Hemoglobin E, malaria and natural selection

Carrier frequency estimation of pathogenic variants of autosomal recessive and X-linked recessive mendelian disorders using exome sequencing data in 1,642 Thais

BACKGROUND

People with autosomal recessive disorders often were born without awareness of the carrier status of their parents. The American College of Medical Genetics and Genomics (ACMG) recommends screening 113 genes known to cause autosomal recessive and X-linked conditions in couples seeking to learn about their risk of having children with these disorders to have an appropriate reproductive plan.

METHODS

We analyzed the exome sequencing data of 1,642 unrelated Thai individuals to identify the pathogenic variant (PV) frequencies in genes recommended by ACMG.

RESULTS

In the 113 ACMG-recommended genes, 165 PV and likely PVs in 60 genes of 559 exomes (34%, 559/1642) were identified. The carrier rate was increased to 39% when glucose-6-phosphate dehydrogenase (G6PD) was added. The carrier rate was still as high as 14.7% when thalassemia and hemoglobinopathies were excluded. In addition to thalassemia, hemoglobinopathies, and G6PD deficiency, carrier frequencies of > 1% were found for Gaucher disease, primary hyperoxaluria, Pendred syndrome, and Wilson disease. Nearly 2% of the couples were at risk of having offsprings with the tested autosomal recessive conditions.

CONCLUSIONS

Based on the study samples, the expanded carrier screening, which specifically targeted common autosomal recessive conditions in Thai individuals, will benefit clinical outcomes, regarding preconception/prenatal genetic carrier screening.

Clinical Outcome, Socioeconomic Status and Psychological Constrains of Patients Undergoing Preimplantation Genetic Testing (PGT) in Northern Greece

Background and objectives: Preimplantation genetic testing (PGT) offers patients the possibility of having a healthy baby free of chromosomal or genetic disorders. The present study focuses on the application of PGT for patients located in Northern Greece, investigating their clinical outcomes, their motives, and their overall physical and emotional experience during the treatment, in association with their socioeconomic background. Materials and Methods: Couples who underwent PGT for a monogenic condition (PGT-M, n = 19 cycles) or aneuploidy (PGT-A, n = 22 cycles) participated in the study. Fertilization, implantation, and pregnancy rates were recorded for all cycles. The couples were asked to fill in a questionnaire about the consultation they had received prior to treatment, their sociodemographic information, and the psychological impact PGT had on both the female and male partner. Results: The fertilization, implantation, and ongoing pregnancy rates for the PGT-M and PGT-A cycles were 81.3%, 70.6%, and 52.9%, and 78.2%, 64.3%, and 57.1%, respectively. Females experienced more intense physical pain than their male partners while psychological pain was encountered by both partners and occasionally in higher instances in males. No typical socioeconomic background of the patients referred for PGT in Northern Greece was noticed. Conclusion: PGT is an attractive alternative to prenatal diagnosis (PND), aiming to establisha healthy pregnancy by identifying and avoiding the transfer of chromosomally or genetically abnormal embryos to the uterus. Although the benefits of PGT were well-received by all patients undergoing the procedure, psychological pain was evident and especially prominent in patients with a previous affected child or no normal embryos for transfer. Holistic counseling is of utmost importance in order to make patients' experience during their journey to have a healthy baby less emotionally demanding and help them make the right choices for the future.

Distinct landscapes of deleterious variants in DNA damage repair system in ethnic human populations

Deleterious variants in the DNA damage repair system can cause genome instability and increase cancer risk. The highly ethnic-specific DDR deleterious variation from this study suggests its potential relationship with different disease susceptibility in ethnic human populations.

Deleterious variants in DNA damage repair (DDR) system can cause genome instability and increase cancer risk. In this study, we analyzed the deleterious variants in DDR system in 16 ethnic human populations. From the genetic variants in 169 DDR genes involved in nine DDR pathways collected from 158,612 individuals of different ethnic background, we identified 1,781 deleterious variants in 81 DDR genes in eight DDR pathways (https://genemutation.fhs.um.edu.mo/dbddr-global/). Our analysis showed although the quantity of deleterious variants was loaded at a similar level, the landscape of the variants differed substantially among different populations that two-third of the variants were present in single ethnic populations, and the rest was mostly shared between the populations with closer geographic and genetic relationship. The highly ethnic-specific DDR deleterious variation suggests its potential relationship with different disease susceptibility in ethnic human populations.

Primate malarias as a model for cross-species parasite transmission

Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.

The prevalence of sickling abnormality in Oman: A review of relevant publications

Sickle cell disease (SCD), caused by a mutation in the β-globin gene HBB, is widely distributed in malaria endemic regions.  The prevalence of sickle cell trait and disease reaches up to 4.8-6% and 0.2% respectively, which is the highest among the Arab Gulf states.  Omani population represents a variability of HbS genotype combinations with other Hb genotypes modify the clinical severity of the disease. The most prevalent sickling abnormality in Oman is Hb S/S (SCA) followed by Hb S/β-thalassemia. Omani children with SCD with high Hb F level had less severe disease. More than two-thirds of SCD cases were running a mild course of the disease due to the high prevalence of  a-thalassemia trait. The severity index has been correlated with the early age of presentation, the absence of  a-thalassemia trait and the lower level of HbF as well as to the existence of different β-globin gene haplotypes.  S/ β0 presented with the same clinical severity of S/S while those with S/ β+ had some splenic function into adulthood and were more prone to splenic sequestration. The unique existence of HbS-Oman (a severe variant of sickle hemoglobinopathy) markedly increased the severity of the disease. Compound heterozygotes HbS-Oman resulted in very severe clinical manifestations with transfusion-dependency and hypersplenism early in life. This paper summarizes and reviews βs gene haplotypes in patients with sickle cell anemia (SCA) in Oman. (www.actabiomedica.it).

Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy

The malaria hypothesis predicts local, balancing selection of deleterious alleles that confer strong protection from malaria. Three protective variants, recently discovered in red cell genes, are indeed more common in African than European populations. Still, up to 89% of the heritability of severe malaria is attributed to many genome-wide loci with individually small effects. Recent analyses of hundreds of genome-wide association studies (GWAS) in humans suggest that most functional, polygenic variation is pleiotropic for multiple traits. Interestingly, GWAS alleles and red cell traits associated with small reductions in malaria risk are not enriched in African populations. We propose that other selective and neutral forces, in addition to malaria prevalence, explain the global distribution of most genetic variation impacting malaria risk.

SARS-CoV-2 and dengue virus coinfection in an adult with beta-thalassemia (trait): A case report from Bangladesh with literature review

Introduction

Coinfections are common in pandemics, however not in recorded patients with hemoglobinopathies. The Coronavirus Disease 2019 (COVID-19) pandemic struck Bangladesh at the beginning of March 2020, which is also an apt period for endemic Dengue fever in this monsoon region.

Case report

We report a 30-year-old man with hemoglobinopathies coinfected with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Dengue virus. Dengue virus was detected by Enzyme-linked Immunosorbent Assay (ELISA). COVID-19 was confirmed by Reverse-transcription Polymerase Chain Reaction (RT-PCR) and Hemoglobin Electrophoresis revealed heterozygous beta-thalassemia or thalassemia trait. The patient was treated successfully at Dhaka Hospital in icddr,b during COVID-19 emergency response with symptomatic supportive treatment for COVID-19 and appropriate fluid therapy for dengue fever in response to daily hematocrit level. The patient's repeated RT-PCR for COVID-19 on day-21 became negative. For thalassemia, the patient was advised to have genetic counseling and family screening on discharge.

Conclusion

The possibility of coinfection between COVID-19 and Dengue fever may be considered in a COVID-19 patient with unremitting fever especially in an area where Dengue fever is epidemic that may further help to attain appropriate management of the patient.

Brain transcriptome analysis reveals genes involved in parental care behaviour in discus fish (Symphysodon haraldi)

Parental care is common in mammals and allows offspring to obtain milk, a substance rich in a range of nutritional and non-nutritional factors crucial to the survival of newborns. The discus fish Symphysodon spp., an Amazonian cichlid, shows an unusual behaviour: Free-swimming fry bite on their parents' skin mucus for growth and development during the first month after hatching. This is similar to the breastfeeding behaviour of mammals, but little is known about the regulatory mechanism by which discus secrete 'milk' and the related genes involved in parental care. Here, transcriptome sequencing was performed by using the brain tissues of female discus fish in parental and non-parental care. The results showed that a total of 86 differentially expressed genes (71 up-regulated genes and 15 down-regulated genes) were obtained by comparing parental with non-parental discus fish, including up-regulated LAPTM, FOXB, SOX1S, OTX2 and NR1F2, and down-regulated EDNRB, PRKCD, H1-5 and HBE. Through functional enrichment analysis, a total of 20 pathways were identified, e.g., estrogen signaling pathway, inflammatory mediator regulation of TRP channels, vascular smooth muscle contraction, GnRH signaling pathway, neurotrophin signaling pathway, NOD-like receptor signaling pathway, Jak-STAT signaling pathway, Fc gamma R-mediated phagocytosis, serotonergic synapse, autophagy-animal and cytokine-cytokine receptor interaction. These pathways and related genes might play important roles in the regulation of discus 'milk' secretion.

Evolutionary history of sickle-cell mutation: implications for global genetic medicine

Resistance afforded by the sickle-cell trait against severe malaria has led to high frequencies of the sickle-cell mutation [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)] in most parts of Africa. High-coverage sequencing and genotype data have now confirmed the single African origin of the sickle-cell gene variant [HBB; c.20T>A, p.Glu6Val; OMIM: 141900 (HBB-βS)]. Nevertheless, the classical HBB-like genes cluster haplotypes remain a rich source of HBB-βS evolutionary information. The overlapping distribution of HBB-βS and other disease-associated variants means that their evolutionary genetics must be investigated concurrently. In this review: (1) we explore the evolutionary history of HBB-βS and its implications in understanding human migration within and out of Africa: e.g. HBB haplotypes and recent migration paths of the Bantu expansion, occurrence of ~7% of the Senegal haplotype in Angola reflecting changes in population/SCD dynamics, and existence of all five classical HBB haplotype in Cameroon and Egypt suggesting a much longer presence of HBB-βS in these regions; (2) we discuss the time estimates of the emergence of HBB-βS in Africa and finally, (3) we discuss implications for genetic medicine in understanding complex epistatic interactions between HBB-βS and other gene variants selected under environmental pressure in Africa e.g. variants in HBB, HBA, G6PD, APOL1, APOE, OSBPL10 and RXRA.

A Southeast Asian Perspective on the COVID-19 Pandemic: Hemoglobin E (HbE)-Trait Confers Resistance Against COVID-19

As of November 25, 2020, over 60 million people have been infected worldwide by COVID-19, causing almost 1.43 million deaths. Puzzling low incidence numbers and milder, non-fatal disease have been observed in Thailand and its Southeast (SE) Asian neighbors. Elusive genetic mechanisms might be operative, as a multitude of genetic factors are widely shared between the SE Asian populations, such as the more than 60 different thalassemia syndromes (principally dominated by the HbE trait). In this study, we have plotted COVID-19 infection and death rates in SE Asian (SEA) countries against heterozygote HbE and thalassemia carrier prevalence. COVID-19 infection and death incidence numbers appear inversely correlated with the prevalence of HbE and thalassemia heterozygote populations. We posit that the evolutionary protective effect of the HbE and other thalassemic variants against malaria and the dengue virus may extend its advantage to resistance to COVID-19 infection, as HbE heterozygote population prevalence appears to be positively correlated with immunity to COVID-19. Host immune system modulations induce antiviral interferon responses and alter structural protein integrity, thereby inhibiting cellular access and viral replication. These changes are possibly engendered by HbE carrier miRNAs. Proving this hypothesis is important, as it may shed light on the mechanism of viral resistance and lead to novel antiviral treatments. This development can thus guide decision-making and action to prevent COVID-19 infection.