Use of selective phenotyping and genotyping to identify rare blood donors in Canada

BACKGROUND AND OBJECTIVES

The distribution of rare and specific red cell phenotypes varies between races and ethnicities. Therefore, the most compatible red cell units for patients with haemoglobinopathies and other rare blood requirements are most likely to be found in donors from similar genetic backgrounds. Our blood service introduced a voluntary question asking donors to provide their racial background/ethnicity. Results triggered additional phenotyping and/or genotyping.

MATERIALS AND METHODS

We analysed the results of additional testing performed between January 2021 and June 2022, and rare donors were added to the Rare Blood Donor database. We determined the incidence of various rare phenotypes and blood group alleles based on donor race/ethnicity.

RESULTS

Over 95% of donors answered the voluntary question; 715 samples were tested, and 25 donors were added to the Rare Blood Donor database, including five k-, four U-, two Jk(a-b-) and two D- - phenotypes.

CONCLUSION

Asking donors about their race/ethnicity was well received by donors, and the resulting selective testing enabled us to identify individuals with a higher likelihood of being rare blood donors, support patients with rare blood requirements and better understand the incidence of common and rare alleles and red blood cell phenotypes in the Canadian donor population.

An open-source python library for detection of known and novel Kell, Duffy and Kidd variants from exome sequencing

BACKGROUND AND OBJECTIVES

Next generation sequencing (NGS) has promising applications in transfusion medicine. Exome sequencing (ES) is increasingly used in the clinical setting, and blood group interpretation is an additional value that could be extracted from existing data sets. We provide the first release of an open-source software tailored for this purpose and describe its validation with three blood group systems.

MATERIALS AND METHODS

The DTM-Tools algorithm was designed and used to analyse 1018 ES NGS files from the ClinSeq® cohort. Predictions were correlated with serology for 5 antigens in a subset of 108 blood samples. Discrepancies were investigated with alternative phenotyping and genotyping methods, including a long-read NGS platform.

RESULTS

Of 116 genomic variants queried, those corresponding to 18 known KEL, FY and JK alleles were identified in this cohort. 596 additional exonic variants were identified KEL, ACKR1 and SLC14A1, including 58 predicted frameshifts. Software predictions were validated by serology in 108 participants; one case in the FY blood group and three cases in the JK blood group were discrepant. Investigation revealed that these discrepancies resulted from (1) clerical error, (2) serologic failure to detect weak antigenic expression and (3) a frameshift variant absent in blood group databases.

CONCLUSION

DTM-Tools can be employed for rapid Kell, Duffy and Kidd blood group antigen prediction from existing ES data sets; for discrepancies detected in the validation data set, software predictions proved accurate. DTM-Tools is open-source and in continuous development.

ABO blood group and COVID-19: a review on behalf of the ISBT COVID-19 working group

Growing evidence suggests that ABO blood group may play a role in the immunopathogenesis of SARS-CoV-2 infection, with group O individuals less likely to test positive and group A conferring a higher susceptibility to infection and propensity to severe disease. The level of evidence supporting an association between ABO type and SARS-CoV-2/COVID-19 ranges from small observational studies, to genome-wide-association-analyses and country-level meta-regression analyses. ABO blood group antigens are oligosaccharides expressed on red cells and other tissues (notably endothelium). There are several hypotheses to explain the differences in SARS-CoV-2 infection by ABO type. For example, anti-A and/or anti-B antibodies (e.g. present in group O individuals) could bind to corresponding antigens on the viral envelope and contribute to viral neutralization, thereby preventing target cell infection. The SARS-CoV-2 virus and SARS-CoV spike (S) proteins may be bound by anti-A isoagglutinins (e.g. present in group O and group B individuals), which may block interactions between virus and angiotensin-converting-enzyme-2-receptor, thereby preventing entry into lung epithelial cells. ABO type-associated variations in angiotensin-converting enzyme-1 activity and levels of von Willebrand factor (VWF) and factor VIII could also influence adverse outcomes, notably in group A individuals who express high VWF levels. In conclusion, group O may be associated with a lower risk of SARS-CoV-2 infection and group A may be associated with a higher risk of SARS-CoV-2 infection along with severe disease. However, prospective and mechanistic studies are needed to verify several of the proposed associations. Based on the strength of available studies, there are insufficient data for guiding policy in this regard.

Promoting access to COVID-19 convalescent plasma in low- and middle-income countries

Low- and middle-income countries (LMICs) remain neglected in the Coronavirus 19 (COVID-19) pandemic. COVID-19 convalescent plasma (CCP) (i.e. plasma collected from individuals after their recovery from COVID-19) has emerged as a leading medical treatment for COVID-19. Studies to date support the safety—and increasingly the efficacy—of CCP to treat COVID-19. This has motivated large-scale procurement and transfusion of CCP, notably in the United States (US), where inventories of CCP have been attained, and government-supported stockpiling of CCP is underway. CCP is a therapy that could be implemented in LMICs. However, systemic and transfusion-specific challenges (e.g. capacity for donor mobilization and collections) impede local procurement of this resource in sufficient volumes to meet clinical demand. This raises the question as to whether there are strategies to facilitate sharing of CCP with LMICs and/or bolstering local capacity for collection to contend with the health crisis. While compelling, there are cost-related, logistical and regulatory barriers to both approaches. For one, there is complexity in diverting national interest (e.g. in the US) away from an epidemic that displays few signs of abating. There are also concerns regarding equitable distribution of CCP in LMICs and how that might be overcome. Further, the barriers to blood donation in general apply to collection of CCP; these obstacles are longstanding, accounting for the inability of many LMICs to meet their blood transfusion needs. Nonetheless, CCP affords dual opportunity for humanitarian outreach while tackling a broader challenge of blood transfusion safety and availability.

Banking with precision: transfusion medicine as a potential universal application in clinical genomics

PURPOSE OF REVIEW

To summarize the most recent scientific progress in transfusion medicine genomics and discuss its role within the broad genomic precision medicine model, with a focus on the unique computational and bioinformatic aspects of this emergent field.

RECENT FINDINGS

Recent publications continue to validate the feasibility of using next-generation sequencing (NGS) for blood group prediction with three distinct approaches: exome sequencing, whole genome sequencing, and PCR-based targeted NGS methods. The reported correlation of NGS with serologic and alternative genotyping methods ranges from 92 to 99%. NGS has demonstrated improved detection of weak antigens, structural changes, copy number variations, novel genomic variants, and microchimerism. Addition of a transfusion medicine interpretation to any clinically sequenced genome is proposed as a strategy to enhance the cost-effectiveness of precision genomic medicine. Interpretation of NGS in the blood group antigen context requires not only advanced immunohematology knowledge, but also specialized software and hardware resources, and a bioinformatics-trained workforce.

SUMMARY

Blood transfusions are a common inpatient procedure, making blood group genomics a promising facet of precision medicine research. Further efforts are needed to embrace transfusion bioinformatic challenges and evaluate its clinical utility.

ABO, Rhesus, and Kell Antigens, Alleles, and Haplotypes in West Bengal, India

Background

Few studies have documented the blood group antigens in the population of eastern India. Frequencies of some common alleles and haplotypes were unknown. We describe phenotype, allele, and haplotype frequencies in the state of West Bengal, India.

Methods

We tested 1,528 blood donors at the Medical College Hospital, Kolkata. The common antigens of the ABO, Rhesus, and Kell blood group systems were determined by standard serologic methods in tubes. Allele and haplotype frequencies were calculated with an iterative method that yielded maximum-likelihood estimates under the assumption of a Hardy-Weinberg equilibrium.

Results

The prevalence of ABO antigens were B (34%), O (32%), A (25%), and AB (9%) with ABO allele frequencies for O = 0.567, A = 0.189, and B = 0.244. The D antigen (RH1) was observed in 96.6% of the blood donors with RH haplotype frequencies, such as for CDe = 0.688809, cde = 0.16983 and CdE = 0.000654. The K antigen (K1) was observed in 12 donors (0.79%) with KEL allele frequencies for K = 0.004 and k = 0.996. Conclusions: For the Bengali population living in the south of West Bengal, we established the frequencies of the major clinically relevant antigens in the ABO, Rhesus, and Kell blood group systems and derived estimates for the underlying ABO and KEL alleles and RH haplotypes. Such blood donor screening will improve the availability of compatible red cell units for transfusion. Our approach using widely available routine methods can readily be applied in other regions, where the sufficient supply of blood typed for the Rh and K antigens is lacking.

Red cell genotyping precision medicine: a conference summary

This review summarizes the salient points of the symposium 'Red Cell Genotyping 2015: Precision Medicine' held on 10 September 2015 in the Masur Auditorium of the National Institutes of Health. The specific aims of this 6th annual symposium were to: (1) discuss how advances in molecular immunohematology are changing patient care; (2) exemplify patient care strategies by case reports (clinical vignettes); (3) review the basic molecular studies and their current implications in clinical practice; (4) identify red cell genotyping strategies to prevent alloimmunization; and (5) compare and contrast future options of red cell genotyping in precision transfusion medicine. This symposium summary captured the state of the art of red cell genotyping and its contribution to the practice of precision medicine.

Abstract A05: The tumor suppressor function of Plk2 in triple-negative breast cancer may be mediated through regulation of Plk1

Triple-negative breast cancers (TNBCs) are highly aggressive, associated with poor prognosis and lack targeted therapies. Current breast cancer therapies target the estrogen (ER), progesterone (PR) and human epidermal growth factor (HER2) receptors, which are absent in TNBCs. Developing new treatment strategies for TNBCs requires a better understanding of the signaling networks regulating TNBCs. Polo-like kinase 1 (Plk1) is a putative oncogene in TNBC. Plk1 is frequently overexpressed and promotes mitotic cell division, making it an attractive target for cancer therapy. Several inhibitors of Plk1 exist, one of which has accelerated to phase III clinical trials for acute myeloid leukemia. However, these drugs also inhibit Plk2, another polo-like kinase family member. The impact that the presence of Plk2 has on the effectiveness of Plk1 inhibitors as a cancer therapy is unknown.

We reported recently that a loss of Plk2 in the developing mammary gland results in increased proliferation, hyperbranching, misoriented mitotic spindle assembly and defects in polarity (Villegas et al Development 2015). Loss of Plk2 was accompanied by increased expression of Plk1. Genetic rescue experiments, knocking down Plk1 in Plk2 null mouse mammary epithelium, and bimolecular fluorescence complementation assays, using wildtype Plk2 and a kinase dead mutant (KD) of Plk2 as bait, revealed that Plk2 regulates these processes through its direct interaction with Plk1. Our preliminary data suggest that loss of Plk2 results in increased Plk1 protein but not RNA expression. We propose that Plk2 functions as a tumor suppressor by decreasing Plk1 stability in TNBCs. Loss of Plk2, therefore, may sensitize tumors to treatment with Plk1 inhibitors if these tumors display Plk1 oncogene addiction. We hypothesize that Plk2, through targeted degradation of Plk1, inhibits tumorigenesis in TNBC.

We observed that loss of Plk2 alone is not sufficient to generate mouse mammary tumors, however more lesions form after multiple pregnancies in Plk2 null glands than wildtype. To examine the tumor suppressor function of Plk2 through its regulation of Plk1 in TNBC, we are generating preclinical mouse mammary tumor models integrating the germline loss of Plk2 with p53 loss or c-Myc overexpression frequently observed in TNBC. Finally, to investigate the clinical relevance of Plk2 in TNBC, we will use available tissue microarrays of TNBC patient derived xenograft (PDX) mouse models to identify those that exhibit loss of Plk2. We will treat the identified PDX models with Plk1 inhibitors to confirm that Plk2 loss promotes Plk1 in human TNBC samples. With these studies, we expect to find that Plk2 is involved in the targeted degradation of Plk1 in TNBC, sensitizing this aggressive breast cancer subtype to treatment with Plk1 inhibitors. The results of these studies should help validate whether Plk2 is a new biomarker for determining which patients will benefit from Plk1 targeted TNBC treatment. Supported by Susan G. Komen Foundation grant SAC110031.

Citation Format: Deanna Acosta, Elizabeth Villegas, Elena Kabotyanski, Celina Montemayor, Sarah J. Kurley, Rocio Dominguez-Vidana, Chad A. Shaw, Thomas F. Westbrook, Jeffrey M. Rosen. The tumor suppressor function of Plk2 in triple-negative breast cancer may be mediated through regulation of Plk1. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A05.

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI

Background

Identification of bona fide direct nuclear receptor gene targets has been challenging but essential for understanding regulation of organismal physiological processes.

Results

We describe a methodology to identify transcription factor binding sites and target genes in vivo by intersecting microarray data, computational binding site queries, and evolutionary conservation. We provide detailed experimental validation of each step and, as a proof of principle, utilize the methodology to identify novel direct targets of the orphan nuclear receptor NR2F1 (COUP-TFI). The first step involved validation of microarray gene expression profiles obtained from wild-type and COUP-TFI^−/− inner ear tissues. Secondly, we developed a bioinformatic tool to search for COUP-TFI DNA binding sites in genomes, using a classification-type Hidden Markov Model trained with 49 published COUP-TF response elements. We next obtained a ranked list of candidate in vivo direct COUP-TFI targets by integrating the microarray and bioinformatics analyses according to the degree of binding site evolutionary conservation and microarray statistical significance. Lastly, as proof-of-concept, 5 specific genes were validated for direct regulation. For example, the fatty acid binding protein 7 (Fabp7) gene is a direct COUP-TFI target in vivo because: i) we identified 2 conserved COUP-TFI binding sites in the Fabp7 promoter; ii) Fapb7 transcript and protein levels are significantly reduced in COUP-TFI^−/− tissues and in MEFs; iii) chromatin immunoprecipitation demonstrates that COUP-TFI is recruited to the Fabp7 promoter in vitro and in vivo and iv) it is associated with active chromatin having increased H3K9 acetylation and enrichment for CBP and SRC-1 binding in the newborn brain.

Conclusion

We have developed and validated a methodology to identify in vivo direct nuclear receptor target genes. This bioinformatics tool can be modified to scan for response elements of transcription factors, cis-regulatory modules, or any flexible DNA pattern.

Sensorineural hearing loss: potential therapies and gene targets for drug development

Recent advances in the developmental biology, genetics and cell biology of the inner ear are guiding research to novel therapeutic modalities - a market currently estimated to be at least US Dollars 10 billion. This article highlights prospects to manipulate the mammalian hearing organ with gene and stem cell delivery to the inner ear to protect, repair or regenerate the hair cells, supporting cells and associated nerves.