Kidney cancer mouse modeling via conditional disruption of Pbrm1 gene

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PBRM1 gene and its correlation with SWI-SNF complexes

Recently, a new kidney cancer-related gene PBRM1 was identified through exome sequencing in a series of primary clear cell renal carcinoma (ccRCC). Study showed that around 40% examined cases carried PBRM1 gene mutations, indicating PBRM1 is the second most important kidney cancer-related gene following VHL genewhose mutations account for approximate 60% of ccRCC cases.

PBRM1 maps to chromosome 3p21 and encodes the BAF180 protein, the chromatin targeting subunit of the PBAF SWI/SNF chromatin remodelling complex. The components of the SWI/SNF chromatin-remodeling complex were initially identified in screens for genes that regulate mating-type switching (SWI) and sucrose nonfermenting (SNF) phenotypes in yeasts (Carlson et al., 1981;N eigeborn and Carlson, 1984, 1987; Stern et al., 1984;Abram s et al., 1986;Nasm yth and Shore, 1987; Carlson and Laurent, 1994). Homolog of SWI/SNF in Drosophila is called BRM (Drosophila homeotic gene brahma). Mammalian cells express homolog BRM as well as a closely related protein called Brahma-related gene-1 (BRG1). Human BRG1 is approximately 74% identical to human BRM (Khavari et al., 1993), 52% identical to Drosophila BRM and 33% identical to yeast SWI2/SNF2 (Fry and Peterson, 2001). The mammalian SWI/SNF complexes contain, in addition to BRM or BRG1, 8–10 subunits, which are referred to as BRM- or BRG1-associated factors or BAFs (Wang et al., 1996a, b).

The mammalian SWI/SNF complexes mediate ATP dependent chromatin remodeling processes that are critical for differentiation, proliferation, and DNA repair. Loss of SWI/SNF subunits has been reported in a number of malignant cell lines and tumors, and a large number of experimental observations suggest that this complex functions as a tumor suppressor (Reisman et al. 2009). There are three types of mammalian SWI/SNF complexes: PBAF complex (BRG1-BAF180-BAF200), BRG1/BAF complex (BRG1-BAF250), and BRM/BAF complex (BRM-BAF250). BRM refers to the Drosophila homeotic gene brahma, whereas BRG1 means Brahma-related gene-1. Each of these proteins contain an Rb binding, ATPase and Bromo domains. Despite these similarities, BRG1 and BRM are only 75% similar at the proteins. BRM differs as it has a poly q section that codes B33 repeating glutamine residues.

（1）SWI/SNF functions as an ATP-dependent chromatin-remodeling complex

（2）The SWI/SNF complex functions as a master regulator of gene expression

（3）The SWI/SNF complex is involved in differentiation

（4）The BAF47 subunit of the SWI/SNF complex is a bona fide tumor suppressor

（5）SWI/SNF subunits and their role in gene regulation and cancer

（6）The SWI/SNF ATPase subunit genes are frequently silenced in cancer

（7）Loss of heterozygosity occurs at the BRG1 and BRM loci

（8）BRM is silenced by epigenetic mechanisms

（9）Transgenic knockout of BRM or BRG1 enhances transformation

（10）BRM and BRG1 play critical roles in the control of cell proliferation

（11）BRM and BRG1 are linked to DNA repair

（12）BRM and BRG1 control the expression of genes that are involved in cellular adhesion

（13）BRM and BRG1 are required for the activity of some nuclear receptors

（14）BRM and BRG1 play important roles in the immune system

（15）BRM and BRG1 exhibit partial functional redundancy

Generally speaking, it is clear that the SWI/SNF complexes are required for a number of processes that are critical for cell cycle checkpoint control and differentiation. Abrogation of the normal control processes is essential for tumor growth and progression,
and loss-of-function mutations in the RB and p53 pathways are among the most common oncogenic events. Mutations that affect cellular adhesion are essential for tumor progression and metastases, and other mutations are required to suppress the process of
anoikis, which is normally triggered by the disruption of cellular adhesion and polarity. There is evidence that links all of these events to SWI/SNF activity, and the preponderance of data suggests that the SWI/SNF complexes function as tumor suppressors. From a
mechanistic standpoint, it is clear that we have much to learn about how the SWI/SNF complexes control these processes. A critical question relates to the numerous observations that suggest that all SWI/SNF components are not equivalent in this respect. For example, loss of BAF47 is rare and is associated with a relatively small subset of tumor types, whereas loss of BRM and BRG1 is relatively common and is observed in a wide variety of solid tumors. Loss of BRM appears to predispose to tumor formation, whereas loss of BRG1 appears to be lethal in non-transformed cells, but to promote tumor progression in cells that have acquired oncogenic mutations. These observations seem to provide a rational basis for understanding why loss of both BRG1 and BRM is more common in tumors than loss of either alone. Furthermore, the connectionbetween BRG1/BRM and tumor suppressors such as RB and p53 suggests that the loss of the SWI/SNF catalytic subunits represents an alternative route to inactivation of checkpoint control in the absence of loss-of-function mutations to the RB and p53 pathways.

SWI/SNF subunits and their role in gene regulation and cancer

The SWI/SNF complexes may be subdivided based upon their subunit composition (Figure 1). The BAF complexes contain BAF250 subunits, which belong to the ARID (AT-rich DNA-interacting domain) gene family. Two different genes encode BAF250 proteins. BAF250A (also known as OSA1 and p270/ARID1A) is encoded by ARID1A, whereas BAF250B (OSA2) is encoded by ARID1B (Hurlstone et al., 2002;Wang et al., 2004b). In addition to the ARID domains, BAF250s also contain EHD1 and EHD2 domains, which map to the C termini and mediate protein binding (Hurlstone et al., 2002). BAF250A has been linked to the functions of steroid receptors (Inoue et al., 2002). ARID1A is located in 1p36.11 (Kozmik et al., 2001), a region frequently deleted in human cancers (Huang et al., 2007), and may be involved in cancer development. BAF250A is lost in two cell lines, C33a and T47D (DeCristofaro et al., 2001), and may be deficient in as many as 30% of renal carcinomas and 10% of breast carcinomas (Wang et al., 2004a). ARID1A- and ARID1B-containing SWI/SNF complexes appear to have antagonistic effects on cell cycle progression, with ARID1A participating in repression and ARID1B in the induction of key cell cycle regulators such as c-MYC (Nagl et al., 2006, 2007). BAF180 (polybromo, PB1, PBRM1)-containing SWI/SNF complexes have different properties from those that contain BAF250 subunits (Nie et al., 2000;Lemon et al., 2001;Wan g et al., 2004c) and are designated polybromo SWI/SNF complexes or PBAF (Figure 1). BAF180 harbors a distinctive set of structural motifs, characteristic of three components of RSC (Xue et al., 2000), another chromatin-remodeling complex in yeast. It also contains a Bromo domain that binds to acetylated histones. The BAF180 gene PBRM1 maps to chromosome 3p21, a frequent site of loss of heterozygosity in human tumors; BAF180 has been reported to be mutated in kidney cancer cells or primary tumors (Varela et al, 2011; Guo et al; Xu et al 2012).

The BAF180 is comprised of 6 bromodomains involved in binding acetylated lysine residues on histone tails, 2 bromo-adjacent homology domains important in protein-protein interaction and an HMG DNA binding domain. PBAF complex-mediated chromatin remodelling is implicated in replication, transcription, DNA repair and control of cell proliferation/differentiation. The SMARCB1 and BRG1 components of this complex have inactivating mutations in rhabdoid tumours and BRG1 mutations have been reported in multiple tumour types.