Recent positive selection signatures reveal phenotypic evolution in the Han Chinese population

Genome diversity and signatures of natural selection in mainland Southeast Asia

Mainland Southeast Asia (MSEA) has rich ethnic and cultural diversity with a population of nearly 300 million1,2. However, people from MSEA are underrepresented in the current human genomic databases. Here we present the SEA3K genome dataset (phase I), generated by deep short-read whole-genome sequencing of 3,023 individuals from 30 MSEA populations, and long-read whole-genome sequencing of 37 representative individuals. We identified 79.59 million small variants and 96,384 structural variants, among which 22.83 million small variants and 24,622 structural variants are unique to this dataset. We observed a high genetic heterogeneity across MSEA populations, reflected by the varied combinations of genetic components. We identified 44 genomic regions with strong signatures of Darwinian positive selection, covering 89 genes involved in varied physiological systems such as physical traits and immune response. Furthermore, we observed varied patterns of archaic Denisovan introgression in MSEA populations, supporting the proposal of at least two distinct instances of Denisovan admixture into modern humans in Asia3. We also detected genomic regions that suggest adaptive archaic introgressions in MSEA populations. The large number of novel genomic variants in MSEA populations highlight the necessity of studying regional populations that can help answer key questions related to prehistory, genetic adaptation and complex diseases.

Contrastive sequence signatures between the both sides of a recombination spot reveal an adaptation at PPARD locus from standing variation for pleiotropy since out-of-Africa dispersal

BACKGROUND

Drug metabolism and transporter genes are a specialized class of genes involved in absorption, distribution, metabolism and excretion. They easily present distinct genetic population differentiation and are vulnerable to natural selection.

RESULTS

We initiated a study using a special panel of informative genetic markers in such genes and dissected the genetic structure in representative Chinese and worldwide populations. A distinctive sub-population stratification was discovered in extensive Eurasians and resulted from divergence at the PPARD locus. The contrastive sequence signatures between the both sides of a recombination spot prove a selective sweep on this locus for genetic hitchhiking effect. A genealogy-based framework demonstrates the positive selection acting from standing variation exerted a moderate pressure in Eurasians, and drove the adaptive allele up to a high frequency. The timing and tempo estimations for the genetic adaptation indicate its onset coincided with the early out-of-Africa migration of modern humans and it lasted over a prolonged evolutionary history. A phenome-wide association analysis reveals an extended cis-regulation on the local gene expression and the pleiotropy implicated in a variety of complex traits. The colocalization analyses between the genetic associations from cis-acting gene expression and complex traits signify the most likely selective pressure from physical capacity, energy metabolism, and immune-related involvement, and provide prioritization for the effective genes and casual variants.

CONCLUSIONS

This work has laid a foundation for following efforts to make full sense of the biological mechanisms underlying the genetic adaptation.

Genetic diversity and dietary adaptations of the Central Plains Han Chinese population in East Asia

The Central Plains Han Chinese (CPHC) is the typical agricultural population of East Asia. Investigating the genome of the CPHC is crucial to understanding the genetic structure and adaptation of the modern humans in East Asia. Here, we perform whole genome sequencing of 492 CPHC individuals and obtained 22.65 million SNPs, 4.26 million INDELs and 41,959 SVs. We found the CPHC has a higher level of genetic diversity and the glycolipid metabolic genes show strong selection signals, e.g. LONP2, FADS2, FGF21 and SLC19A2. Ancient DNA analyses suggest that the domestication of crops, which drove the emergence of the candidate mutations. Notably, East Asian-specific SVs, e.g., DEL_21699 (LINC01749) and DEL_38406 (FAM102A) may be associated with the high prevalence of esophageal squamous carcinoma and primary angle-closure glaucoma. Our results provide an important genetic resource and show that dietary adaptations play an important role in phenotypic evolution in East Asian populations.

Pharmacological Mechanism of Chinese Medicine in Systemic Lupus Erythematosus: A Narrative Review

Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder affecting multiple systems, characterized by the development of harmful autoantibodies and immune complexes that lead to damage in organs and tissues. Chinese medicine (CM) plays a role in mitigating complications, enhancing treatment effectiveness, and reducing toxicity of concurrent medications, and ensuring a safe pregnancy. However, CM mainly solves the disease comprehensively through multi-target and multi-channel regulation process, therefore, its treatment mechanism is often complicated, involving many molecular links. This review introduces the research progress of pathogenesis of SLE from the aspects of genetics, epigenetics, innate immunity and acquired immunity, and then discusses the molecular mechanism and target of single Chinese herbal medicine and prescription that are commonly used and effective in clinic to treat SLE.

Genome-wide investigation of VNTR motif polymorphisms in 8,222 genomes: Implications for biological regulation and human traits

Variable number tandem repeat (VNTR) is a pervasive and highly mutable genetic feature that varies in both length and repeat sequence. Despite the well-studied copy-number variants, the functional impacts of repeat motif polymorphisms remain unknown. Here, we present the largest genome-wide VNTR polymorphism map to date, with over 2.5 million VNTR length polymorphisms (VNTR-LPs) and over 11 million VNTR motif polymorphisms (VNTR-MPs) detected in 8,222 high-coverage genomes. Leveraging the large-scale NyuWa cohort, we identified 2,982,456 (31.8%) NyuWa-specific VNTR-MPs, of which 95.3% were rare. Moreover, we found 1,937 out of 38,685 VNTRs that were associated with gene expression through VNTR-MPs in lymphoblastoid cell lines. Specifically, we clarified that the expansion of a likely causal motif could upregulate gene expression by improving the binding concentration of PU.1. We also explored the potential impacts of VNTR polymorphisms on phenotypic differentiation and disease susceptibility. This study expands our knowledge of VNTR-MPs and their functional implications.

Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle

This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (ARHGAP15, ZNF618, USH2A, PDZRN4, SPATA6, ROR2, KCNIP3, and VWA3B), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle.

STON2 variations are involved in synaptic dysfunction and schizophrenia-like behaviors by regulating Syt1 trafficking

Synaptic dysfunction is a core component of the pathophysiology of schizophrenia. However, the genetic risk factors and molecular mechanisms related to synaptic dysfunction are still not fully understood. The Stonin 2 (STON2) gene encodes a major adaptor for clathrin-mediated endocytosis (CME) of synaptic vesicles. In this study, we showed that the C-C (307Pro-851Ala) haplotype of STON2 increases the susceptibility to schizophrenia and examined whether STON2 variations cause schizophrenia-like behaviors through the regulation of CME. We found that schizophrenia-related STON2 variations led to protein dephosphorylation, which affected its interaction with synaptotagmin 1 (Syt1), a calcium sensor protein located in the presynaptic membrane that is critical for CME. STON2307Pro851Ala knockin mice exhibited deficits in synaptic transmission, short-term plasticity, and schizophrenia-like behaviors. Moreover, among seven antipsychotic drugs, patients with the C-C (307Pro-851Ala) haplotype responded better to haloperidol than did the T-A (307Ser-851Ser) carriers. The recovery of deficits in Syt1 sorting and synaptic transmission by acute administration of haloperidol effectively improved schizophrenia-like behaviors in STON2307Pro851Ala knockin mice. Our findings demonstrated the effect of schizophrenia-related STON2 variations on synaptic dysfunction through the regulation of CME, which might be attractive therapeutic targets for treating schizophrenia-like phenotypes.

Adaptive Selection of Cis-regulatory Elements in the Han Chinese

Cis-regulatory elements have an important role in human adaptation to the living environment. However, the lag in population genomic cohort studies and epigenomic studies, hinders the research in the adaptive analysis of cis-regulatory elements in human populations. In this study, we collected 4,013 unrelated individuals and performed a comprehensive analysis of adaptive selection of genome-wide cis-regulatory elements in the Han Chinese. In total, 12.34% of genomic regions are under the influence of adaptive selection, where 1.00% of enhancers and 2.06% of promoters are under positive selection, and 0.06% of enhancers and 0.02% of promoters are under balancing selection. Gene ontology enrichment analysis of these cis-regulatory elements under adaptive selection reveals that many positive selections in the Han Chinese occur in pathways involved in cell-cell adhesion processes, and many balancing selections are related to immune processes. Two classes of adaptive cis-regulatory elements related to cell adhesion were in-depth analyzed, one is the adaptive enhancers derived from neanderthal introgression, leads to lower hyaluronidase level in skin, and brings better performance on UV-radiation resistance to the Han Chinese. Another one is the cis-regulatory elements regulating wound healing, and the results suggest the positive selection inhibits coagulation and promotes angiogenesis and wound healing in the Han Chinese. Finally, we found that many pathogenic alleles, such as risky alleles of type 2 diabetes or schizophrenia, remain in the population due to the hitchhiking effect of positive selections. Our findings will help deepen our understanding of the adaptive evolution of genome regulation in the Han Chinese.

Asian flush is a potential protective factor against COVID-19: a web-based retrospective survey in Japan

BACKGROUND

Coronavirus disease 2019 (COVID-19), first reported in December 2019, spread worldwide in a short period, resulting in numerous cases and associated deaths; however, the toll was relatively low in East Asia. A genetic polymorphism unique to East Asians, Aldehyde dehydrogenase 2 rs671, has been reported to confer protection against infections.

METHOD

We retrospectively investigated the association between the surrogate marker of the rs671 variant, the skin flushing phenomenon after alcohol consumption, and the timing of COVID-19 incidence using a web-based survey tool to test any protective effects of rs671 against COVID-19.

RESULTS

A total of 807 valid responses were received from 362 non-flushers and 445 flushers. During the 42 months, from 12/1/2019 to 5/31/2023, 40.6% of non-flushers and 35.7% of flushers experienced COVID-19. Flushers tended to have a later onset (Spearman's partial rank correlation test, p = 0.057, adjusted for sex and age). Similarly, 2.5% of non-flushers and 0.5% of flushers were hospitalized because of COVID-19. Survival analysis estimated lower risks of COVID-19 and associated hospitalization among flushers (p = 0.03 and <0.01, respectively; generalized Wilcoxon test). With the Cox proportional hazards model covering 21 months till 8/31/2021, when approximately half of the Japanese population had received two doses of COVID-19 vaccine, the hazard ratio (95% confidence interval) of COVID-19 incidence was estimated to be 0.21 (0.10-0.46) for flusher versus non-flusher, with adjustment for sex, age, steroid use, and area of residence.

CONCLUSIONS

Our study suggests an association between the flushing phenomenon after drinking and a decreased risk of COVID-19 morbidity and hospitalization, suggesting that the rs671 variant is a protective factor. This study provides valuable information for infection control and helps understand the unique constitutional diversity of East Asians.