Investigation of Triple-Negative Breast Cancer Risk Alleles in An International African-Enriched Cohort

doi:10.21203/rs.3.rs-109841/v1

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Investigation of Triple-Negative Breast Cancer Risk Alleles in An International African-Enriched Cohort

https://doi.org/10.21203/rs.3.rs-109841/v1

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published 29 Apr, 2021

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Large-scale efforts to identify breast cancer risk alleles have historically taken place among women on European ancestry, with recent efforts to validate these alleles or identify risk alleles applicable to women of African descent. We investigated the effect of previously reported breast cancer and triple-negative breast cancer (TNBC) risk alleles in our African enriched International Center for the Study of Breast Cancer Subtypes (ICSBCS) cohort. Using case-control and nested case-series approaches, we report that the Duffy-null allele (rs2814778) is associated with TNBC risk (OR = 3.814, p = 0.001), specifically among AA individuals, after adjusting for self-indicated race and west African ancestry (OR = 3.368, p = 0.007). We have also validated the protective effect of the minor allele of the ANKLE1 missense variant rs2363956 among AA for TNBC (OR = 0.4204, p = 0.005). We have shown that differential prevalence of the protective allele may reflect a polymorphic function of ANKLE1 in TNBC breast cancer outcomes. These AA specific risk alleles present opportunities for future studies of therapeutic potential that address race-specific differences in BC and TNBC risk and disease outcome.

TNBC

ICSBCS

ANKLE1

Cancer

Breast cancer (BC) is caused by a combination of dynamic influences, which are typically unique for each individual, but frequently may include underlying heritable genetic risks. Particularly, breast cancer patients who have early onset, or pre-menopausal incidence, typically are carriers of germline mutations in key cancer genes^1,2. However, population studies have shown disparities in BC incidence and mortality among ethnic and racial groups persistently over the past five decades. In the US, White/European Americans (EA) have historically demonstrated the highest incidence of breast cancer, while Black or African Americans (AA) have the highest mortality rates reported in any race/ethnic group^3,4. Interestingly, this mortality gap only emerged in the late 1970s, coinciding with implementation of targeted hormone therapies. The consequential decrease of mortality in EA was not matched in AA, which aside from unequal access to these new therapies, unmasked a race-group bias in breast tumor biology and incidence rates of tumor subtypes. Population studies of hormone receptor (HR) status in breast cancer diagnoses indicates a two-fold increased risk of Triple Negative Breast Cancer (TNBC) in AA compared to EA patients, which persists after adjusting for stage and age at diagnosis^5–8. This trend also extends beyond certain social determinants, with AA having the highest rate of TNBC at every poverty level as well⁹. This finding translates to disproportionate survival benefits in EA patients from the standard-of-care targeted therapies that are primarily designed to target HRs¹⁰, which AA diagnosed with TNBC are not eligible to receive. Clinically, TNBC is a confirmed adverse prognostic feature in patients overall¹¹, and in AA patients specifically¹², and it underscores a need to identify any unique risk of certain breast cancer subtypes. An investigation of genetic risk across self-identified AA groups becomes more informative with the inclusion of an individual’s genetic ancestry composition, as levels of African versus European or other ancestry may be found at varying levels among this admixed population. For example, genetic risk in particular ancestry groups could be unmasked by investigating risk alleles within the predominant ancestry group, as opposed to the traditional risk studies that were devoid of ancestry data¹³. However, there is a severe shortage of genetic and GWAS data in non-white populations^13,14, where less than 10–15% of individuals in population studies are Black, Indigenous, and People of Color (BIPOC), if race or ethnicity groups are reported at all¹³. This tragic limitation stifles our efforts to identify population-specific risk alleles outside of European descendant groups. However, recent studies have investigated race-specific risk; including, the Multi-Ethnic Cohort (MEC)¹⁵, the African American Breast Cancer Epidemiology and Risk (AMBER) Consortium^16–19 (which includes the MEC), and our International Center for the Study of Breast Cancer Subtypes (ICSBCS), along with others^14,20−22, and we are paving the way to more inclusion of AA and African participants in genomic research.

Previous studies inferred that AA-specific risk alleles held race-group specificity due to shared African genetic ancestry among AAs^15,23. Through our Oncologic Anthropology epidemiological studies of breast cancer incidence and prevalence across the African Diaspora^24,25, we have revealed a common trend of lower incidence but higher mortality among women of African descent²⁶. Globally, there is also higher frequency of TNBC among women of western sub-Saharan African descent within every country that has a substantial population of individuals of African descent, and where we could investigate HR status, coupled with higher distribution of poor prognosis in these groups as well^7,27−30. This strikingly correlates with the social history and unparalleled numbers of Africans dispersed during forced migrations of the Trans-Atlantic Slave trade, where over hundreds of years and a dozen generations, enslaved Africans were scattered across Europe, the Americas and the Caribbean.

We previously reported our independent analysis of AA race-group specific risk and our previous findings were able to replicate some, but not all, BC and TNBC-specific risk alleles in our African-enriched ICSBCS cohort³¹. Distinctions in risk associations from hazard models between cohorts could be confounded by bias in shared ancestry, due to differences in composition of genetic admixture among AAs. In this report, we reconsidered our previous risk findings to determine their relevance from a more global perspective, by (i) including additional ancestral populations from contemporary African women, and (ii) adjusting risk models for bias in ancestry background within admixed AAs. These efforts will provide further evidence and methodological insight in the role of shared African ancestry in the shared racial disparity of TNBC incidence across the African diaspora.

All-inclusive analysis of AA-specific BC risk alleles suggests race group specific effects

Our overall BC risk assessment model was an all-inclusive analysis, including all breast cancer subtypes and SIR/ancestry groups, where we have expanded the number of BC cases from Eastern and Western African nations, investigating previously published BC risk alleles that have been validated among African American women in the AMBER consortium³² (Fig. 1A, Table 2). Three alleles replicated previous associations of increased overall BC risk in our unadjusted models. These include rs2981578 (FGFR2), rs4849887 (GLI2), and rs3745185 (BABAM1). Interestingly, we found that the T allele of rs2981578 in the FGFR2 gene was associated with increased risk (OR = 1.508, p = 0.008491), which contrasts with previous reports of the C allele as the risk allele. The C allele of rs4849887 in the GLI2 gene was associated with increased risk (OR = 1.654, p = 0.006122), replicating previous findings. We also replicated the protective A allele of rs3745185 in the BABAM1 gene (OR = 0.67, p = 0.008402).

To determine whether these all-inclusive association models may be confounded by race-specific bias in age or allele frequency, we adjusted the risk model to correct for race and age. Interestingly, each unadjusted risk association loses significance in the combined race group model after adjusting for race and age, indicating that the risk alleles may have higher frequency in one of the SIR groups (See Table 1). Specifically, in the case of the risk (C) allele of rs4849887, we find it is 10–15% lower in populations of West African descent (AA = 35%, Ghanaians = 36%), compared to European Americans (44%) and East Africans (44%) in our cohort. Two additional alleles gained significant overall BC risk associations after race and age adjustments in our all-inclusive model, rs2981579 in the FGFR2 gene (OR = 1.899, p = 0.03038) and rs3112572 in the LOC643714 gene (OR = 2.410, p = 0.03055).

Next, we tested whether the associated BC risk of our candidate alleles was different among SIR groups by performing a nested overall BC risk assessment within each of the SIR groups (Table 2 and Supplemental Table 1). We found that rs4849887, which lost significance in overall risk in our race-adjusted model, is associated with higher overall BC risk in AAs and Ghanaians, but only in Ghanaians after adjusting for age (OR = 2.472, p = 0.001032) (Fig. 1B). There were no significant associations found between the previously identified variants and breast cancer risk among SIR EA in both unadjusted and age-adjusted models (Supplemental Table 1).

AA-specific risk variants, associated TNBC-specific within ancestry groups.

The higher rate of TNBC among women of African descent worldwide begs the question of whether there is a shared genetic risk among the African diaspora, and we have previously shown that quantified West African ancestry was strongly associated with TNBC disease³¹. Using a case-series analysis in our African-enriched cohort, we tested whether previously reported AA-specific risk alleles were associated specifically with TNBC disease risk (Fig. 2A, Table 3 and Supplemental Table 2). Prior to adjusted covariate modeling, five of the nine AA-risk variants showed significant association with TNBC disease risk. Four of these variants were not previously reported as having ER-negative disease specific risk, and four were predicted to have a protective effect; including, rs2981578 in FGFR2 (OR = 0.667, p = 0.0627), rs3745185 in BABAM1 (OR = 0.503, p = 0.009), rs4849887 in GLI2 (OR = 0.414, p = 0.003), and rs2362956 in ANKLE1 (OR = 0.593, p = 0.0149). Only the SNV rs609275 in MYEOV/CCND1(OR = 2.479, p = 5.68E-05) showed higher hazard/risk for TNBC in the unadjusted model. The ANKLE1 variant rs2363956 replicated in the TNBC/ER-negative specific protective effect that was previously reported and was the only variant to retain significance after adjusting for race and age (OR = 0.542, p = 0.014).

Similar to our BC case-control analysis, we used a nested risk analysis within SIR groups to test for SIR-specific risk. For the admixed AA population, we included quantified West African ancestry (WAa) in the adjusted covariate modeling. The rs2363956 variant in the ANKLE1 gene retained a protective effect for TNBC in AAs, even after covariate adjustments, (age and WAa adjusted OR = 0.4204, p = 0.005), indicating this is not a mere artifact of disequilibrium, or biased distribution of the allele in African populations (Fig. 2B and Table 3). Among Ghanaians, the protective effect was observed in unadjusted models, but was lost after age adjustment (unadjusted OR = 0.7904, p = 0.7664; age-adjusted OR = 1.471, p = 0.8163) (Table 3 and Supplemental Table 2).

DARC/ACKR1 alleles in BC and TNBC risk

In addition to the previously implicated AA-risk alleles, we have also included DARC/ACKR1 alleles, including the TNBC risk associated Duffy-null allele³¹, to investigate whether alternative variants may capture risk due to unique biological contributions of either isoforms or distinct gene regulation (Table 1). Our new analysis found that four DARC SNVs also had significant potential to confer overall BC risk in our all-inclusive analysis models (rs2814778 OR = 1.512, p < 0.001, rs17838198, OR = 4.798, p < 0.001, rs3027016 OR = 4.586, p = 0.005 and rs12075 OR = 2.534, p < 0.001, respectively), however, after adjusting for age and race, this is mostly lost (Table 2). In our SIR nested analysis model, the DARC/ACKR1 variant rs3027013 showed a significant protective effect in EA patients, even after age-adjusted modeling (age-adjusted OR = 0.1314, p = 0.03897) (Fig. 1C and Supplemental Table 1).

For DARC/ACKR1 variant associations in TNBC-specific risk we similarly observed that seven out of eight variants were associated with TNBC disease, in which five of the minor alleles presented a protective effect and two showed increased risk, prior to race/age adjustments (rs6676002, OR = 0.191, p = 0.007; rs3027008, OR = 0.134, p = 0.006; rs17838198, OR = 0.367, p = 0.02; rs3027016, OR = 0.39, p = 0.06; rs12075, OR = 0.38, p = 0.003, rs71782098, OR = 3.403, p = 0.019; and rs2814778, OR = 3.062, p < 0.001) (Table 3). Interestingly, as we previously reported with only AA and EA, the Duffy-Null allele, rs2814778, retained significant TNBC-risk association with the addition of East African and West African samples, even after age and SIR adjustments (OR = 3.814, p = 0.001). The Duffy-Null (rs2814778) TNBC-risk association was also retained in our nested SIR analysis among AA, following both age and quantified West African ancestry adjustment (OR = 3.368, p = 0.007) (Fig. 2C and Table 3). This indicates that the TNBC-specific risk conferred by the Duffy-null allele in the DARC/ACKR1 gene is not an artifact of shared ancestry bias, but rather an ancestry-specific risk allele.

Functional consequences of the TNBC-protective rs2362956 variant in ANKLE1

In our TNBC risk analysis, we found that the minor G allele of the rs2363956 ANKLE1 variant was protective against TNBC disease, which has previously been shown for ER-negative disease among AA³². Given its SIR-specific effect, we investigated the frequency of the allele across global 1000 genomes (1 KG) populations³³. Population minor allele frequency (MAF) of the protective G allele is relatively equal among European and African groups (51.5% vs 51.2%, respectively, Table 1). However, among TNBC cases in our ICSBCS cohort, the frequency is much lower in AA patients, compared to EA patients (14% and 43%, respectively). This 40% drop in the minor allele frequency in TNBC cases among AA (Fig. 3B) is what explains the interpreted potentially protective effect of the minor allele, inferring the major allele may somehow drive TNBC frequency higher in AAs.

To date, despite being repeatedly reported as a risk allele in both breast and ovarian cancer^32,34,35, no investigation has linked a functional impact of this variant to risk or survival in this population. Given that the variant causes a dramatic amino acid change of leucine to tryptophan (L184W, Fig. 3A), there is a high probability that the protein structure is impacted, and subsequently have altered the function. We conducted a 3D rendering of the variant, comparing the wildtype structure of the protein with leucine at position 184 to the minor allele change to tryptophan, and found a predicted destabilization of the gene product (Fig. 3A).

The allele’s protective effect through destabilization of ANKLE1 structure, together with its significant loss in AAs who suffer from higher rates of TNBC, suggests the major allele ANKLE1 protein could be a genetic driver of TNBC. We hypothesize that wildtype ANKLE1 expression suppresses TNBC progression, which is most frequently found in EA patients when caused by the rs2363956 variant. To further investigate this theory, we determined whether the expression of ANKLE1 had any impact on survival³⁶. We found that survival trends in TCGA breast cancer cases are significantly impacted by ANKLE1 expression, but that the advantage of ANKLE1 expression only benefits EA patients (Fig. 3C-E). Specifically, we found that when comparing high vs low/medium ANKLE1 expression within SIR groups, EA have a significant survival improvement associated with higher expression (p = 0.035), but AA did not (p = 0.83) (Fig. 3C-E). In fact, when only including patients who had high expression of ANKLE1, EA had a longer survival advantage associated with ANKLE1, compared to AA (Fig. 3E, p = 0.052). This suggests that the benefit of ANKLE1, only found in EA, could be due to the 41–53% chance that EA are expressing the polymorphic version of ANKLE1, which harbors the rs2363956 allele.

While recent findings have delineated breast cancer risk alleles that pose increased or even decreased risk in African Americans specifically, many of these findings do not always replicate in other independent multi-ethnic cohorts. This is likely because of unmeasured individual admixture among the non-white individuals, who through social history are of mixed ancestry (i.e. Caribbean, Latin American and AAs) resulting from recent genetic admixture originating from multiple ancestor lineages^37–39. This complexity of AA ancestry includes heterogeneity of African origins, spanning multiple African parental lineages through dozens of generations. This undoubtedly creates confounding genetic backgrounds that still pose a significant obstacle in identifying causal risk alleles among “African” Americans. However, measuring this genetic and ancestral diversity, and accounting for ancestry substructure would be a key first step toward clarifying the alleles that may be shared among individuals of common ancestry within SIR groups who display common disease/tumor types. Our latest race and West African ancestry adjustments in risk models demonstrate the power of combining diverse ancestry groups and utilizing ancestry estimates to clarify either false-positive or false-negative results if models do not properly consider the underlying ancestry/genetic background of the cohorts.

Our work represents a uniquely powered cohort that is enriched with patients and controls of diverse African ancestry to directly investigate the impact of shared African ancestry in genetic risk for TNBC to account for increased prevalence in women of African descent. However, our analysis is still limited by the paucity of hormone receptor status in African cases and so the limited number of patients we can include in this analysis, thus far. Despite this limitation, we have robust findings that are compelling to expound upon in follow-up molecular and clinical studies. Specifically, African Americans and Ghanaians have the lowest frequency of the protective homozygous minor allele genotype (GG genotype of rs2362956 SNV) among TNBC cases compared to European Americans, where the GG genotype among TNBC cases is 14%, 25% and 43%, respectively (Fig. 3B). This suggests that the major T allele corresponds to a TNBC-specific oncogenic version of the ANKLE1 gene. If validated through additional clinical studies, finding a novel oncogene specific to TNBC could be transformative in two ways: (i) to improve genetic risk models or create AA-tailored risk models, and (ii) to develop prognostic tests to inform survival prediction models, which currently do not include information about ANKLE1. Specifically, if we find that the patients who have longer survival carry the minor protective allele, correlated with higher expression of this polymorphic ANKLE1, we can quickly investigate if this is ultimately related to treatment response. Our preliminary data on survival trends certainly suggests this could be true.

The potential mechanism of action for increased survival would appear to be DNA damage response, as ANKLE1 has repeatedly been shown to be involved in DNA repair pathways in pre-clinical and ex vivo screening, including endonuclease activity^40,41, proliferation, and drug response hits in CRISPR screens in cancer cell lines^42–45. Most intriguingly, one study in non-small-cell lung cancer indicated the combination of ANKLE1 RNAi with paclitaxel increased the efficacy of the drug response⁴⁶. Altogether, this is a very promising avenue for further investigation of targeted/combinatorial therapy, with potential to be transformative in treatment of TNBC, and with specific impact in AA who have higher expression of ANKLE1.

The reported, albeit controversial, findings of TNBC mortality differences between women of African descent compared to women of European descent may be an important indicator of unknown differences in tumor biology. Here, we show that a polymorphic version of a gene is associated with distinct survival outcomes. The allele has repeatedly been associated with breast and ovarian cancer risk and survival^34,35, and this association has been replicated among AA women³². As we investigated the consequences of this variant on the ANKLE1 gene coding region, we uncovered a potential functional reason for race-group risk distinction. Specifically, we are the first to report that the ‘protective’ polymorphic ANKLE1 would be the more likely version expressed in EA patients, compared to AA patients. Intriguingly, this corresponds with differential impact of the gene’s expression on survival when comparing race groups among patients with high expression of the gene. While the functional consequence on mechanistic change is yet unknown, it is a clear indicator of survival and therefore a prognostic indicator. Excitingly, this also reveals a potential opportunity to develop immune-based inhibition of the oncogenic (major allele) version that is more likely expressed in AA. As the frequency of the oncogenic ANKLE1 allele is higher in AA populations, this could present an opportunity for additional research to address its potential in precision therapies to bridge the survival gap in TNBC among race groups. Inclusion of diverse cohorts have powered this discovery and will drive clinical applications in the future.

International Center for the Study of Breast Cancer Subtypes

The mission of the International Center for the Study of Breast Cancer Subtypes (ICSBCS) is to reduce the global breast cancer burden through advances in research and delivery of care to diverse populations worldwide. The ICSBCS brings together an international consortium of breast cancer clinicians and researchers, all of whom share the goal of addressing genetic and phenotypic variation in breast cancer risk and survival outcomes. We accrued prospective breast cancer patients from 2013–2017 as previously described³¹, extracting germline DNA from saliva samples collected at the time of consent at Konfo Anokye Teaching Hospital (KATH) in Kumasi, Ghana, and St. Paul’s Millennium Hospital Medical College in Addis Ababa, Ethiopia. Additional cancer patient samples were collected at the Henry Ford Health System Hospital in Detroit, Michigan, and the University Cancer and Blood Center in Athens, GA (AA and EA). Healthy controls were recruited to the ICSBCS biospecimen registry through various sources of community engagement efforts throughout the US⁴⁷ and the breast cancer screening clinic at KATH²². Informed consent was obtained from all individuals participating in the study, which was approved and under the regulation of the Weill Cornell Medical College (WCM) Institutional Review Board (IRB; protocol number 1807019405). All experiments were performed in accordance with the approved IRB protocol.

Immunohistochemistry for BC tumor subtyping

For our TNBC case-series risk analysis, we determined hormone receptor status in our ICSBCS biospecimen registry via immunohistochemistry (IHC) methods that were described in detail in our previous study³¹. Expression of biomarkers was interpreted in accordance with the American Society of Clinical Oncology / College of American Pathologists guidelines^48,49. Briefly, for estrogen and progesterone receptor IHC, staining of at least 1% was determined as positive. HER2/neu staining score of 0 or 1 + was determined as negative, and 3 + was determined as positive. HER2/neu staining score of 2 + was deemed equivocal and was further evaluated by fluorescent in situ hybridization. ICSBCS cases accrued in the USA were reviewed by the treating facility. IHC and pathology review of Ghanaian and Ethiopian cases was completed in Michigan (University of Michigan and Henry Ford Health System Hospital) and New York (Weill Cornell Medicine).

Allele selection for BC case-control and TNBC case-series analyses

In our previous publication, we investigated nine reported AA BC risk variants in our African-enriched ICSBCS cohort, to determine BC or TNBC-specific risk within self-identified race (SIR) groups in our cohort. We additionally included the Duffy-Null allele (rs2814778), a promoter region variant of the DARC/ACKR1 gene in our panel and demonstrated this allele to be a TNBC-specific risk allele among AA. Building upon our previous findings, we have both increased our number of samples across our SIR groups with genotypes available, and included an additional eight DARC/ACKR1 gene variants in our panel that are implicated as ancestry-specific alleles, or sit in regions that are potentially involved in DARC/ACKR1 gene regulation. These eight DARC/ACKR1 gene variants represent upstream variants, 5’ UTR variants, and variants in the coding region of the gene. All alleles that were assessed in subsequent analyses are described in Table 1. Additionally, our African-enriched ICSBCS cohort allows us to also incorporate African ancestry measurements into the association model (below).

Global Ancestry estimation and genotyping of candidate alleles

Methods to determine global genetic ancestry have been previously reported in detail^31,50. Briefly, DNA extracted from saliva samples were genotyped on the Sequenom MassARRAY iPLEX platform using an AIMs panel containing 100 markers specifically selected and validated for estimating continental ancestry among admixed populations^51,52. The Sequenom TYPER software was used for genotype calls, and STRUCTURE (version 2.3) was used to calculate admixture estimates for each individual⁵³.

Similar to our global ancestry estimations, to obtain genotypes for our candidate variants for risk analyses (Table 1), DNA from saliva samples were genotyped for each of the variants using the Sequenom platform. For the Duffy-Null allele (rs2814778), we have obtained additional genotypes using single-target allele amplification reactions, as previously described³¹.

Risk assessment

From our genotyping data, we used PLINK (version 2.0)⁵⁴ to determine associations between the candidate variants and breast cancer risk in case-control analysis model, and TNBC-specific risk in case-series analysis model as previously described³¹. In both our BC and TNBC-specific risk analyses, we performed associations without covariates (non-adjusted), with SIR adjustment, and with SIR and age adjustments. We additionally investigated variant and risk associations within each SIR race group, where we performed analyses for non-adjusted and age-adjustments. For our analysis within SIR AA, using the genetic ancestry estimates, we were additionally able to adjust for West African ancestry in our models. For the candidate variants, we conducted the risk association using both a dominant and dosage statistical model³¹. In the dominance model where the genotypes are AA, Aa, aa (where a is minor allele), the resulting genotypes would be coded as 0, 1, 1 in the analysis model, where risk is weighted based on having at least one minor dominant allele. In the dosage model using the same genotypes, the resulting genotypes would be coded as 0, 1, 2, where the risk is weighted by the number of minor alleles present. In the main figures and tables, we show and discuss risk assessment output from the dosage models, where the full range of genotypes is considered in the analysis.

For both the BC and TNBC-specific analyses, odds ratio output from the dosage risk assessment analyses were log transformed and plotted using the Forest Plot add-in (v8) within JMP® Pro 15.0.0 statistical software (SAS Institute Inc., Cary, NC, 1989–2019).

3D Modeling of ANKLE1 protein

We used the cBioPortal MutationMapper online program to visualize the ANKLE1 protective variant rs2363956 in the context of the protein domain structure^55,56. For 3D modeling of the wild type and rs2363956 missense variant, the ANKLE1 amino acid sequence in FASTA format was obtained from NCBI using the GrCh37.p13 reference and was submitted to I-TASSER^57–59. The amino acid sequence is 615 residues long, and we performed 3D modeling to obtain the structure with and without the ANKLE1 missense mutation included in our candidate variant analysis (rs2363956, L184W). The estimate of the accuracy of the predictions using I-TASSER is provided based on the confidence score (C-score) of the modeling. The C-score range is between [-5, 2], where a C-score of a higher value suggests a model with higher confidence and vice-versa. Furthermore, Chimera program⁶⁰ (version 1.14) was used for visualization and analysis of the predicted 3D ANKLE1 protein structure from I-TASSER.

ANKLE1 Survival Analysis

The UALCAN online database was accessed to determine potential associations between gene expression and patient survival outcomes in the TCGA BC cohort³⁶. ANKLE1 gene expression was assessed across the patient cohort, and the upper quartile of expression was used to dichotomize expression into high and low/medium ANKLE1 expressing individuals. The log rank p value obtained between comparison groups is reported on the plots.

ACKNOWLEDGEMENTS

Funding- R21 5R21CA210237-03 NIH/NCI (to MD), Susan G Komen (to LN), Fashion Footwear Association of New York Shoes on Sale (to LN), U54-MD007585-26 NIH/NIMHD (to CY) and U54 CA118623 (NIH/NCI) (to CY).

AUTHOR CONTRIBUTIONS

YC, LN and MD designed the study. RM, YC, BJ, IE, JH, RZ, CY, RK and MD were involved in the methodology. RM, YC and MD analyzed and interpreted the data. RM, LN and MD wrote and edited the manuscript. EC, SH, PG, JO, EA, AJ, DC, JB, BA, MB, EA, IK, FA, MA, KA, EO, SN, LJ, EJ, LP, EP, PN, KG are all affiliated with the International Center for the Study of Breast Cancer Subtypes (ICSBCS) Consortium. ICSBCS consortium authors contributed targeted enrollment, biospecimen and data collection, and review of the manuscript. All authors have read and approved the final submitted manuscript.

COMPETING INTERESTS STATEMENT

The authors declare no conflicts of interest.

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Table 1

Population Frequencies of Candidate Alleles for BC and TNBC-specific risk analyses
					ICSBCS Cohort*				1000 Genomes**
SNP	Associated/Neighboring Gene	Chr:Position	Variant Consequence	Minor Allele	AA MAF	EA MAF	G MAF	E MAF	Global MAF	AFR MAF	EUR MAF
rs13000023	TNP1, DIRC3	2:217924394	Intron	A	0.219	0.268	0.244	0.155	0.150	0.130	0.210
rs2363956	ANKLE1	19:17394124	Missense	G	0.482	0.510	0.490	0.683	0.460	0.500	0.570
rs2981578	FGFR2	10:123340311	Intron	T	0.271	0.516	0.364	0.250	0.370	0.080	0.480
rs2981579	FGFR2	10:123337335	Intron	G	0.398	0.551	0.449	0.440	0.510	0.340	0.550
rs3112572	CASC16, LOC643714	16:52600447	Intron	A	0.216	0.011	0.246	0.207	0.120	0.270	0.030
rs3745185	BABAM1	19:17384267	Intron	A	0.191	0.400	0.261	0.369	0.310	0.210	0.480
rs4245739	MDM4	1:204518842	3’ UTR	C	0.271	0.321	0.252	0.145	0.210	0.230	0.260
rs4849887	LOC84934, GLI2	2:121245122	Intergenic	C	0.349	0.495	0.329	0.440	0.790	0.700	0.900
rs609275	MYEOV, CCND1	11:69402915	Regulatory	T	0.491	0.037	0.552	0.085	0.210	0.490	0.000
rs6676002	DARC/ACKR1	1:159173144	Upstream	T	0.027	0.212	0.000	0.195	0.090	0.010	0.180
rs3027008	DARC/ACKR1	1:159173539	Upstream	T	0.027	0.212	0.012	0.195	0.090	0.010	0.180
rs3027013	DARC/ACKR1	1:159174209	5’ UTR	T	0.022	0.087	0.000	0.110	0.030	0.000	0.080
rs71782098	DARC/ACKR1	1:159174347	5’ UTR	DEL	0.080	0.021	0.103	0.060	0.030	0.100	0.000
rs2814778	DARC/ACKR1	1:159174683	5’ UTR	C	0.797	0.005	0.971	0.533	0.270	0.960	0.010
rs17838198	DARC/ACKR1	1:159175005	Intron	T	0.084	0.263	0.005	0.131	0.220	0.010	0.230
rs3027016	DARC/ACKR1	1:159175193	Splice/Intron	G	0.045	0.163	0.000	0.037	0.060	0.000	0.160
rs12075	DARC/ACKR1	1:159175354	Missense	G	0.128	0.398	0.012	0.207	0.460	0.020	0.400
African Americans (AA), European Americans (EA), Ghanaians (G), Ethiopians (E) MAF = Minor allele frequency **1000 Genomes Allele frequencies obtained from ensembl

Table 2

Breast cancer risk assessment (case-control) of previously identified variant alleles
			Overall BC risk (all samples)						SIR African Americans			SIR Ghanaians
			Models without covariates			Models with covariates*			Models with covariates**			Models with covariates**
SNV ID	Associated/ Neighboring Genes	Minor Allele	N	OR (95% CI)	P value	N	OR (95% CI)	P value	N	OR (95% CI)	P value	N	OR (95% CI)	P value
rs13000023	TNP1, DIRC3	A	420	1.048 (0.756, 1.449)	0.775	271	1.061 (0.601, 1.874)	0.838	104	-	-	75	0.909 (0.466, 1.770)	0.780
rs2363956	ANKLE1	G	415	0.847 (0.629, 1.140)	0.273	274	1.272 (0.718, 2.254)	0.409	103	0.916 (0.135, 6.197)	0.928	76	1.409 (0.688, 2.890)	0.349
rs2981578	FGFR2	T	416	1.508 (1.111, 2.047)	0.008	267	1.036 (0.611, 1.759)	0.895	99	-	-	78	0.891 (0.481, 1.650)	0.713
rs2981579	FGFR2	G	418	1.246 (0.928, 1.675)	0.144	269	1.899 (1.063, 3.393)	0.030	99	-	-	77	1.792 (0.905, 3.545)	0.095
rs3112572	CASC16, LOC643714	A	385	1.007 (0.691, 1.467)	0.972	246	2.410(1.086, 5.347)	0.031	96	-	-	65	2.088 (0.948, 4.597)	0.068
rs3745185	BABAM1	A	409	0.666 (0.492, 0.901)	0.008	265	0.618 (0.341, 1.119)	0.112	99	0.787 (0.104, 5.947)	0.816	77	0.590 (0.272, 1.280)	0.182
rs4245739	MDM4	C	409	1.193 (0.860, 1.654)	0.291	264	0.995 (0.569, 1.740)	0.986	97	0.008 (0.000, 20.16)	0.228	75	0.838 (0.427, 1.644)	0.607
rs4849887	LOC84934, GLI2	C	403	1.654 (1.154, 2.371)	0.006	257	0.790 (0.351, 1.776)	0.568	100	0.399 (0.013, 12.43)	0.601	69	0.754 (0.274, 2.073)	0.584
rs609275	MYEOV, CCND1	T	396	1.129 (0.822, 1.552)	0.453	253	1.121 (0.532, 2.361)	0.764	98	0.224 (0.014, 3.646)	0.293	67	0.920 (0.389, 2.176)	0.849
rs6676002	DARC/ACKR1	T	282	1.290 (0.702, 2.368)	0.412	231	0.634 (0.164, 2.454)	0.509	96	-	-	47	-	-
rs3027008	DARC/ACKR1	T	282	1.187 (0.661, 2.131)	0.566	231	0.737 (0.230, 2.369)	0.609	96	-	-	49	2.270 (0.277, 18.60)	0.445
rs3027013	DARC/ACKR1	T	283	0.869 (0.372, 2.033)	0.747	231	0.250 (0.050, 1.241)	0.090	96	-	-	49	-	-
rs71782098	DARC/ACKR1	DEL	291	0.575 (0.307, 1.077)	0.084	238	0.753 (0.280, 2.028)	0.575	96	-	-	52	0.882 (0.298, 2.608)	0.820
rs2814778	DARC/ACKR1	C	712	1.512 (1.263, 1.809)	< 0.001	492	0.772 (0.392, 1.520)	0.454	153	0.696 (0.330, 1.467)	0.340	54	3.657 (0.231, 57.81)	0.357
rs17838198	DARC/ACKR1	T	299	4.798 (2.125, 10.83)	< 0.001	244	3.413 (0.678, 17.20)	0.137	97	1.052 (0.044, 25.41)	0.975	58	-	-
rs3027016	DARC/ACKR1	G	281	4.586 (1.587, 13.26)	0.005	229	2.311 (0.269, 19.88)	0.446	96	-	-	47	-	-
rs12075	DARC/ACKR1	G	292	2.534 (1.498, 4.287)	< 0.001	238	1.131 (0.382, 3.351)	0.824	97	1.108 (0.048, 25.80)	0.949	53	-	-
*Overall analysis models with covariates adjusts for age and SIR
**SIR models with covariates adjusts for age

Table 3

TNBC-specific risk assessment (case-series) of previously identified variant alleles
			Overall BC risk (all samples)						SIR African Americans			SIR Ghanaians
			Models without covariates			Models with covariates*			Models with covariates**			Models with covariates***
SNV ID	Associated/ Neighboring Genes	Minor Allele	N	OR (95% CI)	P value	N	OR (95% CI)	P value	N	OR (95% CI)	P value	N	OR (95% CI)	P value
rs13000023	TNP1, DIRC3	A	197	0.682 (0.410, 1.133)	0.139	190	0.781 (0.439, 1.387)	0.399	96	1.109 (0.538, 2.286)	0.780	6	-	-
rs2363956	ANKLE1	G	201	0.593 (0.389, 0.903)	0.015	194	0.542 (0.332, 0.883)	0.014	95	0.420 (0.230, 0.769)	0.005	8	1.471 (0.057, 38.26)	0.816
rs2981578	FGFR2	T	190	0.667 (0.435, 1.022)	0.063	183	1.248 (0.718, 2.169)	0.432	92	1.304 (0.656, 2.590)	0.449	6	17.55 (0.010, 29760)	0.450
rs2981579	FGFR2	G	193	0.790 (0.515, 1.212)	0.280	186	0.978 (0.599, 1.597)	0.930	92	0.942 (0.530, 1.672)	0.838	6	6.261E-08 (0, -)	0.993
rs3112572	CASC16, LOC643714	A	181	1.546 (0.880, 2.716)	0.130	174	0.748 (0.394, 1.421)	0.375	89	0.714 (0.367, 1.390)	0.322	5	6.976E-49 (0, -)	0.976
rs3745185	BABAM1	A	189	0.503 (0.306, 0.843)	0.009	182	0.682 (0.386, 1.203)	0.180	92	0.584 (0.288, 1.182)	0.135	6	3.304 (0.090, 120.90)	0.515
rs4245739	MDM4	C	190	0.906 (0.571, 1.438)	0.675	183	1.130 (0.658, 1.941)	0.657	90	0.861 (0.440, 1.685)	0.663	6	0.356 (0.004, 34.530)	0.658
rs4849887	LOC84934, GLI2	C	189	0.414 (0.232, 0.738)	0.003	182	0.666 (0.338, 1.313)	0.240	93	0.542 (0.241, 1.221)	0.140	6	0.676 (0.0470, 9.710)	0.773
rs609275	MYEOV, CCND1	T	187	2.479 (1.593, 3.857)	< 0.001	180	1.245 (0.717, 2.163)	0.437	91	1.121 (0.610, 2.061)	0.714	6	14.23 (0.0261, 7750)	0.409
rs6676002	DARC/ACKR1	T	176	0.191 (0.058, 0.635)	0.007	175	0.403 (0.111, 1.460)	0.167	90	-	-	2	-	-
rs3027008	DARC/ACKR1	T	174	0.134 (0.032, 0.568)	0.006	173	0.275 (0.060, 1.261)	0.097	90	-	-	2	-	-
rs3027013	DARC/ACKR1	T	174	-	-	173	-	-	90	-	-	2	-	-
rs71782098	DARC/ACKR1	DEL	178	3.403 (1.231, 9.412)	0.018	177	2.629 (0.796, 8.682)	0.112	90	2.547 (0.668, 9.716)	0.171	2	-	-
rs2814778	DARC/ACKR1	C	339	3.062 (2.249, 4.168)	0.000	304	3.814 (1.710, 8.493)	0.001	95	3.368 (1.390, 8.165)	0.007	16	-	-
rs17838198	DARC/ACKR1	T	178	0.367 (0.164, 0.821)	0.015	177	0.929 (0.355, 2.430)	0.881	91	0.722 (0.190, 2.754)	0.634	2	-	-
rs3027016	DARC/ACKR1	G	174	0.390 (0.144, 1.058)	0.065	173	0.839 (0.270, 2.609)	0.762	90	1.204 (0.226, 6.422)	0.828	2	-	-
rs12075	DARC/ACKR1	G	177	0.380 (0.199, 0.726)	0.003	176	0.846 (0.396, 1.807)	0.666	91	0.922 (0.319, 2.669)	0.881	2	-	-
*Overall analysis models with covariates adjusts for age and SIR
**SIR AA models with covariates adjusts for age and West African ancestry
***SIR Ghanaian models with covariates adjusts for age

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Investigation of Triple-Negative Breast Cancer Risk Alleles in An International African-Enriched Cohort

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Abstract

Figures

Introduction

Results

All-inclusive analysis of AA-specific BC risk alleles suggests race group specific effects

DARC/ACKR1 alleles in BC and TNBC risk

Functional consequences of the TNBC-protective rs2362956 variant in ANKLE1

Discussion

Methods

International Center for the Study of Breast Cancer Subtypes

Immunohistochemistry for BC tumor subtyping

Allele selection for BC case-control and TNBC case-series analyses

Global Ancestry estimation and genotyping of candidate alleles

Risk assessment

3D Modeling of ANKLE1 protein

ANKLE1 Survival Analysis

Declarations

References

Tables

Supplementary Files

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