Heterozygous bi-allelic inactivating mutations in PARD3 and AS3 genes in the LOH -free regions in LNCaP cells. (A). RT-PCR analysis shows the lower mRNA levels in the untreated and the increased levels in caffeine treated LNCaP and 22Rv1 cells for the PARD3 and for AS3 genes, respectively. (B). Sequencing chromatograms show heterozygous deletion of a T in the (T)5 coding repeat in one allele and C to T substitution resulting in the TAA stop codon in the other allele of the PARD3 gene in LNCaP cells (top); heterozygous deletion of a C in the (C)7 repeat in one allele and of an A in the (A)9 repeat in the other allele of the AS3 gene in the 22Rv1 cells (middle); and a homozygous deletion of a C in the (C)2 repeat of the CLPTM1 gene in the LNCaP cells (bottom). (B). Array CGH analysis shows normal genomic content in the PARD3 and AS3 loci in the LNCaP and 22Rv1 cells and the loss of heterozygosity for the CLPTM1 locus in LNCaP cells.