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Distinct Transcript Isoforms of the Atypical Chemokine Receptor 1 (ACKR1)/Duffy Antigen Receptor for Chemokines (DARC) Gene Are Expressed in Lymphoblasts and Altered Isoform Levels Are Associated with Genetic Ancestry and the Duffy-Null Allele.

Davis MB, Walens A, Hire R, Mumin K, Brown AM, Ford D, Howerth EW, Monteil M - PLoS ONE (2015)

Bottom Line: Additional alleles are associated with a myriad of clinical outcomes related to immune responses and inflammation.We conclude that the expression of both isoforms in combination with alternate alleles yields multiple Duffy antigens in ancestry groups, depending upon the haplotypes across the gene.Ultimately, this work will increase knowledge of biological mechanisms underlying disparate clinical outcomes of inflammatory-related diseases among ethnic and geographic ancestry groups.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, United States of America; Department of Molecular Biology and Biochemistry, Georgia Regents University-University of Georgia Medical Partnership, Athens, GA, United States of America.

ABSTRACT
The Atypical ChemoKine Receptor 1 (ACKR1) gene, better known as Duffy Antigen Receptor for Chemokines (DARC or Duffy), is responsible for the Duffy Blood Group and plays a major role in regulating the circulating homeostatic levels of pro-inflammatory chemokines. Previous studies have shown that one common variant, the Duffy Null (Fy-) allele that is specific to African Ancestry groups, completely removes expression of the gene on erythrocytes; however, these individuals retain endothelial expression. Additional alleles are associated with a myriad of clinical outcomes related to immune responses and inflammation. In addition to allele variants, there are two distinct transcript isoforms of DARC which are expressed from separate promoters, and very little is known about the distinct transcriptional regulation or the distinct functionality of these protein isoforms. Our objective was to determine if the African specific Fy- allele alters the expression pattern of DARC isoforms and therefore could potentially result in a unique signature of the gene products, commonly referred to as antigens. Our work is the first to establish that there is expression of DARC on lymphoblasts. Our data indicates that people of African ancestry have distinct relative levels of DARC isoforms expressed in these cells. We conclude that the expression of both isoforms in combination with alternate alleles yields multiple Duffy antigens in ancestry groups, depending upon the haplotypes across the gene. Importantly, we hypothesize that DARC isoform expression patterns will translate into ancestry-specific inflammatory responses that are correlated with the axis of pro-inflammatory chemokine levels and distinct isoform-specific interactions with these chemokines. Ultimately, this work will increase knowledge of biological mechanisms underlying disparate clinical outcomes of inflammatory-related diseases among ethnic and geographic ancestry groups.

No MeSH data available.


Related in: MedlinePlus

The DARC gene structure and frequencies of the two major alleles; Fy- and Fya/b in HAPMAP experimental cohort compared to entire 1000 Genomes (1K) populations.(A). Top, Model of DARC/ACKR1 gene structure indicating the two gene promoter-driven isoforms, DARC1/A and DARC2/B. Primers used for qPCR of transcript variants are indicated as double arrows. Also indicated are the Duffy Null allele (rs2814778) and Fya/b allele (rs12075). The two transcript products result in unique gene products; Duffy isoform A has 338aa and Duffy isoform B has 336aa. Top graph shows the allele frequencies of all documented polymorphisms in the DARC gene region, specifically in the ethnic cohorts of interest; African American (ASW), West African- Yoruba in Ibadan (YRI) and European American (CEPH). The overall ‘world’ variant frequencies are also indicated, summarizing all sampled populations in the 1000 Genomes. The bottom graph details the individual ancestry groups that encompass the global frequencies across the entire 1000 Genomes dataset for the entire DARC gene region. The X-axis matches the gene model with regard to relative gene structure location. The rs# IDs on the X axis of the bottom graph correspond to those on the top graph, for each SNP. The starred locus indicates a deletion polymorphism that resides in the promoter region of the DARC1/A isoform that has not previously been explicitly reported, described in the text (rs17838198). This locus appears to have been under some selection influence in other populations, similar to the as the malaria selection influence on the Duffy Null allele in African populations, as it is the 3rd most prominent variant in the gene and prevalent in most populations. (B). The genotype frequencies for the Fy- and Fya/b loci in our cohort are shown in the inset panel on the left. The allele frequencies of Fy- and Fya/b for the entire corresponding ancestry 1K Genomes panels are shown in the inset panel on the right. The genotype percent distributions of the Fy- genotype across our West African—YRI, African American and European American subpopulations correlate with the high prevalence of the alleles in 1,000 Genome populations. Nearly half of the AA/ASW group is heterozygotes with an additional 40% being CC homozygotes, indicating more than 90% have the Fy- allele, as seen in the adjacent graph. The allele distribution table shows proportion values correlate with previously established numbers and validate our population.
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pone.0140098.g001: The DARC gene structure and frequencies of the two major alleles; Fy- and Fya/b in HAPMAP experimental cohort compared to entire 1000 Genomes (1K) populations.(A). Top, Model of DARC/ACKR1 gene structure indicating the two gene promoter-driven isoforms, DARC1/A and DARC2/B. Primers used for qPCR of transcript variants are indicated as double arrows. Also indicated are the Duffy Null allele (rs2814778) and Fya/b allele (rs12075). The two transcript products result in unique gene products; Duffy isoform A has 338aa and Duffy isoform B has 336aa. Top graph shows the allele frequencies of all documented polymorphisms in the DARC gene region, specifically in the ethnic cohorts of interest; African American (ASW), West African- Yoruba in Ibadan (YRI) and European American (CEPH). The overall ‘world’ variant frequencies are also indicated, summarizing all sampled populations in the 1000 Genomes. The bottom graph details the individual ancestry groups that encompass the global frequencies across the entire 1000 Genomes dataset for the entire DARC gene region. The X-axis matches the gene model with regard to relative gene structure location. The rs# IDs on the X axis of the bottom graph correspond to those on the top graph, for each SNP. The starred locus indicates a deletion polymorphism that resides in the promoter region of the DARC1/A isoform that has not previously been explicitly reported, described in the text (rs17838198). This locus appears to have been under some selection influence in other populations, similar to the as the malaria selection influence on the Duffy Null allele in African populations, as it is the 3rd most prominent variant in the gene and prevalent in most populations. (B). The genotype frequencies for the Fy- and Fya/b loci in our cohort are shown in the inset panel on the left. The allele frequencies of Fy- and Fya/b for the entire corresponding ancestry 1K Genomes panels are shown in the inset panel on the right. The genotype percent distributions of the Fy- genotype across our West African—YRI, African American and European American subpopulations correlate with the high prevalence of the alleles in 1,000 Genome populations. Nearly half of the AA/ASW group is heterozygotes with an additional 40% being CC homozygotes, indicating more than 90% have the Fy- allele, as seen in the adjacent graph. The allele distribution table shows proportion values correlate with previously established numbers and validate our population.

Mentions: The DARC/ACKR1 gene products are traditionally referred to as “Duffy blood group antigens” and vary in their expression among different human populations in several ways. There are several antigens described in various clinical reports which presumably represent variants of the gene product [15]. However, the most commonly described variants are those derived from the two major DARCalleles resulting from common Single Nucleotide Polymorphisms (SNPs). One SNP occurs in the gene regulatory region and yields the “Fy- allele” or “Duffy Null” (rs2814778), and the other SNP is a missense mutation that yields the “Fy B” and “Fy A” alleles (rs12075). The Duffy Null allele nomenclature refers to a phenotype also known as “Erythrocyte Silent” (Fyes) removing expression of DARC on red blood cells (RBCs) and is usually denoted as “Fy-a-b” to reflect the missing blood group antigens. This allele is rare among individuals of either European or Asian descent but is the most common phenotype in most Africans and African Americans. The Fy- allele has a frequency of nearly 100% in West Africans and greater than 80% of African Americans (Fig 1) [16, 17] as it confers resistance to malaria [18] and became fixed in African populations where malaria is endemic[4, 17]. In addition to these DARC variants, there are 4 other alternate Duffy blood group antigens, usually interpreted as DARC gene allele variants, namely; Fy3, Fy4, Fy5 and Fy6. However, the specific immunogenic domain that defines most of these antigens is not fully elucidated [15, 19]. Of note, one additional important yet rare phenotype, Fyx, expresses the Fyb allele, but is believed to have ‘weak’ expression that is not always detected by the anti-Fyb antibody [6, 20], suggesting the epitope is unique and possibly a yet undescribed additional Duffy antigen. One potential explanation for such complexity among Fy antigens could be the co-expression of alternative DARC gene product isoforms and distinct post-translational modifications (i.e. glycosylation) between the isoforms acting as immunogens. This possibility has not yet been addressed.


Distinct Transcript Isoforms of the Atypical Chemokine Receptor 1 (ACKR1)/Duffy Antigen Receptor for Chemokines (DARC) Gene Are Expressed in Lymphoblasts and Altered Isoform Levels Are Associated with Genetic Ancestry and the Duffy-Null Allele.

Davis MB, Walens A, Hire R, Mumin K, Brown AM, Ford D, Howerth EW, Monteil M - PLoS ONE (2015)

The DARC gene structure and frequencies of the two major alleles; Fy- and Fya/b in HAPMAP experimental cohort compared to entire 1000 Genomes (1K) populations.(A). Top, Model of DARC/ACKR1 gene structure indicating the two gene promoter-driven isoforms, DARC1/A and DARC2/B. Primers used for qPCR of transcript variants are indicated as double arrows. Also indicated are the Duffy Null allele (rs2814778) and Fya/b allele (rs12075). The two transcript products result in unique gene products; Duffy isoform A has 338aa and Duffy isoform B has 336aa. Top graph shows the allele frequencies of all documented polymorphisms in the DARC gene region, specifically in the ethnic cohorts of interest; African American (ASW), West African- Yoruba in Ibadan (YRI) and European American (CEPH). The overall ‘world’ variant frequencies are also indicated, summarizing all sampled populations in the 1000 Genomes. The bottom graph details the individual ancestry groups that encompass the global frequencies across the entire 1000 Genomes dataset for the entire DARC gene region. The X-axis matches the gene model with regard to relative gene structure location. The rs# IDs on the X axis of the bottom graph correspond to those on the top graph, for each SNP. The starred locus indicates a deletion polymorphism that resides in the promoter region of the DARC1/A isoform that has not previously been explicitly reported, described in the text (rs17838198). This locus appears to have been under some selection influence in other populations, similar to the as the malaria selection influence on the Duffy Null allele in African populations, as it is the 3rd most prominent variant in the gene and prevalent in most populations. (B). The genotype frequencies for the Fy- and Fya/b loci in our cohort are shown in the inset panel on the left. The allele frequencies of Fy- and Fya/b for the entire corresponding ancestry 1K Genomes panels are shown in the inset panel on the right. The genotype percent distributions of the Fy- genotype across our West African—YRI, African American and European American subpopulations correlate with the high prevalence of the alleles in 1,000 Genome populations. Nearly half of the AA/ASW group is heterozygotes with an additional 40% being CC homozygotes, indicating more than 90% have the Fy- allele, as seen in the adjacent graph. The allele distribution table shows proportion values correlate with previously established numbers and validate our population.
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4608815&req=5

pone.0140098.g001: The DARC gene structure and frequencies of the two major alleles; Fy- and Fya/b in HAPMAP experimental cohort compared to entire 1000 Genomes (1K) populations.(A). Top, Model of DARC/ACKR1 gene structure indicating the two gene promoter-driven isoforms, DARC1/A and DARC2/B. Primers used for qPCR of transcript variants are indicated as double arrows. Also indicated are the Duffy Null allele (rs2814778) and Fya/b allele (rs12075). The two transcript products result in unique gene products; Duffy isoform A has 338aa and Duffy isoform B has 336aa. Top graph shows the allele frequencies of all documented polymorphisms in the DARC gene region, specifically in the ethnic cohorts of interest; African American (ASW), West African- Yoruba in Ibadan (YRI) and European American (CEPH). The overall ‘world’ variant frequencies are also indicated, summarizing all sampled populations in the 1000 Genomes. The bottom graph details the individual ancestry groups that encompass the global frequencies across the entire 1000 Genomes dataset for the entire DARC gene region. The X-axis matches the gene model with regard to relative gene structure location. The rs# IDs on the X axis of the bottom graph correspond to those on the top graph, for each SNP. The starred locus indicates a deletion polymorphism that resides in the promoter region of the DARC1/A isoform that has not previously been explicitly reported, described in the text (rs17838198). This locus appears to have been under some selection influence in other populations, similar to the as the malaria selection influence on the Duffy Null allele in African populations, as it is the 3rd most prominent variant in the gene and prevalent in most populations. (B). The genotype frequencies for the Fy- and Fya/b loci in our cohort are shown in the inset panel on the left. The allele frequencies of Fy- and Fya/b for the entire corresponding ancestry 1K Genomes panels are shown in the inset panel on the right. The genotype percent distributions of the Fy- genotype across our West African—YRI, African American and European American subpopulations correlate with the high prevalence of the alleles in 1,000 Genome populations. Nearly half of the AA/ASW group is heterozygotes with an additional 40% being CC homozygotes, indicating more than 90% have the Fy- allele, as seen in the adjacent graph. The allele distribution table shows proportion values correlate with previously established numbers and validate our population.
Mentions: The DARC/ACKR1 gene products are traditionally referred to as “Duffy blood group antigens” and vary in their expression among different human populations in several ways. There are several antigens described in various clinical reports which presumably represent variants of the gene product [15]. However, the most commonly described variants are those derived from the two major DARCalleles resulting from common Single Nucleotide Polymorphisms (SNPs). One SNP occurs in the gene regulatory region and yields the “Fy- allele” or “Duffy Null” (rs2814778), and the other SNP is a missense mutation that yields the “Fy B” and “Fy A” alleles (rs12075). The Duffy Null allele nomenclature refers to a phenotype also known as “Erythrocyte Silent” (Fyes) removing expression of DARC on red blood cells (RBCs) and is usually denoted as “Fy-a-b” to reflect the missing blood group antigens. This allele is rare among individuals of either European or Asian descent but is the most common phenotype in most Africans and African Americans. The Fy- allele has a frequency of nearly 100% in West Africans and greater than 80% of African Americans (Fig 1) [16, 17] as it confers resistance to malaria [18] and became fixed in African populations where malaria is endemic[4, 17]. In addition to these DARC variants, there are 4 other alternate Duffy blood group antigens, usually interpreted as DARC gene allele variants, namely; Fy3, Fy4, Fy5 and Fy6. However, the specific immunogenic domain that defines most of these antigens is not fully elucidated [15, 19]. Of note, one additional important yet rare phenotype, Fyx, expresses the Fyb allele, but is believed to have ‘weak’ expression that is not always detected by the anti-Fyb antibody [6, 20], suggesting the epitope is unique and possibly a yet undescribed additional Duffy antigen. One potential explanation for such complexity among Fy antigens could be the co-expression of alternative DARC gene product isoforms and distinct post-translational modifications (i.e. glycosylation) between the isoforms acting as immunogens. This possibility has not yet been addressed.

Bottom Line: Additional alleles are associated with a myriad of clinical outcomes related to immune responses and inflammation.We conclude that the expression of both isoforms in combination with alternate alleles yields multiple Duffy antigens in ancestry groups, depending upon the haplotypes across the gene.Ultimately, this work will increase knowledge of biological mechanisms underlying disparate clinical outcomes of inflammatory-related diseases among ethnic and geographic ancestry groups.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, United States of America; Department of Molecular Biology and Biochemistry, Georgia Regents University-University of Georgia Medical Partnership, Athens, GA, United States of America.

ABSTRACT
The Atypical ChemoKine Receptor 1 (ACKR1) gene, better known as Duffy Antigen Receptor for Chemokines (DARC or Duffy), is responsible for the Duffy Blood Group and plays a major role in regulating the circulating homeostatic levels of pro-inflammatory chemokines. Previous studies have shown that one common variant, the Duffy Null (Fy-) allele that is specific to African Ancestry groups, completely removes expression of the gene on erythrocytes; however, these individuals retain endothelial expression. Additional alleles are associated with a myriad of clinical outcomes related to immune responses and inflammation. In addition to allele variants, there are two distinct transcript isoforms of DARC which are expressed from separate promoters, and very little is known about the distinct transcriptional regulation or the distinct functionality of these protein isoforms. Our objective was to determine if the African specific Fy- allele alters the expression pattern of DARC isoforms and therefore could potentially result in a unique signature of the gene products, commonly referred to as antigens. Our work is the first to establish that there is expression of DARC on lymphoblasts. Our data indicates that people of African ancestry have distinct relative levels of DARC isoforms expressed in these cells. We conclude that the expression of both isoforms in combination with alternate alleles yields multiple Duffy antigens in ancestry groups, depending upon the haplotypes across the gene. Importantly, we hypothesize that DARC isoform expression patterns will translate into ancestry-specific inflammatory responses that are correlated with the axis of pro-inflammatory chemokine levels and distinct isoform-specific interactions with these chemokines. Ultimately, this work will increase knowledge of biological mechanisms underlying disparate clinical outcomes of inflammatory-related diseases among ethnic and geographic ancestry groups.

No MeSH data available.


Related in: MedlinePlus