title: Validation and utilization of a TFE3 break-apart FISH assay for Xp11.2 translocation renal cell carcinoma and alveolar soft part sarcoma.
abstract: BACKGROUND
  Xp11.2 or TFE3 translocation renal cell carcinomas (RCC) and alveolar soft part sarcoma (ASPS) are characterized by chromosome translocations involving the Xp11.2 breakpoint resulting in transcription factor TFE3 gene fusions. The most common translocations documented in TFE3 RCCs are t(X;1) (p11.2;q21) and t(X;17) (p11.2;q25) which leads to fusion of TFE3 gene on Xp11.2 with PRCC or ASPL respectively. TFE3 immunohistochemistry (IHC) has been inconsistent over time due to background staining problems in part related to fixation issues. Karyotyping to detect TFE3 gene rearrangement requires typically unavailable fresh tissue. Reverse transcriptase-polymerase chain reaction (RT-PCR) is generally very challenging due to degradation of RNA in archival material. The study objective was to develop and validate a TFE3 break-apart fluorescence in situ hybridization (FISH) assay to confirm Xp11 translocation RCCs and ASPS.
  
  
  METHODS
  Representative sections of formalin-fixed paraffin-embedded tissue blocks were selected in 40 possible cases. Approximately 60 tumor cells were analyzed in the targeted region. The validation of TFE3 FISH was done with 11 negative and two positive cases. Cut off for a positive result was validated as >7.15 % positive nuclei with any pattern of break-apart signals. FISH evaluation was done blinded of the immunohistochemical or karyotype data.
  
  
  RESULTS
  Three out of forty cases were positive for the TFE3 break-apart signals by FISH. The negative cases were reported as clear cell RCC with papillary features (10), clear cell RCC with sarcomatoid areas (2), Papillary RCC with clear cell areas (9), Chromophobe RCC (2), RCC, unclassified type (3) and renal medullary carcinoma (1). 3 of the negative cases were consultation cases for renal tumor with unknown histology. Seven negative cases were soft tissue tumor suspicious for ASPS.
  
  
  CONCLUSIONS
  Our study validates the utility of TFE3 break-apart FISH on formalin-fixed paraffin-embedded tissue sections for diagnosis and confirmation of Xp11.2 translocation RCCs and ASPS.
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. pradhand@upmc.edu.
authors.forename: Dinesh
authors.initials: D
authors.lastname: Pradhan
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. roys@upmc.edu.
authors.forename: Somak
authors.initials: S
authors.lastname: Roy
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. gamaquiga@gmail.com.
authors.forename: Gabriela
authors.initials: G
authors.lastname: Quiroga-Garza
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. cieplykm@upmc.edu.
authors.forename: Kathleen
authors.initials: K
authors.lastname: Cieply
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. luvisonam@upmc.edu.
authors.forename: Alyssa L
authors.initials: AL
authors.lastname: Mahaffey
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. bastackysi@upmc.edu.
authors.forename: Sheldon
authors.initials: S
authors.lastname: Bastacky
authors.affiliation: Department of Pathology, University of Pittsburgh Medical Center, 200 Lothrop Street, Pittsburgh, 15213, PA, USA. dhirr@upmc.edu.
authors.forename: Rajiv
authors.initials: R
authors.lastname: Dhir
authors.affiliation: Wexner Medical Center, The Ohio State University, Columbus, 43210, OH, USA. Anil.Parwani@osumc.edu.
authors.forename: Anil V
authors.initials: AV
authors.lastname: Parwani
mesh_terms: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000378:metabolism*; D002292:Carcinoma, Renal Cell / Q000473:pathology*; D041321:Chromosomes, Human, X / Q000378:metabolism; D015321:Gene Rearrangement / Q000235:genetics; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D007680:Kidney Neoplasms / Q000473:pathology*; D018234:Sarcoma, Alveolar Soft Part / Q000175:diagnosis / Q000473:pathology*; D012983:Soft Tissue Neoplasms / Q000235:genetics*; D014178:Translocation, Genetic
chemical_list: D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C069203:TFE3 protein, human