TFE3 translocation renal cell carcinoma by stimulating N 6-methyladenosine of PARP1 mRNA and downregulating PTEN. J Hematol Oncol 2021; 14:46. [PMID: 33741027 PMCID: PMC7980631 DOI: 10.1186/s13045-021-01059-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
Background NONO-TFE3 translocation renal cell carcinoma (NONO-TFE3 tRCC) is one subtype of RCCs associated with Xp11.2 translocation/TFE3 gene fusions RCC (Xp11.2 tRCCs). Long non-coding RNA (lncRNA) has attracted great attention in cancer research. The function and mechanisms of TRAF3IP2 antisense RNA 1 (TRAF3IP2-AS1), a natural antisense lncRNA, in NONO-TFE3 tRCC remain poorly understood. Methods FISH and qRT-PCR were undertaken to study the expression, localization and clinical significance of TRAF3IP2-AS1 in Xp11.2 tRCC tissues and cells. The functions of TRAF3IP2-AS1 in tRCC were investigated by proliferation analysis, EdU staining, colony and sphere formation assay, Transwell assay and apoptosis analysis. The regulatory mechanisms among TRAF3IP2-AS1, PARP1, PTEN and miR-200a-3p/153-3p/141-3p were investigated by luciferase assay, RNA immunoprecipitation, Western blot and immunohistochemistry. Results The expression of TRAF3IP2-AS1 was suppressed by NONO-TFE3 fusion in NONO-TFE3 tRCC tissues and cells. Overexpression of TRAF3IP2-AS1 inhibited the proliferation, migration and invasion of UOK109 cells which were derived from cancer tissue of patient with NONO-TFE3 tRCC. Mechanistic studies revealed that TRAF3IP2-AS1 accelerated the decay of PARP1 mRNA by direct binding and recruitment of N6-methyladenosie methyltransferase complex. Meanwhile, TRAF3IP2-AS1 competitively bound to miR-200a-3p/153-3p/141-3p and prevented those from decreasing the level of PTEN. Conclusions TRAF3IP2-AS1 functions as a tumor suppressor in NONO-TFE3 tRCC progression and may serve as a novel target for NONO-TFE3 tRCC therapy. TRAF3IP2-AS1 expression has the potential to serve as a novel diagnostic and prognostic biomarker for NONO-TFE3 tRCC detection. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-021-01059-5.
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Affiliation(s)
- Lei Yang
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, Jiangsu, China.,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Yi Chen
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, Jiangsu, China.,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Ning Liu
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, Jiangsu, China.,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, Jiangsu, China
| | - QianCheng Shi
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, Jiangsu, China.,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Xiaodong Han
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, Jiangsu, China.,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, Jiangsu, China
| | - Weidong Gan
- Department of Urology, Affiliated Drum Tower Hospital of Medical School of Nanjing University, Nanjing, 210008, Jiangsu, China.
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, 210093, Jiangsu, China. .,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210093, Jiangsu, China.
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18
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Zhu Y, Pu X, Dong X, Ji C, Guo H, Li D, Zhao X, Gan W. Molecular Heterogeneity of Xp11.2 Translocation Renal Cell Carcinoma: The Correlation Between Split Signal Pattern in FISH and Prognosis. Cancer Manag Res 2021; 13:2419-2431. [PMID: 33758541 PMCID: PMC7979328 DOI: 10.2147/cmar.s297457] [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: 12/15/2020] [Accepted: 02/16/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Xp11.2 translocation renal cell carcinoma (Xp11.2 tRCC) is a distinct subtype of renal cell carcinoma (RCC) characterized by chromosomal translocations involving TFE3 gene. TFE3 break-apart fluorescence in situ hybridization (FISH) assay is an effective tool to diagnose Xp11.2 tRCC. The aim of this study is to evaluate the correlation between split signal pattern in FISH and the clinicopathological characteristics of Xp11.2 tRCC. Patients and Methods We reviewed 2037 RCC patients who underwent partial nephrectomy or radical nephrectomy from January 2007 to March 2020 in our institution. Forty-nine cases were diagnosed as Xp11.2 tRCC and their split signal patterns were evaluated. X-tile software was used to determine the optimal cut-off value of the percentage of split signal in FISH. Kaplan–Meier analysis and Cox regression analysis were performed to assess the relationship between signal pattern of FISH and the prognosis. Results Among the 49 patients, 13 patients and 36 patients were classified into high and low split signal group, respectively. Nine cases showed extra amplification signal pattern and 40 cases showed typical translocation signal pattern. Multivariate analysis demonstrated that high percentage of split signal and amplification signal pattern were the independent predictors for progression-free survival (PFS) whereas only pT stage was associated independently with overall survival (OS). Conclusion Xp11.2 tRCC cases with high percentage of split signals or amplification signal pattern may have a worse outcome, and the two indicators need to be highlighted in clinical practice.
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Affiliation(s)
- Yiqi Zhu
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
| | - Xiaohong Pu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
| | - Xiang Dong
- Department of Urology, Drum Tower Clinical Medical School of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Changwei Ji
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
| | - Hongqian Guo
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
| | - Dongmei Li
- Immunology and Reproduction Biology Laboratory & State Key Laboratory of Analytical Chemistry for Life Science, Medical School, Nanjing University, Nanjing, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, Jiangsu, People's Republic of China
| | - Xiaozhi Zhao
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
| | - Weidong Gan
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, People's Republic of China
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19
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Vu HN, Dilshat R, Fock V, Steingrímsson E. User guide to MiT-TFE isoforms and post-translational modifications. Pigment Cell Melanoma Res 2020; 34:13-27. [PMID: 32846025 DOI: 10.1111/pcmr.12922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/31/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
Abstract
The microphthalmia-associated transcription factor (MITF) is at the core of melanocyte and melanoma fate specification. The related factors TFEB and TFE3 have been shown to be instrumental for transcriptional regulation of genes involved in lysosome biogenesis and autophagy, cellular processes important for mediating nutrition signals and recycling of cellular materials, in many cell types. The MITF, TFEB, TFE3, and TFEC proteins are highly related. They share many structural and functional features and are targeted by the same signaling pathways. However, the existence of several isoforms of each factor and the increasing number of residues shown to be post-translationally modified by various signaling pathways poses a difficulty in indexing amino acid residues in different isoforms across the different proteins. Here, we provide a resource manual to cross-reference amino acids and post-translational modifications in all isoforms of the MiT-TFE family in humans, mice, and zebrafish and summarize the protein accession numbers for each isoform of these factors in the different genomic databases. This will facilitate future studies on the signaling pathways that regulate different isoforms of the MiT-TFE transcription factor family.
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Affiliation(s)
- Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Valerie Fock
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
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20
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Clinicopathologic and Molecular Analysis of the TFEB Fusion Variant Reveals New Members of TFEB Translocation Renal Cell Carcinomas (RCCs): Expanding the Genomic Spectrum. Am J Surg Pathol 2020; 44:477-489. [PMID: 31764220 DOI: 10.1097/pas.0000000000001408] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Xp11 renal cell carcinoma (RCC) with different gene fusions may have different clinicopathologic features. We sought to identify variant fusions in TFEB translocation RCC. A total of 31 cases of TFEB RCCs were selected for the current study; MALAT1-TFEB fusion was identified in 25 cases (81%, 25/31) using fusion probes. The remaining 6 cases (19%, 6/31) were further analyzed by RNA sequencing and 5 of them were detected with TFEB-associated gene fusions, including 2 ACTB-TFEB, 1 EWSR1-TFEB, 1 CLTC-TFEB, and 1 potential PPP1R10-TFEB (a paracentric inversion of the TFEB gene, consistent with "negative" TFEB split FISH result, and advising a potential diagnostic pitfall in detecting TFEB gene rearrangement). Four of the 5 fusion transcripts were successfully validated by reverse transcription-polymerase chain reaction and Sanger sequencing. Morphologically, approximately one third (29%, 9/31) of TFEB RCCs showed typical biphasic morphology. The remaining two thirds of the cases (71%, 22/31) exhibited nonspecific morphology, with nested, sheet-like, or papillary architecture, resembling other types of renal neoplasms, such as clear cell RCC, Xp11 RCC, perivascular epithelioid cell tumor (PEComa), or papillary RCC. Although cases bearing a MALAT1-TFEB fusion demonstrated variable morphologies, all 9 cases featuring typical biphasic morphology were associated with MALAT1-TFEB genotype. Accordingly, typical biphasic morphology suggests MALAT1-TFEB fusion, whereas atypical morphology did not suggest the specific type of fusion. Isolated or clustered eosinophilic cells were a common feature in TFEB RCCs, which may be a useful morphology diagnostic clue for TFEB RCCs. Clinicopathologic variables assessment showed that necrosis was the only morphologic feature that correlated with the aggressive behavior of TFEB RCC (P=0.004). In summary, our study expands the genomic spectrum and the clinicopathologic features of TFEB RCCs, and highlights the challenges of diagnosis and the importance of subtyping of this tumor by combining morphology and multiple molecular techniques.
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21
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Song Y, Yin X, Xia Q, Zheng L, Yao J, Zeng H, Nie L, Gong J, Zhou Q, Chen N. Xp11 translocation renal cell carcinoma with morphological features mimicking multilocular cystic renal neoplasm of low malignant potential: a series of six cases with molecular analysis. J Clin Pathol 2020; 74:171-176. [PMID: 32699116 DOI: 10.1136/jclinpath-2020-206681] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 02/05/2023]
Abstract
AIMS Xp11 translocation renal cell carcinoma (RCC) is a distinctive subtype of RCC with TFE3 (Transcription Factor Binding to IGHM Enhancer 3) gene rearrangement. The gross features in most Xp11 translocation RCCs closely resemble clear cell RCCs. In this study, we report six cases of Xp11 translocation RCCs with a unique multicystic architecture, reminiscent of multilocular cystic renal cell neoplasm of low malignant potential (MCRN-LMP). METHODS AND RESULTS Microscopically, the renal mass was well circumscribed with multilocular cystic architecture. The cyst walls and septa were mostly lined by a single layer of cells with clear cytoplasm and low-grade nuclei, reminiscent of MCRN-LMP. Psammoma bodies were detected in four cases. One particular patient was misdiagnosed with benign cysts in local hospitals and led to second operation. Tumour cells were settled according to the track of the first surgical procedure. TFE3 fluorescence in situ hybridization (FISH) assay confirmed the diagnosis of Xp11 translocation RCCs. FISH and RNA sequencing analyses confirmed MED15-TFE3 gene fusion in all six cases. Respective patients were alive, without any recent evidence of disease recurrence and/or metastasis. CONCLUSIONS Here, we introduce a relatively inertia-variant of Xp11 translocation RCC which mimics MCRN-LMP. The distinctive morphological condition is linked to MED15-TFE3 gene fusion. In fact, renal neoplasms with morphological features of MCRN-LMP, especially those containing psammoma bodies, should be routinely evaluated for evidence of TFE3 gene rearrangements.
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Affiliation(s)
- Yankun Song
- Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoxue Yin
- Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Qiuyuan Xia
- Pathology, Nanjing Jinling Hospital, Nanjing, China
| | - Linmao Zheng
- Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Yao
- Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Zeng
- Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Ling Nie
- Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Jing Gong
- Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Qiao Zhou
- Pathology, West China Hospital, Sichuan University, Chengdu, China
| | - Ni Chen
- Pathology, West China Hospital, Sichuan University, Chengdu, China
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22
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DV200 Index for Assessing RNA Integrity in Next-Generation Sequencing. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9349132. [PMID: 32185225 PMCID: PMC7063185 DOI: 10.1155/2020/9349132] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 12/29/2019] [Accepted: 02/06/2020] [Indexed: 11/28/2022]
Abstract
Poor quality of biological samples will result in an inaccurate analysis of next-generation sequencing (NGS). Therefore, methods to accurately evaluate sample integrity are needed. Among methods for evaluating RNA quality, the RNA integrity number equivalent (RINe) is widely used, whereas the DV200, which evaluates the percentage of fragments of >200 nucleotides, is also used as a quality assessment standard. In this study, we compared the RINe and DV200 RNA quality indexes to determine the most suitable RNA index for the NGS analysis. Seventy-one RNA samples were extracted from formalin-fixed paraffin-embedded tissue samples (n = 30), fresh-frozen samples (n = 25), or cell lines (n = 16). After assessing RNA quality using the RINe and DV200, we prepared two kinds of stranded mRNA sequencing libraries. Finally, we calculated the correlation between each RNA quality index and the amount of library product (1st PCR product per input RNA). The DV200 measure showed stronger correlation with the amount of library product than the RINe (R2 = 0.8208 for the DV200 versus 0.6927 for the RINe). Receiver operating characteristic curve analyses revealed that the DV200 was the better marker for predicting efficient library production than the RINe using a threshold of >10 ng/ng for the amount of the 1st PCR product per input RNA (cutoff value for the RINe and DV200, 2.3 and 66.1%; area under the curve, 0.99 and 0.91; sensitivity, 82% and 92%; and specificity, 93% and 100%, respectively). Our results indicate that NGS libraries prepared using RNA samples with the DV200 value > 66.1% exhibit greater sensitivity and specificity than those prepared with the RINe values > 2.3. These findings suggest that the DV200 is superior to the RINe, especially for low-quality RNA, because it is a more consistent assessment of the amount of the 1st NGS library product per input.
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23
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Argani P, Zhang L, Sung YS, White MJ, Miller K, Hopkins M, Small D, Pratilas CA, Swanson D, Dickson B, Antonescu CR. A novel RBMX-TFE3 gene fusion in a highly aggressive pediatric renal perivascular epithelioid cell tumor. Genes Chromosomes Cancer 2020; 59:58-63. [PMID: 31408245 PMCID: PMC7057291 DOI: 10.1002/gcc.22801] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 01/24/2023] Open
Abstract
We report an Xp11 translocation perivascular epithelioid cell tumor (PEComa) with a novel RBMX-TFE3 gene fusion, resulting from a paracentric X chromosome inversion, inv(X)(p11;q26). The neoplasm occurred in an otherwise healthy 12-year-old boy who presented with a large left renal mass with extension into the inferior vena cava. The patient was found to have multiple pulmonary metastases at diagnosis and died of disease 3 months later. The morphology (epithelioid clear cells with alveolar and nested architecture) and immunophenotype (TFE3 and HMB45 strongly positive; actin, desmin, and PAX8 negative) was typical of an Xp11 translocation PEComa; however, TFE3 rearrangement was initially not detected by routine TFE3 break-apart fluorescence in situ hybridization (FISH). Further RNA sequencing revealed a novel RBMX-TFE3 gene fusion, which was subsequently confirmed by fusion assay FISH, using custom design RBMX and TFE3 come-together probes. This report describes a novel TFE3 gene fusion partner, RBMX, in a pediatric renal PEComa patient associated with a fulminant clinical course. As documented in other intrachromosomal Xp11.2 inversions, such as fusions with NONO, RBM10, or GRIPAP1 genes, the TFE3 break-apart might be below the FISH resolution, resulting in a false negative result.
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Affiliation(s)
- Pedram Argani
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA,Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Lei Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yun-Shao Sung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marissa J. White
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Karin Miller
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Mark Hopkins
- Department of Pathology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Donald Small
- Department of Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Brendan Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada
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24
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Dickson BC, T-S Chung C, Hurlbut DJ, Marrano P, Shago M, Sung YS, Swanson D, Zhang L, Antonescu CR. Genetic diversity in alveolar soft part sarcoma: A subset contain variant fusion genes, highlighting broader molecular kinship with other MiT family tumors. Genes Chromosomes Cancer 2020; 59:23-29. [PMID: 31433528 PMCID: PMC7057290 DOI: 10.1002/gcc.22803] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 01/25/2023] Open
Abstract
Alveolar soft part sarcoma (ASPS) is a rare malignancy that, since its initial description, remains a neoplasm of uncertain histogenesis. The disease-defining molecular event characterizing the diagnosis of ASPS is the ASPSCR1-TFE3 fusion gene. Following identification of an index case of ASPS with a novel TFE3 fusion partner, we performed a retrospective review to determine whether this represents an isolated event. We identified two additional cases, for a total of three cases lacking ASPSCR1 partners. The average patient age was 46 years (range, 17-65); two patients were female. The sites of origin included the transverse colon, foot, and dura. Each case exhibited a histomorphology typical of ASPS, and immunohistochemistry was positive for TFE3 in all cases. Routine molecular testing of the index patient demonstrated a HNRNPH3-TFE3 gene fusion; the remaining cases were found to have DVL2-TFE3 or PRCC-TFE3 fusion products. The latter two fusions have previously been identified in renal cell carcinoma; to our knowledge, this is the first report of a HNRNPH3-TFE3 gene fusion. These findings highlight a heretofore underrecognized genetic diversity in ASPS, which appears to more broadly molecularly overlap with that of translocation-associated renal cell carcinoma and PEComa. These results have immediate implications in the diagnosis of ASPS since assays reliant upon ASPSCR1 may yield a false negative result. While these findings further understanding of the molecular pathogenesis of ASPS, issues related to the histogenesis of this unusual neoplasm remain unresolved.
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Affiliation(s)
- Brendan C. Dickson
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System, Toronto, ON, Canada,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Corresponding Authors: Brendan C. Dickson, Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1X5, , Cristina R. Antonescu, Department of Pathology, Memorial Sloan Kettering Cancer Center New York, NY, USA 10021,
| | - Catherine T-S Chung
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - David J. Hurlbut
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON, Canada
| | - Paula Marrano
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Mary Shago
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada,Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Yun-Shao Sung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Swanson
- Department of Pathology and Laboratory Medicine, Mount Sinai Health System, Toronto, ON, Canada
| | - Lei Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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25
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A Rare Partner of TFE3 in the Xp11 Translocation Renal Cell Carcinoma: Clinicopathological Analyses and Detection of MED15-TFE3 Fusion. BIOMED RESEARCH INTERNATIONAL 2019; 2019:5974089. [PMID: 31828108 PMCID: PMC6881588 DOI: 10.1155/2019/5974089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/29/2019] [Accepted: 10/16/2019] [Indexed: 01/09/2023]
Abstract
Xp11 translocation renal cell carcinoma (RCC), a member of the microphthalmia-associated transcription factor (MiTF) family, is a rare renal tumor characterized by different translocations involving the TFE3 gene. Here, we reported a case of Xp11 translocation RCC with a rare MED15-TFE3 gene fusion by RNA sequencing. Morphologically, the tumor cells were arranged in a solid and small nest pattern. The cytoplasm was voluminous, flocculent eosinophilic, and vacuolated. The nuclei were round or polygon with fine granular chromatin, and the nucleoli were unconspicuous. Psammoma bodies were observed in mesenchyma. Immunohistochemically, the tumor cells were diffuse moderately or strongly positive for CD10, P504S, vimentin, PAX8, RCC, AE1/AE3, and SDHB and focally positive for CK7 and CA IX while negative for cathepsin K, HMB45, Melan-A, Ksp-cadherin, and CD117. The Ki67 proliferation index was approximately 3%. However, TFE3 labeling showed an uncertainly weak nuclear staining and been considered negative. Fluorescence in situ hybridization (FISH) demonstrated a positive result that splits signals with a distance of > 2 signal diameters. Subsequently, RNA sequencing confirmed a fusion of MED15 gene exon 11 on chromosome 22 with TFE3 gene exon 6 in the tumor. The patient was alive with no evidence of recurrence. Our report contributes to the understanding on MED15-TFE3 RCC.
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26
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Xp11 translocation renal cell carcinoma and clear cell renal cell carcinoma with TFE3 strong positive immunostaining: morphology, immunohistochemistry, and FISH analysis. Mod Pathol 2019; 32:1521-1535. [PMID: 31175325 DOI: 10.1038/s41379-019-0283-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022]
Abstract
TFE3 is accepted as a good marker for the diagnosis of Xp11 translocation renal cell carcinoma. However, the significance of TFE3 in other types of renal cell carcinomas remains unclear. We examined the expression of TFE3 using immunohistochemistry by automated Ventana BenchMark XT system in 1818 consecutive renal cell carcinomas and verified the strong positive cases with TFE3 break-apart fluorescence in situ hybridization and RNA sequencing. Among the 27 renal cell carcinomas with TFE3 strong positive immunostaining, 20 cases were diagnosed as Xp11 translocation renal cell carcinoma, and seven cases were diagnosed as clear cell renal cell carcinoma. We further analyzed the morphology, clinicopathological features, and immunohistochemistry markers (CK7, CD117, CD10, P504s, vimentin, CA-IX, AE1/AE3, EMA, HMB45, Melan-A, and cathepsin K) of them. Pale to eosinophilic flocculent cytoplasm and psammomatous calcification were seen only in Xp11 translocation renal cell carcinomas (P < 0.05). Tumor necrosis occurred in all four cases of Xp11 translocation renal cell carcinomas with pT3a stage, which had local recurrence and distant metastasis (two of them died) within 3 years. The expressions of Vimentin, CA-IX, AE1/AE3, and EMA were significantly different between them (P < 0.05). CA-IX was diffusely strong positive in clear cell renal cell carcinomas but negative or focally mild positive in Xp11 translocation renal cell carcinomas. Our study first demonstrates that a very small minority (0.4%) of clear cell renal cell carcinomas with TFE3 strong positive immunostaining, which points out a potential pitfall in diagnosis of Xp11 translocation renal cell carcinomas by TFE3 immunohistochemistry. CA-IX is a good marker to distinguish clear cell renal cell carcinoma with TFE3 strong positive immunostaining from Xp11 translocation renal cell carcinoma. Tumor necrosis could be a potential factor relevant to pT3a stage, which may be a high-risk factor for the patients with Xp11 translocation renal cell carcinomas.
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27
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Gandhi JS, Malik F, Amin MB, Argani P, Bahrami A. MiT family translocation renal cell carcinomas: A 15th anniversary update. Histol Histopathol 2019; 35:125-136. [PMID: 31489603 DOI: 10.14670/hh-18-159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Microphthalmia (MiT) family translocation renal cell carcinomas (RCCs) are a heterogeneous category of renal tumors which all express MiT transcription factors, typically from chromosomal translocation and rarely from gene amplification. This tumor family has two major subtypes [i.e., Xp11 translocation RCC and t(6;11) RCC] and several related neoplasms (i.e., TFEB amplification RCC and melanotic Xp11 translocation renal cancers). Increased understanding of the clinical, pathological, molecular and prognostic heterogeneity of these tumors, since their official recognition in 2004, provides the opportunity to identify prognostic biomarkers and to understand the reasons for tumor aggression. We will review the literature from the past 15 years and highlight the need for a greater understanding of the molecular mechanisms underpinning heterogeneous tumor behavior.
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Affiliation(s)
- Jatin S Gandhi
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Faizan Malik
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Mahul B Amin
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Pedram Argani
- Department of Pathology, John Hopkins University, Baltimore, MD, USA
| | - Armita Bahrami
- Department of Pathology, University of Tennessee Health Science Center, Memphis, TN, USA.,Departments of Pathology and Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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28
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Baba M, Furuya M, Motoshima T, Lang M, Funasaki S, Ma W, Sun HW, Hasumi H, Huang Y, Kato I, Kadomatsu T, Satou Y, Morris N, Karim BO, Ileva L, Kalen JD, Wilan Krisna LA, Hasumi Y, Sugiyama A, Kurahashi R, Nishimoto K, Oyama M, Nagashima Y, Kuroda N, Araki K, Eto M, Yao M, Kamba T, Suda T, Oike Y, Schmidt LS, Linehan WM. TFE3 Xp11.2 Translocation Renal Cell Carcinoma Mouse Model Reveals Novel Therapeutic Targets and Identifies GPNMB as a Diagnostic Marker for Human Disease. Mol Cancer Res 2019; 17:1613-1626. [PMID: 31043488 PMCID: PMC6679785 DOI: 10.1158/1541-7786.mcr-18-1235] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/12/2019] [Accepted: 04/26/2019] [Indexed: 12/16/2022]
Abstract
Renal cell carcinoma (RCC) associated with Xp11.2 translocation (TFE3-RCC) has been recently defined as a distinct subset of RCC classified by characteristic morphology and clinical presentation. The Xp11 translocations involve the TFE3 transcription factor and produce chimeric TFE3 proteins retaining the basic helix-loop-helix leucine zipper structure for dimerization and DNA binding suggesting that chimeric TFE3 proteins function as oncogenic transcription factors. Diagnostic biomarkers and effective forms of therapy for advanced cases of TFE3-RCC are as yet unavailable. To facilitate the development of molecular based diagnostic tools and targeted therapies for this aggressive kidney cancer, we generated a translocation RCC mouse model, in which the PRCC-TFE3 transgene is expressed specifically in kidneys leading to the development of RCC with characteristic histology. Expression of the receptor tyrosine kinase Ret was elevated in the kidneys of the TFE3-RCC mice, and treatment with RET inhibitor, vandetanib, significantly suppressed RCC growth. Moreover, we found that Gpnmb (Glycoprotein nonmetastatic B) expression was notably elevated in the TFE3-RCC mouse kidneys as seen in human TFE3-RCC tumors, and confirmed that GPNMB is the direct transcriptional target of TFE3 fusions. While GPNMB IHC staining was positive in 9/9 cases of TFE3-RCC, Cathepsin K, a conventional marker for TFE3-RCC, was positive in only 67% of cases. These data support RET as a potential target and GPNMB as a diagnostic marker for TFE3-RCC. The TFE3-RCC mouse provides a preclinical in vivo model for the development of new biomarkers and targeted therapeutics for patients affected with this aggressive form of RCC. IMPLICATIONS: Key findings from studies with this preclinical mouse model of TFE3-RCC underscore the potential for RET as a therapeutic target for treatment of patients with TFE3-RCC, and suggest that GPNMB may serve as diagnostic biomarker for TFE3 fusion RCC.
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MESH Headings
- Adolescent
- Adult
- Aged
- Animals
- Apoptosis
- Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/metabolism
- Carcinoma, Renal Cell/pathology
- Cell Cycle Proteins/genetics
- Cell Proliferation
- Child
- Chromosomes, Human, X
- Disease Models, Animal
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Kidney Neoplasms/genetics
- Kidney Neoplasms/metabolism
- Kidney Neoplasms/pathology
- Male
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Inbred C57BL
- Middle Aged
- Neoplasm Proteins/genetics
- Oncogene Proteins, Fusion
- Prognosis
- Survival Rate
- Translocation, Genetic
- Tumor Cells, Cultured
- Young Adult
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Affiliation(s)
- Masaya Baba
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan.
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mitsuko Furuya
- Department of Molecular Pathology, Yokohama City University, Yokohama, Japan
| | | | - Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Shintaro Funasaki
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Wenjuan Ma
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, Maryland
| | - Hisashi Hasumi
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Department of Urology, Yokohama City University, Yokohama, Japan
| | - Ying Huang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ikuma Kato
- Department of Molecular Pathology, Yokohama City University, Yokohama, Japan
| | | | - Yorifumi Satou
- Laboratory of Retroviral Genomics and Transcriptomics, International Research Center for Medical Sciences (IRCMS), Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Nicole Morris
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Baktiar O Karim
- Pathology/Histotechnology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Lilia Ileva
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Joseph D Kalen
- Small Animal Imaging Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Luh Ade Wilan Krisna
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
| | - Yukiko Hasumi
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Aiko Sugiyama
- DSK Project, Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan
| | - Ryoma Kurahashi
- Department of Urology, Kumamoto University, Kumamoto, Japan
- Department of Molecular Genetics, Kumamoto University, Kumamoto, Japan
| | - Koshiro Nishimoto
- Department of Uro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Masafumi Oyama
- Department of Uro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women's Medical University, Tokyo, Japan
| | - Naoto Kuroda
- Department of Pathology, Kochi Red Cross Hospital, Kochi, Japan
| | - Kimi Araki
- Division of Developmental Genetics, Institute of Resource Development and Analysis, Kumamoto University, Kumamoto, Japan
| | - Masatoshi Eto
- Department of Urology, Kyushyu University, Fukuoka, Japan
| | - Masahiro Yao
- Department of Urology, Yokohama City University, Yokohama, Japan
| | - Tomomi Kamba
- Department of Urology, Kumamoto University, Kumamoto, Japan
| | - Toshio Suda
- Laboratory of Stem Cell Regulation, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Japan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore
| | - Yuichi Oike
- Department of Molecular Genetics, Kumamoto University, Kumamoto, Japan
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
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Sharain RF, Gown AM, Greipp PT, Folpe AL. Immunohistochemistry for TFE3 lacks specificity and sensitivity in the diagnosis of TFE3-rearranged neoplasms: a comparative, 2-laboratory study. Hum Pathol 2019; 87:65-74. [DOI: 10.1016/j.humpath.2019.02.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 02/19/2019] [Indexed: 12/17/2022]
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NEAT1-TFE3 and KAT6A-TFE3 renal cell carcinomas, new members of MiT family translocation renal cell carcinoma. Mod Pathol 2019; 32:710-716. [PMID: 30622287 PMCID: PMC6486435 DOI: 10.1038/s41379-018-0191-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 12/31/2022]
Abstract
Microphthalmia-associated transcription factor (MiT) family translocation renal cell carcinoma harbors variable gene fusions involving either TFE3 or TFEB genes. Multiple 5' fusion partners for TFE3 have been reported, including ASPSCR1, CLTC, DVL2, LUC7L3, KHSRP, PRCC, PARP14, NONO, SFPQ1, MED15, and RBM10. Each of these fusion genes activates TFE3 transcription which can be detected by immunostaining. Using targeted RNA-sequencing, TFE3 fusion gene partners were identified in 5 cases of TFE3 immunohistochemistry positive translocation renal cell carcinoma. Three cases demonstrated known fusions: ASPSCR1-TFE3, MED15-TFE3 and RBM10-TFE3. However, two cases showed unreported NEAT1-TFE3 and KAT6A-TFE3 fusion transcripts. The NEAT1-TFE3 RCC arose in a 59-year-old male; which demonstrated overlapping morphological features seen in NEAT2(MALAT1)-TFEB t(6;11) renal cell carcinoma, including biphasic alveolar/nested tumor cells with eosinophilic cytoplasm. The KAT6A-TFE3 renal cell carcinoma demonstrated typical morphological features of TFE3/Xp11 renal cell carcinoma including papillae, eosinophilic cytoplasm with focal clearing and abundant psammoma bodies. KAT6A gene fusion was reported in some cases of acute myeloid leukemia, which has not been previously reported in solid tumors. This report highlights the genetic complexity of TFE3 translocation renal cell carcinoma; and RNA-sequencing is a powerful approach for elucidating the underlying genetic alterations.
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TFE3 fusions escape from controlling of mTOR signaling pathway and accumulate in the nucleus promoting genes expression in Xp11.2 translocation renal cell carcinomas. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:119. [PMID: 30849994 PMCID: PMC6408813 DOI: 10.1186/s13046-019-1101-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
Abstract
Background Xp11.2 translocation renal cell carcinoma (tRCC) is mainly caused by translocation of the TFE3 gene located on chromosome Xp11.2 and is characterized by overexpression of the TFE3 fusion gene. Patients are diagnosed with tRCC usually before 45 years of age with poor prognosis. We investigated this disease using two tRCC cell lines, UOK109 and UOK120, in this study. Methods The purpose of this study was to investigate the pathogenic mechanism of TFE3 fusions in tRCC based on its subcellular localization, nuclear translocation and transcriptional activity. The expression of TFE3 fusions and other related genes were analyzed by quantitative reverse transcription PCR (qRT-PCR) and Western blot. The subcellular localization of TFE3 was determined using immunofluorescence. The transcriptional activity of TFE3 fusions was measured using a luciferase reporter assay and ChIP analysis. In some experiments, TFE3 fusions were depleted by RNAi or gene knockdown. The TFE3 fusion segments were cloned into a plasmid expression system for expression in cells. Results Our results demonstrated that TFE3 fusions were overexpressed in tRCC with a strong nuclear retention irrespective of treatment with an mTORC1 inhibitor or not. TFE3 fusions lost its co-localization with lysosomal proteins and decreased its interaction with the chaperone 14–3-3 proteins in UOK109 and UOK120 cells. However, the fusion segments of TFE3 could not translocate to the nucleus and inhibition of Gsk3β could increase the cytoplasmic retention of TFE3 fusions. Both the luciferase reporter assay and ChIP analysis demonstrated that TFE3 fusions could bind to the promoters of the target genes as a wild-type TFE3 protein. Knockdown of TFE3 results in decreased expression of those genes responsible for lysosomal biogenesis and other target genes. The ChIP-seq data further verified that, in addition to lysosomal genes, TFE3 fusions could regulate genes involved in cellular responses to hypoxic stress and transcription. Conclusions Our results indicated that the overexpressed TFE3 fusions were capable of escaping from the control by the mTOR signaling pathway and were accumulated in the nucleus in UOK109 and UOK120 cells. The nuclear retention of TFE3 fusions promoted the expression of lysosomal genes and other target genes, facilitating cancer cell resistance against an extreme environment. Electronic supplementary material The online version of this article (10.1186/s13046-019-1101-7) contains supplementary material, which is available to authorized users.
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Abstract
The identity of a cell or an organism is at least in part defined by its gene expression and therefore analyzing gene expression remains one of the most frequently performed experimental techniques in molecular biology. The development of the RNA-Sequencing (RNA-Seq) method allows an unprecedented opportunity to analyze expression of protein-coding, noncoding RNA and also de novo transcript assembly of a new species or organism. However, the planning and design of RNA-Seq experiments has important implications for addressing the desired biological question and maximizing the value of the data obtained. In addition, RNA-Seq generates a huge volume of data and accurate analysis of this data involves several different steps and choices of tools. This can be challenging and overwhelming, especially for bench scientists. In this chapter, we describe an entire workflow for performing RNA-Seq experiments. We describe critical aspects of wet lab experiments such as RNA isolation, library preparation and the initial design of an experiment. Further, we provide a step-by-step description of the bioinformatics workflow for different steps involved in RNA-Seq data analysis. This includes power calculations, setting up a computational environment, acquisition and processing of publicly available data if desired, quality control measures, preprocessing steps for the raw data, differential expression analysis, and data visualization. We particularly mention important considerations for each step to provide a guide for designing and analyzing RNA-Seq data.
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Eikrem Ø, Walther TC, Flatberg A, Beisvag V, Strauss P, Farstad M, Beisland C, Koch E, Mueller TF, Marti HP. Fine needle aspirates of kidneys: a promising tool for RNA sequencing in native and transplanted kidneys. BMC Nephrol 2018; 19:221. [PMID: 30185151 PMCID: PMC6126030 DOI: 10.1186/s12882-018-1012-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/23/2018] [Indexed: 01/17/2023] Open
Abstract
Background Transcriptome analysis is emerging as emerging as a promising tool to enhance precision of diagnosis and monitoring in solid organ transplantation. Clinical progress has however been hampered by the current reliance on samples from core needle biopsies. This proof-of-principle study examined whether fine needle aspirates, being less invasive, permit the ascertainment of the identical molecular information as core biopsies. Methods We collected fine needles aspirates from various needle sizes (G19, 21, 23, 25) and the corresponding core biopsies (G16 needle) of non-tumor tissue of full nephrectomy specimens from patients suffering from clear cell renal cell carcinoma (n = 11). RNA expression patterns of two gene sets (156 genes) were executed using targeted RNA sequencing in samples from fine needle vs. core needle samples. A subgroup of kidneys (n = 6) also underwent whole transcriptome RNA sequencing from core biopsies of tumor and peri-tumoral normal tissue (Tru Seq RNA Access, Illumina). Results Samples from all needle sizes except two G25 aspirates yielded RNA potentially suitable for sequencing of both gene sets. The mRNA expression patterns of the two gene sets were highly correlated between fine needle aspirates (G23) and corresponding (G16) core biopsies (r = 0.985 and 0.982, respectively). This close correlation was further documented by heat map, Principal Component Analyses (PCA) and whole transcription RNA sequencing. The similarity between fine neddle aspirates and core needle biopsies was additionally confirmed in the subgroup with complete RNA sequencing. Conclusions Fine needle biopsies yield similar genomic information to core needle biopsies. The less invasive nature of fine needle biopsies may therefore permit more frequent molecular monitoring and a more targeted use of core needle biopsies in native and especially in transplanted kidneys.
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Affiliation(s)
- Øystein Eikrem
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Tedd C Walther
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Magnus Farstad
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway.,Department of Urology, Haukeland University Hospital, Bergen, Norway
| | - Even Koch
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Thomas F Mueller
- Division of Nephrology, Department of Medicine, University Hospital of Zurich, Zurich, Switzerland
| | - Hans-Peter Marti
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway. .,Department of Medicine, Haukeland University Hospital, Bergen, Norway.
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RNA sequencing of Xp11 translocation-associated cancers reveals novel gene fusions and distinctive clinicopathologic correlations. Mod Pathol 2018; 31:1346-1360. [PMID: 29713041 DOI: 10.1038/s41379-018-0051-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/27/2018] [Accepted: 02/28/2018] [Indexed: 12/20/2022]
Abstract
Both Xp11 translocation renal cell carcinomas and the corresponding mesenchymal neoplasms are characterized by a variety of gene fusions involving TFE3. It has been known that tumors with different gene fusions may have different clinicopathologic features; however, further in-depth investigations of subtyping Xp11 translocation-associated cancers are needed in order to explore more meaningful clinicopathologic correlations. A total of 22 unusual cases of Xp11 translocation-associated cancers were selected for the current study; 20 cases were further analyzed by RNA sequencing to explore their TFE3 gene fusion partners. RNA sequencing identified 17 of 20 cases (85%) with TFE3-associated gene fusions, including 4 ASPSCR1/ASPL-TFE3, 3 PRCC-TFE3, 3 SFPQ/PSF-TFE3, 1 NONO-TFE3, 4 MED15-TFE3, 1 MATR3-TFE3, and 1 FUBP1-TFE3. The results have been verified by fusion fluorescence in situ hybridization (FISH) assays or reverse transcriptase polymerase chain reaction (RT-PCR). The remaining 2 cases with specific pathologic features highly suggestive of MED15-TFE3 renal cell carcinoma were identified by fusion FISH assay. We provide the detailed morphologic and immunophenotypic description of the MED15-TFE3 renal cell carcinomas, which frequently demonstrate extensively cystic architecture, similar to multilocular cystic renal neoplasm of low malignant potential, and expressed cathepsin K and melanotic biomarker Melan A. This is the first time to correlate the MED15-TFE3 renal cell carcinoma with specific clinicopathologic features. We also report the first case of the corresponding mesenchymal neoplasm with MED15-TFE3 gene fusion. Additional novel TFE3 gene fusion partners, MATR3 and FUBP1, were identified. Cases with ASPSCR1-TFE3, SFPQ-TFE3, PRCC-TFE3, and NONO-TFE3 gene fusion showed a wide variability in morphologic features, including invasive tubulopapillary pattern simulating collecting duct carcinoma, extensive calcification and ossification, and overlapping and high columnar cells with nuclear grooves mimicking tall cell variant of papillary thyroid carcinoma. Furthermore, we respectively evaluated the ability of TFE3 immunohistochemistry, TFE3 FISH, RT-PCR, and RNA sequencing to subclassify Xp11 translocation-associated cancers. In summary, our study expands the list of TFE3 gene fusion partners and the clinicopathologic features of Xp11 translocation-associated cancers, and highlights the importance of subtyping Xp11 translocation-associated cancers combining morphology, immunohistochemistry, and multiple molecular techniques.
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Strauss P, Marti HP, Beisland C, Scherer A, Lysne V, Leh S, Flatberg A, Koch E, Beisvag V, Landolt L, Skogstrand T, Eikrem Ø. Expanding the Utilization of Formalin-Fixed, Paraffin-Embedded Archives: Feasibility of miR-Seq for Disease Exploration and Biomarker Development from Biopsies with Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2018. [PMID: 29534467 PMCID: PMC5877664 DOI: 10.3390/ijms19030803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Novel predictive tools for clear cell renal cell carcinoma (ccRCC) are urgently needed. MicroRNAs (miRNAs) have been increasingly investigated for their predictive value, and formalin-fixed paraffin-embedded biopsy archives may potentially be a valuable source of miRNA sequencing material, as they remain an underused resource. Core biopsies of both cancerous and adjacent normal tissues were obtained from patients (n = 12) undergoing nephrectomy. After small RNA-seq, several analyses were performed, including classifier evaluation, obesity-related inquiries, survival analysis using publicly available datasets, comparisons to the current literature and ingenuity pathway analyses. In a comparison of tumour vs. normal, 182 miRNAs were found with significant differential expression; miR-155 was of particular interest as it classified all ccRCC samples correctly and correlated well with tumour size (R² = 0.83); miR-155 also predicted poor survival with hazard ratios of 2.58 and 1.81 in two different TCGA (The Cancer Genome Atlas) datasets in a univariate model. However, in a multivariate Cox regression analysis including age, sex, cancer stage and histological grade, miR-155 was not a statistically significant survival predictor. In conclusion, formalin-fixed paraffin-embedded biopsy tissues are a viable source of miRNA-sequencing material. Our results further support a role for miR-155 as a promising cancer classifier and potentially as a therapeutic target in ccRCC that merits further investigation.
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Affiliation(s)
- Philipp Strauss
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Urology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Andreas Scherer
- Spheromics, 81100 Kontiolahti, Finland;
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00100 Helsinki, Finland
| | - Vegard Lysne
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (A.F.); (V.B.)
| | - Even Koch
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (A.F.); (V.B.)
| | - Lea Landolt
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Trude Skogstrand
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway;
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence: ; Tel.: +47-4544-6008
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TFE3-Fusion Variant Analysis Defines Specific Clinicopathologic Associations Among Xp11 Translocation Cancers. Am J Surg Pathol 2017; 40:723-37. [PMID: 26975036 DOI: 10.1097/pas.0000000000000631] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Xp11 translocation cancers include Xp11 translocation renal cell carcinoma (RCC), Xp11 translocation perivascular epithelioid cell tumor (PEComa), and melanotic Xp11 translocation renal cancer. In Xp11 translocation cancers, oncogenic activation of TFE3 is driven by the fusion of TFE3 with a number of different gene partners; however, the impact of individual fusion variant on specific clinicopathologic features of Xp11 translocation cancers has not been well defined. In this study, we analyze 60 Xp11 translocation cancers by fluorescence in situ hybridization using custom bacterial artificial chromosome probes to establish their TFE3 fusion gene partner. In 5 cases RNA sequencing was also used to further characterize the fusion transcripts. The 60 Xp11 translocation cancers included 47 Xp11 translocation RCC, 8 Xp11 translocation PEComas, and 5 melanotic Xp11 translocation renal cancers. A fusion partner was identified in 53/60 (88%) cases, including 18 SFPQ (PSF), 16 PRCC, 12 ASPSCR1 (ASPL), 6 NONO, and 1 DVL2. We provide the first morphologic description of the NONO-TFE3 RCC, which frequently demonstrates subnuclear vacuoles leading to distinctive suprabasal nuclear palisading. Similar subnuclear vacuolization was also characteristic of SFPQ-TFE3 RCC, creating overlapping features with clear cell papillary RCC. We also describe the first RCC with a DVL2-TFE3 gene fusion, in addition to an extrarenal pigmented PEComa with a NONO-TFE3 gene fusion. Furthermore, among neoplasms with the SFPQ-TFE3, NONO-TFE3, DVL2-TFE3, and ASPL-TFE3 gene fusions, the RCCs are almost always PAX8 positive, cathepsin K negative by immunohistochemistry, whereas the mesenchymal counterparts (Xp11 translocation PEComas, melanotic Xp11 translocation renal cancers, and alveolar soft part sarcoma) are PAX8 negative, cathepsin K positive. These findings support the concept that despite an identical gene fusion, the RCCs are distinct from the corresponding mesenchymal neoplasms, perhaps due to the cellular context in which the translocation occurs. We corroborate prior data showing that the PRCC-TFE3 RCCs are the only known Xp11 translocation RCC molecular subtype that are consistently cathepsin K positive. In summary, our data expand further the clinicopathologic features of cancers with specific TFE3 gene fusions and should allow for more meaningful clinicopathologic associations to be drawn.
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江 海, 李 平, 张 梅, 张 锋, 苏 丽. RNA-Seq技术及其在胃肠肿瘤研究中的应用现状. Shijie Huaren Xiaohua Zazhi 2017; 25:1564-1571. [DOI: 10.11569/wcjd.v25.i17.1564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
转录组是特定的细胞或组织在特定的时间或状态下转录出来的RNA集合, 转录组研究能够从整体水平研究基因功能以及基因结构, 并能很好的显示处于表达状态的基因数量和活跃程度. 作为转录组学新一代高通量测序技术之一, RNA-Seq技术能够更为快速、准确地为人们提供更多的生物体转录信息, 在生物医学研究中已经得到广泛应用. 随着全球胃肠肿瘤发病率的逐年提高, RNA-Seq技术在胃肠肿瘤研究领域进行全转录组测序分析的应用越来越多, 并取得了一些新的进展. 本文将就RNA-Seq技术原理、优势及其在胃肠肿瘤研究中的具体应用进行论述.
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Landolt L, Eikrem Ø, Strauss P, Scherer A, Lovett DH, Beisland C, Finne K, Osman T, Ibrahim MM, Gausdal G, Ahmed L, Lorens JB, Thiery JP, Tan TZ, Sekulic M, Marti HP. Clear Cell Renal Cell Carcinoma is linked to Epithelial-to-Mesenchymal Transition and to Fibrosis. Physiol Rep 2017; 5:e13305. [PMID: 28596300 PMCID: PMC5471444 DOI: 10.14814/phy2.13305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/27/2017] [Accepted: 05/01/2017] [Indexed: 12/14/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) represents the most common type of kidney cancer with high mortality in its advanced stages. Our study aim was to explore the correlation between tumor epithelial-to-mesenchymal transition (EMT) and patient survival. Renal biopsies of tumorous and adjacent nontumorous tissue were taken with a 16 g needle from our patients (n = 26) undergoing partial or radical nephrectomy due to ccRCC RNA sequencing libraries were generated using Illumina TruSeq® Access library preparation protocol and TruSeq Small RNA library preparation kit. Next generation sequencing (NGS) was performed on Illumina HiSeq2500. Comparative analysis of matched sample pairs was done using the Bioconductor Limma/voom R-package. Liquid chromatography-tandem mass spectrometry and immunohistochemistry were applied to measure and visualize protein abundance. We detected an increased generic EMT transcript score in ccRCC Gene expression analysis showed augmented abundance of AXL and MMP14, as well as down-regulated expression of KL (klotho). Moreover, microRNA analyses demonstrated a positive expression correlation of miR-34a and its targets MMP14 and AXL Survival analysis based on a subset of genes from our list EMT-related genes in a publicly available dataset showed that the EMT genes correlated with ccRCC patient survival. Several of these genes also play a known role in fibrosis. Accordingly, recently published classifiers of solid organ fibrosis correctly identified EMT-affected tumor samples and were correlated with patient survival. EMT in ccRCC linked to fibrosis is associated with worse survival and may represent a target for novel therapeutic interventions.
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Affiliation(s)
- Lea Landolt
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Andreas Scherer
- Spheromics, Kontiolahti, Finland
- Institute for Molecular Medicine Finland (FIMM) University of Helsinki, Helsinki, Finland
| | - David H Lovett
- Department of Medicine, San Francisco VAMC University of California San Francisco, San Francisco, California
| | - Christian Beisland
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Urology, Haukeland University Hospital, Bergen, Norway
| | - Kenneth Finne
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Tarig Osman
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | | | | | | | - James B Lorens
- BerGenBio AS, Bergen, Norway
- Department of Biomedicine, Center for Cancer Biomarkers University of Bergen, Bergen, Norway
| | - Jean Paul Thiery
- Department of Biomedicine, Center for Cancer Biomarkers University of Bergen, Bergen, Norway
- INSERM UMR 1186, Integrative Tumor Immunology and Genetic Oncology Gustave Roussy EPHE Fac. de médecine-Univ. Paris-Sud Université Paris-Saclay, Villejuif, France
| | - Tuan Zea Tan
- Science Institute of Singapore National University of Singapore, Singapore, Singapore
| | - Miroslav Sekulic
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Xp11 Translocation Renal Cell Carcinomas (RCCs) With RBM10-TFE3 Gene Fusion Demonstrating Melanotic Features and Overlapping Morphology With t(6;11) RCC. Am J Surg Pathol 2017; 41:663-676. [DOI: 10.1097/pas.0000000000000837] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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RBM10-TFE3 Renal Cell Carcinoma: A Potential Diagnostic Pitfall Due to Cryptic Intrachromosomal Xp11.2 Inversion Resulting in False-negative TFE3 FISH. Am J Surg Pathol 2017; 41:655-662. [PMID: 28296677 DOI: 10.1097/pas.0000000000000835] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Xp11 translocation renal cell carcinoma (RCC) are defined by chromosome translocations involving the Xp11 breakpoint which results in one of a variety of TFE3 gene fusions. TFE3 break-apart florescence in situ hybridization (FISH) assays are generally preferred to TFE3 immunohistochemistry (IHC) as a means of confirming the diagnosis in archival material, as FISH is less sensitive to the variable fixation which can result in false positive or false negative IHC. Prompted by a case report in the cytogenetics literature, we identify 3 cases of Xp11 translocation RCC characterized by a subtle chromosomal inversion involving the short arm of the X chromosome, resulting in an RBM10-TFE3 gene fusion. TFE3 rearrangement was not detected by conventional TFE3 break-apart FISH, but was suggested by strong diffuse TFE3 immunoreactivity in a clean background. We then developed novel fosmid probes to detect the RBM10-TFE3 gene fusion in archival material. These cases validate RBM10-TFE3 as a recurrent gene fusion in Xp11 translocation RCC, illustrate a source of false-negative TFE3 break-apart FISH, and highlight the complementary role of TFE3 IHC and TFE3 FISH.
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Classe M, Malouf GG, Su X, Yao H, Thompson EJ, Doss DJ, Grégoire V, Lenobin J, Fantoni JC, Sudour-Bonnange H, Khayat D, Aubert S, Tannir NM, Leroy X. Incidence, clinicopathological features and fusion transcript landscape of translocation renal cell carcinomas. Histopathology 2017; 70:1089-1097. [DOI: 10.1111/his.13167] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 01/16/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Marion Classe
- Département de Pathologie; Hôpital Lariboisière; Assistance Publique Hôpitaux de Paris; Paris France
| | - Gabriel G Malouf
- Département d'Oncologie Médicale; Groupe Hospitalier Pitié-Salpêtrière; Assistance Publique Hôpitaux de Paris; Faculté de Médecine Pierre et Marie Curie; Institut Universitaire de Cancérologie GRC5; Paris France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Hui Yao
- Department of Bioinformatics and Computational Biology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Erika J Thompson
- Department of Genetics; The University of Texas MD Anderson Cancer Center; Houston Texas USA
| | - Denaha J Doss
- Department of Genetics; The University of Texas MD Anderson Cancer Center; Houston Texas USA
| | - Valérie Grégoire
- Département de Pathologie; Centre Hospitalier Régional Universitaire; Lille France
| | - Julien Lenobin
- Département d'Urologie; Centre Hospitalier Régional Universitaire; Lille France
| | | | | | - David Khayat
- Département d'Oncologie Médicale; Groupe Hospitalier Pitié-Salpêtrière; Assistance Publique Hôpitaux de Paris; Faculté de Médecine Pierre et Marie Curie; Institut Universitaire de Cancérologie GRC5; Paris France
| | - Sébastien Aubert
- Département de Pathologie; Centre Hospitalier Régional Universitaire; Lille France
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Xavier Leroy
- Département de Pathologie; Centre Hospitalier Régional Universitaire; Lille France
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Xia QY, Wang Z, Chen N, Gan HL, Teng XD, Shi SS, Wang X, Wei X, Ye SB, Li R, Ma HH, Lu ZF, Zhou XJ, Rao Q. Xp11.2 translocation renal cell carcinoma with NONO-TFE3 gene fusion: morphology, prognosis, and potential pitfall in detecting TFE3 gene rearrangement. Mod Pathol 2017; 30:416-426. [PMID: 27934879 DOI: 10.1038/modpathol.2016.204] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 12/12/2022]
Abstract
Xp11 translocation renal cell carcinomas are characterized by several different translocations involving the TFE3 gene. Tumors with different specific gene fusions may have different clinicopathological manifestations. Fewer than 10 renal cell carcinoma cases with NONO-TFE3 have been described. Here we examined eight additional cases of this rare tumor using clinicopathological, immunohistochemical, and molecular analyses. The male-to-female ratio of our study cohort was 1:1, and the median age was 30 years. The most distinctive feature of the tumors was that they exhibited glandular/tubular or papillary architecture that was lined with small-to-medium cuboidal to high columnar cells with indistinct cell borders and an abundantly clear or flocculent eosinophilic cytoplasm. The nuclei were oriented toward the luminal surface and were round and uniform in shape, which resulted in the appearance of secretory endometrioid subnuclear vacuolization. The distinct glandular/tubular or papillary architecture was often accompanied by sheets of epithelial cells that presented a biphasic pattern. Immunohistochemically, all eight cases demonstrated moderate (2+) or strong (3+) positive staining for TFE3, CD10, RCC marker, and PAX-8. None of the tumors were immunoreactive for CK7, Cathepsin K, Melan-A, HMB45, Ksp-cadherin, Vimentin, CA9, 34βE12 or CD117. NONO-TFE3 fusion transcripts were identified in six cases by RT-PCR. All eight cases showed equivocal split signals with a distance of nearly 2 signal diameters and sometimes had false-negative results. Furthermore, we developed a fluorescence in situ hybridization (FISH) assay to serve as an adjunct diagnostic tool for the detection of the NONO-TFE3 fusion gene and used this method to detect the fusion gene in all eight cases. Long-term follow-up (range, 10-102 months) was available for 7 patients. All 7 patients were alive with no evidence of recurrent disease or disease progression after their initial resection. This report adds to the known data regarding NONO-TFE3 renal cell carcinoma.
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Affiliation(s)
- Qiu-Yuan Xia
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhe Wang
- Department of Pathology, State Key Laboratory of Cancer Biology, Xi Jing Hospital, Fourth Military Medical University, Xi'an, China
| | - Ni Chen
- Department of Pathology, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Hua-Lei Gan
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xiao-Dong Teng
- Department of Pathology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Shan-Shan Shi
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xuan Wang
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xue Wei
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Sheng-Bing Ye
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Rui Li
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Heng-Hui Ma
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Zhen-Feng Lu
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Xiao-Jun Zhou
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qiu Rao
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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Eikrem OS, Strauss P, Beisland C, Scherer A, Landolt L, Flatberg A, Leh S, Beisvag V, Skogstrand T, Hjelle K, Shresta A, Marti HP. Development and confirmation of potential gene classifiers of human clear cell renal cell carcinoma using next-generation RNA sequencing. Scand J Urol 2016; 50:452-462. [PMID: 27739342 DOI: 10.1080/21681805.2016.1238007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE A previous study by this group demonstrated the feasibility of RNA sequencing (RNAseq) technology for capturing disease biology of clear cell renal cell carcinoma (ccRCC), and presented initial results for carbonic anhydrase-9 (CA9) and tumor necrosis factor-α-induced protein-6 (TNFAIP6) as possible biomarkers of ccRCC (discovery set) [Eikrem et al. PLoS One 2016;11:e0149743]. To confirm these results, the previous study is expanded, and RNAseq data from additional matched ccRCC and normal renal biopsies are analyzed (confirmation set). MATERIALS AND METHODS Two core biopsies from patients (n = 12) undergoing partial or full nephrectomy were obtained with a 16 g needle. RNA sequencing libraries were generated with the Illumina TruSeq® Access library preparation protocol. Comparative analysis was done using linear modeling (voom/Limma; R Bioconductor). RESULTS The formalin-fixed and paraffin-embedded discovery and confirmation data yielded 8957 and 11,047 detected transcripts, respectively. The two data sets shared 1193 of differentially expressed genes with each other. The average expression and the log2-fold changes of differentially expressed transcripts in both data sets correlated, with R² = .95 and R² = .94, respectively. Among transcripts with the highest fold changes were CA9, neuronal pentraxin-2 and uromodulin. Epithelial-mesenchymal transition was highlighted by differential expression of, for example, transforming growth factor-β1 and delta-like ligand-4. The diagnostic accuracy of CA9 was 100% and 93.9% when using the discovery set as the training set and the confirmation data as the test set, and vice versa, respectively. These data further support TNFAIP6 as a novel biomarker of ccRCC. TNFAIP6 had combined accuracy of 98.5% in the two data sets. CONCLUSIONS This study provides confirmatory data on the potential use of CA9 and TNFAIP6 as biomarkers of ccRCC. Thus, next-generation sequencing expands the clinical application of tissue analyses.
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Affiliation(s)
- Oystein S Eikrem
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway.,b Department of Medicine , Haukeland University Hospital , Bergen , Norway
| | - Philipp Strauss
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway.,b Department of Medicine , Haukeland University Hospital , Bergen , Norway
| | - Christian Beisland
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway.,c Department of Urology , Haukeland University Hospital , Bergen , Norway
| | - Andreas Scherer
- d Spheromics , Kontiolahti , Finland.,e Institute for Molecular Medicine Finland (FIMM), University of Helsinki , Helsinki , Finland
| | - Lea Landolt
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway
| | - Arnar Flatberg
- f Department of Cancer Research and Molecular Medicine , Norwegian University of Science and Technology , Trondheim , Norway
| | - Sabine Leh
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway.,g Department of Pathology , Haukeland University Hospital , Bergen , Norway
| | - Vidar Beisvag
- f Department of Cancer Research and Molecular Medicine , Norwegian University of Science and Technology , Trondheim , Norway
| | - Trude Skogstrand
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway
| | - Karin Hjelle
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway.,c Department of Urology , Haukeland University Hospital , Bergen , Norway
| | - Anjana Shresta
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway
| | - Hans-Peter Marti
- a Department of Clinical Medicine , University of Bergen , Bergen , Norway.,b Department of Medicine , Haukeland University Hospital , Bergen , Norway
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Ishiguro N, Yoshida H. ASPL-TFE3 Oncoprotein Regulates Cell Cycle Progression and Induces Cellular Senescence by Up-Regulating p21. Neoplasia 2016; 18:626-635. [PMID: 27673450 PMCID: PMC5037204 DOI: 10.1016/j.neo.2016.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 01/30/2023] Open
Abstract
Alveolar soft part sarcoma is an extremely rare soft tissue sarcoma with poor prognosis. It is characterized by the unbalanced recurrent chromosomal translocation der(17)t(X;17)(p11;q25), resulting in the generation of an ASPL-TFE3 fusion gene. ASPL-TFE3 oncoprotein functions as an aberrant transcriptional factor and is considered to play a crucial role in the tumorigenesis of alveolar soft part sarcoma. However, the underlying molecular mechanisms are poorly understood. In this study, we identified p21 (p21WAF1/CIP1) as a direct transcriptional target of ASPL-TFE3. Ectopic ASPL-TFE3 expression in 293 cells resulted in cell cycle arrest and significant increases in protein and mRNA levels of p21. ASPL-TFE3 activated p21 expression in a p53-independent manner through direct transcriptional interactions with the p21 promoter region. When ASPL-TFE3 was expressed in human bone marrow–derived mesenchymal stem cells in a tetracycline-inducible manner, we observed the up-regulation of p21 expression and the induction of senescence-associated β-galactosidase activity. Suppression of p21 significantly decreased the induction of ASPL-TFE3-mediated cellular senescence. Furthermore, ASPL-TFE3 expression in mesenchymal stem cells resulted in a significant up-regulation of proinflammatory cytokines associated with senescence-associated secretory phenotype (SASP). These results show that ASPL-TFE3 regulates cell cycle progression and induces cellular senescence by up-regulating p21 expression. In addition, our data suggest a potential mechanism by which ASPL-TFE3-induced senescence may play a role in tumorigenesis by inducing SASP, which could promote the protumorigenic microenvironment.
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Affiliation(s)
- Naoko Ishiguro
- Department of Pathobiological Science and Technology, Faculty of Medicine, Tottori University, 86 Nishimachi, Yonago, Tottori 683-8503, Japan.
| | - Haruhiko Yoshida
- Department of Pathology, Yonago Medical Center, 4-17-1 Kuzumo, Yonago, Tottori 683-0006, Japan
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45
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Hirsch MS, Signoretti S, Dal Cin P. Adult Renal Cell Carcinoma: A Review of Established Entities from Morphology to Molecular Genetics. Surg Pathol Clin 2016; 8:587-621. [PMID: 26612217 DOI: 10.1016/j.path.2015.09.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
According to the current World Health Organization (WHO), renal cell carcinomas (RCCs) that primarily affect adults are classified into 8 major subtypes. Additional emerging entities in renal neoplasia have also been recently recognized and these are discussed in further detail by Mehra et al (Emerging Entities in Renal Neoplasia, Surgical Pathology Clinics, 2015, Volume 8, Issue 4). In most cases, the diagnosis of a RCC subtype can be based on morphologic criteria, but in some circumstances the use of ancillary studies can aid in the diagnosis. This review discusses the morphologic, genetic, and molecular findings in RCCs previously recognized by the WHO, and provides clues to distinction from each other and some of the newer subtypes of RCC. As prognosis and therapeutic options vary for the different subtypes of RCC, accurate pathologic distinction is critical for patient care.
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Affiliation(s)
- Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA
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46
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Iacobas DA. The Genomic Fabric Perspective on the Transcriptome Between Universal Quantifiers and Personalized Genomic Medicine. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s13752-016-0245-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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47
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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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48
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Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval. Exp Mol Pathol 2016; 100:482-92. [PMID: 27185020 DOI: 10.1016/j.yexmp.2016.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 12/27/2022]
Abstract
Attempts to establish a tissue bank from autopsy samples have led to uncovering of the secrets of many diseases. Here, we examined the length of time that the RNA from postmortem tissues is available for microarray analysis and reported the gene expression profile for up- and down-regulated genes during the postmortem interval. We extracted RNA from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) brains and livers of three different groups of mice: 1) mice immediately after death, 2) mice that were stored at room temperature for 3h after death, and 3) mice that were stored at 4°C for 18h after death, as this storage resembles the human autopsy process in Japan. The RNA quality of the brain and the liver was maintained up to 18h during the postmortem interval. Based on the microarray analysis, we selected genes that were altered by >1.3-fold or <0.77-fold and classified these genes using hierarchical cluster analysis following DAVID gene ontology analysis. These studies revealed that cytoskeleton-related genes were enriched in the set of up-regulated genes, while serine protease inhibitors were enriched in the set of down-regulated genes. Interestingly, although the RNA quality was maintained due to high RNA integrity number (RIN) values, up-regulated genes were not validated by quantitative PCR, suggesting that these genes may become fragmented or modified by an unknown mechanism. Taken together, our findings suggest that under typical autopsy conditions, gene expression profiles that reflect disease pathology can be examined by understanding comprehensive recognition of postmortem fluctuation of gene expression.
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49
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Wang XT, Xia QY, Ni H, Wang ZY, Ye SB, Li R, Wang X, Lv JH, Shi SS, Ma HH, Lu ZF, Shen Q, Zhou XJ, Rao Q. Xp11 neoplasm with melanocytic differentiation of the prostate harbouring the novel NONO-TFE3 gene fusion: report of a unique case expanding the gene fusion spectrum. Histopathology 2016; 69:450-8. [PMID: 26844676 DOI: 10.1111/his.12949] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/16/2022]
Abstract
Recently, an increasing number of TFE3 rearrangement-associated tumours have been reported, such as TFE3 rearrangement-associated perivascular epithelioid cell tumours (PEComas), melanotic Xp11 translocation renal cancers and melanotic Xp11 neoplasms. We have suggested that these tumours belong to a single clinicopathological spectrum. 'Xp11 neoplasm with melanocytic differentiation' or 'melanotic Xp11 neoplasm' have been proposed to designate this unique neoplasm. Herein, we describe the first case of an Xp11 neoplasm with melanocytic differentiation to be described in the prostate, bearing the novel NONO-TFE3 gene fusion. This study both adds to the spectrum regarding melanotic Xp11 neoplasms and expands its gene fusion spectrum. Moreover, we discuss the relationship of these rare tumours to neoplasms such as conventional PEComas, alveolar soft part sarcomas, malignant melanomas, clear cell sarcomas and Xp11 translocation renal cancers.
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Affiliation(s)
- Xiao-Tong Wang
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China.,Department of Pathology, Jinling Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Qiu-Yuan Xia
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Hao Ni
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China.,Department of Pathology, Jinling Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zi-Yu Wang
- School of Basic Medical Sciences, Nanjing University of Traditional Chinese Medicine, Nanjing, China
| | - Sheng-Bing Ye
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Rui Li
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Xuan Wang
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Jing-Huan Lv
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Shan-Shan Shi
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Heng-Hui Ma
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Zhen-Feng Lu
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Qin Shen
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Xiao-Jun Zhou
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China
| | - Qiu Rao
- Department of Pathology, Nanjing Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu, China.,Department of Pathology, Jinling Clinical Medical College, Nanjing Medical University, Nanjing, Jiangsu, China
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50
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Eikrem O, Beisland C, Hjelle K, Flatberg A, Scherer A, Landolt L, Skogstrand T, Leh S, Beisvag V, Marti HP. Transcriptome Sequencing (RNAseq) Enables Utilization of Formalin-Fixed, Paraffin-Embedded Biopsies with Clear Cell Renal Cell Carcinoma for Exploration of Disease Biology and Biomarker Development. PLoS One 2016; 11:e0149743. [PMID: 26901863 PMCID: PMC4764764 DOI: 10.1371/journal.pone.0149743] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are an underused resource for molecular analyses. This proof of concept study aimed to compare RNAseq results from FFPE biopsies with the corresponding RNAlater® (Qiagen, Germany) stored samples from clear cell renal cell carcinoma (ccRCC) patients to investigate feasibility of RNAseq in archival tissue. From each of 16 patients undergoing partial or full nephrectomy, four core biopsies, such as two specimens with ccRCC and two specimens of adjacent normal tissue, were obtained with a 16g needle. One normal and one ccRCC tissue specimen per patient was stored either in FFPE or RNAlater®. RNA sequencing libraries were generated applying the new Illumina TruSeq® Access library preparation protocol. Comparative analysis was done using voom/Limma R-package. The analysis of the FFPE and RNAlater® datasets yielded similar numbers of detected genes, differentially expressed transcripts and affected pathways. The FFPE and RNAlater datasets shared 80% (n = 1106) differentially expressed genes. The average expression and the log2 fold changes of these transcripts correlated with R2 = 0.97, and R2 = 0.96, respectively. Among transcripts with the highest fold changes in both datasets were carbonic anhydrase 9 (CA9), neuronal pentraxin-2 (NPTX2) and uromodulin (UMOD) that were confirmed by immunohistochemistry. IPA revealed the presence of gene signatures of cancer and nephrotoxicity, renal damage and immune response. To simulate the feasibility of clinical biomarker studies with FFPE samples, a classifier model was developed for the FFPE dataset: expression data for CA9 alone had an accuracy, specificity and sensitivity of 94%, respectively, and achieved similar performance in the RNAlater dataset. Transforming growth factor-ß1 (TGFB1)-regulated genes, epithelial to mesenchymal transition (EMT) and NOTCH signaling cascade may support novel therapeutic strategies. In conclusion, in this proof of concept study, RNAseq data obtained from FFPE kidney biopsies are comparable to data obtained from fresh stored material, thereby expanding the utility of archival tissue specimens.
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Affiliation(s)
- Oystein Eikrem
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, Urology, University of Bergen, Bergen, Norway
| | - Karin Hjelle
- Department of Clinical Medicine, Urology, University of Bergen, Bergen, Norway
| | - Arnar Flatberg
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Lea Landolt
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Trude Skogstrand
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Vidar Beisvag
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, Nephrology, University of Bergen, Bergen, Norway
- Department of Medicine, Nephrology, Haukeland University Hospital, Bergen, Norway
- * E-mail:
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