PRCC-TFE3 dual-fusion FISH assay: A new method for identifying PRCC-TFE3 renal cell carcinoma in paraffin-embedded tissue

Xiong, Lei; Chen, Xiancheng; Gan, Weidong; Wang, Zhen; Miao, Baolei; Gan, Weidong; Li, Dongmei; Guo, Hongqian

doi:10.1371/journal.pone.0185337

Cited by 12 publications

(26 citation statements)

References 39 publications

(64 reference statements)

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“…Therefore, all eligible patients were diagnosed by TFE3-IHC combined with the TFE3 break-apart FISH assay in the present research. Interestingly, it has been confirmed that dual-fusion FISH probes were useful for identifying ASPL-TFE3 and PRCC-TFE3 RCC 18,19 , and other probes are worthy of designing to diagnose the remaining known subtypes of Xp11 translocation RCCs.…”

Section: Discussionmentioning

confidence: 93%

Comparative Clinicopathologic Characteristics and Outcomes of Paediatric and Adult Xp11 Translocation Renal Cell Carcinomas: a Retrospective Multicentre Study in China

Liu

Zhuang

et al. 2020

Sci Rep

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This study aimed to compare the clinicopathologic features and prognosis in patients with Xp11 translocation renal cell carcinomas (RCCs). In total, 8083 RCCs were screened at five centres from January 2007 to December 2018, including 8001 adults (≥18 years) and 82 children (<18 years). Finally, 73 adults and 17 children were identified as Xp11 translocation RCCs, accounting for 1.1% (90 of 8083) of the RCCs. However, 4 children and 1 adult were excluded because of loss to follow-up when performing the survival analysis. The proportion of paediatric and adult Xp11 translocation RCCs was 20.7% (17 of 82) and 0.9% (73 of 8001) of RCCs, respectively, and the incidence in children and adults was significantly different (P < 0.01). Lymph node positivity (LN+) most commonly occurred in children (58.8%) compared with adults (28.8%; P = 0.02), but children with LN+ showed significantly higher fiveyear overall survival and progression-free rates (OS: 75.0%; PFS: 64.8%) than adult patients (OS: 40.3%; PFS: 0%) (log-rank P pfS < 0.01; P oS = 0.04). Multivariable analysis indicated that local lymph node metastasis was associated with both PFS (HR = 0.10; 95% CI 0.02-0.51; P = 0.01) and OS (HR = 0.11; 95% CI 0.01-0.98; P = 0.04) in adults. Adult patients with LN+ may indicate a worse prognosis than paediatric patients.Xp11 translocation renal cell carcinomas (RCCs) are characterized by several different chromosomal translocations involving Xp11 and the formation of TFE3 fusion genes, followed by overexpression of TFE3 protein 1 . The first case was a 2.4-year-old child diagnosed by karyotype analysis in 1986 2 . In 2004, Xp11 translocation RCCs were classified as a distinct entity of RCC by the World Health Organization (WHO) 3 . Recent reports have found that RCC associated with t(6; 11) (p2l; q12)/TFEB gene fusions is exceedingly similar to Xp11 translocation RCCs with respect to clinical characteristics, pathology, and molecular genetics 4 . Given that both TFE3 and TFEB pertain to the microphthalmia-associated transcription factor family, Xp11 translocation RCCs and RCC associated 1

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Section: Discussionmentioning

confidence: 93%

Comparative Clinicopathologic Characteristics and Outcomes of Paediatric and Adult Xp11 Translocation Renal Cell Carcinomas: a Retrospective Multicentre Study in China

Liu

Zhuang

et al. 2020

Sci Rep

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“…FISH is currently the most convenient and effective method for identifying gene alteration by using custom BAC probes on FFPE tissue sections. Utilizing ASPSCR1-TFE3 and PRCC-TFE3 dual-fusion FISH assays www.nature.com/scientificreports/ previously designed by us 5,13 , 8 cases each of ASPSCR1-TFE3 RCC and PRCC-TFE3 RCC were identified (Table 1).…”

Section: Discussionmentioning

confidence: 99%

“…In addition, 15 randomly chosen cases each of clear cell renal cell carcinoma (ccRCC) and papillary renal cell carcinoma (pRCC) and UOK 109 cells 10 (generously gifted by Dr. W. Marston Linehan, National Cancer Institute, Bethesda, MD) were used as controls. All 13 cases of unclassified Xp11.2 translocation RCC were identified by the TFE3 break-apart FISH probe, but were excluded from ASPSCR1-TFE3 RCC and PRCC-TFE3 RCC, by previously reported dual-fusion FISH assays reported by us 5,13 . The 5 suspected cases showed moderate (2+) to strong (3+) immunoblotting response to the TFE3 antibody but equivocal split signals to the TFE3 probe.…”

Section: Methodsmentioning

confidence: 99%

“…However, TFE3 immunoreactivity only reflects the expression levels of TFE3 protein, and the FISH split signal merely indicates rearrangements in TFE3. Identification of fusion patterns still relies on fusion FISH assays 5,13 , reverse transcription-polymerase chain reactions (RT-PCR), cytogenetic karyotypic analysis 10 , or sequencing 14 . However, the fusion FISH assay represents the most inexpensive and accessible method, due to economic difficulties and complicated sample requirements of the other methods.…”

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confidence: 99%

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The suitability of NONO-TFE3 dual-fusion FISH assay as a diagnostic tool for NONO-TFE3 renal cell carcinoma

Liu

Guo

Shi

et al. 2020

Sci Rep

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NONO-TFE3 RCC is a subtype of Xp11.2 translocation renal cell carcinoma (RCC). So far, only a small amount of NONO-TFE3 RCC have been reported owing to lack of effective diagnosis methods. Utilizing the novel dual-fusion fluorescence in situ hybridization (FISH) probe reported here, 5 cases of NONO-TFE3 RCC were identified and were ultimately confirmed by RT-PCR. Histopathology, all 5 cases were consisted by sheets of epithelial cells and papillary architecture. The cytoplasm was abundantly clear, and nucleoli was not prominent. Besides, the nuclear palisading, subnuclear vacuoles and psammoma bodies were identified. The most distinctive features were strong positive TFE3 staining but equivocal split signals of the TFE3 probe, which might lead to the misdiagnosis of Xp11.2 translocation RCC. The median age and median tumor size of the five patients were 41.2 years and 3.6 cm, respectively. A median following follow-up of 27 months showed moderate disease progression and prognosis in NONO-TFE3 RCC patients. In conclusion, the present study demonstrates the effectiveness and reliability of the NONO-TFE3 dual-fusion FISH probe for diagnosing NONO-TFE3 RCC. Suspected cases of Xp11.2 translocation RCC showing biphasic pattern, strong positive TFE3 staining, and equivocal split signals in the TFE3 FISH assay indicated a possibility of NONO-TFE3 RCC.

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“…Two other chromosome contacts with PEAR1 involve two genes whose abnormal expression is reported to lead to growth of several tumours [ 66 , 67 , 68 , 69 , 70 ]. PRCC is involved in mRNA splicing and reported to have a role in cell cycle delay.…”

Section: Discussionmentioning

confidence: 99%

Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes

Izzi

Noro

Cludts

et al. 2018

IJMS

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Chromosomal interactions connect distant enhancers and promoters on the same chromosome, activating or repressing gene expression. PEAR1 encodes the Platelet-Endothelial Aggregation Receptor 1, a contact receptor involved in platelet function and megakaryocyte and endothelial cell proliferation. PEAR1 expression during megakaryocyte differentiation is controlled by DNA methylation at its first CpG island. We identified a PEAR1 cell-specific methylation sensitive region in endothelial cells and megakaryocytes that showed strong chromosomal interactions with ISGL20L2, RRNAD1, MRLP24, HDGF and PRCC, using available promoter capture Hi-C datasets. These genes are involved in ribosome processing, protein synthesis, cell cycle and cell proliferation. We next studied the methylation and expression profile of these five genes in Human Umbilical Vein Endothelial Cells (HUVECs) and megakaryocyte precursors. While cell-specific PEAR1 methylation corresponded to variability in expression for four out of five genes, no methylation change was observed in their promoter regions across cell types. Our data suggest that PEAR1 cell-type specific methylation changes may control long distance interactions with other genes. Further studies are needed to show whether such interaction data might be relevant for the genome-wide association data that showed a role for non-coding PEAR1 variants in the same region and platelet function, platelet count and cardiovascular risk.

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PRCC-TFE3 dual-fusion FISH assay: A new method for identifying PRCC-TFE3 renal cell carcinoma in paraffin-embedded tissue

Cited by 12 publications

References 39 publications

Comparative Clinicopathologic Characteristics and Outcomes of Paediatric and Adult Xp11 Translocation Renal Cell Carcinomas: a Retrospective Multicentre Study in China

Comparative Clinicopathologic Characteristics and Outcomes of Paediatric and Adult Xp11 Translocation Renal Cell Carcinomas: a Retrospective Multicentre Study in China

The suitability of NONO-TFE3 dual-fusion FISH assay as a diagnostic tool for NONO-TFE3 renal cell carcinoma

Cell-Specific PEAR1 Methylation Studies Reveal a Locus that Coordinates Expression of Multiple Genes

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