Mechanisms of genetically-based resistance to malaria

Interaction models matter: an efficient, flexible computational framework for model-specific investigation of epistasis

PURPOSE

Epistasis, the interaction between two or more genes, is integral to the study of genetics and is present throughout nature. Yet, it is seldom fully explored as most approaches primarily focus on single-locus effects, partly because analyzing all pairwise and higher-order interactions requires significant computational resources. Furthermore, existing methods for epistasis detection only consider a Cartesian (multiplicative) model for interaction terms. This is likely limiting as epistatic interactions can evolve to produce varied relationships between genetic loci, some complex and not linearly separable.

METHODS

We present new algorithms for the interaction coefficients for standard regression models for epistasis that permit many varied models for the interaction terms for loci and efficient memory usage. The algorithms are given for two-way and three-way epistasis and may be generalized to higher order epistasis. Statistical tests for the interaction coefficients are also provided. We also present an efficient matrix based algorithm for permutation testing for two-way epistasis. We offer a proof and experimental evidence that methods that look for epistasis only at loci that have main effects may not be justified. Given the computational efficiency of the algorithm, we applied the method to a rat data set and mouse data set, with at least 10,000 loci and 1,000 samples each, using the standard Cartesian model and the XOR model to explore body mass index.

RESULTS

This study reveals that although many of the loci found to exhibit significant statistical epistasis overlap between models in rats, the pairs are mostly distinct. Further, the XOR model found greater evidence for statistical epistasis in many more pairs of loci in both data sets with almost all significant epistasis in mice identified using XOR. In the rat data set, loci involved in epistasis under the XOR model are enriched for biologically relevant pathways.

CONCLUSION

Our results in both species show that many biologically relevant epistatic relationships would have been undetected if only one interaction model was applied, providing evidence that varied interaction models should be implemented to explore epistatic interactions that occur in living systems.

Awareness of sickle cell disease among nursing undergraduates in Farasan: Its interference with malaria

Aim

The present study was conducted to generate data on awareness and incidence of sickle cell disease (SCD) and also to adduce the widespread myths peddled about SCD.

Materials and Methods

Students studying in the Department of Nursing were recruited. A pretested, self-administered sickle cell assessment questionnaire was distributed electronically through WhatsApp group to collect necessary data. Participants were screened for malaria by thin blood smear analyses, and their hemoglobin (Hb) contents (g/dL) were determined by Sahli's haemoglobinometer. Statistical analyses were done using Origin (version 8.1, USA). A reliability study was performed for the validity of questionnaire data.

Results

Study participants had significantly high awareness regarding SCDs (89.9%, P < 0.001). Most participants (96.3%) were aware about government policy regarding premarital screening for genetic disorders and replied that the government has strict health policies backed by equally robust laboratory diagnostics. Moreover, none of the participants had SCDs, although their parents had a consanguineous marriage. Thin blood smear analyses of participants did not reveal any cases of Plasmodium falciparum. However, significant percentages (33.1%) were found to be anemic, probably due to their dietary habits and lifestyles, as has been reflected by questionnaire analyses. Furthermore, a very less number of students had knowledge about genetic variations that might occur in malaria-endemic regions after long exposure to offer protection from malaria. Knowledge about management practices was also lacking among study participants (29%).

Conclusion

This research points to the necessity that the nursing study plan should focus on providing specific training on management skills and preventive measures for SCDs, which is of paramount importance.

Reconciling Mouse and Human Immunology at the Altar of Genetics

Immunity to infection has been extensively studied in humans and mice bearing naturally occurring or experimentally introduced germline mutations. Mouse studies are sometimes neglected by human immunologists, on the basis that mice are not humans and the infections studied are experimental and not natural. Conversely, human studies are sometimes neglected by mouse immunologists, on the basis of the uncontrolled conditions of study and small numbers of patients. However, both sides would agree that the infectious phenotypes of patients with inborn errors of immunity often differ from those of the corresponding mutant mice. Why is that? We argue that this important question is best addressed by revisiting and reinterpreting the findings of both mouse and human studies from a genetic perspective. Greater caution is required for reverse-genetics studies than for forward-genetics studies, but genetic analysis is sufficiently strong to define the studies likely to stand the test of time. Genetically robust mouse and human studies can provide invaluable complementary insights into the mechanisms of immunity to infection common and specific to these two species.

Therapeutics through glycobiology: an approach for targeted elimination of malaria

The emergence of drug resistance in Plasmodium jeopardises worldwide malaria eradication efforts necessitating novel therapeutic approaches and therefore the identification of key metabolic pathways of parasite and human host for drug development garners importance. Enzymopathies like glucose-6-phosphate-dehydrogenase (G6PD) and pyruvate kinase (PK) deficiencies have been shown to protect against the severe consequences of malaria. Glycome profiles and the regulatory mechanisms involving the microRNAs or transcription factors' expression related to the histo-blood group glycogenes may add up to resolve the underlying pathogenesis. The glycan derivatives viz. heparin-like molecules (HLMs) interrupt parasite proliferation that can be exploited as leads for alternative therapies. The Plasmodium invasion of erythrocytes involve events of receptor recognition, adhesion, and ligand interactions. Since post translational modifications like N-glycosylation of merozoite surface proteins and several erythrocyte cluster of differentiation (CD) antigens and complement receptor, among others, are crucial to parasite invasion, understanding of post translational modification of proteins involved in the parasite-host interactions should identify viable antimalarial strategies.

Versatile tools of synthetic biology applied to drug discovery and production

Although synthetic biology is an emerging research field, which has come to prominence within the last decade, it already has many practical applications. Its applications cover the areas of pharmaceutical biotechnology and drug discovery, bringing essential novel methods and strategies such as metabolic engineering, reprogramming the cell fate, drug production in genetically modified organisms, molecular glues, functional nucleic acids and genome editing. This review discusses the main avenues for synthetic biology application in pharmaceutical biotechnology. The authors believe that synthetic biology will reshape drug development and drug production to a similar extent as the advances in organic chemical synthesis in the 20th century. Therefore, synthetic biology already plays an essential role in pharmaceutical, biotechnology, which is the main focus of this review.

Toxicological Implications of Biological Heterogeneity

From a micro to macro scale of biological organization, macromolecular diversity and biological heterogeneity are fundamental properties of biological systems. Heterogeneity may result from genetic, epigenetic, and non-genetic characteristics (e.g., tissue microenvironment). Macromolecular diversity and biological heterogeneity are tolerated as long as the sustenance and propagation of life are not disrupted. They also provide the raw materials for microevolutionary changes that may help organisms adapt to new selection pressures arising from the environment. Sequence evolution, functional divergence, and positive selection of gene and promoter dosage play a major role in the evolution of life's diversity including complex metabolic networks, which is ultimately reflected in changes in the allele frequency over time. Robustness in evolvable biological systems is conferred by functional redundancy that is often created by macromolecular diversity and biological heterogeneity. The ability to investigate biological macromolecules at an increasingly finer level has uncovered a wealth of information in this regard. Therefore, the dynamics of biological complexity should be taken into consideration in biomedical research.

Novel Highlight in Malarial Drug Discovery: Aspartate Transcarbamoylase

Malaria remains one of the most prominent and dangerous tropical diseases. While artemisinin and analogs have been used as first-line drugs for the past decades, due to the high mutational rate and rapid adaptation to the environment of the parasite, it remains urgent to develop new antimalarials. The pyrimidine biosynthesis pathway plays an important role in cell growth and proliferation. Unlike human host cells, the malarial parasite lacks a functional pyrimidine salvage pathway, meaning that RNA and DNA synthesis is highly dependent on the de novo synthesis pathway. Thus, direct or indirect blockage of the pyrimidine biosynthesis pathway can be lethal to the parasite. Aspartate transcarbamoylase (ATCase), catalyzes the second step of the pyrimidine biosynthesis pathway, the condensation of L-aspartate and carbamoyl phosphate to form N-carbamoyl aspartate and inorganic phosphate, and has been demonstrated to be a promising target both for anti-malaria and anti-cancer drug development. This is highlighted by the discovery that at least one of the targets of Torin2 – a potent, yet unselective, antimalarial – is the activity of the parasite transcarbamoylase. Additionally, the recent discovery of an allosteric pocket of the human homology raises the intriguing possibility of species selective ATCase inhibitors. We recently exploited the available crystal structures of the malarial aspartate transcarbamoylase to perform a fragment-based screening to identify hits. In this review, we summarize studies on the structure of Plasmodium falciparum ATCase by focusing on an allosteric pocket that supports the catalytic mechanisms.

Association of TNF-Alpha, MBL2, NOS2, and G6PD with Malaria Outcomes in People in Southern Ghana

Background

One major issue that has set back the gains of the numerous malaria control interventions that national malaria control programs have implemented is asymptomatic malaria. Certain host genetic factors are known to influence symptomatic malaria; however, not much is known about how host genetics influences the acquisition of asymptomatic malaria.

Methods

Genomic DNA was extracted from whole blood collected from 60 symptomatic and 149 nonfebrile (asymptomatic, N = 109, and uninfected, N = 40) volunteers aged between 2 and 69 years from a high (Obom) and a low (Asutsuare) malaria transmission setting in Southern Ghana. Restriction fragment length polymorphism (RFLP) was used to determine polymorphisms at the MBL2 54, TNF-α 308, NOS2 954, and G6PD 202/376 gene loci.

Results

Polymorphisms at the MBL2 54 and TNF-α 308 loci were significantly different amongst the three categories of volunteers in both Asutsuare (p = 0.006) and Obom (p=0.05). In Asutsuare, a low malaria transmission area, the allele G has significantly higher odds (3.15) of supporting asymptomatic malaria as against symptomatic malaria. There were significantly higher odds of TNF-α genotype GA being associated with symptomatic malaria as against asymptomatic malaria in both sites, Obom (p=0.027) and Asutsuare (p=0.027). The allele B of the G6PD gene was more prevalent in symptomatic rather than asymptomatic parasite-infected individuals in both Obom (p=0.001) and Asutsuare (p=0.003).

Conclusion

Individuals in Southern Ghana carrying the TNF-α 308 GA genotype are more likely to exhibit symptoms of malaria when infected with the malaria parasite as opposed to harboring an asymptomatic infection. Also, the B allele of the G6PD gene is likely to prevent a P. falciparum-infected person from exhibiting symptoms and thereby promote asymptomatic parasite carriage.

The Myth of the Genetically Sick African

Western medicine has an unfortunate history where it has been applied to address the health of African Americans. At its origins, it was aligned with the objectives of colonialism and chattel slavery. The degree to which medical “science” concerned itself with persons of African descent was to keep them alive for sale on the auction block, or to keep them healthy as they toiled to generate wealth for their European owners. Medicine in early America relied upon both dead and live African bodies to test its ideas to benefit Europeans. As medicine moved from quackery to a discipline based in science, its understanding of human biological variation was flawed. This was not a problem confined to medicine alone, but to the biological sciences in general. Biology had no solid theoretical basis until after 1859. As medicine further developed in the 20th century, it never doubted the difference between Europeans and Africans, and also asserted the innate inferiority of the latter. The genomic revolution in the latter 20th century produced tools that were deployed in a biomedical culture still mired in “racial” medicine. This lack of theoretical perspective still misdirects research associated with health disparity. In contrast to this is evolutionary medicine, which relies on a sound unification of evolutionary (ultimate) and physiological, cellular, and molecular (proximate) mechanisms. Utilizing the perspectives of evolutionary medicine is a prerequisite for an effective intervention in health disparity and finally dispelling the myth of the genetically sick African.

Prevalence of Glucose-6-Phosphate Dehydrogenase (G6PD) Deficiency among Malaria Patients in Southern Thailand: 8 Years Retrospective Study

Erythrocytes deficient in glucose-6-phosphate dehydrogenase (G6PD) is more susceptible to oxidative damage from free radical derived compounds. The hemolysis triggered by oxidative agents such as primaquine (PQ) is used for the radical treatment of hypnozoites of P. vivax. Testing of G6PD screening before malaria treatment is not a common practice in Thailand, which poses patients at risk of hemolysis. This retrospective study aimed to investigate the prevalence of G6PD in malaria patients who live in Southern Thailand. Eight hundred eighty-one malaria patients were collected for 8-year from 2012 to 2019, including 785 (89.1%) of P. vivax, 61 (6.9%) of P. falciparum, 27 (3.1%) of P. knowlesi, and 8 (0.9%) of mixed infections. The DiaPlexC genotyping kit (Asian type) and PCR-RFLP were employed to determine the G6PD variants. The result showed that 5 different types of G6PD variants were identified in 26 cases (2.9%); 12/26 (46.2%) had Mahidol (487G>A) and 11/26 (42.3%) had Viangchan (871G>A) variants, while the rest had Kaiping (1388G>A), Union (1360C>T), and Mediterranean (563C>T) variants. G6PD Songklanagarind (196T>A) variant was not found in the study. Our result did not show a significant difference in the malaria parasite densities in patients between G6PD-deficient and G6PD-normal groups. According to our findings, testing G6PD deficiency and monitoring the potential PQ toxicity in patients who receive PQ are highly recommended.

Linking functional and molecular mechanisms of host resilience to malaria infection

It remains challenging to understand why some hosts suffer severe illnesses, while others are unscathed by the same infection. We fitted a mathematical model to longitudinal measurements of parasite and red blood cell density in murine hosts from diverse genetic backgrounds to identify aspects of within-host interactions that explain variation in host resilience and survival during acute malaria infection. Among eight mouse strains that collectively span 90% of the common genetic diversity of laboratory mice, we found that high host mortality was associated with either weak parasite clearance, or a strong, yet imprecise response that inadvertently removes uninfected cells in excess. Subsequent cross-sectional cytokine assays revealed that the two distinct functional mechanisms of poor survival were underpinned by low expression of either pro- or anti-inflammatory cytokines, respectively. By combining mathematical modelling and molecular immunology assays, our study uncovered proximate mechanisms of diverse infection outcomes across multiple host strains and biological scales.

Heat Shock Proteins as Targets for Novel Antimalarial Drug Discovery

Plasmodium falciparum, the parasitic agent that is responsible for a severe and dangerous form of human malaria, has a history of long years of cohabitation with human beings with attendant negative consequences. While there have been some gains in the fight against malaria through the application of various control measures and the use of chemotherapeutic agents, and despite the global decline in malaria cases and associated deaths, the continual search for new and effective therapeutic agents is key to achieving sustainable development goals. An important parasite survival strategy, which is also of serious concern to the scientific community, is the rate at which the parasites continually develop resistance to drugs. Among the key players in the parasite's ability to develop resistance, maintain cellular integrity, and survives within an unusual environment of the red blood cells are the molecular chaperones of the heat shock proteins (HSP) family. HSPs constitute a novel avenue for antimalarial drug discovery and by exploring their ubiquitous nature and multifunctional activities, they may be suitable targets for the discovery of multi-targets antimalarial drugs, needed to fight incessant drug resistance. In this chapter, features of selected families of plasmodial HSPs that can be exploited in drug discovery are presented. Also, known applications of HSPs in small molecule screening, their potential usefulness in high throughput drug screening, as well as possible challenges are highlighted.

Multiple-ancestry genome-wide association study identifies 27 loci associated with measures of hemolysis following blood storage

BackgroundThe evolutionary pressure of endemic malaria and other erythrocytic pathogens has shaped variation in genes encoding erythrocyte structural and functional proteins, influencing responses to hemolytic stress during transfusion and disease.MethodsWe sought to identify such genetic variants in blood donors by conducting a genome-wide association study (GWAS) of 12,353 volunteer donors, including 1,406 African Americans, 1,306 Asians, and 945 Hispanics, whose stored erythrocytes were characterized by quantitative assays of in vitro osmotic, oxidative, and cold-storage hemolysis.ResultsGWAS revealed 27 significant loci (P < 5 × 10-8), many in candidate genes known to modulate erythrocyte structure, metabolism, and ion channels, including SPTA1, ALDH2, ANK1, HK1, MAPKAPK5, AQP1, PIEZO1, and SLC4A1/band 3. GWAS of oxidative hemolysis identified variants in genes encoding antioxidant enzymes, including GLRX, GPX4, G6PD, and SEC14L4 (Golgi-transport protein). Genome-wide significant loci were also tested for association with the severity of steady-state (baseline) in vivo hemolytic anemia in patients with sickle cell disease, with confirmation of identified SNPs in HBA2, G6PD, PIEZO1, AQP1, and SEC14L4.ConclusionsMany of the identified variants, such as those in G6PD, have previously been shown to impair erythrocyte recovery after transfusion, associate with anemia, or cause rare Mendelian human hemolytic diseases. Candidate SNPs in these genes, especially in polygenic combinations, may affect RBC recovery after transfusion and modulate disease severity in hemolytic diseases, such as sickle cell disease and malaria.

Molecular characterization of Plasmodium falciparum PHISTb proteins as potential targets of naturally-acquired immunity against malaria

Background: Plasmodium falciparum causes the deadliest form of malaria in humans. Upon infection, the host’s infected red blood cells (iRBCs) are remodelled by exported parasite proteins to provide a niche for parasite development and maturation. Methods: Here we analysed the role of three PHISTb proteins Pf3D7_0532400, Pf3D7_1401600, and Pf3D7_1102500 by expressing recombinant proteins and evaluated antibody responses against these proteins using immune sera from malaria-exposed individuals from Kenya and The Gambia in Africa. Results: Children and adults from malaria-endemic regions recognized the three PHISTb proteins. Responses against PHISTb proteins varied with malaria transmission intensity in three different geographical sites in Kenya (Siaya and Takaungu) and The Gambia (Sukuta). Antibody responses against PHISTb antigens Pf3D7_1102500 and Pf3D7_1401600 were higher in Sukuta, a low transmission region in Gambia, compared to Siaya, a high transmission region in western Kenya, unlike Pf3D7_0532400. Anti-PHIST responses indicate negative correlation between antibody levels and malaria transmission intensity for Pf3D7_1102500 and Pf3D7_1401600. We report a correlation in antibody responses between schizont and gametocyte extract, but this is not statistically significant (cor=0.102, p=0.2851, CI=95%) and, Pf3D7_0532400 (cor=0.11, p=0.249, CI=95%) and Pf3D7_1401600 (cor=0.02, p=0.7968, CI=95%). We report a negative correlation in antibody responses between schizont and Pf3D7_1102500 (cor=-0.008, p=0.9348, CI=95%). There is a correlation between gametocyte extract and Pf3D7_1401600 (cor=-0.0402, p=0.6735, CI=95%), Pf3D7_1102500 (cor=0.0758, p=0.4271, CI=95%) and Pf3D7_0532400 (cor=0.155, p=0.1028, CI=95%). Acquisition of anti-PHIST antibodies correlates with exposure to malaria for Pf3D7_0532400 (p=0.009) but not Pf3D7_1102500 and Pf3D7_1401600 (p=0.507 and p=0.15, respectively, CI=95%). Children aged below 2 years had the lowest antibody levels which do not correlate with age differences. Conclusions: Collectively, these findings provide evidence of natural immunity against PHISTb antigens that varies with level of malaria exposure and underscore their potential as possible serological markers to P. falciparum infection aimed at contributing to malaria control through vaccine development.

Ticks, Hair Loss, and Non-Clinging Babies: A Novel Tick-Based Hypothesis for the Evolutionary Divergence of Humans and Chimpanzees

Human straight-legged bipedalism represents one of the earliest events in the evolutionary split between humans (Homo spp.) and chimpanzees (Pan spp.), although its selective basis is a mystery. A carrying-related hypothesis has recently been proposed in which hair loss within the hominin lineage resulted in the inability of babies to cling to their mothers, requiring mothers to walk upright to carry their babies. However, a question remains for this model: what drove the hair loss that resulted in upright walking? Observers since Darwin have suggested that hair loss in humans may represent an evolutionary strategy for defence against ticks. The aim of this review is to propose and evaluate a novel tick-based evolutionary hypothesis wherein forest fragmentation in hominin paleoenvironments created conditions that were favourable for tick proliferation, selecting for hair loss in hominins and grooming behaviour in chimpanzees as divergent anti-tick strategies. It is argued that these divergent anti-tick strategies resulted in different methods for carrying babies, driving the locomotor divergence of humans and chimpanzees.

Diversity of KIR genes and their HLA-C ligands in Ugandan populations with historically varied malaria transmission intensity

BACKGROUND

Malaria is one of the most serious infectious diseases in the world. The malaria burden is greatly affected by human immunity, and immune responses vary between populations. Genetic diversity in KIR and HLA-C genes, which are important in immunity to infectious diseases, is likely to play a role in this heterogeneity. Several studies have shown that KIR and HLA-C genes influence the immune response to viral infections, but few studies have examined the role of KIR and HLA-C in malaria infection, and these have used low-resolution genotyping. The aim of this study was to determine whether genetic variation in KIR and their HLA-C ligands differ in Ugandan populations with historically varied malaria transmission intensity using more comprehensive genotyping approaches.

METHODS

High throughput multiplex quantitative real-time PCR method was used to genotype KIR genetic variants and copy number variation and a high-throughput real-time PCR method was developed to genotype HLA-C1 and C2 allotypes for 1344 participants, aged 6 months to 10 years, enrolled from Ugandan populations with historically high (Tororo District), medium (Jinja District) and low (Kanungu District) malaria transmission intensity.

RESULTS

The prevalence of KIR3DS1, KIR2DL5, KIR2DS5, and KIR2DS1 genes was significantly lower in populations from Kanungu compared to Tororo (7.6 vs 13.2%: p = 0.006, 57.2 vs 66.4%: p = 0.005, 33.2 vs 46.6%: p < 0.001, and 19.7 vs 26.7%: p = 0.014, respectively) or Jinja (7.6 vs 18.1%: p < 0.001, 57.2 vs 63.8%: p = 0.048, 33.2 vs 43.5%: p = 0.002, and 19.7 vs 30.4%: p < 0.001, respectively). The prevalence of homozygous HLA-C2 was significantly higher in populations from Kanungu (31.6%) compared to Jinja (21.4%), p = 0.043, with no significant difference between Kanungu and Tororo (26.7%), p = 0.296.

CONCLUSIONS

The KIR3DS1, KIR2DL5, KIR2DS5 and KIR2DS1 genes may partly explain differences in transmission intensity of malaria since these genes have been positively selected for in places with historically high malaria transmission intensity. The high-throughput, multiplex, real-time HLA-C genotyping PCR method developed will be useful in disease-association studies involving large cohorts.

COVID-19: The Effect of Host Genetic Variations on Host-Virus Interactions

Spurred into action by the COVID-19 pandemic, the global scientific community has, in a short of period of time, made astonishing progress in understanding and combating COVID-19. Given the known human protein machinery for (a) SARS-CoV-2 entry, (b) the host innate immune response, and (c) virus-host interactions (protein-protein and RNA-protein), the potential effects of human genetic variation in this machinery, which may contribute to clinical differences in SARS-CoV-2 pathogenesis and help determine individual risk for COVID-19 infection, are explored. The Genome Aggregation Database (gnomAD) was used to show that several rare germline exome variants of proteins in these pathways occur in the human population, suggesting that carriers of these rare variants (especially for proteins of innate immunity pathways) are at risk for severe symptoms (like the severe symptoms in patients who are known to be rare variant carriers), whereas carriers of other variants could have a protective advantage against infection. The occurrence of genetic variation is thus expected to motivate the experimental probing of natural variants to understand the mechanistic differences in SARS-CoV-2 pathogenesis from one individual to another.

Syk Kinase Inhibitors Synergize with Artemisinins by Enhancing Oxidative Stress in Plasmodium falciparum-Parasitized Erythrocytes

Although artemisinin-based combination therapies (ACTs) treat Plasmodium falciparum malaria effectively throughout most of the world, the recent expansion of ACT-resistant strains in some countries of the Greater Mekong Subregion (GMS) further increased the interest in improving the effectiveness of treatment and counteracting resistance. Recognizing that (1) partially denatured hemoglobin containing reactive iron (hemichromes) is generated in parasitized red blood cells (pRBC) by oxidative stress, (2) redox-active hemichromes have the potential to enhance oxidative stress triggered by the parasite and the activation of artemisinin to its pharmaceutically active form, and (3) Syk kinase inhibitors block the release of membrane microparticles containing hemichromes, we hypothesized that increasing hemichrome content in parasitized erythrocytes through the inhibition of Syk kinase might trigger a virtuous cycle involving the activation of artemisinin, the enhancement of oxidative stress elicited by activated artemisinin, and a further increase in hemichrome production. We demonstrate here that artemisinin indeed augments oxidative stress within parasitized RBCs and that Syk kinase inhibitors further increase iron-dependent oxidative stress, synergizing with artemisinin in killing the parasite. We then demonstrate that Syk kinase inhibitors achieve this oxidative enhancement by preventing parasite-induced release of erythrocyte-derived microparticles containing redox-active hemichromes. We also observe that Syk kinase inhibitors do not promote oxidative toxicity to healthy RBCs as they do not produce appreciable amounts of hemichromes. Since some Syk kinase inhibitors can be taken daily with minimal side effects, we propose that Syk kinase inhibitors could evidently contribute to the potentiation of ACTs.

Inter- and intrabreed diversity of the major histocompatibility complex (MHC) in primitive and draft horse breeds

Background

Polymorphism of major histocompatibility complex (MHC) genes ensures effective immune responses against a wide array of pathogens. However, artificial selection, as performed in the case of domestic animals, may influence MHC diversity. Here, we investigate and compare the MHC diversity of three populations of horses, for which different breeding policies were applied, to evaluate the impact of artificial selection and the environment on MHC polymorphism.

Methods

Samples of DNA were taken from 100 Polish draft horses, 38 stabled Konik Polski horses and 32 semiferal Konik Polski horses. MHC alleles and haplotype diversity within and between these populations of horses was estimated from 11 MHC microsatellite loci.

Results

MHC diversity measured based on allelic richness, observed heterozygosity, expected heterozygosity and polymorphism content was similar across the MHC microsatellite loci in all three populations. The highest expected heterozygosity was detected in semiferal primitive horses (He = 0.74), while the lowest was calculated for draft horses (He = 0.65). In total, 203 haplotypes were determined (111 in Polish draft horses, 43 in semiferal Konik Polski horses and 49 in stabled Konik Polski horses), and four haplotypes were shared between the two populations of Koniks. None of these haplotypes were present in any of the previously investigated horse breeds. Intra-MHC recombination events were detected in all three populations. However, the population of semiferal Konik horses showed the highest recombination frequency among the three horse populations. In addition, three recombination events were detected.

Conclusions

These results showed that despite the different breeding policies, the MHC allele and haplotype diversity was similarly high in all three horse populations. Nevertheless, the proportion of new haplotypes in the offspring was the highest in semiferal Konik Polski horses, which indicates the influence of the environment on MHC diversity in horses. Thus, we speculate that the genetic makeup of the domestic horse MHC might be more strongly influenced by the environment than by artificial selection. Moreover, intra-MHC conversion, insertion, and deletion and intra-MHC recombination may be proposed as mechanisms underlying the generation of new MHC haplotypes in horses.

Life History Transitions at the Origins of Agriculture: A Model for Understanding How Niche Construction Impacts Human Growth, Demography and Health

Over recent millennia, human populations have regularly reconstructed their subsistence niches, changing both how they obtain food and the conditions in which they live. For example, over the last 12,000 years the vast majority of human populations shifted from foraging to practicing different forms of agriculture. The shift to farming is widely understood to have impacted several aspects of human demography and biology, including mortality risk, population growth, adult body size, and physical markers of health. However, these trends have not been integrated within an over-arching conceptual framework, and there is poor understanding of why populations tended to increase in population size during periods when markers of health deteriorated. Here, we offer a novel conceptual approach based on evolutionary life history theory. This theory assumes that energy availability is finite and must be allocated in competition between the functions of maintenance, growth, reproduction, and defence. In any given environment, and at any given stage during the life-course, natural selection favours energy allocation strategies that maximise fitness. We argue that the origins of agriculture involved profound transformations in human life history strategies, impacting both the availability of energy and the way that it was allocated between life history functions in the body. Although overall energy supply increased, the diet composition changed, while sedentary populations were challenged by new infectious burdens. We propose that this composite new ecological niche favoured increased energy allocation to defence (immune function) and reproduction, thus reducing the allocation to growth and maintenance. We review evidence in support of this hypothesis and highlight how further work could address both heterogeneity and specific aspects of the origins of agriculture in more detail. Our approach can be applied to many other transformations of the human subsistence niche, and can shed new light on the way that health, height, life expectancy, and fertility patterns are changing in association with globalization and nutrition transition.

Complete genome and bimodal genomic structure of the amoebal symbiont Neochlamydia strain S13 revealed by ultra-long reads obtained from MinION

Neochlamydia strain S13 is an amoebal symbiont of an Acanthamoeba sp. The symbiont confers resistance to Legionella pneumophila on its host; however, the molecular mechanism underlying this resistance is not completely understood. Genome analyses have been crucial for understanding the complicated host-symbiont relationship but segregating the host's genome DNA from the symbiont's DNA is often challenging. In this study, we successfully identified a bimodal genomic structure in Neochlamydia strain S13 using PacBio RS II supported by ultra-long reads derived from MinION. One mode consisted of circular sequences of 2,586,667 and 231,307 bp; the other was an integrated sequence of the two via long homologous regions. They encoded 2175 protein-coding regions, some of which were implied to be acquired via horizontal gene transfer. They were specifically conserved in the genus Neochlamydia and formed a cluster in the genome, presumably by multiplication through genome replication. Moreover, it was notable that the sequenced DNA was obtained without segregating the symbiont DNA from the host. This is an easy and versatile technique that facilitates the characterization of diverse hosts and symbionts in nature.

The glucose-6-phosphate dehydrogenase Mahidol variant protects against uncomplicated Plasmodium vivax infection and reduces disease severity in a Kachin population from northeast Myanmar

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is one of the most common red cell disorders in the world. The aim of this study was to investigate whether the G6PD Mahidol variant and haplotype 1311 T/93C, which are prevalent in the Kachin ethnic population along the China-Myanmar border area, offer protection against Plasmodium vivax infection. Malaria was monitored in nine villages near the Laiza township, Kachin State, Myanmar, where 258 cases of uncomplicated P. vivax were identified in 2013-2017. From the same villages, 250 unrelated, malaria-free participants were recruited to serve as the control cohort. Quantitative enzyme activity analysis in 100 healthy individuals identified that both male hemizygotes and female heterozygotes of the G6PD Mahidol variant had on average ~40% lower enzyme activity relative to the wild-type individuals. Compared with the overall prevalence of 25.2% in the control cohort, the G6PD Mahidol variant had a significantly lower prevalence (7.0%) among the 258 vivax patients (P <  .0001, χ2 test). Logistic regression analysis of G6PD genotypes stratified by sex showed that the individuals with the Mahidol 487A allele had dramatically reduced odds of having acute vivax malaria (adjusted odds ratio = 0.213 for male 487A hemizygotes, P < .0001, and 0.248 for female 487GA heterozygotes, P < .001). Furthermore, both 487A hemizygous male and 487GA heterozygous female patients had significantly lower asexual parasitemias than the wild-type patients, suggesting a potential effect on alleviating disease severity. In contrast, the silent mutation haplotype 1311 T/93C was highly prevalent (49.6%) in the study population, but it was not associated with altered G6PD enzymatic activities nor did it seem to provide protection against vivax infection or disease severity. Taken together, this study provided evidence that the Mahidol G > A mutation offers protection against P. vivax infection and potentially reduces disease severity in a Kachin population.

Immunoglobulin G responses against falciparum malaria specific antigens are higher in children with homozygous sickle cell trait than those with normal hemoglobin

BACKGROUND

High Immunoglobulin G (IgG) response to Plasmodium falciparum antigens is associated with partial malaria protection in sickle hemoglobin (HbS) children. However, this response has been more studied in children with heterozygous sickle cell trait (HbAS) but little explored in those with homozygous sickle cell trait (HbSS). The current study was conducted to determine the IgG responses against specific Plasmodium falciparum antigens in children with homozygous sickle cell trait (HbSS) by comparing to those with normal hemoglobin (HbAA).

METHODS

A cross sectional study was conducted between April and July 2018 in Dar es Salaam tertiary hospitals. Parents were consented for their child to give about 5 ml of venous blood. IgG concentration from the blood plasma of 220 children (110 HbAA vs. 110 HbSS) were determined using indirect Enzyme Linked Immunosorbent Assay (ELISA). Then IgG medians were compared between the groups with prism 5 software (GraphPad) using Mann Whitney U test. Where the differences in age, hemoglobin levels and body weight between the groups was analyzed using independent sample t test. Multiple linear regressions were used to control cofounding variables such as body weight, age and hemoglobin level using statistical package for social sciences software (SPSS version 23). P value <0.05 was considered statistically significant.

RESULTS

The median IgG concentration to PfEBA-175, Pfg27, yPfs28C antigens were HbSS; 20.7 ng/ml (IQR; 18.1-25.6) vs. HbAA; 2.3 ng/ml (IQR; 1.21-3.04), HbSS; 2.76 ng/ml (IQR: 2.08-5.69) vs. HbAA; 1.36 ng/ml (IQR: 1.28-1.76), and HbSS; 26,592 ng/ml (IQR: 10817-41,462) vs. HbAA; 14,164 ng/ml (IQR; 3069-24,302) respectively (p < 0.0001 for all IgG). In both groups; age, body weight and hemoglobin level had no impact on the levels of IgG responses to Plasmodium falciparum antigens except for HbAA group which showed a significant increase in IgG against Pfg27 by 0.004 ng/ml with 1 g/dl increase in Hb level (p = 0.028).

CONCLUSIONS

This study found significant higher levels of specific Plasmodium falciparum IgG responses in children with homozygous sickle cell trait than those with normal hemoglobin.

Glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase: characterization of the Plasmodium vivax enzyme and inhibitor studies

BACKGROUND

Since malaria parasites highly depend on ribose 5-phosphate for DNA and RNA synthesis and on NADPH as a source of reducing equivalents, the pentose phosphate pathway (PPP) is considered an excellent anti-malarial drug target. In Plasmodium, a bifunctional enzyme named glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase (GluPho) catalyzes the first two steps of the PPP. PfGluPho has been shown to be essential for the growth of blood stage Plasmodium falciparum parasites.

METHODS

Plasmodium vivax glucose 6-phosphate dehydrogenase (PvG6PD) was cloned, recombinantly produced in Escherichia coli, purified, and characterized via enzyme kinetics and inhibitor studies. The effects of post-translational cysteine modifications were assessed via western blotting and enzyme activity assays. Genetically encoded probes were employed to study the effects of G6PD inhibitors on the cytosolic redox potential of Plasmodium.

RESULTS

Here the recombinant production and characterization of PvG6PD, the C-terminal and NADPH-producing part of PvGluPho, is described. A comparison with PfG6PD (the NADPH-producing part of PfGluPho) indicates that the P. vivax enzyme has higher K_M values for the substrate and cofactor. Like the P. falciparum enzyme, PvG6PD is hardly affected by S-glutathionylation and moderately by S-nitrosation. Since there are several naturally occurring variants of PfGluPho, the impact of these mutations on the kinetic properties of the enzyme was analysed. Notably, in contrast to many human G6PD variants, the mutations resulted in only minor changes in enzyme activity. Moreover, nanomolar IC₅₀ values of several compounds were determined on P. vivax G6PD (including ellagic acid, flavellagic acid, and coruleoellagic acid), inhibitors that had been previously characterized on PfGluPho. ML304, a recently developed PfGluPho inhibitor, was verified to also be active on PvG6PD. Using genetically encoded probes, ML304 was confirmed to disturb the cytosolic glutathione-dependent redox potential of P. falciparum blood stage parasites. Finally, a new series of novel small molecules with the potential to inhibit the falciparum and vivax enzymes were synthesized, resulting in two compounds with nanomolar activity.

CONCLUSION

The characterization of PvG6PD makes this enzyme accessible to further drug discovery activities. In contrast to naturally occurring G6PD variants in the human host that can alter the kinetic properties of the enzyme and thus the redox homeostasis of the cells, the naturally occurring PfGluPho variants studied here are unlikely to have a major impact on the parasites' redox homeostasis. Several classes of inhibitors have been successfully tested and are presently being followed up.

Membrane protein carbonylation of Plasmodium falciparum infected erythrocytes under conditions of sickle cell trait and G6PD deficiency

Deficiency of glucose-6-phosphate dehydrogenase (G6PD) and sickle cell trait (SCT) are described as the polymorphic disorders prevalent in erythrocytes. Both are considered the result of the selective pressure exerted by Plasmodium parasites over human genome, due to a certain degree of resistance to the clinical symptoms of severe malaria. There exist in both a prooxidant environment that favors the oxidative damage on membrane proteins, which probably is part of molecular protector mechanisms. Nevertheless, mechanisms are not completely understood at molecular level for each polymorphism yet, and even less if are commons for several of them. Here, synchronous cultures at high parasitemia levels of P. falciparum 3D7 were used to quantify oxidative damage in membrane proteins of erythrocytes with G6PD deficient and SCT. Carbonyl index by dot blot assay was used to calculate the variation of oxidative damage during the asexual phases. Besides, protein carbonylation profiles were obtained by Western blot and complemented with mass spectrometry using MALDI-TOF-TOF analysis. Erythrocytes with G6PD deficient and SCT showed higher carbonyl index values than control and similar profiles of carbonylated proteins; moreover, cytoskeletal and stress response proteins were identified as the main targets of oxidative damage. Therefore, both polymorphisms promote carbonylation on the same membrane proteins. Finally, these results allowed to reinforce the hypothesis of oxidative damage in erythrocyte membrane proteins as molecular mechanism of human adaptation to malaria infection.

Intradonor reproducibility and changes in hemolytic variables during red blood cell storage: results of recall phase of the REDS-III RBC-Omics study

BACKGROUND

Genetic determinants may underlie the susceptibility of red blood cells (RBCs) to hemolyze in vivo and during routine storage. This study characterized the reproducibility and dynamics of in vitro hemolysis variables from a subset of the 13,403 blood donors enrolled in the RBC-Omics study.

STUDY DESIGN AND METHODS

RBC-Omics donors with either low or high hemolysis results on 4°C-stored leukoreduced (LR)-RBC samples from enrollment donations stored for 39 to 42 days were recalled 2 to 12 months later to donate LR-RBCs. Samples of stored LR-RBCs from the unit and from transfer bags were evaluated for spontaneous and stress-induced hemolysis at selected storage time points. Intradonor reproducibility of hemolysis variables was evaluated in transfer bags over two donations. Hemolysis data at serial storage time points were generated on LR-RBCs from parent bags and analyzed by site, sex, race/ethnicity, and donation frequency.

RESULTS

A total of 664 donors were successfully recalled. Analysis of intradonor reproducibility revealed that osmotic and oxidative hemolysis demonstrated good and moderate reproducibility (Pearson's r = 0.85 and r = 0.53, respectively), while spontaneous hemolysis reproducibility was poor (r = 0.40). Longitudinal hemolysis in parent bags showed large increases over time in spontaneous (508.6%) and oxidative hemolysis (399.8%) and smaller increases in osmotic (9.4%) and mechanical fragility (3.4%; all p < 0.0001).

CONCLUSION

Spontaneous hemolysis is poorly reproducible in donors over time and may depend on site processing methods, while oxidative and osmotic hemolysis were reproducible in donors and hence could reflect consistent heritable phenotypes attributable to genetic traits. Spontaneous and oxidative hemolysis increased over time of storage, whereas osmotic and mechanical hemolysis remained relatively stable.

Plasmodium genomics: an approach for learning about and ending human malaria

Malaria causes high levels of morbidity and mortality in human beings worldwide. According to the World Health Organization (WHO), about half a million people die of this disease each year. Malaria is caused by six species of parasites belonging to the Plasmodium genus: P. falciparum, P. knowlesi, P. vivax, P. malariae, P. ovale curtisi, and P. ovale wallikeri. Currently, malaria is being kept under control with varying levels of elimination success in different countries. The development of new molecular tools as well as the use of next-generation sequencing (NGS) technologies and novel bioinformatic approaches has improved our knowledge of malarial epidemiology, diagnosis, treatment, vaccine development, and surveillance strategies. In this work, the genetics and genomics of human malarias have been analyzed. Since the first P. falciparum genome was sequenced in 2002, various population-level genetic and genomic surveys, together with transcriptomic and proteomic studies, have shown the importance of molecular approaches in supporting malaria elimination.

Effects of hydroxyurea on CNV induction in the mouse germline

Copy number variants (CNVs) are important in genome variation and genetic disease, with new mutations arising frequently in the germline and somatic cells. Replication stress caused by aphidicolin and hydroxyurea (HU) is a potent inducer of de novo CNVs in cultured mammalian cells. HU is used extensively for long-term management of sickle cell disease. Here, we examined the effects of HU treatment on germline CNVs in vivo in male mice to explore whether replication stress can act as a CNV mutagen in germline mitotic divisions as in cultured cells and whether this would support a concern for increased CNV mutations in offspring of men treated with HU. Several trials of HU administration were performed by oral gavage and subcutaneous pump, with CNVs characterized in C57BL/6 x C3H/HeJ hybrid mouse offspring by microarray and mate-pair sequencing. HU had a short half-life of ~14 min and a narrow dose window over which studies could be performed while maintaining fertility. Tissue histopathology and reticulocyte micronucleus assays verified that doses had a substantial tissue and genetic toxicity. CNVs were readily detected in offspring that originated in both paternal and maternal mouse strains, as de novo and inherited events. However, HU did not increase CNV formation above baseline levels. These results reveal a high rate of CNV mutagenesis in the mouse germline but do not support the hypothesis that HU would increase CNV formation during mammalian spermatogenesis, perhaps due to highly toxic effects on sperm development or experimental variables related to HU pharmacology in mice. Environ. Mol. Mutagen. 59:698-714, 2018. © 2018 Wiley Periodicals, Inc.

Associations between erythrocyte polymorphisms and risks of uncomplicated and severe malaria in Ugandan children: A case control study

Background

Evidence for association between sickle cell and alpha thalassemia trait and severe malaria is compelling. However, for these polymorphisms associations with uncomplicated malaria, and for G6PD deficiency associations with uncomplicated and severe malaria, findings have been inconsistent. We studied samples from a three-arm case-control study with the objective of determining associations between common host erythrocyte polymorphisms and both uncomplicated and severe malaria, including different severe malaria phenotypes.

Method

We assessed hemoglobin abnormalities, α-thalassemia, and G6PD deficiency by molecular methods in 325 children with severe malaria age-matched to 325 children with uncomplicated malaria and 325 healthy community controls. Conditional logistic regression was used to measure associations between specified genotypes and malaria outcomes.

Results

No tested polymorphisms offered significant protection against uncomplicated malaria. α-thalassemia homozygotes (_α/_α) had increased risk of uncomplicated malaria (OR 2.40; 95%CI 1.15, 5.03, p = 0.020). HbAS and α-thalassemia heterozygous (_α/αα) genotypes protected against severe malaria compared to uncomplicated malaria (HbAS OR 0.46; 0.23, 0.95, p = 0.036; _α/αα OR 0.51; 0.24, 0.77; p = 0.001) or community (HbAS OR 0.23; 0.11, 0.50; p<0.001; _α/αα; OR 0.49; 0.32, 0.76; p = 0.002) controls. The α-thalassemia homozygous (_α/_α) genotype protected against severe malaria when compared to uncomplicated malaria controls (OR 0.34; 95%CI 0.156, 0.73, p = 0.005), but not community controls (OR 1.03; 0.46, 2.27, p = 0.935). Stratifying by the severe malaria phenotype, compared to community controls, the protective effect of HbAS was limited to children with severe anemia (OR 0.17; 95%CI 0.04, 0.65; p = 0.009) and that of _α/αα to those with altered consciousness (OR 0.24; 0.09, 0.59; p = 0.002). A negative epistatic effect was seen between HbAS and _α/αα; protection compared to uncomplicated malaria controls was not seen in individuals with both polymorphisms (OR 0.45; 0.11, 1.84; p = 0.269). G6PD deficiency was not protective against severe malaria.

Conclusion

Associations were complex, with HbAS principally protective against severe anemia, _α/αα against altered consciousness, and negative epistasis between the two polymorphisms.

Realizing effectiveness across continents with hydroxyurea: Enrollment and baseline characteristics of the multicenter REACH study in Sub-Saharan Africa

Despite its well-described safety and efficacy in the treatment of sickle cell anemia (SCA) in high-income settings, hydroxyurea remains largely unavailable in sub-Saharan Africa, where more than 75% of annual SCA births occur and many comorbidities exist. Realizing Effectiveness Across Continents with Hydroxyurea (REACH, ClinicalTrials.gov NCT01966731) is a prospective, Phase I/II open-label trial of hydroxyurea designed to evaluate the feasibility, safety, and benefits of hydroxyurea treatment for children with SCA in four sub-Saharan African countries. Following comprehensive training of local research teams, REACH was approved by local Ethics Committees and achieved full enrollment ahead of projections with 635 participants enrolled over a 30-month period, despite half of families living >12 km from their clinical site. At enrollment, study participants (age 5.4 ± 2.4 years) had substantial morbidity, including a history of vaso-occlusive pain (98%), transfusion (68%), malaria (85%), and stroke (6%). Significant differences in laboratory characteristics were noted across sites, with lower hemoglobin concentrations (P < .01) in Angola (7.2 ± 1.0 g/dL) and the DRC (7.0 ± 0.9 g/dL) compared to Kenya (7.4 ± 1.1 g/dL) and Uganda (7.5 ± 1.1 g/dL). Analysis of known genetic modifiers of SCA demonstrated a high frequency of α-thalassemia (58.4% with at least a single α-globin gene deletion) and G6PD deficiency (19.7% of males and 2.4% of females) across sites. The CAR β-globin haplotype was present in 99% of participants. The full enrollment to REACH confirms the feasibility of conducting high-quality SCA research in Africa; this study will provide vital information to guide safe and effective dosing of hydroxyurea for children with SCA living in Africa.

The Assessment and Sustainable Management of Sickle Cell Disease in the Indigenous Tharu Population of Nepal

Sickle cell disease is an inherited hemoglobinopathy associated with significant morbidity and mortality. Reports suggest a high sickle cell disease burden among the indigenous Tharu population of Nepal, who for centuries have inhabited regions where malaria is endemic. Unfortunately, health care resources are limited and often inaccessible for Tharu individuals suffering from sickle cell disease. We conducted a large-scale screening effort to estimate the prevalence of Hb S (HBB: c.20A>T) among the Tharu population and delivered community-based education sessions to increase sickle cell disease awareness. A total of 2899 Tharu individuals aged 6 months to 40 years in the rural district of Dang in Western Nepal were screened using a sickling test, of whom, 271 [9.3%; 95% confidence interval (95% CI): 8.3-10.4%] screened positive for Hb S. Those who screened positive were offered diagnostic gel electrophoresis testing. Of the 133 individuals who underwent diagnostic testing, 75.9% (n = 101) were confirmed to be Hb AS heterozygotes, 4.5% (n = 6) were confirmed to be Hb SS homozygotes and 19.5% (n = 26) were false positives. These findings support a large burden of sickle cell disease among the Tharu population and highlight the importance of appropriate resource allocation and management. With a positive predictive value of 80.0% (95% CI: 73.0-87.0%), the sickling test in conjunction with raising local sickle cell disease awareness may be a simple and sustainable way to promote access to health resources.

Antibody responses to P. falciparum Apical Membrane Antigen 1(AMA-1) in relation to haemoglobin S (HbS), HbC, G6PD and ABO blood groups among Fulani and Masaleit living in Western Sudan

Fulani and Masaleit are two sympatric ethnic groups in western Sudan who are characterised by marked differences in susceptibility to Plasmodium falciparum malaria. It has been demonstrated that Glucose-6-phosphate dehydrogenase (G6PD) deficiency and Sickle cell trait HbAS carriers are protected from the most severe forms of malaria. This study aimed to investigate a set of specific IgG subclasses against P. falciparum Apical Membrane Antigen 1 (AMA-1 3D7), haemoglobin variants and (G6PD) in association with malaria susceptibility among Fulani ethnic group compared to sympatric ethnic group living in Western Sudan. A total of 124 children aged 5-9 years from each tribe living in an area of hyper-endemic P. falciparum unstable malaria transmission were recruited and genotyped for the haemoglobin (Hb) genes, (G6PD) and (ABO) blood groups. Furthermore, the level of plasma IgG antibody subclasses against P. falciparum antigen (AMA-1) were measured using enzyme linked immunosorbent assays (ELISA). Higher levels of anti-malarial IgG1, IgG2 and IgG3 but not IgG4 antibody were found in Fulani when compared to Masaleit. Individuals carrying the HbCC phenotype were significantly associated with higher levels of IgG1 and IgG2. Furthermore, individuals having the HbAS phenotype were associated with higher levels of specific IgG2 and IgG4 antibodies. In addition, patients with G6PD A/A genotype were associated with higher levels of specific IgG2 antibody compared with those carrying the A/G and G/G genotypes. The results indicate that the Fulani ethnic group show lower frequency of HbAS, HbSS and HbAC compared to the Masaleit ethnic group. The inter-ethnic analysis shows no statistically significant difference in G6PD genotypes (P value = 0.791). However, the intra-ethnic analysis indicates that both ethnic groups have less A/A genotypes and (A) allele frequency of G6PD compared to G/G genotypes, while the HbSA genotype was associated with higher levels of IgG2 (AMA-1) and IgG4 antibodies. In addition, patients carrying the G6PD A/A genotype were associated with higher levels of specific IgG2 antibody compared with those carrying the A/G and G/G genotypes. The present results revealed that the Fulani ethnic group has statistically significantly lower frequency of abnormal haemoglobin resistant to malaria infection compared to the Masaleit ethnic group.

Prevalence and incidence of congenital anomalies amongst babies born to women with sickle cell disease and exposed to hydroxyurea during pregnancy: a systematic review protocol

REVIEW QUESTION/OBJECTIVE

What is the prevalence and incidence of congenital anomalies among babies born to women with sickle cell disease (SCD) and who have been exposed to hydroxyurea (HU) therapy at any time in their pregnancy?The objective of this review is to identify the proportion of babies born with congenital anomalies among babies born to mothers with SCD who have been exposed to HU therapy at any point during pregnancy and to describe the specific types of congenital anomalies encountered.

Alloimmunization in Thalassemia Patients: New Insight for Healthcare

Background:

Development of alloantibodies against the foreign red blood cell (RBC) (alloimmunization) is a well-known complication in thalassemia patients when performing multiple transfusions. The study was conducted to know the prevalence of alloimmunization in thalassemia patients, in the Caspian Sea coastline.

Methods:

This study is a descriptive, retrospective analysis of transfusion records of 190 patients with β-thalassemia major who received regular transfusions. To detect the type of alloantibodies, two cells panel tests (kits; Iranian Blood Transfusion Organization [IBTO], 3 RBC cells and IBTO, 11 RBC cells) were used.

Results:

Forty-seven patients were positive for alloantibodies (24.7%). Of them, 18.4% (35 cases) had only one alloantibody, and 6.3% (12 cases) had at least two or more of alloantibodies. The vast majority of alloantibodies were anti-Kell followed by anti-E, and anti-D, respectively.

Conclusions:

Blood matching for Rh and K antigens in patients with transfusion-dependent thalassemia could reduce the rate of RBC alloinununization.

The HLA-B landscape of Africa: Signatures of pathogen-driven selection and molecular identification of candidate alleles to malaria protection

Human leukocyte antigen (HLA) genes play a key role in the immune response to infectious diseases, some of which are highly prevalent in specific environments, like malaria in sub-Saharan Africa. Former case-control studies showed that one particular HLA-B allele, B*53, was associated with malaria protection in Gambia, but this hypothesis was not tested so far within a population genetics framework. In this study, our objective was to assess whether pathogen-driven selection associated with malaria contributed to shape the HLA-B genetic landscape of Africa. To that aim, we first typed the HLA-A and -B loci in 484 individuals from 11 populations living in different environments across the Sahel, and we analysed these data together with those available for 29 other populations using several approaches including linear modelling on various genetic, geographic and environmental parameters. In addition to relevant signatures of populations' demography and migrations history in the genetic differentiation patterns of both HLA-A and -B loci, we found that the frequencies of three HLA alleles, B*53, B*78 and A*74, were significantly associated with Plasmodium falciparum malaria prevalence, suggesting their increase through pathogen-driven selection in malaria-endemic environments. The two HLA-B alleles were further identified, by high-throughput sequencing, as B*53:01:01 (in putative linkage disequilibrium with one HLA-C allele, C*04:01:01:01) and B*78:01 in all but one individuals tested, making them appropriate candidates to malaria protection. These results highlight the role of environmental factors in the evolution of the HLA polymorphism and open key perspectives for functional studies focusing on HLA peptide-binding properties.

Malaria

Malaria is caused in humans by five species of single-celled eukaryotic Plasmodium parasites (mainly Plasmodium falciparum and Plasmodium vivax) that are transmitted by the bite of Anopheles spp. mosquitoes. Malaria remains one of the most serious infectious diseases; it threatens nearly half of the world's population and led to hundreds of thousands of deaths in 2015, predominantly among children in Africa. Malaria is managed through a combination of vector control approaches (such as insecticide spraying and the use of insecticide-treated bed nets) and drugs for both treatment and prevention. The widespread use of artemisinin-based combination therapies has contributed to substantial declines in the number of malaria-related deaths; however, the emergence of drug resistance threatens to reverse this progress. Advances in our understanding of the underlying molecular basis of pathogenesis have fuelled the development of new diagnostics, drugs and insecticides. Several new combination therapies are in clinical development that have efficacy against drug-resistant parasites and the potential to be used in single-dose regimens to improve compliance. This ambitious programme to eliminate malaria also includes new approaches that could yield malaria vaccines or novel vector control strategies. However, despite these achievements, a well-coordinated global effort on multiple fronts is needed if malaria elimination is to be achieved.

Ethnicity, sex, and age are determinants of red blood cell storage and stress hemolysis: results of the REDS-III RBC-Omics study

Genetic polymorphisms in blood donors may contribute to donor-specific differences in the survival of red blood cells (RBCs) during cold storage and after transfusion. Genetic variability is anticipated to be high in donors with racial admixture from malaria endemic regions such as Africa and Asia. The purpose of this study was to test the hypothesis that donor genetic background, reflected by sex and self-reported ethnicity, significantly modulates RBC phenotypes in storage. High throughput hemolysis assays were developed and used to evaluate stored RBC samples from 11 115 African American, Asian, white, and Hispanic blood donors from 4 geographically diverse regions in the United States. Leukocyte-reduced RBC concentrate-derived samples were stored for 39 to 42 days (1-6°C) and then evaluated for storage, osmotic, and oxidative hemolysis. Male sex was strongly associated with increased susceptibility to all 3 hemolysis measures (P < .0001). African American background was associated with resistance to osmotic hemolysis compared with other racial groups (adjusted P < .0001). Donor race/ethnicity was also associated with extreme (>1%) levels of storage hemolysis exceeding US Food and Drug Administration regulations for transfusion (hemolysis >1% was observed in 3.51% of Asian and 2.47% of African American donors vs 1.67% of white donors). These findings highlight the impact of donor genetic traits on measures of RBC hemolysis during routine cold storage, and they support current plans for genome-wide association studies, which may help identify hereditable variants with substantive effects on RBC storage stability and possibly posttransfusion outcomes.

Co-inheritance of glucose-6-phosphate dehydrogenase deficiency mutations and hemoglobin E in a Kachin population in a malaria-endemic region of Southeast Asia

Glucose-6-phosphate dehydrogenase (G6PD) deficiency and hemoglobin E (HbE, β26 Glu-Lys) are two common red cell disorders in Southeast Asia. G6PD deficiency produces hemolytic anemia, which can be triggered by certain drugs or infections. HbE is asymptomatic or is manifested as microcytic, minimally hemolytic anemia. The association between G6PD deficiency and HbE is little understood. This study aimed to investigate G6PD deficiency and HbE in a Kachin ethnic group in the China-Myanmar border area. G6PD enzyme activity was measured using a quantitative G6PD assay, G6PD variants genotyped by the SNaPshot assay, and an HbE gene mutation identified by an amplification refractory mutation system and subsequently confirmed by using a reverse dot blot hybridization assay from 100 unrelated individuals in the study area. G6PD enzyme activity ranged from 0.4 to 24.7 U/g Hb, and six males had severe G6PD deficiency (<0.12-1.2 U/g Hb), while six males and 12 females had mild G6PD deficiency (>1.2-4.5 U/g Hb). Among the 24 G6PD-deficient subjects, 22 (92%) had the Mahidol 487G>A mutation (12 male hemizygotes, one female homozygote, and nine female heterozygotes), while the G6PD genotypes in two female subjects were unknown. HbE was identified in 39 subjects (20 males and 19 females), including 15 HbEE (seven males and eight females) and 24 HbAE (13 males and 11 females). Twenty-three subjects co-inherited both G6PD deficiency and HbE (22 with HbAE and one with HbEE). Whereas mean Hb levels were not significantly different between the HbA and HbE groups, G6PD-deficient males had significantly lower Hb levels than G6PD-normal males (P < 0.05, t-test). However, it is noteworthy that two G6PD-deficient hemizygous males with HbAE were severely anemic with Hb levels below 50 g/L. This study revealed high prevalence of co-inheritance of G6PD deficiency with HbAE in the Kachin ethnicity, and a potential interaction of the G6PD Mahidol 487G>A and HbAE in males leading to severe anemia. The presence of 6% males with severe G6PD deficiency raised a major concern in the use of primaquine for radical cure of vivax malaria.

What Is Known about the Immune Response Induced by Plasmodium vivax Malaria Vaccine Candidates?

Malaria caused by Plasmodium vivax continues being one of the most important infectious diseases around the world; P. vivax is the second most prevalent species and has the greatest geographic distribution. Developing an effective antimalarial vaccine is considered a relevant control strategy in the search for means of preventing the disease. Studying parasite-expressed proteins, which are essential in host cell invasion, has led to identifying the regions recognized by individuals who are naturally exposed to infection. Furthermore, immunogenicity studies have revealed that such regions can trigger a robust immune response that can inhibit sporozoite (hepatic stage) or merozoite (erythrocyte stage) invasion of a host cell and induce protection. This review provides a synthesis of the most important studies to date concerning the antigenicity and immunogenicity of both synthetic peptide and recombinant protein candidates for a vaccine against malaria produced by P. vivax.

Molecular basis of human cerebral malaria development

Cerebral malaria is still a deleterious health problem in tropical countries. The wide spread of malarial drug resistance and the lack of an effective vaccine are obstacles for disease management and prevention. Parasite and human genetic factors play important roles in malaria susceptibility and disease severity. The malaria parasite exerted a potent selective signature on the human genome, which is apparent in the genetic polymorphism landscape of genes related to pathogenesis. Currently, much genomic data and a novel body of knowledge, including the identification of microRNAs, are being increasingly accumulated for the development of laboratory testing cassettes for cerebral malaria prevention. Therefore, understanding of the underlying complex molecular basis of cerebral malaria is important for the design of strategy for cerebral malaria treatment and control.

Comparative Microbial Genomics and Forensics

Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

Apolipoprotein L1 and Kidney Disease in African Americans

Genetic variants in the Apolipoprotein L1 (APOL1) gene cause high rates of kidney disease in African Americans. These variants, found only in individuals with recent African ancestry, confer enhanced innate immunity against African trypanosomes. Although they are among the most powerful disease-causing common variants discovered to date, we are just beginning to understand how they promote kidney injury. Since APOL1 is present in only a few primate species, much of our current knowledge has come from natural experiments in humans and in vitro studies while awaiting the development of transgenic animal models. Understanding more about the function of ApoL1 and how the high-risk variants behave differently from other ApoL1 molecules is a high priority in kidney disease research.

Type 2 Diabetes Prevention: Implications of Hemoglobin A1c Genetics

Hemoglobin A1c (HbA1c) is a biomarker used for population-level screening of type 2 diabetes (T2D) and risk stratification. Large-scale, genome-wide association studies have identified multiple genomic loci influencing HbA1c. We discuss the challenges of classifying these genomic loci as influencing HbA1c through glycemic or nonglycemic pathways, based on their probable biology and pleiotropic associations with erythrocyte traits. We show that putative nonglycemic genetic variants have a measurable, albeit small, impact on the classification of T2D status by HbA1c in white and Asian populations. Accounting for their effect on HbA1c may be relevant when screening populations with higher frequencies of nonglycemic HbA1c-altering alleles. As carriers of such HbA1c-altering alleles have HbA1c levels that may not accurately reflect overall glycemia, we describe how accounting for genotype may improve the performance of HbA1c in T2D prediction models and risk stratification, allowing for lifestyle intervention strategies to be directed towards those who are truly at elevated risk for developing T2D. In a Mendelian randomization framework, genetic variants can be used as instrumental variables to estimate causal relationships between HbA1c and T2D-related complications. This approach may help to support or refute HbA1c as an appropriate biomarker for long-term health outcomes in the general population.

Decreased erythrocyte nucleoside transport and hENT1 transporter expression in glucose 6-phosphate dehydrogenase deficiency

BACKGROUND

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is associated with erythrocyte sensitivity to oxidative damage and hemolytic crises. In β-thalassemia major, where hemoglobin instability imposes oxidative stress, erythrocytes show reduced hENT1 nucleoside transporter expression and decreased nucleoside uptake. This study investigated hENT1 expression and nucleoside transport in G6PD-deficient erythrocytes to determine if decreased hENT1 activity might be a contributory feature in the variable pathology of this enzymopathy.

METHODS

Uptake of (3)H-uridine was measured at room temperature using an inhibitor-oil stop protocol and 5-s incubations. Erythrocyte membranes were analyzed by SDS-PAGE and nucleoside (hENT1), glucose (GLUT-1), and anion exchange (Band 3) transporter polypeptides quantitated on immunoblots.

RESULTS

In G6PD-deficient cells, uridine uptake (mean 8.18, 95 % CI 5.6-10.7 vs controls mean 12.35, 95 % CI 9.2-15.5, pmol uridine/gHb/min; P = 0.031) and expression of hENT1 (mean 50.4 %, 95 % CI 38.1-62.7 %, arbitrary units n = 11 vs controls mean 95.23 %, 95 % CI 88.38-102.1 % arbitrary units, n = 8; P < 0.001) were significantly lower; expression of GLUT-1 (mean 106.9 %, vs control mean 99.75 %; P = 0.308) and Band 3 polypeptides (mean 100.1 %, vs control mean 102.84 %; P = 0.329) were unchanged.

CONCLUSIONS

Nucleoside transporter activity in human erythrocytes sustains intracellular purine nucleotide levels and assists in control of plasma adenosine levels; decreased hENT1 expression and activity in G6PD-deficiency could affect red metabolism and influence a wide spectrum of responses mediated by adenosine receptors.

Clinical Role of Human Leukocyte Antigen in Health and Disease

Most of the genes in the major histocompatibility complex (MHC) region express high polymorphism that is fundamental for their function. The most important function of human leukocyte antigen (HLA) molecule is in the induction, regulation of immune responses and the selection of the T cell repertoire. A clinician's attention is normally drawn to a system only when it malfunctions. The HLA system is no exception in this regard, but in contrast to other systems, it also arouses interest when it functions well - too well, in fact. Population studies carried out over the last several decades have identified a long list of human diseases that are significantly more common among individuals that carry particular HLA alleles including inflammatory, autoimmune and malignant disorders. HLA-disease association is the name of this phenomenon, and the mechanism underlying is still a subject of hot debate. Social behaviours are affected by HLA genes and preference for HLA disparate mates may provide 'good genes' for an individual's offspring. Also, certain HLA genes may be associated with shorter life and others with longer lifespan, but the effects depend both on the genetic background and on the environmental conditions. The following is a general overview of the important functional aspects of HLA in health and diseases.

Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase is a potential drug target

The malarial parasite Plasmodium falciparum is exposed to substantial redox challenges during its complex life cycle. In intraerythrocytic parasites, haemoglobin breakdown is a major source of reactive oxygen species. Deficiencies in human glucose-6-phosphate dehydrogenase, the initial enzyme in the pentose phosphate pathway (PPP), lead to a disturbed redox equilibrium in infected erythrocytes and partial protection against severe malaria. In P. falciparum, the first two reactions of the PPP are catalysed by the bifunctional enzyme glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase (PfGluPho). This enzyme differs structurally from its human counterparts and represents a potential target for drugs. In the present study we used epitope tagging of endogenous PfGluPho to verify that the enzyme localises to the parasite cytosol. Furthermore, attempted double crossover disruption of the PfGluPho gene indicates that the enzyme is essential for the growth of blood stage parasites. As a further step towards targeting PfGluPho pharmacologically, ellagic acid was characterised as a potent PfGluPho inhibitor with an IC50 of 76 nM. Interestingly, pro-oxidative drugs or treatment of the parasites with H2O2 only slightly altered PfGluPho expression or activity under the conditions tested. Furthermore, metabolic profiling suggested that pro-oxidative drugs do not significantly perturb the abundance of PPP intermediates. These data indicate that PfGluPho is essential in asexual parasites, but that the oxidative arm of the PPP is not strongly regulated in response to oxidative challenge.

Glioma Association and Balancing Selection of ZFPM2

ZFPM2, encoding a zinc finger protein and abundantly expressed in the brain, uterus and smooth muscles, plays important roles in cardiac and gonadal development. Abnormal expression of ZFPM2 in ovarian tumors and neuroblastoma has been reported but hitherto its genetic association with cancer and effects on gliomas have not been studied. In the present study, the hexamer insertion-deletion polymorphism rs71305152, located within a large haplotype block spanning intron 1 to intron 3 of ZFPM2, was genotyped in Chinese cohorts of glioma (n = 350), non-glioma cancer (n = 354) and healthy control (n = 463) by direct sequencing and length polymorphism in gel electrophoresis, and ZFPM2 expression in glioma tissues (n = 69) of different grades was quantified by real-time RT-PCR. Moreover, potential natural selection pressure acting on the gene was investigated. Disease-association analysis showed that the overall genotype of rs71305152 was significantly associated with gliomas (P = 0.016), and the heterozygous genotype compared to the combined homozygous genotypes was less frequent in gliomas than in controls (P = 0.005) or non-glioma cancers (P = 0.020). ZFPM2 mRNA expression was negatively correlated with the grades of gliomas (P = 0.002), with higher expression levels in the low-grade gliomas. In the astrocytoma subtype, higher ZFPM2 expression was also correlated with the rs71305152 heterozygous genotype (P = 0.028). In addition, summary statistics tests gave highly positive values, demonstrating that the gene is under the influence of balancing selection. These findings suggest that ZFPM2 is a glioma susceptibility gene, its genotype and expression showing associations with incidence and severity, respectively. Moreover, the balancing selection acting on ZFPM2 may be related to the important roles it has to play in multiple organ development or associated disease etiology.