Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals

Tissue-specific genes as an underutilized resource in drug discovery

Tissue-specific genes are believed to be good drug targets due to improved safety. Here we show that this intuitive notion is not reflected in phase 1 and 2 clinical trials, despite the historic success of tissue-specific targets and their 2.3-fold overrepresentation among targets of marketed non-oncology drugs. We compare properties of tissue-specific genes and drug targets. We show that tissue-specificity of the target may also be related to efficacy of the drug. The relationship may be indirect (enrichment in Mendelian disease and PTVesc genes) or direct (elevated betweenness centrality scores for tissue-specifically produced enzymes and secreted proteins). Reduced evolutionary conservation of tissue-specific genes may represent a bottleneck for drug projects, prompting development of novel models with smaller evolutionary gap to humans. We show that the opportunities to identify tissue-specific drug targets are not exhausted and discuss potential use cases for tissue-specific genes in drug research.

Hemoglobin E protects against acute Plasmodium vivax infections in a Kachin population at the China-Myanmar border

OBJECTIVES

Hemoglobin E (HbE, β^{26 Glu-Lys}) is the most prevalent hemoglobinopathy in Southeast Asia. This study aimed to determine whether HbE protects against clinical Plasmodium vivax malaria in Southeast Asia.

METHODS

In a case-control study performed in villages along the China-Myanmar border, we determined the prevalence of HbE in 257 villagers who had acute P. vivax infections and in 157 control healthy villagers.

RESULTS

HbE in P. vivax patients (17.4%) was significantly less prevalent than in the healthy villager population (36.3%). Moreover, there was a complete lack of HbEE homozygotes in the vivax patients as compared to 9.5% prevalence in the healthy villagers. Using the HbAA group as the reference, both the HbEA heterozygotes and HbEE homozygotes had significantly lower odds of presenting with acute P. vivax infections. Furthermore, HbEA heterozygotes also had significantly lower P. vivax asexual parasite densities. HbEA did not affect the proportion of P. vivax patients with gametocytemia nor the gametocyte densities.

CONCLUSIONS

HbE offers significant protection against the occurrence and parasite density of acute P. vivax infections and provides a renewed perspective on P. vivax malaria as a potentially strong driving force behind the high frequencies of HbE in the Kachin population.

The genomic landscape of African populations in health and disease

A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research. In the case of pharmacogenomics, for instance, variants of consequence are not limited to those identified in other populations, and diversity within African ancestry populations precludes summarizing risk across different African ethnic groups. Exposure of Africans to fatal pathogens, such as Plasmodium falciparum, Lassa Virus and Trypanosoma brucei rhodesiense, has resulted in elevated frequencies of alleles conferring survival advantages for infectious diseases, but that are maladaptive in modern-day environments. Illustrating with cardiometabolic traits, we show that while genomic research in African ancestry populations is still in early stages, there are already many examples of novel and African ancestry-specific disease loci that have been discovered. Furthermore, the shorter haplotypes in African genomes have facilitated fine-mapping of loci discovered in other human ancestry populations. Given the insights already gained from the interrogation of African genomes, it is imperative to continue and increase our efforts to describe genomic risk in and across African ancestry populations.

Revealing phenotype-associated functional differences by genome-wide scan of ancient haplotype blocks

Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data. By applying this pipeline to the genotypes in the International HapMap project database, we show that genes in the detected regions are enriched in pathways related to the immune system and infectious diseases. The detected regions also contain SNPs reported to be associated with cancers and metabolic diseases, obesity-related traits, type 2 diabetes, and allergic sensitization. These SNPs were further mapped to biological pathways to determine the associations between phenotypes and molecular functions. Assessments of candidate regions to identify functions associated with variations in incidence rates of these diseases are needed in the future.