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McGowan EC, Wu PC, Hellberg Å, Lopez GH, Hyland CA, Olsson ML. A Bioinformatically Initiated Approach to Evaluate GATA1 Regulatory Regions in Samples with Weak D, Del, or D- Phenotypes Despite Normal RHD Exons. Transfus Med Hemother 2024; 51:252-264. [PMID: 39021419 PMCID: PMC11250534 DOI: 10.1159/000538469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 03/19/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction With over 360 blood group antigens in systems recognized, there are antigens, such as RhD, which demonstrate a quantitative reduction in antigen expression due to nucleotide variants in the non-coding region of the gene that result in aberrant splicing or a regulatory mechanism. This study aimed to evaluate bioinformatically predicted GATA1-binding regulatory motifs in the RHD gene for samples presenting with weak or apparently negative RhD antigen expression but showing normal RHD exons. Methods Publicly available open chromatin region data were overlayed with GATA1 motif candidates in RHD. Genomic DNA from weak D, Del or D- samples with normal RHD exons (n = 13) was used to confirm RHD zygosity by quantitative PCR. Then, RHD promoter, intron 1, and intron 2 regions were amplified for Sanger sequencing to detect potential disruptions in the GATA1 motif candidates. Electrophoretic mobility shift assay (EMSA) was performed to assess GATA1-binding. Luciferase assays were used to assess transcriptional activity. Results Bioinformatic analysis identified five of six GATA1 motif candidates in the promoter, intron 1 and intron 2 for investigation in the samples. Luciferase assays showed an enhancement in transcription for GATA1 motifs in intron 1 and for intron 2 only when the R 2 haplotype variant (rs675072G>A) was present. GATA1 motifs were intact in 12 of 13 samples. For one sample with a Del phenotype, a novel RHD c.1-110A>C variant disrupted the GATA1 motif in the promoter which was supported by a lack of a GATA1 supershift in the EMSA and 73% transcriptional activity in the luciferase assay. Two samples were D+/D- chimeras. Conclusion The bioinformatic predictions enabled the identification of a novel DEL allele, RHD c.1-110A>C, which disrupted the GATA1 motif in the proximal promoter. Although the majority of the samples investigated here remain unexplained, we provide GATA1 targets which may benefit future RHD regulatory investigations.
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Affiliation(s)
- Eunike C. McGowan
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Ping Chun Wu
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Åsa Hellberg
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Genghis H. Lopez
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD, Australia
- School of Health, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Catherine A. Hyland
- Research and Development, Australian Red Cross Lifeblood, Brisbane, QLD, Australia
- Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Martin L. Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
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Wu PC, McGowan EC, Lee YQ, Ghosh S, Hansson J, Olsson ML. Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci. Transfusion 2024; 64:1083-1096. [PMID: 38644556 DOI: 10.1111/trf.17840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/23/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Blood typing is essential for safe transfusions and is performed serologically or genetically. Genotyping predominantly focuses on coding regions, but non-coding variants may affect gene regulation, as demonstrated in the ABO, FY and XG systems. To uncover regulatory loci, we expanded a recently developed bioinformatics pipeline for discovery of non-coding variants by including additional epigenetic datasets. METHODS Multiple datasets including ChIP-seq with erythroid transcription factors (TFs), histone modifications (H3K27ac, H3K4me1), and chromatin accessibility (ATAC-seq) were analyzed. Candidate regulatory regions were investigated for activity (luciferase assays) and TF binding (electrophoretic mobility shift assay, EMSA, and mass spectrometry, MS). RESULTS In total, 814 potential regulatory sites in 47 blood-group-related genes were identified where one or more erythroid TFs bound. Enhancer candidates in CR1, EMP3, ABCB6, and ABCC4 indicated by ATAC-seq, histone markers, and co-occupancy of 4 TFs (GATA1/KLF1/RUNX1/NFE2) were investigated but only CR1 and ABCC4 showed increased transcription. Co-occupancy of GATA1 and KLF1 was observed in the KEL promoter, previously reported to contain GATA1 and Sp1 sites. TF binding energy scores decreased when three naturally occurring variants were introduced into GATA1 and KLF1 motifs. Two of three GATA1 sites and the KLF1 site were confirmed functionally. EMSA and MS demonstrated increased GATA1 and KLF1 binding to the wild-type compared to variant motifs. DISCUSSION This combined bioinformatics and experimental approach revealed multiple candidate regulatory regions and predicted TF co-occupancy sites. The KEL promoter was characterized in detail, indicating that two adjacent GATA1 and KLF1 motifs are most crucial for transcription.
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Affiliation(s)
- Ping Chun Wu
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Eunike C McGowan
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Yan Quan Lee
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Sudip Ghosh
- Department of Experimental Medical Science and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Jenny Hansson
- Department of Experimental Medical Science and Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine and the Lund Stem Cell Center, Lund University, Lund, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Sweden
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3
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Wu PC, Lee YQ, Möller M, Storry JR, Olsson ML. Elucidation of the low-expressing erythroid CR1 phenotype by bioinformatic mining of the GATA1-driven blood-group regulome. Nat Commun 2023; 14:5001. [PMID: 37591894 PMCID: PMC10435571 DOI: 10.1038/s41467-023-40708-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 08/08/2023] [Indexed: 08/19/2023] Open
Abstract
Genetic determinants underlying most human blood groups are now clarified but variation in expression levels remains largely unexplored. By developing a bioinformatics pipeline analyzing GATA1/Chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets, we identify 193 potential regulatory sites in 33 blood-group genes. As proof-of-concept, we aimed to delineate the low-expressing complement receptor 1 (CR1) Helgeson phenotype on erythrocytes, which is correlated with several diseases and protects against severe malaria. We demonstrate that two candidate CR1 enhancer motifs in intron 4 bind GATA1 and drive transcription. Both are functionally abolished by naturally-occurring SNVs. Erythrocyte CR1-mRNA and CR1 levels correlate dose-dependently with genotype of one SNV (rs11117991) in two healthy donor cohorts. Haplotype analysis of rs11117991 with previously proposed markers for Helgeson shows high linkage disequilibrium in Europeans but explains the poor prediction reported for Africans. These data resolve the longstanding debate on the genetic basis of inherited low CR1 and form a systematic starting point to investigate the blood group regulome.
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Affiliation(s)
- Ping Chun Wu
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Yan Quan Lee
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Mattias Möller
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics and Pathology, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Jill R Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.
- Department of Clinical Immunology and Transfusion Medicine, Office for Medical Services, Region Skåne, Lund, Sweden.
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Ajore R, Niroula A, Pertesi M, Cafaro C, Thodberg M, Went M, Bao EL, Duran-Lozano L, Lopez de Lapuente Portilla A, Olafsdottir T, Ugidos-Damboriena N, Magnusson O, Samur M, Lareau CA, Halldorsson GH, Thorleifsson G, Norddahl GL, Gunnarsdottir K, Försti A, Goldschmidt H, Hemminki K, van Rhee F, Kimber S, Sperling AS, Kaiser M, Anderson K, Jonsdottir I, Munshi N, Rafnar T, Waage A, Weinhold N, Thorsteinsdottir U, Sankaran VG, Stefansson K, Houlston R, Nilsson B. Functional dissection of inherited non-coding variation influencing multiple myeloma risk. Nat Commun 2022; 13:151. [PMID: 35013207 PMCID: PMC8748989 DOI: 10.1038/s41467-021-27666-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/02/2021] [Indexed: 12/16/2022] Open
Abstract
Thousands of non-coding variants have been associated with increased risk of human diseases, yet the causal variants and their mechanisms-of-action remain obscure. In an integrative study combining massively parallel reporter assays (MPRA), expression analyses (eQTL, meQTL, PCHiC) and chromatin accessibility analyses in primary cells (caQTL), we investigate 1,039 variants associated with multiple myeloma (MM). We demonstrate that MM susceptibility is mediated by gene-regulatory changes in plasma cells and B-cells, and identify putative causal variants at six risk loci (SMARCD3, WAC, ELL2, CDCA7L, CEP120, and PREX1). Notably, three of these variants co-localize with significant plasma cell caQTLs, signaling the presence of causal activity at these precise genomic positions in an endogenous chromosomal context in vivo. Our results provide a systematic functional dissection of risk loci for a hematologic malignancy.
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Affiliation(s)
- Ram Ajore
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Abhishek Niroula
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
| | - Maroulio Pertesi
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Caterina Cafaro
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Malte Thodberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Erik L Bao
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Laura Duran-Lozano
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | | | | | - Nerea Ugidos-Damboriena
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden
| | - Olafur Magnusson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Mehmet Samur
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Caleb A Lareau
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Asta Försti
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
- Hopp Children's Cancer Center, Heidelberg, Germany
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University Hospital of Heidelberg, 69120, Heidelberg, Germany
| | - Kari Hemminki
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
- Faculty of Medicine and Biomedical Center in Pilsen, Charles University in Prague, Prague, 30605, Czech Republic
| | | | - Scott Kimber
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Adam S Sperling
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Martin Kaiser
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Kenneth Anderson
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Nikhil Munshi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Thorunn Rafnar
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Niels Weinhold
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
- Department of Internal Medicine V, University Hospital of Heidelberg, 69120, Heidelberg, Germany
| | | | - Vijay G Sankaran
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
| | - Kari Stefansson
- deCODE Genetics/Amgen Inc., Sturlugata 8, 101, Reykjavik, Iceland
| | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 123 Old Brompton Road, London, SW7 3RP, United Kingdom
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, 221 84, Lund, Sweden.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, 415 Main Street, Boston, MA, 02142, USA.
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Srivastava K, Fratzscher AS, Lan B, Flegel WA. Cataloguing experimentally confirmed 80.7 kb-long ACKR1 haplotypes from the 1000 Genomes Project database. BMC Bioinformatics 2021; 22:273. [PMID: 34039276 PMCID: PMC8150616 DOI: 10.1186/s12859-021-04169-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Background Clinically effective and safe genotyping relies on correct reference sequences, often represented by haplotypes. The 1000 Genomes Project recorded individual genotypes across 26 different populations and, using computerized genotype phasing, reported haplotype data. In contrast, we identified long reference sequences by analyzing the homozygous genomic regions in this online database, a concept that has rarely been reported since next generation sequencing data became available. Study design and methods Phased genotype data for a 80.6 kb region of chromosome 1 was downloaded for all 2,504 unrelated individuals of the 1000 Genome Project Phase 3 cohort. The data was centered on the ACKR1 gene and bordered by the CADM3 and FCER1A genes. Individuals with heterozygosity at a single site or with complete homozygosity allowed unambiguous assignment of an ACKR1 haplotype. A computer algorithm was developed for extracting these haplotypes from the 1000 Genome Project in an automated fashion. A manual analysis validated the data extracted by the algorithm. Results We confirmed 902 ACKR1 haplotypes of varying lengths, the longest at 80,584 nucleotides and shortest at 1,901 nucleotides. The combined length of haplotype sequences comprised 19,895,388 nucleotides with a median of 16,014 nucleotides. Based on our approach, all haplotypes can be considered experimentally confirmed and not affected by the known errors of computerized genotype phasing. Conclusions Tracts of homozygosity can provide definitive reference sequences for any gene. They are particularly useful when observed in unrelated individuals of large scale sequence databases. As a proof of principle, we explored the 1000 Genomes Project database for ACKR1 gene data and mined long haplotypes. These haplotypes are useful for high throughput analysis with next generation sequencing. Our approach is scalable, using automated bioinformatics tools, and can be applied to any gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04169-6.
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Affiliation(s)
- Kshitij Srivastava
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anne-Sophie Fratzscher
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bo Lan
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Willy Albert Flegel
- Laboratory Services Section, Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, 20892, USA.
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SMIM1, carrier of the Vel blood group, is a tail-anchored transmembrane protein and readily forms homodimers in a cell-free system. Biosci Rep 2021; 40:222673. [PMID: 32301496 PMCID: PMC7953501 DOI: 10.1042/bsr20200318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/17/2020] [Accepted: 03/24/2020] [Indexed: 01/05/2023] Open
Abstract
Antibodies to the Vel blood group antigen can cause adverse hemolytic reactions unless Vel-negative blood units are transfused. Since the genetic background of Vel-negativity was discovered in 2013, DNA-based typing of the 17-bp deletion causing the phenotype has facilitated identification of Vel-negative blood donors. SMIM1, the gene underlying Vel, encodes a 78-amino acid erythroid transmembrane protein of unknown function. The transmembrane orientation of SMIM1 has been debated since experimental data supported both the N- and C-termini being extracellular. Likewise, computational predictions of its orientation were divided and potential alternatives such as monotopic or dual-topology have been discussed but not investigated. We used a cell-free system to explore the topology of SMIM1 when synthesized in the endoplasmic reticulum (ER). SMIM1 was tagged with an opsin-derived N-glycosylation reporter at either the N- or C-terminus and synthesized in vitro using rabbit reticulocyte lysate supplemented with canine pancreatic microsomes as a source of ER membrane. SMIM1 topology was then determined by assessing the N-glycosylation of its N- or C-terminal tags. Complementary experiments were carried out by expressing the same SMIM1 variants in HEK293T/17 cells and establishing their membrane orientation by immunoblotting and flow cytometry. Our data consistently indicate that SMIM1 has its short C-terminus located extracellularly and that it most likely belongs to the tail-anchored class of membrane proteins with the bulk of the polypeptide located in the cytoplasm. Having established its membrane orientation in an independent model system, future work can now focus on functional aspects of SMIM1 as a potential regulator of erythropoiesis.
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van der Rijst MVE, Abay A, Aglialoro F, van der Schoot CE, van den Akker E. SMIM1 missense mutations exert their effect on wild type Vel expression late in erythroid differentiation. Transfusion 2020; 61:236-245. [PMID: 33128268 DOI: 10.1111/trf.16169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND Vel expression on erythrocytes is variable due to polymorphisms, complicating Vel typing. Weak Vel expression can be caused by mutations within SMIM1 in a heterozygous setting, suggesting a dominant negative effect of SMIM1 mutants on wild type (wt)SMIM1 expression. Here we report how SMIM1 expression is regulated during erythropoiesis, to understand its variable expression on erythrocytes. STUDY DESIGN AND METHODS Peripheral blood reticulocytes at different stages, cultured erythroid precursors and HEK293T cells were used to investigate expression and putative competition between wtSMIM1 and mutated SMIM1 VEL*01W.01, (c.152T>A (p.Met51Lys)), VEL*01W.02 (c.152T>G (p.Met51Arg)), and VEL*01W.03 (c.161T>C (p.Leu54Pro)). RESULTS Depending on the mutations in SMIM1 an effect on total and membrane expression of SMIM1 was observed in transfected HEK293T cells, but co-expression of wtSMIM1 and mutatedSMIM1 did not have an effect on wtSMIM1 membrane expression. During differentiation of donors expressing VEL*01W.01, VEL*01W.03, Vel-positive, Vel-negative (homozygote SMIM1*64_80del), and Vel-heterozygote SMIM1*64_80del primary human erythroblasts no overt defect was found in Vel expression dynamics or total SMIM1 expression levels when compared with wtSMIM1 erythroblasts. However, during enucleation, total Vel expression was significantly lower on reticulocytes of Vel-weak donors expressing heterozygote mutated SMIM1 compared to Vel-positive or Vel-heterozygote SMIM1*64_80del donors, while Vel expression on extruded nuclei was maintained. In addition, reticulocyte maturation in vivo showed further loss of Vel expression in these individuals and nearly absent on erythrocytes. CONCLUSION These results suggest that SMIM1 mutations exert a dominant negative effect on wtSMIM1 probably by affecting SMIM1 multimerization and thereby Vel epitope presentation at the latest stages of erythroid differentiation.
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Affiliation(s)
- Marea V E van der Rijst
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands.,Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - Asena Abay
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - Francesca Aglialoro
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - Emile van den Akker
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
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Roulis E, Schoeman E, Hobbs M, Jones G, Burton M, Pahn G, Liew YW, Flower R, Hyland C. Targeted exome sequencing designed for blood group, platelet, and neutrophil antigen investigations: Proof-of-principle study for a customized single-test system. Transfusion 2020; 60:2108-2120. [PMID: 32687227 DOI: 10.1111/trf.15945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 01/14/2023]
Abstract
BACKGROUND Immunohematology reference laboratories provide red blood cell (RBC), platelet (PLT), and neutrophil typing to resolve complex cases, using serology and commercial DNA tests that define clinically important antigens. Broad-range exome sequencing panels that include blood group targets provide accurate blood group antigen predictions beyond those defined by serology and commercial typing systems and identify rare and novel variants. The aim of this study was to design and assess a panel for targeted exome sequencing of RBC, PLT, and neutrophil antigen-associated genes to provide a comprehensive profile in a single test, excluding unrelated gene targets. STUDY DESIGN AND METHODS An overlapping probe panel was designed for the coding regions of 64 genes and loci involved in gene expression. Sequencing was performed on 34 RBC and 17 PLT/neutrophil reference samples. Variant call outputs were analyzed using software to predict star allele diplotypes. Results were compared with serology and previous sequence genotyping data. RESULTS Average coverage exceeded 250×, with more than 94% of targets at Q30 quality or greater. Increased coverage revealed a variant in the Scianna system that was previously undetected. The software correctly predicted allele diplotypes for 99.5% of RBC blood groups tested and 100% of PLT and HNA antigens excepting HNA-2. Optimal throughput was 12 to 14 samples per run. CONCLUSION This single-test system demonstrates high coverage and quality, allowing for the detection of previously overlooked variants and increased sample throughput. This system has the potential to integrate genomic testing across laboratories within hematologic reference settings.
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Affiliation(s)
- Eileen Roulis
- Australian Red Cross Lifeblood Research and Development, Kelvin Grove, Queensland, Australia
| | - Elizna Schoeman
- Australian Red Cross Lifeblood Research and Development, Kelvin Grove, Queensland, Australia
| | - Matthew Hobbs
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Greg Jones
- Australian Red Cross Lifeblood Platelet and Granulocyte Reference Laboratory, Kelvin Grove, Queensland, Australia
| | - Mark Burton
- Australian Red Cross Lifeblood Platelet and Granulocyte Reference Laboratory, Kelvin Grove, Queensland, Australia
| | - Gail Pahn
- Australian Red Cross Lifeblood Platelet and Granulocyte Reference Laboratory, Kelvin Grove, Queensland, Australia
| | - Yew-Wah Liew
- Australian Red Cross Lifeblood Red Cell Reference Laboratory, Kelvin Grove, Queensland, Australia
| | - Robert Flower
- Australian Red Cross Lifeblood Research and Development, Kelvin Grove, Queensland, Australia
| | - Catherine Hyland
- Australian Red Cross Lifeblood Research and Development, Kelvin Grove, Queensland, Australia
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Flesch BK, Scherer V, Just B, Opitz A, Ochmann O, Janson A, Steitz M, Zeiler T. Molecular Blood Group Screening in Donors from Arabian Countries and Iran Using High-Throughput MALDI-TOF Mass Spectrometry and PCR-SSP. Transfus Med Hemother 2020; 47:396-408. [PMID: 33173458 DOI: 10.1159/000505495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/14/2019] [Indexed: 12/11/2022] Open
Abstract
Background and Aims Only little is known about blood groups other than ABO blood groups and Rhesus factors in Arabian countries and Iran. During the last years, increased migration to Central Europe has put a focus on the question how to guarantee blood supply for patients from these countries, particularly because hemoglobinopathies with the need of regular blood support are more frequent in patients from that region. Therefore, blood group allele frequencies should be determined in individuals from Arabian countries and Iran by molecular typing and compared to a German rare donor panel. Methods 1,111 samples including 800 individuals from Syria, 147 from Iran, 123 from the Arabian Peninsula, and 41 from Northern African countries were included in a MALDI-TOF MS assay to detect polymorphisms coding for Kk, Fy(a/b), Fy<sub>null</sub>, C<sub>w</sub>, Jk(a/b), Jo(a+/a-), Lu(a/b), Lu(8/14), Ss, Do(a/b), Co(a/b), In(a/b), Js(a/b), Kp(a/b), and variant alleles RHCE*c.697C>G and RHCE *c.733C>G. Yt(a/b), S-s-U-, Vel<sub>null</sub>, Co<sub>null</sub>, and RHCE *c.667G>T were tested by PCR-SSP. Results Of the Arabian donors, 2% were homozygous for the FY *02.01N allele (Fy<sub>null</sub>), and 15.7% carried the heterozygous mutation. However, 0.8% of the German donors also carried 1 copy of the allele. 3.6% of all and 29.3% of Northern African donors were heterozygous for the RHCE *c.733C>G substitution, 0.4% of the Syrian probands were heterozygous for DO *01/DO *01.-05, a genotype that was lacking in German donors. Whereas the KEL *02.06 allele coding for the Js(a) phenotype was missing in Germans; 0.8% of the Syrian donors carried 1 copy of this allele. 1.8% of the Syrian but only 0.3% of the German donors were negative for YT *01. One donor from Northern Africa homo-zygously carried the GYPB *270+5g>t mutation, inducing the S-s-U+<sup>w</sup> phenotype, and in 2 German donors a GYPB *c.161G>A exchange, which induces the Mit+ phenotype, caused a GYPB *03 allele dropout in the MALDI assay. The overall failure rate of the Arabian panel was 0.4%. Conclusions Some blood group alleles that are largely lacking in Europeans but had been described in African individuals are present in Arabian populations at a somewhat lower frequency. In single cases, it could be challenging to provide immunized Arabian patients with compatible blood.
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Affiliation(s)
- Brigitte Katharina Flesch
- German Red Cross Blood Service Rhineland-Palatinate and Saarland, Bad Kreuznach, Germany.,German Red Cross Blood Service West, Hagen, Germany
| | - Vanessa Scherer
- German Red Cross Blood Service Rhineland-Palatinate and Saarland, Bad Kreuznach, Germany
| | | | - Andreas Opitz
- German Red Cross Blood Service Rhineland-Palatinate and Saarland, Bad Kreuznach, Germany
| | - Oswin Ochmann
- German Red Cross Blood Service Rhineland-Palatinate and Saarland, Bad Kreuznach, Germany
| | - Anne Janson
- German Red Cross Blood Service Rhineland-Palatinate and Saarland, Bad Kreuznach, Germany
| | - Monika Steitz
- German Red Cross Blood Service Rhineland-Palatinate and Saarland, Bad Kreuznach, Germany
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10
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Kelley LP, Nylander A, Arnaud L, Schmoker AM, St Clair RM, Gleason LA, Souza JM, Storry JR, Olsson ML, Ballif BA. Dimerization of small integral membrane protein 1 promotes cell surface presentation of the Vel blood group epitope. FEBS Lett 2020; 594:1261-1270. [PMID: 31879955 DOI: 10.1002/1873-3468.13726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/03/2019] [Indexed: 01/04/2023]
Abstract
The Vel blood group antigen is carried on the short extracellular segment of the 78-amino-acid-long, type II transmembrane protein SMIM1 of unknown function. Here, using biochemical analysis and flow cytometry of cells expressing wild-type and mutant alleles of SMIM1, we demonstrate that dimerization of SMIM1 promotes cell surface display of the Vel epitope. We show that SMIM1 dimerization is mediated both by an extracellular Cys77-dependent, homomeric disulfide linkage and via a GxxxG helix-helix interaction motif in the transmembrane domain. These results provide important context for the observed variability in reactivity patterns of clinically important anti-Vel identified in patient sera.
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Affiliation(s)
- Liam P Kelley
- Department of Biology, University Vermont, Burlington, VT, USA
| | - Anja Nylander
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Department of Internal Medicine, Hässleholm-Kristianstad Hospitals, Kristianstad, Sweden
| | - Lionel Arnaud
- Department of Biology, University Vermont, Burlington, VT, USA
| | - Anna M Schmoker
- Department of Biology, University Vermont, Burlington, VT, USA
| | | | | | - Jessica M Souza
- Department of Biology, University Vermont, Burlington, VT, USA
| | - Jill R Storry
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Martin L Olsson
- Division of Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Office of Medical Services, Region Skåne, Lund, Sweden
| | - Bryan A Ballif
- Department of Biology, University Vermont, Burlington, VT, USA
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11
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Aniweh Y, Nyarko PB, Quansah E, Thiam LG, Awandare GA. SMIM1 at a glance; discovery, genetic basis, recent progress and perspectives. Parasite Epidemiol Control 2019; 5:e00101. [PMID: 30906890 PMCID: PMC6416411 DOI: 10.1016/j.parepi.2019.e00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/28/2018] [Accepted: 03/06/2019] [Indexed: 11/18/2022] Open
Abstract
Recent elucidation of the genetic basis of the Vel blood group system has offered the field of blood transfusion medicine an additional consideration in determining the causes of hemolytic reactions after a patient is transfused. The identification of the SMIM1 gene to be responsible for the Vel blood group allows molecular based tools to be developed to further dissect the function of this antigen. Genetic signatures such as the homozygous 17 bp deletion and the heterozygous 17 bp deletion in combination with other single nucleotide polymorphisms (SNPs) and insertion sequences regulate the expression level of the gene. With this knowledge, it is now possible to study this antigen in-depth.
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Affiliation(s)
- Yaw Aniweh
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Prince B. Nyarko
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Evelyn Quansah
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Laty Gaye Thiam
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Gordon A. Awandare
- West Africa Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
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12
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Dezan MR, Costa-Neto A, Gomes CN, Ribeiro IH, Oliveira VB, Conrado MCAV, Oliveira TGM, Carvalho MLP, Aranha AF, Bosi SRA, Salles NA, Krieger JE, Pereira AC, Sabino EC, Rocha V, Mendrone-Junior A, Dinardo CL, Levi JE. SMIM1 intron 2 gene variations leading to variability in Vel antigen expression among Brazilian blood donors. Blood Cells Mol Dis 2019; 77:23-28. [PMID: 30939337 DOI: 10.1016/j.bcmd.2019.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND There is a significant inter-individual heterogeneity of Vel antigen expression which can lead to inaccuracies on Vel phenotyping of blood donors and, potentially, to hemolytic post-transfusion reactions. Our aim was to evaluate the impact of genetic variants in the SMIM1 intron 2 on the expression of Vel antigen among Brazilian blood donors harboring the c.64_80del17 deletion in heterozygosity. METHODS Donors presenting the SMIM1 c.64_80del17 in heterozygosity were included in the study and subjected to SMIM1 intron 2 direct sequencing aiming to genotype the following polymorphisms: rs143702418, rs1181893, rs191041962, rs6673829, rs1175550 and rs9424296. RESULTS SMIM1 intron 2 sequencing was performed on two hundred donors presenting one c.64_80del17 allele. The rs1175550 polymorphism significantly impacted on Vel antigen expression. Variations in the strength of agglutination on Vel phenotyping were also observed according to the rs6673829 genotype, but this difference did not persist with statistical relevance after multivariate analysis. CONCLUSION The presence of the rs1175550A allele of SMIM1 is significantly and independently associated with a decrease in Vel antigen expression. Even though the population in Brazil is intensely mixed, the allele frequencies obtained in the current study were very similar to that reported for Europeans.
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Affiliation(s)
- Marcia Regina Dezan
- Fundação Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil; Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, Brazil.
| | - Abel Costa-Neto
- Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Disciplina de Hematologia, Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | | | - Théo Gremen M Oliveira
- Fundação Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil; Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of Sao Paulo School of Medicine, Brazil
| | - Mariana L P Carvalho
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of Sao Paulo School of Medicine, Brazil
| | - Aline Fernanda Aranha
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of Sao Paulo School of Medicine, Brazil
| | - Silvia R A Bosi
- Fundação Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil
| | - Nanci A Salles
- Fundação Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil
| | - José Eduardo Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of Sao Paulo School of Medicine, Brazil
| | - Alexandre Costa Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute (InCor), University of Sao Paulo School of Medicine, Brazil
| | | | - Vanderson Rocha
- Fundação Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil; Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Disciplina de Hematologia, Universidade de Sao Paulo, Sao Paulo, Brazil; Churchill Hospital, NHSBT, Oxford University, Oxford, UK
| | | | - Carla Luana Dinardo
- Fundação Pro-Sangue Hemocentro de Sao Paulo, Sao Paulo, Brazil; Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, Brazil.
| | - José Eduardo Levi
- Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, Brazil
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13
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van der Rijst MVE, Lissenberg-Thunnissen SN, Ligthart PC, Visser R, Jongerius JM, Voorn L, Veldhuisen B, Vidarsson G, van den Akker E, van der Schoot CE. Development of a recombinant anti-Vel immunoglobulin M to identify Vel-negative donors. Transfusion 2019; 59:1359-1366. [PMID: 30702752 DOI: 10.1111/trf.15147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/28/2018] [Accepted: 12/03/2018] [Indexed: 01/10/2023]
Abstract
BACKGROUND Alloimmunization against the high-frequency Vel blood group antigen may result in transfusion reactions or hemolytic disease of fetus and newborn. Patients with anti-Vel alloantibodies require Vel-negative blood but Vel-negative individuals are rare (1:4000). Identification of Vel-negative donors ensures availability of Vel-negative blood; however, accurate Vel blood group typing is difficult due to variable Vel antigen expression and limited availability of anti-Vel typing sera. We report the production of a recombinant anti-Vel that also identifies weak Vel expression. STUDY DESIGN AND METHODS A recombinant anti-Vel monoclonal antibody was produced by cloning the variable regions from an anti-Vel-specific B cell isolated from an alloimmunized patient into a vector harboring the constant regions of immunoglobulin (Ig)G1-kappa or IgM-kappa. Antibody Vel specificity was tested by reactivity to SMIM1-transfected HEK293T cells and by testing various red blood cells (RBCs) of donors with normal, weak, or no Vel expression. High-throughput donor screening applicability was tested using an automated blood group analyzer. RESULTS A Vel-specific IgM class antibody was produced. The antibody was able to distinguish between Vel-negative and very weak Vel antigen-expressing RBCs by direct agglutination and in high-throughput settings using a fully automated blood group analyzer and performed better than currently used human anti-Vel sera. High-throughput screening of 13,288 blood donations identified three new Vel-negative donors. CONCLUSION We generated a directly agglutinating recombinant anti-Vel IgM, M3F5S-IgM, functional in manual, automated agglutination assays and flow cytometry settings. This IgM anti-Vel will improve diagnostics by facilitating the identification of Vel-negative blood donors.
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Affiliation(s)
- Marea V E van der Rijst
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands.,Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | | | - Peter C Ligthart
- Department of Immunohematology Diagnostic Services, Sanquin, Amsterdam, The Netherlands
| | - Remco Visser
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - John M Jongerius
- Department of Research and Lab Services, National Screening Laboratory Sanquin, Sanquin, Amsterdam, the Netherlands
| | - Lesley Voorn
- Department of Research and Lab Services, National Screening Laboratory Sanquin, Sanquin, Amsterdam, the Netherlands
| | - Barbera Veldhuisen
- Department of Immunohematology Diagnostic Services, Sanquin, Amsterdam, The Netherlands
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - Emile van den Akker
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
| | - C Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, AUMC, Amsterdam, The Netherlands
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14
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Jongruamklang P, Gassner C, Meyer S, Kummasook A, Darlison M, Boonlum C, Chanta S, Frey BM, Olsson ML, Storry JR. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of 36 blood group alleles among 396 Thai samples reveals region-specific variants. Transfusion 2018; 58:1752-1762. [PMID: 29656499 DOI: 10.1111/trf.14624] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Blood group phenotype variation has been attributed to potential resistance to pathogen invasion. Variation was mapped in blood donors from Lampang (northern region) and Saraburi (central region), Thailand, where malaria is endemic. The previously unknown blood group allele profiles were characterized and the data were correlated with phenotypes. The high incidence of the Vel-negative phenotype previously reported in Thais was investigated. STUDY DESIGN AND METHODS DNA from 396 blood donors was analyzed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Outliers were investigated by serology and DNA sequencing. Allele discrimination assays for SMIM1 rs1175550A/G and ACKR1 rs118062001C/T were performed and correlated with antigen expression. RESULTS All samples were phenotyped for Rh, MNS, and K. Genotyping/phenotyping for RhD, K, and S/s showed 100% concordance. Investigation of three RHCE outliers revealed an e-variant antigen encoded by RHCE*02.22. Screening for rs147357308 (RHCE c.667T) revealed a frequency of 3.3%. MN typing discrepancies in 41 samples revealed glycophorin variants, of which 40 of 41 were due to Mia . Nine samples (2.3%) were heterozygous for FY*01W.01 (c.265C > T), and six samples (1.5%) were heterozygous for JK*02N.01. All samples were wildtype SMIM1 homozygotes with 97% homozygosity for rs1175550A. CONCLUSIONS Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry is an efficient method for rapid routine genotyping and investigation of outliers identified novel variation among our samples. The expected high prevalence of the Mi(a+) phenotype was observed from both regions. Of potential clinical relevance in a region where transfusion-dependent thalassemia is common, we identified two RHCE*02 alleles known to encode an e-variant antigen.
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Affiliation(s)
- Philaiphon Jongruamklang
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Christoph Gassner
- Molecular Diagnostics & Research (MOC), Blood Transfusion Service Zürich, Zürich-Schlieren, Switzerland
| | - Stefan Meyer
- Molecular Diagnostics & Research (MOC), Blood Transfusion Service Zürich, Zürich-Schlieren, Switzerland
| | - Aksarakorn Kummasook
- Department of Medical Technology, School of Allied Health Sciences, University of Phayao, Phayao, Thailand
| | - Marion Darlison
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Chayanun Boonlum
- Transfusion Medicine, Department of Medical Technology and Clinical Laboratory, Saraburi Hospital, Saraburi, Thailand
| | - Surin Chanta
- Transfusion Medicine, Department of Medical Technology and Clinical Laboratory, Lampang Hospital, Lampang, Thailand
| | - Beat M Frey
- Molecular Diagnostics & Research (MOC), Blood Transfusion Service Zürich, Zürich-Schlieren, Switzerland
| | - Martin L Olsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, Lund, Sweden
| | - Jill R Storry
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden.,Clinical Immunology and Transfusion Medicine, Laboratory Medicine, Office of Medical Services, Lund, Sweden
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15
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Jakobsen MA, Dellgren C, Sheppard C, Yazer M, Sprogøe U. The use of next-generation sequencing for the determination of rare blood group genotypes. Transfus Med 2017; 29:162-168. [PMID: 29265667 DOI: 10.1111/tme.12496] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/13/2017] [Accepted: 11/26/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Next-generation sequencing (NGS) for the determination of rare blood group genotypes was tested in 72 individuals from different ethnicities. BACKGROUND Traditional serological-based antigen detection methods, as well as genotyping based on specific single nucleotide polymorphisms (SNPs) or single nucleotide variants (SNVs), are limited to detecting only a limited number of known antigens or alleles. NGS methods do not have this limitation. METHODS NGS using Ion torrent Personal Genome Machine (PGM) was performed with a customised Ampliseq panel targeting 15 different blood group systems on 72 blood donors of various ethnicities (Caucasian, Hispanic, Asian, Middle Eastern and Black). RESULTS Blood group genotypes for 70 of 72 samples could be obtained for 15 blood group systems in one step using the NGS assay and, for common SNPs, are consistent with previously determined genotypes using commercial SNP assays. However, particularly for the Kidd, Duffy and Lutheran blood group systems, several SNVs were detected by the NGS assay that revealed additional coding information compared to other methods. Furthermore, the NGS assay allowed for the detection of genotypes related to VEL, Knops, Gerbich, Globoside, P1PK and Landsteiner-Wiener blood group systems. CONCLUSIONS The NGS assay enables a comprehensive genotype analysis of many blood group systems and is capable of detecting common and rare alleles, including alleles not currently detected by commercial assays.
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Affiliation(s)
- M A Jakobsen
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark.,University of Southern Denmark, Odense, Denmark
| | - C Dellgren
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - C Sheppard
- Virginia Blood Services, Richmond, Virginia, USA
| | - M Yazer
- University of Southern Denmark, Odense, Denmark.,Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - U Sprogøe
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
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16
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Affiliation(s)
- A. K. Hult
- Division of Laboratory Medicine; Clinical Immunology and Transfusion Medicine; Office of Medical Services; Lund Sweden
- Division of Hematology and Transfusion Medicine; Department of Laboratory Medicine; Lund University; Lund Sweden
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17
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Liu TX, Liu YC, Ma L, Zhao F, Zhang RY, Shi LL. Molecular screening of Vel-blood donors using DNA pools in Nanjing, China. Transfus Med 2017; 27:457-459. [PMID: 28881066 DOI: 10.1111/tme.12460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/22/2017] [Accepted: 08/10/2017] [Indexed: 11/30/2022]
Affiliation(s)
- T X Liu
- Immunohematology Laboratory, Jiangsu Province Blood Center, Nanjing, China
| | - Y C Liu
- Immunohematology Laboratory, Jiangsu Province Blood Center, Nanjing, China
| | - L Ma
- Immunohematology Laboratory, Jiangsu Province Blood Center, Nanjing, China
| | - F Zhao
- Immunohematology Laboratory, Jiangsu Province Blood Center, Nanjing, China
| | - R Y Zhang
- Immunohematology Laboratory, Jiangsu Province Blood Center, Nanjing, China
| | - L L Shi
- Immunohematology Laboratory, Jiangsu Province Blood Center, Nanjing, China
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