To the Editor: The SWI–SNF chromatin-remodeling complex regulates gene expression patterns and plays critical roles in development, differentiation, and proliferation of cells (1). AT-rich interactive domain-containing protein 1A (ARID1A) is a large subunit of the SWI–SNF complex and is considered to perform a tumor suppressor function (1). Initially, frequent somatic mutation of ARID1A gene was reported in clear cell and endometrioid carcinomas of ovary (2, 3). In nonovarian tumors, gastric (GC), colorectal (CRC), urinary bladder, and other cancers [pancreas, breast, lung, prostate (PCA), and brain cancers] have been reported to harbor ARID1A mutations (4–6). In the GC and CRC cancers, approximately 50% of the mutations were detected in cancers with microsatellite instability (MSI)(4, 6). In contrast, in pancreas, breast, lung, PCA, and brain cancers, all except one mutation were detected in cancers with stable MSI (MSS)(6). Wang et al.(4) analyzed ARID1A expression in GC and found that loss of ARID1A expression was observed in 83% of the GC with ARID1A mutations, but the loss of expression was also observed in 19% of those without ARID1A mutation. In breast cancers, low expression of ARID1A was observed in 56% of the cases (7). Together, these data suggest that loss of ARID1A expression in cancers may vary depending on tissue types and MSI status. To see whether loss of ARID1A expression is present and dependent on MSI status, we analyzed GC, CRC, and PCA with high MSI (MSI-H) and those with MSS in the present study. There is a mononucleotide repeat (G7 in exon 20) in the coding sequences of human ARID1A gene (http://genome. cse. ucsc. edu/). Frameshift mutation of genes at mononucleotide repeats is a feature of cancers with MSI, and most of the ARID1A mutations in cancers with MSI have been detected in this repeat (4, 6). We analyzed this repeat in ARID1A gene in 91 GC, 100 CRC, and 90 PCA by polymerase chain reaction (PCR) and single-strand conformation polymorphism (SSCP) assay as described previously (8, 9). The GC consisted of 32 GC with high MSI (MSI-H), 14 GC with low MSI (MSI-L), 45 GC with stable MSI (MSS), 40 CRC with MSI-H, 15 GC with MSI-L, and 45 CRC with MSS. All of the PCA were MSS. Genomic DNA each from tumor cells and corresponding normal cells were amplified with seven primer pairs for by PCR. Radioisotope ([32P] dCTP) was incorporated into the PCR products for detection by SSCP autoradiogram. PCR-SSCP and DNA sequencing analysis identified aberrant bands in eight of the GC with MSI-H (8/32; 25%), one of the GC with MSI-L (1/14; 7%), and four of the CRC with MSI-H (4/40; 10%), but neither in those with MSS (GC, CRC, and PCA) and the CRC with MSI-L. All the mutations were detected in the G7 repeat and were frameshift mutations (c. 5548delG and c. 5548dupG). DNA from normal tissue showed no shifts in SSCP, indicating the mutations had risen somatically.

To see whether ARID1A protein is altered in the cancers, we used tissue microarray (TMA) blocks that contained paraffin-embedded GC (N= 100), CRC (N= 100), and PCA (N= 100) tissues. Each case has cores representing cancers as well as those representing corresponding normal epithelial tissues. The TMA included GC with MSI-H (N= 20) and CRC with MSI-H (N= 20), which showed ARID1A mutations in three and two cancers, respectively. All other GC, CRC, and PCA were MSS and did not harbor ARID1A mutation. For immunohistochemistry, we used DAKO REAL EnVision System (DAKO, Glostrup, Denmark) with a rabbit polyclonal antibody against human ARID1A (Sigma, Saint Louis, MO …