Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer

Abstract

Inherited mutations in the BRCA2-interacting protein PALB2 are known to be associated with increased risks of developing breast cancer. To evaluate the contribution of PALB2 to familial breast cancer in the United States, we sequenced the coding sequences and flanking regulatory regions of the gene from constitutional genomic DNA of 1,144 familial breast cancer patients with wild-type sequences at BRCA1 and BRCA2. Overall, 3.4% (33/972) of patients not selected by ancestry and 0% (0/172) of patients specifically of Ashkenazi Jewish ancestry were heterozygous for a nonsense, frameshift, or frameshift-associated splice mutation in PALB2. Mutations were detected in both male and female breast cancer patients. All mutations were individually rare: the 33 heterozygotes harbored 13 different mutations, 5 previously reported and 8 novel mutations. PALB2 heterozygotes were 4-fold more likely to have a male relative with breast cancer (P = 0.0003), 6-fold more likely to have a relative with pancreatic cancer (P = 0.002), and 1.3-fold more likely to have a relative with ovarian cancer (P = 0.18). Compared with their female relatives without mutations, increased risk of developing breast cancer for female PALB2 heterozygotes was 2.3-fold (95% CI: 1.5-4.2) by age 55 and 3.4-fold (95% CI: 2.4-5.9) by age 85. Loss of the wild-type PALB2 allele was observed in laser-dissected tumor specimens from heterozygous patients. Given this mutation prevalence and risk, consideration might be given to clinical testing of PALB2 by complete genomic sequencing for familial breast cancer patients with wild-type sequences at BRCA1 and BRCA2.

Figure 1

Truncating mutations in PALB2. Thirteen different truncating mutations in PALB2 were detected in familial breast cancer patients. On the PALB2 gene sequence, frameshift mutations are indicated in red, nonsense mutations in purple, and splice mutations in blue. On the PALB2 protein, yellow symbols indicate low complexity regions (LCR), the red symbol the coiled coil domain, and green symbols the WD40-like repeats that comprise beta propeller structures.

Figure 2

Splice mutations in PALB2. Effects on splicing of single bp genomic substitutions in PALB2 were evaluated by sequencing transcripts. PALB2 c.2559C>T leads to altered splicing and deletion of 29 bp in the PALB2 message. PALB2 c.3113G>A produces three different PALB2 messages: complete deletion of exon 10 (117 bp), use of an alternate splice site within exon 10 and deletion of 31 bp, and an immediate stop at codon 1038.

Figure 3

Loss of heterozygosity of wildtype PALB2 alleles in tumor tissue. Tumor tissue was available from seven patients with five different mutations. In all cases, cancer cells isolated by laser dissection carried only the mutant PALB2 allele. Each panel indicates the sequence at the mutant allele (arrow) for a wildtype control (WT), for constitutional genomic DNA from the carrier (MUT), and for laser-dissected tumor cells (Tumor).