A Rare Germline HOXB13 Variant Contributes to Risk of Prostate Cancer in Men of African Ancestry

Abstract

A rare African ancestry–specific germline deletion variant in HOXB13 (X285K, rs77179853) was recently reported in Martinican men with early-onset prostate cancer. Given the role of HOXB13 germline variation in prostate cancer, we investigated the association between HOXB13 X285K and prostate cancer risk in a large sample of 22 361 African ancestry men, including 11 688 prostate cancer cases. The risk allele was present only in men of West African ancestry, with an allele frequency in men that ranged from 0.40% in Ghana and 0.31% in Nigeria to 0% in Uganda and South Africa, with a range of frequencies in men with admixed African ancestry from North America and Europe (0–0.26%). HOXB13 X285K was associated with 2.4-fold increased odds of prostate cancer (95% confidence interval [CI] =1.5–3.9, p = 2 × 10^–4), with greater risk observed for more aggressive and advanced disease (Gleason ≥8: odds ratio [OR] = 4.7, 95% CI = 2.3–9.5, p = 2 × 10^–5; stage T3/T4: OR = 4.5, 95% CI = 2.0–10.0, p = 2 × 10^–4; metastatic disease: OR = 5.1, 95% CI = 1.9–13.7, p = 0.001). We estimated that the allele arose in West Africa 1500–4600 yr ago. Further analysis is needed to understand how the HOXB13 X285K variant impacts the HOXB13 protein and function in the prostate. Understanding who carries this mutation may inform prostate cancer screening in men of West African ancestry.

Patient summary:

A rare African ancestry–specific germline deletion in HOXB13, found only in men of West African ancestry, was reported to be associated with an increased risk of prostate cancer. Understanding of who carries this mutation may help inform screening for prostate cancer in men of West African ancestry.

A rare African ancestry–specific germline deletion in HOXB13 (X285K) was associated with an increased risk of overall and advanced prostate cancer and was found only in men of West African ancestry. Men carrying this variant may benefit from earlier prostate cancer screening.

The nonsynonymous rare germline HOXB13 G84E variant (rs138213197) is a major risk factor for prostate cancer, accounting for ~5% of hereditary prostate cancer in men of European ancestry [1,2]. Rare prostate cancer HOXB13 risk variants have also been observed in other populations, including missense variants G132E in Japanese men (rs1286034091; allele frequency = 0.04%) [3] and G135E in Chinese men (rs769634543; allele frequency = 0.004%) [4]. Recently, a rare African ancestry–specific germline deletion variant in HOXB13 (rs77179853, allele frequency = 0.2%), which removes the stop codon (X285K) and elongates the HOXB13 protein, was observed in three Martinican men (French West Indies) with early-onset prostate cancer (allele frequency = 3.2%) [5]. Given the critical role of HOXB13 germline variation in prostate cancer, we investigated the association between the HOXB13 X285K variant and prostate cancer risk in a large sample of men of African ancestry.

This investigation included 11 688 prostate cancer cases and 10 673 controls from the African Ancestry Prostate Cancer (AAPC) Consortium, ELLIPSE/PRACTICAL OncoArray Consortium, California/Uganda Prostate Cancer Study, Ghana Prostate Study, and Men of African Descent and Carcinoma of the Prostate (MADCaP) Network (Supplementary Tables 1 and 2). The HOXB13 X285K variant was not included on genome-wide association studies (GWAS) arrays used in the African ancestry prostate cancer studies and was imputed separately using the Trans-Omics for Precision Medicine (TOPMed) r2 and 1000 Genomes Project (1KGP) phase 3 reference panels; the variant was observed in approximately 126 of 97 256 TOPMed participants and three of 2504 1KGP participants (Supplementary material). We imputed 101 carriers among 22 361 men in the African ancestry studies when using the TOPMed panel (imputation info score range across studies: 0.92–0.97) versus 60 when using 1KGP (imputation info score range across studies: 0.68–0.82; Supplementary Table 3). The carrier concordance between imputation panels was 0% (Supplementary Fig. 1). Confirmatory genotyping of 82 TOPMed imputed carriers, 42 1KGP imputed carriers, and 1431 imputed noncarriers confirmed 81 of 82 TOPMed but none of the 1KGP imputed genotypes (Supplementary Fig. 1 and Supplementary material). Other pathogenic and deleterious variants in HOXB13 were observed in our African ancestry populations (Supplementary Table 4), but were extremely rare and not able to be imputed with high confidence and tested in the current study.

HOXB13 X285K was present only in men of West African ancestry (Fig. 1 and Supplementary Fig. 2), with an allele frequency ranging from 0% in men from Uganda and South Africa to 0.31% in controls from Nigeria and 0.40% in controls from Ghana (Supplementary Table 5). Allele frequencies ranged from 0% to 0.26% in African ancestry controls from North America, the UK, and France (Supplementary Table 5), likely due to the high degree of European admixture in these populations. Of the 22 361 men, those with greater West African ancestry were found to have larger risk allele frequencies, ranging from 0.05% in cases with 0–20% West African ancestry to 0.90% in cases with 80–100% West African ancestry (Fisher’s exact test p = 2 × 10^–4; Supplementary Fig. 3 and Supplementary material).

Fig. 1 –

Distribution of HOXB13 rs77179853 by genetic ancestry comparing principal components 1 and 2 calculated in our sample of 22 361 men of African ancestry. Men carrying the rs77179853 delA risk allele are highlighted by black triangles.

In studies where the variant was observed (10 477 cases and 9688 controls; Supplementary Table 2), the HOXB13 X285K variant was significantly associated with 2.4-fold increased odds of prostate cancer (95% confidence interval [CI] = 1.5–3.9, p = 2 × 10^–4; allele frequency in cases = 0.35% and controls = 0.14%; Table 1 and Supplementary material). The allele frequency was more common in cases with higher Gleason scores (0.29% in men with Gleason ≤6 tumors [odds ratio {OR} = 2.6, 95% CI = 1.3–5.2, p = 0.01], 0.36% in men with Gleason 7 tumors [OR = 2.3, 95% CI = 1.2–4.2, p = 0.01], and 0.84% in men with Gleason ≥8 tumors [OR = 4.7, 95% CI = 2.3–9.5, p = 2 × 10^–5]), in cases diagnosed with higher-stage disease (0.34% in men with stage T1/T2 disease [OR = 2.3, 95% CI = 1.3–4.1, p = 0.01] and 0.73% in men with stage T3/T4 disease [OR = 4.5, 95% CI = 2.0–10.0, p = 2 × 10^–4]), and in cases with metastatic (or prostate-specific antigen ≥100 ng/ml) disease (1.08% [OR = 5.1, 95% CI = 1.9–13.7, p = 0.001]; Table 1 and Supplementary Table 6).

Table 1 –

Association of HOXB13 germline variant rs77179853 with prostate cancer risk and disease aggressiveness^a

Group	n	Carriers, n	Risk allele frequency (%)	Carrier frequency (%)	OR (95% CI)	p value
Overall prostate cancer
Controls (reference)	9688	28	0.14	0.29	–	–
Cases	10 477	73	0.35	0.70	2.42 (1.52–3.87)	2 × 10−4
Men of African ancestry from North America
Controls (reference)	8766	21	0.12	0.24	–	–
Cases	9192	44	0.24	0.48	1.98 (1.16–3.38)	0.01
Men of African ancestry from West African countries (Ghana, Nigeria, and Senegal)
Controls (reference)	922	7	0.38	0.76	–	–
Cases	920	22	1.20	2.39	3.99 (1.46–10.9)	0.01
Disease aggressiveness
Controls (reference)	9180	28	0.15	0.31	–	–
Gleason ≤6 tumors	3319	19	0.29	0.57	2.58 (1.28–5.18)	0.01
Gleason 7 tumors	3056	22	0.36	0.72	2.28 (1.22–4.24)	0.01
Gleason ≥8 tumorsb	1126	19	0.84	1.69	4.65 (2.28–9.47)	2 × 10–5
Controls (reference)	8918	28	0.16	0.31	–	–
Stage T1/T2	4784	33	0.34	0.69	2.30 (1.28–4.14)	0.01
Stage T3/T4	959	14	0.73	1.46	4.48 (2.01–9.98)	2 × 10–4
Controls (reference)	6526	20	0.15	0.31	–	–
Metastatic or PSA ≥100 ng/ml	511	11	1.08	2.15	5.08 (1.88–13.7)	0.001
Controls (reference)	9688	28	0.14	0.29	–	–
Cases with low-risk diseasec,d	2795	12	0.21	0.43	1.84 (0.87–3.88)	0.11
Cases with intermediate-risk diseasec	2721	12	0.22	0.44	1.51 (0.73–3.15)	0.27
Cases with high-risk disease	3082	33	0.54	1.07	3.09 (1.75–5.45)	1 × 10–4

CI = confidence interval; OR = odds ratio; PSA = prostate-specific antigen; RAF = risk allele frequency.

^aAnalyses were limited to studies that carried the variant (see Supplementary Table 2).

^bCompared with 8329 controls (25 carriers, RAF = 0.15%) as the CA UG study did not have Gleason ≥8 tumor case carriers.

^cCompared with 9400 controls (27 carriers, RAF = 0.14%) as MADCaP did not have low- or intermediate-risk case carriers.

^dLow risk disease: Gleason <7, stage T1/T2, and PSA <10 ng/ml; intermediate-risk disease: Gleason = 7, stage T1/T2, and PSA = 10–20 ng/ml; high-risk disease: Gleason 8–10, stage T3/T4, PSA >20 ng/ml, metastatic disease, or died of prostate cancer.

The absolute risk of prostate cancer was 15.9% (95% CI = 15.9–16.0%) in noncarriers and 32.9% (95% CI = 22.0–44.6%) in carriers by age 85 yr (Supplementary Fig. 4). We did not observe associations between the variant and age at diagnosis (Supplementary Tables 7 and 8), family history of prostate cancer (Supplementary Table 9), or prostate-specific antigen levels (Supplementary Table 10).

We estimated that the HOXB13 X285K variant arose approximately 1500–4600 yr ago (refer to Supplementary Fig. 5 and Supplementary material for details on allelic age estimates based on two complementary approaches) and likely occurred after the Bantu migration from Western to Southern and Eastern Africa [6], which may explain why it is found only in men of West African ancestry. These findings, together with the established prostate cancer susceptibility G84E founder mutation that is more prevalent in Scandinavian populations [7] and the East Asian–specific G132E and G135E mutations [3,4], underscore the importance of ancestry-specific germline prostate cancer risk variants in the HOXB13 gene.

The HOXB13 X285K variant adds to growing evidence of regional differences in Africa for prostate cancer risk variants [8,9] and provides the first evidence of a genetic factor that is limited to specific African ancestry populations, although studies in other populations are needed to better understand the distribution of this variant in Africa. This investigation also demonstrates the importance and necessity of building diverse reference panels to facilitate the discovery of rare ancestry-specific risk variants and the need for larger sequencing studies in prostate cancer. At an exome-wide significance threshold of p < 5 × 10^–7, 18 000 cases and 18 000 controls would be needed to detect an OR of 2.4 for an allele frequency of 0.14% (eg, HOXB13 X285K) with 90% power. The X285K stop codon is predicted to result in a 34% elongation of the HOXB13 protein, extending it by 96 amino acids [10]. Further studies are needed to understand how the HOXB13 X285K variant impacts the function of this homeobox transcription factor in the prostate. Understanding who carries this mutation may help inform screening for prostate cancer in men of West African ancestry.