Estonian Biocentre

Abstract Ancient DNA is a valuable data source for the understanding of our past. However, to effectively interpret this data, it is essential to know the age of the samples from which the DNA is obtained. Although the field of palaeogenomics has been recognised for its robust open data sharing practices, dating information associated with analysed samples is not reported consistently across palaeogenomic studies, nor is it included as metadata in most genetic data repositories. Here, we describe the addition of standardised precise dating information for ancient microbial genomes into the AncientMetagenomeDir metadata repository of published ancient metagenomic samples. This extension currently includes dating information for over 700 ancient microbial genomic datasets, of which 333 are dated using historical, contextual, or stratigraphic methods, and 405 are radiocarbon dated. We quantitatively assess the quality of radiocarbon date reporting and find that, despite established reporting conventions, radiocarbon dating information is often reported inconsistently across ancient metagenomic studies. This new resource provides ancient microbial researchers with standardised dating information that facilitates more accurate and consistent analysis of metagenomic sequencing data. The dataset also highlights the need for greater standardisation of radiocarbon date reporting in original publications in order to allow effective reuse of this and future ancient microbial data.

The gut microbiome has been shown to be affected by the use of many human-targeted medications, and the interaction can be bidirectional. This has been clearly demonstrated for type 2 diabetes medications that have been in clinical use for several decades. However, the bidirectional effects of novel type 2 diabetes drugs semaglutide, empagliflozin, and the gut microbiome have yet to be clearly described. Considering this, we investigate the effect of semaglutide and empagliflozin initiation on the gut microbiome of type 2 diabetes patients. In addition, we analyze whether the pre-treatment gut microbiome can predict the treatment efficacy. In the study, patients with type 2 diabetes donated gut microbiome fecal samples at four timepoints (Baseline, Month 1, Month 3, Month 12) that were studied using 16S ribosomal RNA gene sequencing and analysis. Subjects additionally donated plasma and urine samples for quantitative measurement of clinical markers before treatment initiation and at Months 3 and 12. Repeated measures ANOVA paired with paired t-tests were used to analyze the effects of drug initiation on the gut microbiome. Pearson correlation was used to identify microbial features associated with the change in clinical parameters. First, semaglutide and empagliflozin use is associated with changes in the gut microbiome after treatment initiation, but changes in microbial diversity were not detected. Moreover, the baseline gut microbiome predicted changes in glycohemoglobin for semaglutide and empagliflozin users. Based on the results, our findings suggest that semaglutide and empagliflozin impact the gut microbial community during treatment. In addition, the baseline gut microbiome can predict semaglutide treatment effects.

ABSTRACT In humans, 19 Wnt ligands interact with 10 Frizzled (Fzd) receptors and the co-receptors LRP5/6 to initiate signaling. Wnts and Fzds are highly promiscuous, making it challenging to dissect the specific outcomes of individual Wnt-Fzd interactions. Developing Wnt surrogates with specificity for individual Fzd subtypes could be pivotal. We present a modular, potent, and Fzd7-specific Wnt surrogate that consists of three de novo designed modules, a Fzd7 binder, an LRP6 binder and a homodimeric protein. The Fzd7-specific module was designed by targeting two less conserved surface patches on the cysteine-rich domain (CRD) of Fzds to achieve both selectivity and affinity. It exhibits a strong binding affinity (K D < 2.3 nM) for the very closely related Fzd7 subtype members (Fzd7, Fzd1, Fzd2) with no measurable binding to the CRDs of the other seven Fzd receptors. This Wnt surrogate induced spheroid organoid formation from intestinal stem cells at subnanomolar concentration, and promoted full hair follicle regeneration and robust hair growth in mice. These results suggest that our strategy could be extended to design modular Wnt surrogates capable of selectively activating individual Fzd receptors, providing a valuable tool kit for development and differentiation, organoid cultures and targeted regeneration.

Abstract Genome-wide association studies (GWAS) have significantly advanced the understanding of genetic mechanisms underlying complex human diseases and traits by systematically identifying genetic variants linked to diverse phenotype traits across diverse populations. Large-scale analyses that combine multiple phenotypes are especially valuable, as they can reveal shared genetic architectures and patterns of comorbidity, refining disease classification and risk prediction.Here, we conducted comprehensive GWAS analyses based on Estonian Biobank EHR data, focusing on 4,884 ICD-10-based disease phenotypes, in a cohort of 206,159 Estonian Biobank participants. By analysing their genotype data, altogether 18,977,777 SNV and indel variants (including common, low-frequency and rare variants), our analyses revealed 2,127 unique genome-wide significant loci, including 778 putatively novel locus-phenotype associations.Further investigation into coding variants revealed 835 significant associations, including well-established ACMG pathogenic variants and multiple putatively novel associations. Notably, a missense variant inSCN11A, which encodes the Nav1.9 sodium channel involved in pain signalling, was associated with decreased migraine risk, while an Estonian-enrichedGOT1variant considerably affected aspartate transaminase enzymatic function.Our study highlights the potential of population-based biobanks in discovering both common and rare genetic associations, contributing to the identification of novel disease associated loci and expanding the catalog of human disease related genetic variants.

The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.

Abstract Highlanders and lowlanders of Papua New Guinea (PNG) have faced distinct environmental conditions. These environmental differences lead to specific stress on PNG highlanders and lowlanders, such as hypoxia and environment-specific pathogen exposure, respectively. We hypothesise that these constraints induced specific selective pressures that shaped the genomes of both populations. In this study, we explored signatures of selection in newly sequenced whole genomes of 54 PNG highlanders and 74 PNG lowlanders. Based on multiple methods to detect selection, we investigated the 21 and 23 genomic top candidate regions for positive selection in PNG highlanders and PNG lowlanders, respectively. To identify the most likely candidate SNP driving selection in each of these regions, we computationally reconstructed allele frequency trajectories of variants in each of these regions and chose the SNP with the highest likelihood of being under selection with CLUES. We show that regions with signatures of positive selection in PNG highlanders genomes encompass genes associated with the hypoxia-inducible factors pathway, brain development, blood composition, and immunity, while selected genomic regions in PNG lowlanders contain genes related to immunity and blood composition. We found that several candidate driver SNPs are associated with haematological phenotypes in the UK biobank. Moreover, using phenotypes measured from the sequenced Papuans, we found that two candidate SNPs are significantly associated with altered heart rates in PNG highlanders and lowlanders. Furthermore, we found that 16 of the 44 selection candidate regions harboured archaic introgression. In four of these regions, the selection signal might be driven by the introgressed archaic haplotypes, suggesting a significant role of archaic admixture in local adaptation in PNG populations.

Abstract Atopic dermatitis (AD) is a common inflammatory skin condition and prior genome-wide association studies have identified 71 associated loci. In the current study we conducted the largest AD GWAS to date (discovery N=1,086,394, replication N=3,604,027), combining previously reported cohorts with additional available data. We identified 81 loci (29 novel) in the European-only analysis and 15 additional loci in the multi-ancestry analysis (6 novel). All 81 variants replicated in a separate European analysis. Eleven variants from the multi-ancestry analysis replicated in at least one of the populations tested (European, Latino or African). While four variants appeared to be specific to individuals of Japanese ancestry. AD loci showed enrichment for DNAse I hypersensitivity and eQTL signals in blood. At each locus we prioritised candidate genes by integrating multi-omic data. The implicated genes are predominantly in immune pathways of relevance to atopic inflammation and some offer drug repurposing opportunities.

Gibbons are the most speciose family of living apes, characterized by a diverse chromosome number and rapid rate of large-scale rearrangements. Here we performed single-cell template strand sequencing (Strand-seq), molecular cytogenetics, and deep in silico analysis of a southern white-cheeked gibbon genome, providing the first comprehensive map of 238 previously hidden small-scale inversions. We determined that more than half are gibbon specific, at least fivefold higher than shown for other primate lineage-specific inversions, with a significantly high number of small heterozygous inversions, suggesting that accelerated evolution of inversions may have played a role in the high sympatric diversity of gibbons. Although the precise mechanisms underlying these inversions are not yet understood, it is clear that segmental duplication–mediated NAHR only accounts for a small fraction of events. Several genomic features, including gene density and repeat (e.g., LINE-1) content, might render these regions more break-prone and susceptible to inversion formation. In the attempt to characterize interspecific variation between southern and northern white-cheeked gibbons, we identify several large assembly errors in the current GGSC Nleu3.0/nomLeu3 reference genome comprising more than 49 megabases of DNA. Finally, we provide a list of 182 candidate genes potentially involved in gibbon diversification and speciation.

ObjectivesContemporary archeological theory emphasizes the economic and social complexity of Eurasian steppe populations. As a result, old notions of “nomadic” cultures as homogenously mobile and economically simple are now displaced by more nuanced interpretations. Large part of the literature on diet and mobility among Eurasian pastoralists is focused on the Bronze and Iron Ages. The underrepresentation of more recent contexts hampers a full discussion of possible chronological trajectories. In this study we explore diet and mobility at Tunnug1 (Republic of Tuva, 2nd–4th century CE), and test their correlation with social differentiation.Materials and MethodsWe compare demographic patterns (by age‐at‐death and sex) of carbon, nitrogen, and sulfur stable isotope ratios (δ13C, δ15N, and δ34S) among 65 humans and 12 animals from Tunnug1 using nonparametric tests and Bayesian modeling. We then compare isotopic data with data on perimortal skeletal lesions of anthropic origin and funerary variables.ResultsOur analyses show that: (1) diet at Tunnug1 was largely based on C4 plants (likely millet) and animal proteins; (2) few individuals were nonlocals, although their geographic origin remains unclarified; (3) no differences in diet separates individuals based on sex and funerary treatment. In contrast, individuals with perimortal lesions show carbon and nitrogen stable isotope ratios consistent with a diet incorporating a lower consumption of millet and animal proteins.DiscussionOur results confirm the previously described socioeconomic variability of steppe populations, providing at the same time new data about the economic importance of millet in Southern Siberia during the early centuries CE.