A novel mutation +5904 C>T of RUNX1 site in the erythroid cell-specific regulatory element decreases the ABO antigen expression in Chinese population

Novel regulatory variant in ABO intronic RUNX1 binding site inducing A3 phenotype

BACKGROUND AND OBJECTIVES

Mixed-field agglutination in ABO phenotyping (A3, B3) has been linked to genetically different blood cell populations such as in chimerism, or to rare variants in either ABO exon 7 or regulatory regions. Clarification of such cases is challenging and would greatly benefit from sequencing technologies that allow resolving full-gene haplotypes at high resolution.

MATERIALS AND METHODS

We used long-read sequencing by Oxford Nanopore Technologies to sequence the entire ABO gene, amplified in two overlapping long-range PCR fragments, in a blood donor presented with A3B phenotype. Confirmation analyses were carried out by Sanger sequencing and included samples from other family members.

RESULTS

Our data revealed a novel heterozygous g.10924C>A variant on the ABO*A allele located in the transcription factor binding site for RUNX1 in intron 1 (+5.8 kb site). Inheritance was shown by the results of the donor's mother, who shared the novel variant and the anti-A specific mixed-field agglutination.

CONCLUSION

We discovered a regulatory variant in the 8-bp RUNX1 motif of ABO, which extends current knowledge of three other variants affecting the same motif and also leading to A3 or B3 phenotypes. Overall, long-range PCR combined with nanopore sequencing proved powerful and showed great potential as an emerging strategy for resolving cases with cryptic ABO phenotypes.

Detection and phenotype analysis of a novel Ael blood group allele

BACKGROUND AND OBJECTIVES

The presence of blood subtypes may lead to difficulties in blood group identification; however, third-generation sequencing (TGS) can help in accurately identifying difficult blood groups, and study the serological characteristics and molecular mechanism of Ael subtypes.

MATERIALS AND METHODS

ABO blood group was identified by the standard serological technique, weak blood group antigen was identified by adsorption-elution experiments, ABH substance in the saliva was determined and glycosyltransferase activity of A and B was detected. The ABO gene full-length sequence and promoter region were amplified by specific primers using single-molecule real-time sequencing, with the amplified products being sequenced directly and analysed in real time.

RESULTS

The patient was serologically identified as Ael subtype, and TGS analysis revealed new intron mutations in Ael patients (c.467C>T; c.29-10T>A).

CONCLUSION

The discovery of the new allele and the identification of ABO subtypes can be combined with serological characterization and molecular biological methods.

Emergence of an erythroid cell-specific regulatory region in ABO intron 1 attributable to A- or B-antigen expression on erythrocytes in Hominoidea

A- and B-antigens are present on red blood cells (RBCs) as well as other cells and secretions in Hominoidea including humans and apes such as chimpanzees and gibbons, whereas expression of these antigens on RBCs is subtle in monkeys such as Japanese macaques. Previous studies have indicated that H-antigen expression has not completely developed on RBCs in monkeys. Such antigen expression requires the presence of H-antigen and A- or B-transferase expression in cells of erythroid lineage, although whether or not ABO gene regulation is associated with the difference of A- or B-antigen expression between Hominoidea and monkeys has not been examined. Since it has been suggested that ABO expression on human erythrocytes is dependent upon an erythroid cell-specific regulatory region or the + 5.8-kb site in intron 1, we compared the sequences of ABO intron 1 among non-human primates, and demonstrated the presence of sites orthologous to the + 5.8-kb site in chimpanzees and gibbons, and their absence in Japanese macaques. In addition, luciferase assays revealed that the former orthologues enhanced promoter activity, whereas the corresponding site in the latter did not. These results suggested that the A- or B-antigens on RBCs might be ascribed to emergence of the + 5.8-kb site or the corresponding regions in ABO through genetic evolution.

Analysis of the Genomic Sequence of ABO Allele Using Next-Generation Sequencing Method

Background

Although many molecular diagnostic methods have been used for ABO genotyping, there are few reports on the full-length genomic sequence analysis of the ABO gene. Recently, next-generation sequencing (NGS) has been shown to provide fast and high-throughput results and is widely used in the clinical laboratory. Here, we established an NGS method for analyzing the sequence of the start codon to the stop codon in the ABO gene.

Study Design and Methods

Two pairs of primers covering the partial 5’-untranslated region (UTR) to 3’-UTR of the ABO gene were designed. The sequences covering from the start codon to the stop codon of the ABO gene were amplified using these primers, and an NGS method based on the overlap amplicon was developed. A total of 110 individuals, including 88 blood donors with normal phenotypes and 22 ABO subtypes, were recruited and analyzed. All these specimens were first detected by serological tests and then determined by polymerase chain reaction sequence-based typing (PCR-SBT) and NGS. The sequences, including all the intron regions for the specimens, were analyzed by bioinformatics software.

Results

Among the 88 blood donors with a normal phenotype, 48 homozygous individuals, 39 heterozygous individuals, and one individual with a novel O allele were found according to the results of the PCR-SBT method. Some single-nucleotide variants (SNV) in intronic regions were found to be specific for different ABO alleles from 48 homozygous individuals using the NGS method. Sequences in the coding region of all specimens using the NGS method were the same as those of the PCR-SBT method. Three intronic SNVs were found to be associated with the ABO subtypes, including one novel intronic SNV (c.28+5956T>A). Moreover, six specimens were found to exhibit DNA recombination.

Conclusion

An NGS method was established to analyze the sequence from the start codon to the stop codon of the ABO gene. Two novel ABO alleles were identified, and DNA recombination was found to exist in the ABO alleles.

Application of Blood Group Genotyping by Next-Generation Sequencing in Various Immunohaematology Cases

BACKGROUND

Next-generation sequencing (NGS) technology has been recently introduced into blood group genotyping; however, there are few studies using NGS-based blood group genotyping in real-world clinical settings. In this study, we applied NGS-based blood group genotyping into various immunohaematology cases encountered in routine clinical practice.

METHODS

This study included 4 immunohaematology cases: ABO subgroup, ABO chimerism, antibody to a high-frequency antigen (HFA), and anti-CD47 interference. We designed a hybridization capture-based NGS panel targeting 39 blood group-related genes and applied it to the 4 cases.

RESULTS

NGS analysis revealed a novel intronic variant (NM_020469.3:c.29-10T>G) in a patient with an Ael phenotype and detected a small fraction of ABO*A1.02 (approximately 3-6%) coexisting with the major genotype ABO*B.01/O.01.02 in dizygotic twins. In addition, NGS analysis found a homozygous stop-gain variant (NM_004827.3:c.376C>T, p.Gln126*; ABCG2*01N.01) in a patient with an antibody to an HFA; consequently, this patient's phenotype was predicted as Jr(a-). Lastly, blood group phenotypes predicted by NGS were concordant with those determined by serology in 2 patients treated with anti-CD47 drugs.

CONCLUSION

NGS-based blood group genotyping can be used for identifying ABO subgroup alleles, low levels of blood group chimerism, and antibodies to HFAs. Furthermore, it can be applied to extended blood group antigen matching for patients treated with anti-CD47 drugs.

New ABO intron 1 variant alleles

Unusual and discrepant ABO phenotypes are often due to genetic variants that lead to altered levels or activity of ABO transferases and consequently to altered expression of ABO antigens. This report describes eight genetic alterations found in 15 cases with reduced or undetectable expression of ABO antigens. Forward and reverse ABO grouping was performed by standard gel or tube methods. Adsorption-heat elution and saliva testing for H and A substances followed the AABB technical manual procedures. Genomic DNA extracted from whole blood was PCR-amplified to cover the entire ABO coding sequence, splice junctions, proximal promoter, and intron 1 enhancer. Amplification products were sequenced by next-generation or Sanger dideoxy methods, either directly or after cloning into a bacterial plasmid vector. Eight unreported alleles were found in the 15 cases analyzed. Alleles ABO*A(28+1C) and ABO*A(29-5G) harbor variants that alter the consensus sequence at the intron 1 donor and acceptor splice sites, respectively. The other alleles harbor variants that alter the consensus sequence at transcription factor-binding sites in the intron 1 enhancer: specifically, ABO*A(28+5792T), ABO*A(28+5859A), and ABO*A(28+5860G) at GATA-1 sites; ABO*B(28+5877T) and ABO*B(28+5878G) at a RUNX1 site; and ABO*A(28+5843A) at or near a C/EBP site. Molecular and serologic characterization of ABO alleles can help in their future identification and in the resolution of discrepancies.

Unusual and discrepant ABO phenotypes are often due to genetic variants that lead to altered levels or activity of ABO transferases and consequently to altered expression of ABO antigens. This report describes eight genetic alterations found in 15 cases with reduced or undetectable expression of ABO antigens. Forward and reverse ABO grouping was performed by standard gel or tube methods. Adsorption-heat elution and saliva testing for H and A substances followed the AABB technical manual procedures. Genomic DNA extracted from whole blood was PCR-amplified to cover the entire ABO coding sequence, splice junctions, proximal promoter, and intron 1 enhancer. Amplification products were sequenced by next-generation or Sanger dideoxy methods, either directly or after cloning into a bacterial plasmid vector. Eight unreported alleles were found in the 15 cases analyzed. Alleles ABO*A(28+1C) and ABO*A(29–5G) harbor variants that alter the consensus sequence at the intron 1 donor and acceptor splice sites, respectively. The other alleles harbor variants that alter the consensus sequence at transcription factor–binding sites in the intron 1 enhancer: specifically, ABO*A(28+5792T), ABO*A(28+5859A), and ABO*A(28+5860G) at GATA-1 sites; ABO*B(28+5877T) and ABO*B(28+5878G) at a RUNX1 site; and ABO*A(28+5843A) at or near a C/EBP site. Molecular and serologic characterization of ABO alleles can help in their future identification and in the resolution of discrepancies.

Reduction of blood group A antigen on erythrocytes in a patient with myelodysplastic syndrome harboring somatic mutations in RUNX1 and GATA2

BACKGROUND

Reduction of blood group ABO antigens on red blood cells (RBCs) is well known in patients with leukemias, and this reduction of ABO expression is strongly associated with DNA methylation of the ABO promoter. Previously, we reported a two-nucleotide deletion in RUNX1 encoding an abnormally elongated protein lacking the trans-activation domain in a patient with myelodysplastic syndrome (MDS) showing A-antigen loss on RBCs. This prompted us to investigate the underlying mechanism responsible for A-antigen reduction on RBCs in another patient with MDS.

STUDY DESIGN AND METHODS

Screening of somatic mutations was carried out using a targeted sequencing panel with genomic DNA from peripheral blood mononuclear cells from the patient and eleven MDS controls without A- or B-antigen loss. DNA methylation of the ABO promoter was examined by bisulfite genomic sequencing. Transient transfection assays were performed for functional evaluation of mutations.

RESULTS

Screening of somatic mutations showed missense mutations in RUNX1 and GATA2 in the patient, while no mutation was found in exons of those genes in the controls. There was no significant difference in ABO promoter methylation between the patient and the controls. Transient transfection experiments into COS-7 and K562 cells suggested that the amino acid substitutions encoded by those mutations reduced or lost the trans-activation potential of the ABO expression.

CONCLUSION

Considering the discrepancy between the variant frequencies of these mutations and the ratios of the RBCs with A-antigens loss, the antigen reduction might be associated with these somatic mutations and hypermethylation of the ABO promoter.

Molecular basis of weak A subgroups in the Korean population: Identification of three novel subgroup-causing variants in the ABO regulatory regions

BACKGROUND

Recent studies on Chinese and Japanese populations have shown that weak ABO subgroups could be caused by variants in the major regulatory regions of ABO, the proximal promoter, +5.8-kb site, and CCAAT-binding factor/NF-Y binding site. We investigated the molecular basis of weak A subgroups in the Korean population.

STUDY DESIGN AND METHODS

This study included 11 samples suspected to have a weak A subgroup. These samples were subjected to sequencing analysis of ABO exons 6 and 7. If no subgroup-causing variants were detected in this region, exons 1-5 and three major regulatory regions were sequenced.

RESULTS

Sequencing analysis of exons 6 and 7 detected two known subgroup alleles (ABO*AW.10, n = 5; ABO*AEL.02, n = 2). The remaining four samples contained a sequence variant in the proximal promoter (g.4944C>T, n = 1; g.4954G>T, n = 1) or +5.8-kb site (g.10843T>C, n = 1; g.10935C>T, n = 1). Notably, three of the four variants (g.4944C>T, g.4954G>T, and g.10843T>C) have not been reported previously in weak ABO subgroups.

CONCLUSION

This study provides the first evidence that alterations in the proximal promoter and + 5.8-kb site could account for a substantial proportion of weak A subgroups in the Korean population.

A historical overview of advances in molecular genetic/genomic studies of the ABO blood group system

In 1990, 90 years after the discovery of ABO blood groups by Karl Landsteiner, my research team at the Molecular Biology Laboratory of the now-defunct Biomembrane Institute elucidated the molecular genetic basis of the ABO polymorphism. Henrik Clausen, Head of the Immunology Laboratory, initiated the project by isolating human group A transferase (AT), whose partial amino acid sequence was key to its success. Sen-itiroh Hakomori, the Scientific Director, provided all the institutional support. The characterization started from the 3 major alleles (A1, B, and O), and proceeded to the alleles of A2, A3, Ax and B3 subgroups and also to the cis-AB and B(A) alleles, which specify the expression of A and B antigens by single alleles. In addition to the identification of allele-specific single nucleotide polymorphism (SNP) variations, we also experimentally demonstrated their functional significance in glycosyltransferase activity and sugar specificity of the encoded proteins. Other scientists interested in blood group genes later characterized more than 250 ABO alleles. However, recent developments in next-generation sequencing have enabled the sequencing of millions of human genomes, transitioning from the era of genetics to the era of genomics. As a result, numerous SNP variations have been identified in the coding and noncoding regions of the ABO gene, making ABO one of the most studied loci for human polymorphism. As a tribute to Dr. Hakomori's scientific legacy, a historical overview in molecular genetic/genomic studies of the human ABO gene polymorphism is presented, with an emphasis on early discoveries made at his institute.

Sequence variants in the proximal promoter and +5.8-kb site of ABO in Koreans with weak B phenotypes

BACKGROUND AND OBJECTIVES

Several studies on Chinese and Japanese populations have revealed that a substantial proportion of weak B subgroups are caused by variants in the major regulatory regions of ABO, the proximal promoter, CCAAT-binding factor/NF-Y binding site and +5.8-kb site. We performed molecular analyses of these regions in Koreans with weak B phenotypes.

MATERIALS AND METHODS

This study included 16 samples with weak B phenotypes (4 B₃ , 1 B_w , 5 A₁ B₃ and 6 A₁ B_w ) harbouring no subgroup-causing variants in ABO exons 6 and 7. These samples were subjected to sequencing analysis of exons 1-5 and the major regulatory regions of ABO.

RESULTS

Of the 16 samples, 14 were found to carry a sequence variant either in the proximal promoter (g.4991_5008del [n = 3]) or the +5.8-kb site (g.10893G>A [n = 4] and g.10925C>T [n = 7]). The remaining two samples were found to contain no subgroup-causing variants.

CONCLUSION

Our study demonstrates that sequence variants in the proximal promoter and +5.8-kb site account for a substantial proportion of weak B subgroups in Koreans, suggesting that molecular analysis of these regions is essential for the accurate determination of ABO genotypes in Koreans with weak B phenotypes.

[Genetic analysis of weakened expression of ABO blood group antigen in 20 cases]

OBJECTIVE

To explore the molecular mechanism for weakened expression of ABO blood group antigens in 20 cases.

METHODS

Blood samples were collected from 20 cases with weakened expression of ABO blood group antigens, including 12 children undergoing elective surgery and 8 of their parents or grandparents. Serological identification of the ABO blood group was performed using microcolumn agglutination method and saline test tube method. The PCR products of exons 1-7 and their upstream promoter region of the ABO gene were directly sequenced for genotyping.

RESULTS

In 11 of the cases, the ABO genotype could be determined by pedigree analysis (including 1 case of ABO*A2.01/ABO*B.01, 1 case of ABO*A2.01/ ABO*O01.01, 1 case of A1.02/B3.04, 2 cases of B3.04/O.01.01, 2 cases of B3.02/O.01.02, and 4 cases of Bw.12/O.01.01). Pedigree analysis revealed deletion mutation at -35_-18 nt in the ABO promoter region in 3 cases, indicating that the mutation occurred in the B allele; a C > T mutation occurred at -119 nt in the ABO promoter region in 1 case; a C deletion at 1054 nt in exon 7 was identified in 1 case; no mutation was found in exons 1-7 and their regulatory region of ABO gene in 4 cases.

CONCLUSION

The C > T mutation at-119 nt in the promoter region and the deletion mutation at 1054 nt in exon 7 of ABO gene are probably new mutations leading to abnormal expression of ABO blood group antigens. Some ABO subtypes may be associated with abnormal introns or mRNA synthesis.

Mechanism evaluation for an amino acid substitution p.Y246C of B-glycosyltransferase enzyme with Bweak phenotype

BACKGROUND

The amino acid substitutions caused by ABO gene variants are usually predicted to impact the glycosyltransferase function. Here, the effect of an amino acid substitution in the vicinity of the catalytic active region of the B-glycosyltransferase was explored in vitro and in silico study, which is important for further recognizing the ABO subgroup.

METHODS

The ABO serological tests were performed by the routine methods. The ABO genotype was analyzed by polymerase chain reaction and sequenced bidirectionally. The haplotype of the variant allele was separated using single-strand amplification and sequencing with allele-specific primers. Stably expression cell lines with variant were constructed for study in vitro. 3D structure of the B-glycosyltransferase (GTB) variant was simulated by PyMOL software. The free energy change (ΔΔG) was calculated by FoldX.

RESULTS

A variant c.737A > G was identified in a Chinese individual with Bweak phenotype, which led to an amino acid substitution p.Y246C in the vicinity of the catalytic active region of GTB enzyme. The stably expression cell lines with variant and wild type were successfully established and showed that the variant caused a decrease in protein levels and/or enzyme activity. The 3D structural of the GTB modelling found the amino acid substitution p.Y246C caused the hydrogen bond of the protein changes. Meanwhile, the free energy change (ΔΔG) value predicted the destabilizing effect on the variant GTB.

DISCUSSION

The p.Y246C variant in the vicinity of the enzyme active centre reduced the antigen expression because of greatly destabilizing effect on the GTB variant.

Molecular Basis of ABO Variants Including Identification of 16 Novel ABO Subgroup Alleles in Chinese Han Population

Introduction

The characteristic of ABO blood subgroup is crucial for elucidating the mechanisms of such variant phenotypes and offering useful information in blood transfusion.

Methods

In total, 211 ABO variants including part of available family members were investigated in this study. The phenotypes of these individuals were typed with serologic methods. The full coding regions of ABO gene and the erythroid cell-specific regulatory elements in intron 1 of them were amplified with polymerase chain reaction and then directly sequenced. The novel alleles were confirmed by cloning and sequencing. Phylogenetic tree was made using CLUSTAL W software. 3D structural analyses of the glycosyltransferases (GTs) with some typical mutations were performed by PyMOL software.

Results

Forty-eight distinctly rare ABO alleles were identified in 211 Chinese variant individuals, including 16 novel ABO alleles. All of the alleles were categorized as 5 groups: 16 ABO*A alleles, 23 ABO*B alleles, 4 ABO*BA alleles, 4 ABO*cisAB alleles, and 1 ABO*O alleles. ABO*A2.08 and ABO*BA.02 were the relatively predominant A and B subgroup alleles, respectively. According to the phylogenetic tree, 28 alleles (5 common alleles and 23 alleles identified in our laboratory) were classified into 3 major allelic lineages. The structural analysis of 3D homology modeling predicted reduced protein stability of the mutant GTs and may explain the reduced ABO antigen expression.

Conclusions

The molecular basis of ABO variants was analyzed, and 16 novel ABO alleles were identified. The results extended the information of ABO variants and provided a basis for better transfusion strategies and helped to improve blood transfusion safety.