Germline BLM mutations and metastatic prostate cancer

Abstract

Background:

Biallelic loss-of-function BLM mutations result in Bloom syndrome: a genetic disorder characterized by growth deficiencies, photosensitivity, and multiple cancer susceptibilities. There are conflicting reports about whether or not heterozygous BLM carriers are at a higher risk of various cancers. Without BLM protein functionality, there is evidence of increased sister chromatid exchange and chromosomal instability.

Methods:

Metastatic prostate cancer patients (N = 796) underwent germline genetic testing as part of routine care at three academic centers. Patients with heterozygous BLM mutations were identified. Tumor tissue was analyzed for somatic alterations in those patients who had a germline pathogenic mutation. Control data using a population sample were extracted from the Genome Aggregation Database.

Results:

Heterozygous BLM germline mutations in 5 of 796 patients (prevalence, 0.63%). All mutations were loss-of-function truncating alterations. None of the mutations were BLM^Ash. The control population (gnomAD) frequency of pathogenic or likely pathogenic BLM mutations was 0.18% (212 of 116 653). The relative risk (RR) of BLM mutations in metastatic prostate cancer patients was 3.4 (95% CI, 1.42-8.33; P < .0062) compared to gnomAD controls. Tumor DNA sequencing in the BLM carriers showed no evidence of somatic BLM mutations. Interestingly, 3 of 5 BLM germline carriers had bi-allelic BRCA2 inactivation evident on tumor sequencing. One patient had both germline and somatic mutations in BRCA2. Excluding the patient with the germline BRCA2 mutation (BLM prevalence, 4 of 796: 0.50%) still yielded a statistically significant finding vs the gnomAD controls (RR, 2.8; 95% CI, 1.02-7.39; P < .04).

Conclusion:

Truncating BLM germline mutations occur at a higher frequency in patients with advanced prostate cancer as compared to control populations. Though no biallelic loss of BLM was no noted in cancers, a surprising number of the BLM germline heterozygotes had pathogenic BRCA2 mutations in their tumor.

1 |. INTRODUCTION

The BLM gene encodes a RecQ DNA helicase involved in maintenance of genomic integrity and regulation of homologous recombination. In particular, this helicase participates in the unwinding of DNA in 3′-to-5′ direction and is involved with 5′ resection during DNA double-strand break repair. Without BLM protein functionality, there is an increase in sister chromatid exchange resulting in greater chromosomal instability.

Biallelic loss-of-function BLM mutations result in Bloom syndrome: a genetic disorder characterized by growth deficiencies, photosensitivity, and multiple cancer susceptibilities often developing at an early age.¹ The most frequent BLM mutation (c.2281delATCTGAinsTAGATTC), also known as BLM^Ash, is a relatively common founder mutation found in the Ashkenazi Jewish population. There are conflicting reports about whether or not heterozygous BLM carriers are at a higher risk of various cancers, with most studies examining colorectal carcinoma risk.² Previous case-control studies have not found an association between BLM carrier status and prostate or ovarian cancer.³ However, in prostate cancer, both a genome-wide haplotype association study in the Chinese population and a study of familial prostate cancer have preliminarily identified certain risk variants associated with the BLM gene.^4,5 Germline mutations in DNA-repair genes occur at higher incidence in metastatic prostate cancer patients⁶; however, the potential role of BLM in prostate cancer remains unknown. Herein we examined the potential significance of germline pathogenic BLM mutations in prostate cancer patients.

2 |. MATERIALS AND METHODS

A total of 796 metastatic prostate cancer patients underwent germline genetic testing as part of routine clinical care at 3 academic centers. Patients with heterozygous BLM mutations were identified from Tulane Cancer Center (TCC), Johns Hopkins (JH), and University of Washington (UW). The clinical testing was performed through commercial germline testing (Invitae), the UW-BROCA panel, or whole-exome sequencing. Tumor tissue was also analyzed for somatic alterations in those patients who had a germline pathogenic mutation. Control data using a population sample were extracted from the Genome Aggregation Database (gnomad.broadinstitute.org).

3 |. RESULTS

Of the 796 prostate cancer patients interrogated, 5 heterozygous BLM germline mutations (prevalence, 0.63%) were identified; 2 of 295 TCC patients, 2 of 172 JH patients, and 1 of 302 UW patients (see Table 1). All mutations were loss-of-function truncating alterations (see Table 2). None of the mutations were BLM^Ash. The control population (gnomAD) frequency of pathogenic or likely pathogenic BLM mutations was much lower at 0.18% (212 of 116 653). The relative risk (RR) of BLM mutations in metastatic prostate cancer patients was 3.4 (95% CI, 1.42-8.33; P < .0062) compared to gnomAD controls. Tumor DNA sequencing in all 5 BLM carriers showed no evidence of “second hit” somatic BLM mutations. Interestingly, 3 of 5 BLM carriers on tumor sequencing had bi-allelic BRCA2 inactivation; one of these patients had both germline and somatic mutations in BRCA2. Excluding the patient with the germline BRCA2 mutation (BLM prevalence, 4 of 796: 0.50%) still yielded a statistically significant finding when comparing prostate cancer patients with BLM mutations vs the gnomAD controls (RR, 2.8; 95% CI, 1.02-7.39; P < 0.04).

TABLE 1.

BLM mutation carriers

Patient	Site	Age at diagnosis	Race	Gleason score	Time between diagnosis and metastatic disease	Family history
1	JH	59	Caucasian	5 + 4	5 mo	Mother with breast cancer, and brother with Hodgkin lymphoma
2	JH	68	Caucasian	4 + 4	At diagnosis	Father with colorectal cancer
3	TCC	62	Caucasian	4 + 3	Undetermined	Mother with breast and skin cancer, and brother with skin cancer
4	TCC	63	Caucasian	4 + 3	At diagnosis	Father with prostate and lung cancer, and grandfather with prostate cancer
5	UW	63	Caucasian	4 + 4	11 y	Mother and grandmother with colon cancer

Note: Clinical characteristics and family history for BLM mutation carriers.

Abbreviations: JH, Johns Hopkins; TCC, Tulane Cancer Center; UW, University of Washington.

TABLE 2.

BLM alterations detected in five prostate cancer patients

Patient	Site	Position	Reference allele	Variant allele	Gene	Protein change	Annotation	Concurrent BRCA2 (somatic)
1	JH	chr15:91290721	G	A	BLM	splicing	NM_000057, c.98 + 1 G > A	Yesa
2	JH	chr15:91337589	-	T	BLM	splicing	NM_000057.3, c.3210 + 2delT	Yes
3	TCC	chr15:91310196	-	AAAT	BLM	p.L751Kfs*25	NM_000057, c.2250_2251insAAAT	No
4	TCC	chr15:91337405	G	-	BLM	p.D1010Mfs*24	NM_000057, c.3028del	No
5	UW	chr15:91310151	ATCTGA	TAGATTC	BLM	p.Y736Lfs*5	NM_000057.2, c.2207_2212delATCTGAinsTAGATTC	Yes

Abbreviations: JH, Johns Hopkins; TCC, Tulane Cancer Center; UW, University of Washington.

^aPatient 1 has both germline and somatic BRCA2 variants.

4 |. DISCUSSION

In conclusion, pathogenic germline BLM mutations may influence risk of developing metastatic prostate cancer as evidenced by the increased frequency of BLM pathogenic mutations in these analyses. Though these findings are intriguing, the frequency of germline BLM alterations in prostate cancer patients should be validated and assessed in a larger study population. The concurrent somatic BRCA2 inactivation found in a subset of prostatic tumors is notable, and may suggest a cancer-specific interaction between these two genes known to be involved in homologous recombination.