Biological predictors of variable vaccine responses are lacking. We hypothesized that variability in prevaccine innate immune responses, specifically for type I interferons (IFN-I), is predictive of postvaccine antigen-specific responses. To test this, we assessed prevaccine immune responses at protein and transcriptomic levels following whole blood stimulation with Toll-like receptor (TLR) viral agonists in healthy adolescents and adults. Four weeks after the second vaccine dose, with either the BNT162b2 mRNA or CoronaVac inactivated virus vaccine, we assessed antigen-specific T cell cytokine responses and plasma antibody levels. BNT162b2 vaccinees had increased production of the antigen-specific T cell cytokines interleukin-2 (IL-2), interferon-γ, and IL-21 after severe acute respiratory syndrome coronavirus 2 spike stimulation, as well as increased antibody levels and serum pseudo-neutralization compared with CoronaVac recipients. In direct support of our hypothesis, we find that prevaccine poly(I:C) (polyinosine-polycytidylic acid; TLR3 viral agonist) IFN-I responses were significantly associated with the postvaccine T cell cytokine responses. In an independent cohort of 990 healthy donors, we confirmed the significant association between poly(I:C)-induced IFN-α and spike-induced cytokines in mRNA vaccine recipients. We further confirmed this specific association in a cohort of healthy Europeans and identified a common genetic polymorphism in TLR3 that affects IFN-I induction and subsequent vaccine-specific T cell responses. This study shows that preexisting innate immune variability can predict the effectiveness of vaccine responses and identifies pathways relevant to mRNA vaccination. Targeting the specific innate immune pathway relevant for a vaccine may provide a new approach for tailoring vaccines to different populations.

Motivation:Epigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. Results:We developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG- searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. Availability and implementation:The eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

Human immune responses vary across individuals due to both genetic and environmental factors. We previously established the Milieu Intérieur cohort to define boundaries of healthy immune variation and identify their determinants. To evaluate how immune responses change over time and test whether immune states can predict future disease, we conducted a 10-year follow-up of the cohort. Here we show widespread changes in humoral responses to pathogens over this period, including unexpected seroreversion of cytomegalovirus (CMV) status, despite a general age-related increase in CMV antibodies. We also investigated whether immune profiles at initial recruitment are associated with disease development a decade later. Strikingly, whole blood transcriptional responses to Staphylococcus aureus and Candida albicans stimulation were predictive of subsequent infectious disease. Collectively, the Milieu Intérieur longitudinal study represents a valuable resource for evaluating immune aging and may help identify predictors of adverse health outcomes.

Antibodies are central to immune defenses. Despite advances in understanding the mechanisms of antibody generation, a comprehensive model of how intrinsic and external factors shape human humoral responses to viruses has been lacking. Here we apply phage immunoprecipitation sequencing to investigate the effects of demographic factors-including 108 lifestyle and health-related variables-and genetic variation on antibody reactivity to over 97,000 viral peptides in 1,212 healthy adults. We demonstrate that age, sex and continent of birth extensively affect not only the viruses but also the specific viral epitopes targeted by the antibody repertoire. Notably, we find that antibodies against rapidly evolving epitopes of influenza A virus decrease with age, whereas immunoreactivity to conserved epitopes increases. Furthermore, we identify strong associations between antibodies against 34 viruses and genetic variants at HLA, FUT2, IGH and IGK loci, some of which increase autoimmune disease risk. These findings offer a valuable resource for understanding the factors affecting antibody-mediated immunity, laying the groundwork for optimizing vaccine strategies.

Homozygosity for rare loss-of-function IL23R variants abolishes IL-23-dependent IFN-γ production by lymphocytes, including NK and innate-like T cells, thereby underlying clinical disease due to weakly virulent mycobacterial species. We report selective enrichment in homozygosity for four hypomorphic IL23R variants in our cohort of patients with tuberculosis. Three of these IL23R alleles are rare (G300V, G149R, and L372F), with a minor allele frequency (MAF) under 1%, but the fourth (R381Q) is surprisingly common, with an MAF as high as 10.2% in certain populations. The other 15 missense alleles found in the homozygous state in public databases are isomorphic. The four hypomorphic IL-23R variants identified dimerize with IL-12Rβ1 and bind IL-23. However, their function is impaired by low levels of cell surface expression (R381Q, G300V) and/or as a consequence of conformational changes altering agonist efficacy. IFN-γ production in response to IL-23 is impaired in innate-like T cells and NK cells. These data suggest that recessive partial IL-23R deficiency, whether due to rare or common variants, confers a predisposition to tuberculosis while preserving immunity to less virulent mycobacteria.

Yakut communities from northeastern Siberia inhabit some of the coldest environments on Earth, preserving an extraordinary archaeological record. Their history was profoundly reshaped by the Russian conquest, which introduced cereals, pathogens and Christianity beginning in 1632 (refs. 1-5). However, the biological impact of these transformations remains unknown. Here we generated extensive ancient DNA data to elucidate contemporary changes in Yakut genomic diversity and oral microbiomes. We found Yakut origins tracing back to local populations that admixed with Trans-Baikal groups migrating as the Great Mongol Empire spread. Despite the Russian conquest, the Yakut gene pool and oral microbiomes appeared largely stable, although smallpox strains distinct from those documented in Europe by approximately 1650 circulated. Marital practices generally maintained low consanguinity, with the exception of one female bearing the latest markers of traditional shamanism, who was the daughter of second-degree relatives.

Homozygosity for rare loss-of-function IL23R variants abolishes IL-23-dependent IFN-γ production by lymphocytes, including NK and innate-like T cells, thereby underlying clinical disease due to weakly virulent mycobacterial species. We report selective enrichment in homozygosity for four hypomorphic IL23R variants in our cohort of patients with tuberculosis. Three of these IL23R alleles are rare (G300V, G149R and L372F), with a minor allele frequency (MAF) under 1%, but the fourth (R381Q) is surprisingly common, with a MAF as high as 10.2% in certain populations. The other 15 missense alleles found in the homozygous state in public databases are isomorphic. The four hypomorphic IL-23R variants identified dimerize with IL-12Rβ1 and bind IL-23. However, their function is impaired by low levels of cell-surface expression (R381Q, G300V) and/or as a consequence of conformational changes altering agonist efficacy. IFN-γ production in response to IL-23 is impaired in innate-like T cells and NK cells. These data suggest that recessive partial IL-23R deficiency, whether due to rare or common variants, confers a predisposition to tuberculosis while preserving immunity to less virulent mycobacteria. One sentence summary:Homozygous hypomorphic IL23R variants impair IL-23-dependent IFN-γ production and underlie tuberculosis.

Neanderthal and Denisovan introgression have left a pervasive footprint in the human genome, yet its regulatory consequences remain poorly understood. Here we use a massively parallel reporter assay to characterize the cis-regulatory activity of 4,161 high-frequency introgressed variants across respiratory (A549), hepatic (HepG2), and hematopoietic (K562) cells exposed to immune and infectious stimuli. We find that ~18% of variants show differential activity between archaic and modern alleles, including 94 whose effects are revealed or modulated by stimulation, often in a cell type-specific manner. We identify loci, including STAT2, IL23A , and RNF41 , where clusters of introgressed alleles exert coordinated regulatory effects consistent with adaptive programs. Finally, we dissect the mechanisms underlying the association between Neanderthal introgression and COVID-19 severity and show that the risk allele rs17713054-A, which displays the strongest effect in our assay, increases activity of a TNF-α-responsive enhancer in lung epithelial cells, directly upregulating SLC6A20 .Together, these findings reveal widespread context-dependent regulatory effects of archaic introgression, with broad evolutionary and biomedical implications.

Naïve T cell output from the thymus varies across the human lifespan and is a key determinant of health, differing between individuals by age, sex, and genetics. How thymic output is dynamically regulated early in life in response to initial microbial colonization remains unclear. We report longitudinal thymic output dynamics, measured as T cell receptor excision circles (TRECs), in 136 newborns from Stockholm, Sweden. Thymic output increases after birth following initial microbial colonization, peaking at 3-4 mo. Peak height correlates with plasma levels of RANKL and lymphotoxin-α and with a common genetic variant in the TCRD locus previously linked to adult thymopoiesis. B cell lymphopoiesis measured by KRECs reveals divergent dynamics between B and T cell branches of the adaptive immune system in early life. Findings are corroborated by thymic tissue analyses, in which local RANKL secretion correlates with medullary, but not cortical, epithelial cell numbers. These results illuminate the establishment of healthy immune-microbe interactions in early human life.

Aging is associated with genome-wide changes in DNA methylation in humans, facilitating the development of epigenetic age prediction models. However, these models have been trained primarily on European-ancestry individuals and none account for the impact of methylation quantitative trait loci (meQTL). To address these gaps, we analyze the relationships between age, genotype, and CpG methylation in 3 understudied populations: central African Baka (n = 35), southern African ‡Khomani San (n = 52), and southern African Himba (n = 51). We show that published prediction methods yield higher mean errors in these cohorts compared to European-ancestry individuals and find that unaccounted-for DNA sequence variation may be a significant factor underlying this loss of accuracy. We leverage information about the associations between DNA genotype and CpG methylation to develop an age predictor that is minimally influenced by meQTL and show that this model remains accurate across a broad range of genetic backgrounds. Intriguingly, we also find that the older individuals and those with lower epigenetic age acceleration carry more genetic variants linked to reduced epigenetic age. These findings support the hypothesis that multiple heritable factors collectively influence healthspan and longevity in human populations.

The gut microbiome is a complex ecosystem characterized not only by its marginal taxonomic composition but also by its emergent properties. Bacteria develop local interactions to form coherent functional communities, whose effects on health and diseases cannot be predicted from the behavior of individual members. Understanding the factors underlying variability in these communities may therefore provide critical insights on the biological links between the gut microbiome and human phenotypes. Here, we examined the effect of a range of host factors, including demographics, medical history, and dietary habits, on these communities in 938 healthy individuals using MANOCCA, a covariance-based approach developed to address existing limitations. Increased age and smoking were associated with a significant overall decrease in co-abundance, and conversely a higher body mass index was associated with increased co-abundance. At the taxon level, a core of 200 genera were systematically impacted in their co-abundance with other taxa, suggesting a central role in structuring the network. Finally, we demonstrate that our approach offers a powerful framework for prediction purposes, with taxa co-abundance being able to predict the age of participants with an accuracy three-fold higher than a model based on abundance only.

Background The ABO blood group system is associated with differential susceptibility to thrombotic vascular diseases. ABO is also known to be a strong trans-protein quantitative trait locus for plasma proteins involved in cell adhesion and hemostasis.Study Design and Method To further investigate these associations, we integrated epigenomic, genomic, and proteomic data from the Milieu Int & eacute;rieur cohort. We used the rs8176719 SNP to classify donors as either type O or non-O, and used linear models to compare levels of 229 plasma proteins in 400 donors, including age, sex, cytomegalovirus serostatus, and secretor status as covariates.Results We observed increased levels of soluble E-selectin and decreased levels of von Willebrand Factor (vWF) in O donors compared with non-O donors. By performing an epigenome-wide association study, we identified 23 differentially methylated CpG sites between blood types, which were all located in the ABO gene. Notably, CpG sites in the ABO promoter region of type O donors were less methylated than those of the non-O donors. Using mediation analysis, we found that these differences in DNA methylation partially explained the effects of blood group on differential E-selectin and vWF plasma levels.Discussion We find differentially methylated CpG sites between blood types and provide new evidence that ABO blood group status affects circulating levels of specific proteins.

Background::Gout, which manifests as severe inflammation caused by excessive serum urate levels and monosodium urate deposits in the joints, is associated with multiple genomic loci in Europeans. In this exploratory work, we aimed to identify additional gene variants in Melanesian families from New Caledonia, a population in which the disease is highly prevalent. Methods::Two families from Lifou Island (New Caledonia) in which multiple members were diagnosed with gout were selected. Whole exome sequencing and/or targeted sequencing of a panel of genes involved in immunity was performed in patients and their healthy relatives. Rare variants in Melanesian populations were selected using an autosomal dominant segregation model.Results::Several variants were identified in genes not previously involved in immune diseases or hyperuricemia, several of which were not observed in control individuals from Remote Oceania.Conclusion::This work highlights new candidate susceptibility loci for gout in New Caledonians, an underrepresented population in genomic studies, and suggests that novel pathways are likely involved in gout pathogenesis.

Steroid hormone levels vary greatly among individuals, between sexes, with age, and across health and disease. What drives variance in steroid hormones and how they vary in individuals over time are not well studied. To address these questions, we measured 17 steroid hormones in a sex-balanced cohort of 949 healthy donors aged 20 to 69 years. We investigated associations between steroid levels and biological sex, age, clinical and demographic data, genetics, and plasma proteomics. Steroid hormone levels were strongly affected by sex and age, and a high number of lifestyle habits. Key observations were the broad impact of hormonal birth control in female donors and the relationship with smoking in male donors. In a 10-year follow-up study, we identified significant associations between steroid hormone levels and health status only in male donors. These observations highlight biological and lifestyle parameters affecting steroid hormones, and underlie the importance of considering sex, age, and potentially gendered behaviors in the treatment of hormone-related diseases.

Human body temperature is sexually dimorphic, with females averaging 0.1-0.5°C warmer than males. Body temperature is also linked to immune responses through highly conserved fever and heat shock pathways. We hypothesized that subtle temperature differences observed between sexes could mediate sex differences in immune responses, with potential clinical implications. To test this, we analyzed 973 healthy adults from the Milieu Intérieur cohort, first confirming significant sex and age effects on body temperature within the homeostatic range. Strikingly, within the narrow 36-38°C healthy range, we observed significant, sex-specific associations with both baseline and induced immune responses upon stimulation. In males, higher temperature was associated with decreased type I IFN pathway responses following bacterial and viral ligand stimulation, whereas in females, it correlated with decreased type II IFN responses after superantigen stimulation. Using precise ex vivo stimulation at fever temperatures and single-cell readouts, we confirmed that temperature-immune associations persist beyond homeostatic levels, highlighting their relevance in pathological conditions. This study provides new insights into how natural variation in body temperature across individuals and throughout life may contribute to the immune variation underlying sex disparities in disease.

P. vivax, the most geographically widespread human malaria parasite with millions of clinical cases per year, is however quasi absent in sub-Saharan Africa. Positive selection targeting the rs2814778 protective mutation, also known as the Duffy-null allele, may explain the absence (or quasi absence) of vivax in sub-Saharan Africa by a progressive purge of the pathogen due to a quasi-fixation of the Duffy-null allele and the resulting high rates of protected carriers in western, central and eastern populations. Yet, while positive selection has been clearly evidenced in admixed populations coexisting with vivax, the selection model currently admitted poorly explains the lack of the Duffy-null allele in Europe, or in Asia where the pathogen is mainly observed. In this article, several validated Deep Learning methods applied to high coverage sequence data obtained in 589 African individuals resolved this retention of the Duffy-null resistance to vivax in Africa. The CNN and GAN algorithms implemented in this study also predict a rise in frequency of the Duffy-null mutation due to selection 25-35 kya years ago in the western part of Africa, a geographical region and a time frame overlapping with the rise of another protective mutation, βS, the sickle-cell mutation protective at heterozygous state against the malaria caused by P. falciparum. In addition, the pattern of Duffy-null haplotypes highlights a quick spread of the Duffy-null allele in sub-Saharan Africa due to post-admixture selection events following the road of the recent Bantu expansion. Independent lines of evidence describing malaria as a life-threatening disease in West Africa from ~30 kya, together with a rise in frequency followed by recent disseminations of the Duffy-null resistance, open new perspectives about both the history of malaria as a major human disease and the history of the main protective mutations in Africa. ### Competing Interest Statement The authors have declared no competing interest.

Human genetic admixture, involving the contact between two or more previously isolated populations, can be a complex process influenced by social dynamics. In this study, we aim to reconstruct complex admixture histories in São Tomé, an island in the Gulf of Guinea where the Portuguese established one of the first plantation-based slave societies. Since the 15th century, migration waves from Africa and Europe, slavery, marooning, and indentured labour led to profound demographic shifts and social stratification on the island. Examining 2.5 million SNPs newly genotyped in 96 São Toméans, we observed patterns of genetic differentiation that were more complex than those of other populations descended from enslaved Africans on either side of the Atlantic. Using local ancestry inference and Identical-by-Descent methods, we identified five genetic clusters in São Tomé and reconstructed shared ancestries between each cluster and 70 African and European population samples, including an extensive sample from the Cabo Verde archipelago. Our findings align with historical records, retracing the major slave trade routes and labour-driven migrations after the abolition of slavery. We also identified gene flow between recently admixed groups that were previously isolated on the island. We call this process, creating multiple layers of genetic ancestry in admixed genomes, nested admixture. We suggest that changing social structures in São Tomé transformed the genetic structure of its population and influenced the admixture process. This study demonstrates how successive admixture and isolation events during and after the Trans-Atlantic Slave Trade shaped extant genetic diversity patterns at local scale in Africa.

Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype-based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post-Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC-based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease-risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases.