Novel alleles at the JK blood group locus explain the absence of the erythrocyte urea transporter in European families

Resolving Genotype-Phenotype Discrepancies of the Kidd Blood Group System Using Long-Read Nanopore Sequencing

Due to substantial improvements in read accuracy, third-generation long-read sequencing holds great potential in blood group diagnostics, particularly in cases where traditional genotyping or sequencing techniques, primarily targeting exons, fail to explain serological phenotypes. In this study, we employed Oxford Nanopore sequencing to resolve all genotype-phenotype discrepancies in the Kidd blood group system (JK, encoded by SLC14A1) observed over seven years of routine high-throughput donor genotyping using a mass spectrometry-based platform at the Blood Transfusion Service, Zurich. Discrepant results from standard serological typing and donor genotyping were confirmed using commercial PCR-SSP kits. To resolve discrepancies, we amplified the entire coding region of SLC14A1 (~24 kb, exons 3 to 10) in two overlapping long-range PCRs in all samples. Amplicons were barcoded and sequenced on a MinION flow cell. Sanger sequencing and bridge-PCRs were used to confirm findings. Among 11,972 donors with both serological and genotype data available for the Kidd system, we identified 10 cases with unexplained conflicting results. Five were linked to known weak and null alleles caused by variants not included in the routine donor genotyping. In two cases, we identified novel null alleles on the JK*01 (Gly40Asp; c.119G>A) and JK*02 (Gly242Glu; c.725G>A) haplotypes, respectively. Remarkably, the remaining three cases were associated with a yet unknown deletion of ~5 kb spanning exons 9-10 of the JK*01 allele, which other molecular methods had failed to detect. Overall, nanopore sequencing demonstrated reliable and accurate performance for detecting both single-nucleotide and structural variants. It possesses the potential to become a robust tool in the molecular diagnostic portfolio, particularly for addressing challenging structural variants such as hybrid genes, deletions and duplications.

Jknull alleles in two patients with anti-Jk3

BACKGROUND

As of publication, a total of 41 null alleles have been acknowledged by the International Society of Blood Transfusion (ISBT) to cause the rare Jknull phenotype, but none have been discovered in Austria thus far.

MATERIALS AND METHODS

Two patients with anti-Jk3 were serologically identified by a positive antibody screening and typed as Jk(a-b-). The initial genotyping using an SSP-PCR method for the common 838A/G polymorphism indicated a JK*02/02, or JK*01/02 genotype, respectively. To find the disruptive mutations, Sanger sequencing was performed and results were compared to the reference sequence. The patient's antibodies were characterized with a monocyte monolayer assay (MMA) for their potential clinical significance.

RESULTS

Three novel null-mutations of the SLC14A1 gene were found in two patients. Patient 1 was homozygous for a 10bp deletion in exon 4 (c.157_166del on JK*02). Testing of her family members revealed Mendelian inheritance of the deletional allele. The other patient was compound heterozygous for two mutations: one allele carrying a single base deletion in exon 4 (c.267delC on JK*01) and the other a splice site mutation in intron 3 (c.152-1g>a on JK*02). The MMA results suggest high clinical significance of the anti-Jk3 in both patients.

DISCUSSION

The detected mutations led to Jknull phenotypes and are the first description of JKnull alleles in the Austrian population.

DNA sequence analysis and Jk blood group genotype-phenotype assessment

Background

The Kidd (JK) blood group is critical for clinical blood transfusion. Various methods for Jk typing have been commonly used, including urea hemolysis, serological test, and genotyping. However, the application of molecular methods has so far been restricted to selected samples and not been applied to the population-scale analysis.

Methods

One hundred eighty-three blood samples, containing 174 samples collected from voluntary blood donors of Chinese Han individuals, together with 3 Jk (aw+b-) and 6 Jk (a-b-) samples, were investigated by standard serology urea hemolysis test and Sanger-sequencing. Complete coverage of exons 4-11 and intron-exon borders have been sequenced.

Results

We report the frequencies of three SNPs in exon 4, 7, and intron 9. Besides, sequence analysis revealed the simultaneous DNA variants of intron 7 (-68) and exon 9 (838) found in all samples, suggesting the co-inheritance of these SNPs-taking the observed SNPs frequencies into account. Further, we discuss the potential of the sequencing technique for high-resolution genotyping.

Conclusions

The described sequencing method for Jk exons delivers a genotyping technique for Jk molecular characterization. According to the co-inheritance of these DNA variants in intron 7 (-68) and exon 9 (838), and their regularity linkage with Jk phenotypes, these two sites offer a potential sequencing target for rapid and far more simplified Jk typing that can supplement routine serology and urea hemolysis tests.

Emerging strategies of blood group genotyping for patients with hemoglobinopathies

Red cell alloimmunization is a serious problem in chronically transfused patients. A number of high-throughput DNA assays have been developed to extend or replace traditional serologic antigen typing. DNA-based typing methods may be easily automated and multiplexed, and provide reliable information on a patient. Molecular genotyping promises to become cheaper, being not dependent on serologic immunoglobulin reagents. Patients with hemoglobinopathies could benefit from receiving extended genomic typing. This could limit post transfusional complications depending on subtle antigenic differences between donors and patients. Patient/donor compatibility extended beyond the phenotype Rh/Kell may allows improved survival of transfused units of red blood cells (RBC) and lead to reduced need for blood transfusion and leading to less iron overload and reduced risk of alloimmunization. Here we discuss the advantages and limitations of current techniques, that detect only predefined genetic variants. In contrast, target enrichment next-generation sequencing (NGS) has been used to detect both known and de novo genetic polymorphisms, including single-nucleotide polymorphisms, indels (insertions/deletions), and structural variations. NGS approaches can be used to develop an extended blood group genotyping assay system.

The Kidd (JK) Blood Group System

The Kidd blood group system was discovered in 1951 and is composed of 2 antithetical antigens, Jk^a and Jk^b, along with a third high-incidence antigen, Jk3. The Jk3 antigen is expressed in all individuals except those with the rare Kidd-null phenotype. Four Kidd phenotypes are therefore possible: Jk(a+b-), Jk(a-b+), Jk(a+b+), and Jk(a-b-). The glycoprotein carrying the Kidd antigens is a 43-kDa, 389-amino acid protein with 10 membrane-spanning domains which functions as a urea transporter on endothelial cells of the renal vasa recta as well as erythrocytes. The HUT11/UT-B/JK (SLC14A1) gene encoding this glycoprotein is located on chromosome 18q12-q21. The Jk^a and Jk^b antigens are the result of a single-nucleotide polymorphism present at nucleotide 838 resulting in an aspartate or asparagine amino acid at position 280, respectively. The Kidd blood group can create several difficult transfusion situations. Besides the typical acute hemolytic transfusion reactions common to all clinically relevant blood group antigens, the Kidd antigens are notorious for causing delayed hemolytic transfusion reactions due to the strong anamnestic response exhibited by antibodies directed against Kidd antigens. The Kidd-null phenotype is extremely rare in most ethnic groups, but is clinically significant due to the ability of those with the Kidd-null phenotype to produce antibodies directed against the high-incidence Jk3 antigen. Anti-Jk3 antibodies behave in concordance with anti-Jk^a or anti-Jk^b possessing the capability to cause both acute and delayed hemolytic reactions. Antibodies against any of the 3 Kidd antigens can also be a cause of hemolytic disease of the fetus and newborn, although this is generally mild. In this review, we will outline the makeup of the Kidd system from its historical discovery to the details of the Kidd gene and glycoprotein, and then discuss the practical aspects of Kidd antibodies and transfusion reactions with an extended focus on the Kidd-null phenotype. We will end with a brief discussion of the donor aspects related to the screening and supply management of blood from donors with the rare Jk(a-b-) phenotype.

Molecular genetic analysis of the Jk(a-b-) phenotype in Chinese: A novel silent recessive JK allele

The Jk(a-b-) phenotype, referred to as Jknull, is rare in most populations. This blood type is characterized by the absence of Kidd glycoprotein on the surface of red blood cells (RBCs) and moderately reduced ability to concentrate urine. The molecular basis for Jknull phenotype includes splice-site mutations, missense mutations, and a partial gene deletion in the JK(SLC14A1) gene that encodes the human urea transporter protein. In this study, we have analyzed 10 Chinese Jknull samples to determine their molecular bases. In addition to the well known Polynesian Jknull allele, three Jknull alleles were detected including one novel Jknull allele: JKA (130A, 220G).

Genes and proteins of urea transporters

A urea transporter protein in the kidney was first proposed in 1987. The first urea transporter cDNA was cloned in 1993. The SLC14a urea transporter family contains two major subgroups: SLC14a1, the UT-B urea transporter originally isolated from erythrocytes; and SLC14a2, the UT-A group originally isolated from kidney inner medulla. Slc14a1, the human UT-B gene, arises from a single locus located on chromosome 18q12.1-q21.1, which is located close to Slc14a2. Slc14a1 includes 11 exons, with the coding region extending from exon 4 to exon 11, and is approximately 30 kb in length. The Slc14a2 gene is a very large gene with 24 exons, is approximately 300 kb in length, and encodes 6 different isoforms. Slc14a2 contains two promoter elements: promoter I is located in the typical position, upstream of exon 1, and drives the transcription of UT-A1, UT-A1b, UT-A3, UT-A3b, and UT-A4; while promoter II is located within intron 12 and drives the transcription of UT-A2 and UT-A2b. UT-A1 and UT-A3 are located in the inner medullary collecting duct, UT-A2 in the thin descending limb and liver, UT-A5 in testis, UT-A6 in colon, UT-B1 primarily in descending vasa recta and erythrocytes, and UT-B2 in rumen.

Clinical aspects of urea transporters

Jk antigens, which were identified as urea transporter B (UT-B) in the plasma membrane of erythrocytes, and which determine the Kidd blood type in humans, are involved in transfusion medicine, and even in organ transplantation. The Jk(a-b-) blood type is a consequence of a silent Slc14A1 gene caused by various mutations related to lineage. In addition, the specific mutations related to hypertension and metabolic syndrome cannot be ignored. Genome-wide association studies established Slc14A1 as a related gene of bladder cancer and some genotypes are associated with higher morbidity. This chapter aims to introduce the clinical significance of urea transporters.

Genomic characterisation of the Jk(a-b-) phenotype in Thai blood donors

BACKGROUND

The Kidd (JK) blood group antigens are encoded by the JK gene. The rare Jk(a-b-) phenotype can be caused by homozygosity for a silent JK allele. Currently, JK(null) alleles have been identified among different populations; however, information on its presence among Thais is not available.

MATERIALS AND METHODS

Screening for the Jk(a-b-) phenotype by the urea lysis test was performed in 25,340 blood samples from Thai blood donors. The Jk(a-b-) phenotypes were confirmed by an indirect antiglobulin test (IAT). Additionally, polymerase chain reaction amplification and sequence analysis of the JK gene were performed using previously described methods.

RESULTS

Five samples were confirmed as having a Jk(a-b-) phenotype by a urea lysis test and IAT; four of these samples were investigated. Two samples of JK*02 alleles were homozygous for a g>a mutation at the 3' acceptor splice site of intron 5 of the JK gene, as in previous studies in Asians and Polynesians. Moreover, one sample of JK*02 alleles was homozygous for an 896G>A mutation at exon 9 (Gly299Glu), as in a previous study in Polynesians. Interestingly, missense dual mutations of JK*01 alleles from a female blood donor were identified. The first mutation was 956C>T (Thr319Met) in exon 10, as in a recent study in African-Americans. The second mutation was 130G>A (Glu44Lys) at exon 4, as in previous studies among Caucasians.

CONCLUSION

There are various different molecular bases of the Jk(a-b-) phenotype. This is the first report of JK(null) alleles among Thais. The information presented in this study could be beneficial in planning genotyping strategies for blood donors and patients.

The emerging physiological roles of the SLC14A family of urea transporters

In mammals, urea is the main nitrogenous breakdown product of protein catabolism and is produced in the liver. In certain tissues, the movement of urea across cell membranes is specifically mediated by a group of proteins known as the SLC14A family of facilitative urea transporters. These proteins are derived from two distinct genes, UT-A (SLC14A2) and UT-B (SLC14A1). Facilitative urea transporters play an important role in two major physiological processes - urinary concentration and urea nitrogen salvaging. Although UT-A and UT-B transporters both have a similar basic structure and mediate the transport of urea in a facilitative manner, there are a number of significant differences between them. UT-A transporters are mainly found in the kidney, are highly specific for urea, have relatively lower transport rates and are highly regulated at both gene expression and cellular localization levels. In contrast, UT-B transporters are more widespread in their tissue location, transport both urea and water, have a relatively high transport rate, are inhibited by mercurial compounds and currently appear to be less acutely regulated. This review details the fundamental research that has so far been performed to investigate the function and physiological significance of these two types of urea transporters.

Urea transport in the kidney

Urea transport proteins were initially proposed to exist in the kidney in the late 1980s when studies of urea permeability revealed values in excess of those predicted by simple lipid-phase diffusion and paracellular transport. Less than a decade later, the first urea transporter was cloned. Currently, the SLC14A family of urea transporters contains two major subgroups: SLC14A1, the UT-B urea transporter originally isolated from erythrocytes; and SLC14A2, the UT-A group with six distinct isoforms described to date. In the kidney, UT-A1 and UT-A3 are found in the inner medullary collecting duct; UT-A2 is located in the thin descending limb, and UT-B is located primarily in the descending vasa recta; all are glycoproteins. These transporters are crucial to the kidney's ability to concentrate urine. UT-A1 and UT-A3 are acutely regulated by vasopressin. UT-A1 has also been shown to be regulated by hypertonicity, angiotensin II, and oxytocin. Acute regulation of these transporters is through phosphorylation. Both UT-A1 and UT-A3 rapidly accumulate in the plasma membrane in response to stimulation by vasopressin or hypertonicity. Long-term regulation involves altering protein abundance in response to changes in hydration status, low protein diets, adrenal steroids, sustained diuresis, or antidiuresis. Urea transporters have been studied using animal models of disease including diabetes mellitus, lithium intoxication, hypertension, and nephrotoxic drug responses. Exciting new animal models are being developed to study these transporters and search for active urea transporters. Here we introduce urea and describe the current knowledge of the urea transporter proteins, their regulation, and their role in the kidney.

High-resolution melting analysis for genotyping Duffy, Kidd and Diego blood group antigens

High-resolution melting (HRM) analysis is a simpler genotyping method than allele-specific PCR, PCR-restriction fragment length polymorphism and multiplex PCR. Duffy, Kidd and Diego are clinically important blood group antigens. We used a novel method to genotype these three blood group antigens. Purified genomic DNA extracts of blood samples (354 Duffy, 347 Kidd and 457 Diego) were amplified using specific amplification primers. HRM curves were obtained by HRM analysis. Results were in complete concordance with those obtained for previous phenotypes and genotypes. Nucleotide substitutions for these blood group antigens were differentiated by the HRM curves. HRM analysis is a simple genotyping method and is an alternative to serological typing. Our results suggest that HRM analysis can also be used for genotyping blood group antigens whose allotype specificity is determined by single nucleotide substitutions.

Identification of gene networks associated with erythroid differentiation

Erythropoiesis is a multistep process involving a large number of genes, which balance between proliferation, differentiation and survival of the erythroid cells. To understand the molecular mechanisms of erythropoiesis and related pathological aberrations, we analyzed three stages of in vitro differentiating human erythroid cells by expression profiling. We identified distinct clusters of genes, each with a unique expression pattern during differentiation. As JAK2 was shown to play a central role in myeloproliferative disorders, we focused on one cluster which includes JAK2 and other genes with high correlation to JAK2 expression. These genes had a low expression at the early erythroblast which increased in the intermediate stage and further slightly increased in the last stage of differentiation. Our results indicate that gene networks may associate with JAK2 expression in erythroid differentiation. It is intriguing to determine whether the pathogenesis of polycythemia vera (PV), harboring a common or uncommon JAK2 mutation, involves alterations in independent gene pathways that underlie the normal erythropoietic process.

Two novel Jk(null) alleles derived from 222C>A in Exon 5 and 896G>A in Exon 9 of the JK gene

BACKGROUND

Polynesian Jk(null) is well known for its mutation as Intron 5 g>a at the 3' splice acceptor site. After sequencing analysis, however, it was noticed that only three of eight samples with the Jknull phenotype carried typical homozygous Polynesian Jk(null) mutation. Five others were noted to be unreported heterozygous Polynesian Jk(null) mutation. An investigation was then conducted to characterize the underlying mechanism leading to this particular Jk(null) genotype.

STUDY DESIGN AND METHODS

Genomic DNA covering 5'-untranslated region exons and intervening introns of the JK gene was amplified by polymerase chain reaction, and the fragments were directly sequenced. The sequencing results were compared with those published in literature and related biologic Web sites.

RESULTS

In all five samples with a heterozygous Polynesian Jk(null) mutation, additional mutations were identified. Two samples carried missense mutations: 222C>A (Asn74Lys) in Exon 5 and 499A>G (Met167Val) in Exon 7. Three others had missense mutation 896G>A (Gly299Glu) in Exon 9. These substituted amino acids were located either near or at transmembrane domains, respectively. In addition, two polymorphic nucleotides at positions -103 (a>g) and -119(c>a) from the 3' end of Intron 1 were also Polynesian mutation-related.

CONCLUSIONS

In contrast to the typical homozygous Polynesian Jk(null) mutation, two novel heterozygous Jk(null) alleles were noted to be associated with the Jknull phenotype. One carried missense mutation 222C>A in Exon 5, and the other had 896G>A missense mutation in Exon 9. These findings may have implications in designing a molecular screening assay for people with the Jknull phenotype.

Erythroid urea transporter deficiency due to novel JKnull alleles

BACKGROUND

The Kidd blood group antigens Jka and Jkb are encoded by the red blood cell (RBC) urea transporter gene. Homozygosity for silent JK alleles results in the rare Jk(a-b-) phenotype. To date, seven JKnull alleles have been identified, and of these, two are more frequent in the Polynesians and Finns. This study reports the identification of other JKnull alleles in Jk(a-b-) individuals of different ethnic or geographic origins.

STUDY DESIGN AND METHODS

Nine Jk(a-b-) samples and a sample from a Jk(a-b+) mother of a Jk(a+b-) baby were investigated. Polymerase chain reaction amplification and sequence analysis of the JK gene was performed. Western blotting and urea lysis were used to confirm Jk(a-b-) RBCs.

RESULTS

Four novel alleles were identified: two different nonsense mutations, 202C>T (Gln68Stop) and 723delA (Ile262Stop) were identified on otherwise consensus JK*1 and JK*2 alleles, respectively. A missense mutation, 956C>T (Thr319Met), was identified in a JK*1 allele from an African-American and a JK*2 allele in two people of subcontinental Indian descent. Immunoblotting and urea lysis confirmed absence of JK glycoprotein in RBC membranes from a sample carrying the 956C>T mutation. Other previously described JKnull mutations were found in samples of origins other than in which they were first identified.

CONCLUSION

The molecular bases of the Jk(a-b-) phenotype are diverse and this is the first report of JKnull alleles in individuals of African and subcontinental Indian descent. Although rare, these alleles should be taken into consideration when planning genotyping strategies for blood donors and patients.

ADP acting on P2Y13 receptors is a negative feedback pathway for ATP release from human red blood cells

Red blood cells may regulate tissue circulation and O2 delivery by releasing the vasodilator ATP in response to hypoxia. When released extracellularly, ATP is rapidly degraded to ADP in the circulation by ectonucleotidases. In this study, we show that ADP acting on P2Y13 receptors on red blood cells serves as a negative feedback pathway for the inhibition of ATP release. mRNA of the ADP receptor P2Y13 was highly expressed in human red blood cells and reticulocytes. The stable ADP analogue 2-MeSADP decreased ATP release from red blood cells by inhibition of cAMP. The P2Y12 and P2Y13 receptor antagonist AR-C67085 (30 micromol/L), but not the P2Y1 blocker MRS2179, inhibited the effects of 2-MeSADP. At doses where AR-C67085 only blocks P2Y12 (100 nmol/L), it had no effect. AR-C67085 and the nucleotidase apyrase increased cAMP per se, indicating a constant cAMP inhibitory effect of endogenous extracellular ADP. 2-MeSADP reduced plasma ATP concentrations in an in vivo pig model. Our results indicate that the ATP degradation product ADP inhibits ATP release by acting on the red blood cell P2Y13 receptor. This negative feedback system could be important in the control of plasma ATP levels and tissue circulation.

Genetic basis of blood group diversity

In the last 18 years the genes that encode all but one of the 29 blood group systems present on red blood cells (RBCs) have been identified. This body of knowledge has permitted the application of molecular techniques to characterize the common blood group antigens and to elucidate the background for some of the variant phenotypes. Just as the RBC was used as a model for the biochemical characterization of cell membranes, so the genes encoding blood groups provide a readily accessible model for the study of gene expression and diversity. The application of genotyping techniques to identify fetuses at risk of haemolytic disease of the newborn is now the standard of care, and the expansion of nucleic acid testing platforms to include both disease testing and blood typing in the blood centre is on the horizon. This review summarizes the molecular basis of blood groups and illustrates the mechanisms that generate diversity through specific examples.

Clinical investigation of posttransfusion Kidd blood group typing using a rapid normalized quantitative polymerase chain reaction

BACKGROUND

Accurate typing of a patient's RBCs in the setting of prior transfusion or a hemolytic transfusion reaction is crucial in the selection of compatible blood but is time consuming, technically difficult, and sometimes impossible. To address this problem, a simple, rapid, and inexpensive quantitative PCR method was developed to identify the single nucleotide polymorphism (SNP) of the Kidd blood group. We applied this method in a clinical investigation of 54 multiple-transfusion patients.

STUDY DESIGN AND METHODS

Patients were eligible if they had received at least one RBC transfusion within 30 days and had a sample referred to our regional reference lab for assistance with compatibility testing requiring reticulocyte separation, hypotonic saline treatment, or chemical modification to remove IgG. We compared serologic result to the normalized quantitative PCR. For discrepants, or where no serologic type could be assigned, DNA sequencing characterized the patient's Kidd SNP.

RESULTS

Of the 54 patients, the reference lab could assign a serologic Kidd type for 33. Quantitative PCR assigned a Kidd type for 53 of the 54. In three cases, where serology and PCR were discrepant, and for all cases where serology could not assign a Kidd type, DNA sequencing verified the Kidd typing assigned by PCR.

CONCLUSION

A simple, rapid, and accurate technique has been developed. The assay performs well in the clinical setting. With further study, and inclusion of other blood group systems, this may become an important supplemental technique for selected patients in the immunohematology reference laboratory.

Antigenic and functional properties of the human red blood cell urea transporter hUT-B1

The Kidd (JK) blood group locus encodes the urea transporter hUT-B1, which is expressed on human red blood cells and other tissues. The common JK*A/JK*B blood group polymorphism is caused by a single nucleotide transition G838A changing Asp-280 to Asn-280 on the polypeptide, and transfection of erythroleukemic K562 cells with hUT-B1 cDNAs carrying either the G838 or the A838 nucleotide substitutions resulted in the isolation of stable clones that expressed the Jk(a) or Jk(b) antigens, respectively, thus providing the first direct demonstration that the hUT-B1 gene encodes the Kidd blood group antigens. In addition, immunochemical analysis of red blood cells demonstrated that hUT-B1 also exhibits ABO determinants attached to the single N-linked sugar chain at Asn-211. Moreover, immunoadsorption studies, using inside-out and right-side-out red cell membrane vesicles as competing antigen, demonstrated that the C- and N-terminal ends of hUT-B1 are oriented intracellularly. Mutagenesis and functional studies by expression in Xenopus oocytes revealed that both cysteines Cys-25 and Cys-30 (but not alone) are essential for plasma membrane addressing. Conversely, the transport function was not affected by the JK*A/JK*B polymorphism, C-terminal deletion (residues 360-389), or mutation of the extracellular N-glycosylation consensus site and remains poorly para-chloromercuribenzene sulfonate (pCMBS)-sensitive. However, transport studies by stopped flow light scattering using Jk-K562 transfectants demonstrated that the hUT-B1-mediated urea transport is pCMBS-sensitive in an erythroid context, as reported previously for the transporter of human red blood cells. Mutagenesis analysis also indicated that Cys-151 and Cys-236, at least alone, are not involved in pCMBS inhibition. Altogether, these antigenic, topologic, and functional properties might have implications into the physiology of hUT-B1 and other members of the urea transporter family.