Fig 1.
Validation of the antibodies used for IHC.
Kidney cancer cell lines stably expressing control shRNA or shRNA against ARID1A, PBRM1, BRG1, BRM, and SETD2 were used for western blot analysis with indicated antibodies.
Fig 2.
Immunohistochemical analysis of ccRCC foci from TMAs.
A) Two FFPE ccRCC tissue blocks from one tumor with four cores excised (indicated by arrows). B) H&E stained foci from three tumor samples. C) Representative foci stained for different markers showing different scores. The arrows point to stromal cells that stained positive for the markers.
Fig 3.
Summary of losses of expression of protein markers in ccRCC tumors and foci.
A) Overall losses of each marker in tumor and foci. Loss of individual marker in different tumor stages: PBRM1 (B), ARID1A (C), SETD2 (D), BRG1 (E), BRM (F).
Fig 4.
Phylogenetic trees of protein losses in ccRCC tumors.
A) Depiction of the way in which a phylogenetic tree was constructed. A: ARID1A loss; M: BRM loss; P: PBRM1 loss, G: BRG12 loss; S: SETD2 loss. AM = losses of AIRD1A and BRM. PG = losses of PBRM1 and BRG1. R1, R2, R3 refer to the foci. Presentation of phylogenetic trees of stage I (B), stage II (C), stage III (D), and stage IV (E) ccRCCs. F) A summary of phylogenetic trees in tumors.
Fig 5.
Co-losses of protein markers in both tumor and foci.
A) Co-loss of ARID1A and PBRM1 expression in tumors/foci. B) Co-loss of BRM and BRG1 expression in tumors/foci. C) Statistical analysis of co-losses of the different protein markers in ccRCC tumors and foci. Co-losses of any two parameters considered here were found to be non-random.
Fig 6.
ARID1A loss seemed to have greater tumor-promoting effects than PBRM1 loss.
A) Western blots showing suppression of PBRM1 and ARID1A expression. B, D, F, H) Representative photographs of excised tumors from tumor-bearing recipient mice. C, E, G, I) Summary of xenograft studies comparing tumor growth of the indicated cell lines. N.S.: not significant. n indicates the number of mice used in each experiment.