Immunohistochemical Profiling of Molecular Markers

Immunohistochemistry was conducted in 5 μm FFPE whole tissue or tissue microarray sections using automated Ventana Discovery system or Ventana Benchmark system (Ventana Medical Systems). The primary antibodies used included NF2 (1:100, D3S3W, Cell Signaling Technology), YAP/TAZ (1:50, D24E4, Cell Signaling Technology), phospho-YAP (Ser127) (1:500, D9W2I, Cell Signaling Technology), phospho-S6 (Ser235/236; 1:100, D57.2.2E, Cell Signaling Technology), phospho-4EBP1 (Thr37/46; 1:400, 236B4, Cell Signaling Technology), 2SC (Dr Norma Frizzell, Univ. of South Carolina)42 (link), FH (1:1,000, Clone J-13, Santa Cruz Biotechnology), INI1 (1:100, BAF47, BD Bioscience) and H3K36me3 (1:200, MABI-0333, Active Motif). For the semi-quantitive or quantitative (H-scores) analysis of staining, the pathologists were blinded to the group designation of cases on tissue microarray slides.

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Chen Y.B., Xu J., Skanderup A.J., Dong Y., Brannon A.R., Wang L., Won H.H., Wang P.I., Nanjangud G.J., Jungbluth A.A., Li W., Ojeda V., Hakimi A.A., Voss M.H., Schultz N., Motzer R.J., Russo P., Cheng E.H., Giancotti F.G., Lee W., Berger M.F., Tickoo S.K., Reuter V.E, & Hsieh J.J. (2016). Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets. Nature Communications, 7, 13131.

Publication 2016

Ventana Discovery system Ventana Benchmark system D9W2I Clone J-13 BAF47 MABI-0333

4ebp1 Antibodies Clone Immunohistochemistry Ini1 Mabi Microarray Pathologists Tissue

Corresponding Organization : Memorial Sloan Kettering Cancer Center

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Variable analysis

independent variables

Primary antibodies used: NF2, YAP/TAZ, phospho-YAP (Ser127), phospho-S6 (Ser235/236), phospho-4EBP1 (Thr37/46), 2SC, FH, INI1, H3K36me3

dependent variables

Immunohistochemistry staining patterns in 5 μm FFPE whole tissue or tissue microarray sections

control variables

Tissue sample preparation: 5 μm FFPE whole tissue or tissue microarray sections
Automated staining systems: Ventana Discovery system or Ventana Benchmark system (Ventana Medical Systems)
Pathologists were blinded to the group designation of cases on tissue microarray slides for semi-quantitive or quantitative (H-scores) analysis of staining

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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