Genome-wide analyses disclose the distinctive HLA architecture and the pharmacogenetic landscape of the Somali population

Prognostic Role of Human Leukocyte Antigen Alleles and Cytokine Single-Nucleotide Polymorphisms in Patients with Chronic Myeloid Leukemia Treated with Tyrosine Kinase Inhibitor Drugs

Tyrosine kinase inhibitor (TKI) drugs have significantly improved chronic myeloid leukemia (CML) outcomes. Neopeptides from CML cells may induce specific immune responses, which are crucial for deep molecular (DMR) and treatment-free remission (TFR). In this study of Ethiopian patients with CML (n = 162), the HLA alleles and single-nucleotide polymorphisms of five cytokines revealed significant associations with clinical outcomes. Clinically unfavorable outcomes correlated with HLA alleles A*03:01/02, A*23:17:01, B*57:01/02/03, and HLA-DRB4*01:01 (p-value = 0.0347, p-value = 0.0285, p-value = 0.037, and p-value = 0.0127, respectively), while HLA-DRB4*01:03:01 was associated with favorable outcomes (p-value = 0.0058). After assigning values for the 'low', 'intermediate', and 'high' gene expression of the SNPs' respective cytokine genes, Kaplan-Meier estimates for relapse-free survival, adjusted for age, treatment duration, and relapse risk among patients after the administration of TKIs, indicated that a gene expression ratio above the overall median of TNF-α, IL-6, and the combination of TGF-β1/IL-10, IFNγ, and IL-6/IL-10 TGF-β1 was correlated with a higher likelihood of treatment failure ((RR: 3.01; 95% CI: 1.1-8.3; p-value = 0.0261) and (RR: 2.4; 95% CI: 1.1-5.2; p-value = 0.022), respectively). Multi-SNPs, surpassing single-SNPs, and HLA allele polymorphisms showed promise in predicting outcomes of patients with CML during TKI treatment, prompting further exploration into their potential utility.

Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students

Here, salivary microbiota and major histocompatibility complex (MHC) human leukocyte antigen (HLA) alleles were compared between 47 (12.6%) young adults with recent suicidal ideation (SI) and 325 (87.4%) controls without recent SI. Several bacterial taxa were correlated with SI after controlling for sleep issues, diet, and genetics. Four MHC class II alleles were protective for SI including DRB1*04, which was absent in every subject with SI while present in 21.7% of controls. Increased incidence of SI was observed with four other MHC class II alleles and two MHC class I alleles. Associations between these HLA alleles and salivary bacteria were also identified. Furthermore, rs10437629, previously associated with attempted suicide, was correlated here with SI and the absence of Alloprevotella rava, a producer of an organic acid known to promote brain energy homeostasis. Hence, microbial-genetic associations may be important players in the diathesis-stress model for suicidal behaviors.

ABO and Rhesus Blood Group Distribution in Mogadishu, Somalia

Purpose

Our aim in this study is to reveal the blood group distribution by investigating retrospectively the blood types of around 60 thousand patients and donors who applied to Mogadishu Somalia Turkey Recep Tayyip Erdogan Training and Research Hospital between 2018 and 2021.

Patients and Methods

The blood group data of 59,442 people were included in this study. 20,414 (34.35%) of the study’s participants were female, 39,023 (65.65%) were male. The blood groups of participants were determined using the slide method and the gel column technique. The frequencies and percentages of O, A, B, AB and Rh blood groups were calculated.

Results

The frequencies of ABO blood group distribution indicated that blood group O and Rh+ were predominant in Mogadishu O group: 60.30%, A group: 26.50%, B group: 11.27%, AB group: 1.93%, Rh+ group: 96.49%, Rh− group: 3.43%.

Conclusion

This is the first study about blood group distribution in Mogadishu based on a large number of blood type tests and hospital data. The findings of our study can guide the blood center administrators make decisions concerning blood stocking and supply. This study can give an idea about how much fluctuations may occur in the frequency of blood group types in emigrant populations over many years.

Rhesus negative males have an enhanced IFNγ-mediated immune response to influenza A virus

The Rhesus D antigen (RhD) has been associated with susceptibility to several viral infections. Reports suggest that RhD-negative individuals are better protected against infectious diseases and have overall better health. However, potential mechanisms contributing to these associations have not yet been defined. Here, we used transcriptomic and genomic data from the Milieu Interieur cohort of 1000 healthy individuals to explore the effect of Rhesus status on the immune response. We used the rs590787 SNP in the RHD gene to classify the 1000 donors as either RhD-positive or -negative. Whole blood was stimulated with LPS, polyIC, and the live influenza A virus and the NanoString human immunology panel of 560 genes used to assess donor immune response and to investigate sex-specific effects. Using regression analysis, we observed no significant differences in responses to polyIC or LPS between RhD-positive and -negative individuals. However, upon sex-specific analysis, we observed over 40 differentially expressed genes (DEGs) between RhD-positive (n = 384) and RhD-negative males (n = 75) after influenza virus stimulation. Interestingly these Rhesus-associated differences were not seen in females. Further investigation, using gene set enrichment analysis, revealed enhanced IFNγ signalling in RhD-negative males. This amplified IFNγ signalling axis may explain the increased viral resistance previously described in RhD-negative individuals.

Cross-ethnic analysis of common gene variants in hemostasis show lopsided representation of global populations in genetic databases

A majority of studies reporting human genetic variants were performed in populations of European ancestry whereas other global populations, and particularly many ethnolinguistic groups in other continents, are heavily underrepresented in these studies. To investigate the extent of this disproportionate representation of global populations concerning variants of significance to thrombosis and hemostasis, 845 single nucleotide polymorphisms (SNPs) in and around 34 genes associated with thrombosis and hemostasis and included in the commercial Axiom Precision Medicine Research Array (PMRA) were evaluated, using gene frequencies in 3 African (Somali and Luhya in East Africa, and Yoruba in West Africa) and 14 non-African (admixed American, East Asian, European, South Asian, and sub-groups) populations. Among the populations studied, Europeans were observed to be the best represented population by the hemostatic SNPs included in the PMRA. The European population also presented the largest number of common pharmacogenetic and pathogenic hemostatic variants reported in the ClinVar database. The number of such variants decreased the farther the genetic distance a population was from Europeans, with Yoruba and East Asians presenting the least number of clinically significant hemostatic SNPs in ClinVar while also being the two genetically most distinct populations from Europeans among the populations compared. Current study shows the lopsided representation of global populations as regards to hemostatic genetic variants listed in different commercial SNP arrays, such as the PMRA, and reported in genetic databases while also underlining the importance of inclusion of non-European ethnolinguistic populations in genomics studies designed to discover variants of significance to bleeding and thrombotic disorders.