Abstract Introduction Even in “healthy” aging, adaptive immune cells become dysregulated, increasing age-associated B cells and exhausted and senescent T cells in the circulation. Although the clinical consequence of this dysregulation remains poorly understood, we previously reported that aged B cells, through the induction of cytolytic CD8+ T cells, can be responsible for the surprising suppression of orthotopic B16-F10 melanoma in aged C57BL/6 mice. Despite this, it remains unclear why this pathway fails to prevent the age-associated increase in other cancers. Methods We performed comprehensive flocytometric analysis combined with scRNA-seq and ATC-seq of adaptive immune cells in young (8-20 weeks old) and aged (17-20 months old) mice. Results While the age-related cancer increase can be explained by exhaustion or senescence of T cells, we do not detect significant accumulation of these cells in aged mice. Instead, we find that aged mice markedly increase a previously unknown subset of CD8+ cells expressing CXCR6 and adenosine-generating CD39 and CD73. These cells (termed DP8), which are also induced by aged B cells, appear to play the key role in the increase of cancer in aged mice. Unlike cancers that regress, cancers that progress in aged mice recruit DP8 cells through the production of CXCL16, which then suppress antitumor CD4+ T cells by generating immunoregulatory adenosine using their ectonucleotidases CD39 and CD73. Conclusion Our results underscore the importance of aged B cells in cancer. By targeting B cells, aging elicits both cancer-promoting and cancer-blocking CD8+ T cells. Funding Source This work was supported by the Intramural Research Program, National Institute on Aging Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

The ε4 allele of the apolipoprotein E (APOE4+) genotype and aging synergistically contribute to the risk of Alzheimer's disease (AD), but the mechanisms underlying their influence are not completely understood. The methylation of ELOVL2 DNA accounts for 70% of the variance in the aging epigenetic clock. The ELOVL2 gene is essential for synthesizing long polyunsaturated fatty acids, crucial for cell membrane integrity, inflammation modulation, and energy maintenance. This study investigated the impact of APOE genotype and ELOVL2 methylation on EEG alpha rhythm and functional MRI (fMRI) resting-state functional connectivity (rsFC) of brain networks in non-demented adults during aging. We examined EEG alpha sub-bands power and individual alpha peak frequency (IAPF) and the fMRI rsFC in 151 non-demented volunteers, age range 20-84 years, stratified by APOE genotype. APOE ε3/ε3 subgroup (APOE4-) included 104 subjects, APOE ε4/ε3 (APOE4+) subgroup – 47 subjects. ELOVL2 cg16867657 methylation was examined in the blood in subgroup of 56 individuals (35 APOE4- and 21 APOE4+). The individuals underwent fMRI tsFC of the brain using the CONN Matlab/SPM-based toolbox (Whitfield-Gabrieli and Nieto-Castanon, 2012). Informed written consent was obtained from all participants. All subjects underwent a neurological examination and cognitive screening. The presence of the APOE4+ genotype was associated with more pronounced alpha rhythm slowing and more pronounced decrease of fMRI rsFC during aging. Age-related increase of ELOVL2 methylation was observed. The partial correlation analysis, with age as a covariate, revealed a significant correlation between ELOVL2 methylation and IAPF. More pronounced alpha rhythm slowing and fMRI rsFC reduction in APOE4+ carriers during aging can be linked to synaptic dysfunction and deterioration of white matter integrity. Impaired lipid metabolism, driven by age-dependent ELOVL2 methylation, may accelerate the impact of the APOE4+ genotype on neurophysiological alterations during aging. These changes increase the risk of AD developed. Funding : This study was supported by Russian Science Foundation (Project No. 19-75-30039 to TA genotyping; Project No. 22-15-00448 to NP, RK, VF, EK EEG and fMRI analysis and MP for genotyping) and by Ministry of Science and Higher Education of the Russian Federation (Agreement 075-10-2021-093 project GEN-RND-2017).

Human longevity is a sex-biased process in which sex chromosomes and sex-specific immunity may play a crucial role in the health and lifespan disparities between men and women. Generally, women have a higher life expectancy than men, exhibiting lower infection rates for a broad range of pathogens, which results in a higher prevalence of female centenarians compared to males. Investigation of the immunological changes that occur during the process of healthy aging, while taking into account the differences between sexes, can significantly enhance our understanding of the mechanisms that underlie longevity. In this review, we aim to summarize the current knowledge on sexual dimorphism in the human immune system and gut microbiome during aging, with a particular focus on centenarians, based exclusively on human data.

Great Scythia was the ancient Greek name for the area stretching from the northern Black Sea coast to the Middle Don. Using high-quality genomic data generated from 131 ancient individuals from Great Scythia and neighboring regions of the Bronze Age and the Iron Age, we established the genetic structure of the Scythians, revealing their diverse origin with major European Bronze Age ancestral components, and genetic traces of migration and invasions. We uncovered relationships between Scythians, including elite Scythians. Substantial endogamy in the Scythian clan was found. We examined Scythians' phenotypes and medical-genetic background and found a harmful gene mutation causing fructose intolerance. This ancient "Scythian" mutation has spread throughout West Eurasia and has become the most prevalent genetic cause of fructose intolerance in contemporary European populations.

BACKGROUND:Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type-whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). METHODS:We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. RESULTS:Applied to 66 human samples Exo-C achieved 100% recall and 73% precision in detecting chromosomal translocations and SNVs. We further benchmarked its performance for inversions and CNVs and demonstrated its utility in detecting mosaic SVs and resolving diagnostically challenging cases. CONCLUSIONS:Through several case studies, we demonstrate how Exo-C's multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders.

Cervical artery dissection (CeAD) is the primary cause of ischemic stroke in young adults. Monogenic heritable connective tissue diseases account for fewer than 5% of cases of CeAD. The remaining sporadic cases have known risk factors. The clinical, radiological, and histological characteristics of systemic vasculopathy and undifferentiated connective tissue dysplasia are present in up to 70% of individuals with sporadic CeAD. Genome-wide association studies identified CeAD-associated genetic variants in the non-coding genomic regions that may impact the gene transcription and RNA processing. However, global gene expression profile analysis has not yet been carried out for CeAD patients. We conducted bulk RNA sequencing and differential gene expression analysis to investigate the expression profile of protein-coding genes in the peripheral blood of 19 CeAD patients and 18 healthy volunteers. This was followed by functional annotation, heatmap clustering, reports on gene–disease associations and protein–protein interactions, as well as gene set enrichment analysis. We found potential correlations between CeAD and the dysregulation of genes linked to nucleolar stress, senescence-associated secretory phenotype, mitochondrial malfunction, and epithelial–mesenchymal plasticity.

INTRODUCTION:The most significant genetic risk factor for late-onset Alzheimer's disease (AD) is APOE4, with evidence for gain- and loss-of-function mechanisms. A clinical need remains for therapeutically relevant tools that potently modulate APOE expression. METHODS:We optimized small interfering RNAs (di-siRNA, GalNAc) to potently silence brain or liver Apoe and evaluated the impact of each pool of Apoe on pathology. RESULTS:In adult 5xFAD mice, siRNAs targeting CNS Apoe efficiently silenced Apoe expression and reduced amyloid burden without affecting systemic cholesterol, confirming that potent silencing of brain Apoe is sufficient to slow disease progression. Mechanistically, silencing Apoe reduced APOE-rich amyloid cores and activated immune system responses. DISCUSSION:These results establish siRNA-based modulation of Apoe as a viable therapeutic approach, highlight immune activation as a key pathway affected by Apoe modulation, and provide the technology to further evaluate the impact of APOE silencing on neurodegeneration.

For the first time, this paper presents a complex study of the burial of the ancient Russian woman from the classic “Vyatich” mound from the Kremenyie burial site (Moscow region). The mounds and synchronized ground cremation burials are combined at this unique 12th-century burial site. The aim of this research is to examine the historical details of the person from the mound using conventional archaeological, anthropological, and archae-oparasitology methodologies along with modern paleogenetics methods. The burial site is characterized by a general “archaic” rite, manifested in the late preservation of the cremation rite along with the burial. According to anthropological data, an elderly woman, over forty, was buried there. She was identified as a member of the local population by radiogenic strontium isotope (87Sr/86Sr) study. Rich grave content and the fact that the body was buried in the middle of the mound indicate the woman's high social standing in the community. According to ar-chaeoparasitological data, the eating habits of the woman appear to be characterized by the consumption of un-cooked or insufficiently thermally prepared freshwater fish. The complete mtDNA sequence reconstruction indi-cates that it belongs to haplogroup V1a1, one of the Western Eurasian haplogroup V branches. To date, this represents the first case of the V1a1 mitogroup being found in the Russian Plain during ancient times. A repre-sentative of the Danish Viking clan from the Oxford burial site of the XI century was the closest of the ancient samples to the mtDNA of the studied woman, which indicates a genetic relationship on the maternal lineage with the medieval Northwestern European population. Single nucleotide substitution A7299G in the mitogenome of the woman clusters her with present-day Russians from the Belgorod and Pskov regions and shows the continuity of the modern Russian population with the Ancient Russians. Thus, the results of our study demonstrate the private details of the individual as common historical features, which include the ceremonial side of burial and belonging to the maternal genetic lineage preserved in the modern gene pool of the Russian population.

The genetic structure of the population of Northern Europe of the Mesolithic-Neolithic period currently remains poorly investigated due to the small number of materials available for research. For the first time, the complete genome of an individual from the multilayer Meso-Neolithic site Ivanovskoe VII, located in the Upper Volga region in Yaroslavl Oblast, was studied. According to stratigraphic data, an isolated skull of an adult male without a lower jaw was found in layer II containing ceramics of the Upper Volga Early Neolithic Culture. AMS date obtained from the scull bone. The calibrated age of the collagen sample was determined with a probability of 1σ (68 %) in the interval 6588–6498 cal.y.b. (UGAMS-67431 OxCal v4.4), wich corresponds to the Late Mesolithic. The dates of the peat containing layer II of the culture lie between 6000 and 7000 radiocarbon years ago. The main aim of the study is to elucidate the position of this individual in the context of the genomic landscape of Mesolithic and Neolithic Europe. It is shown that the genetic profile of the studied individual (DM5) fully coincides with the genetic diversity profile of the Eastern Hunter-Gatherers (EHG). Haplogroups of mitochondrial DNA (U5a2+16294) and Y-chromosome (R1b1a1) testify to its genetic connection with ancient Mesolithic populations of Europe. The DM5 sample has an additional substitution at position 54 of mtDNA in common with the most ancient samples of this mitochondrial haplogroup from the territory of Western Europe (England and France), which suggests the existence of a probable ancestor belonging to an even earlier period (Late Paleolithic), possibly on the territory of Western Europe. Specimen DM5 is clustered together with several ancient territorially and chronologically separated groups. First, with representatives of Mesolithic hunter-gatherers of northern Eastern Europe (South Oleniy Island, Karelia; Minino I and II, Vologda region; Peschanitsa, and Popovo, Arkhangelsk region). Second, DM5 is similar to Early Mesolithic materials from the Middle Volga region — the oldest representative of Mesolithic hunter-gatherers from Sidelkino and an Eneolithic specimen from Lebyazhinka, Samara region. Third, in the cluster of individuals close to DM5 there are representatives of later groups — from the Early Neolithic Yazykovo I, Tver region, Middle Neolithic Karavaikha, Vologda region and Eneolithic layers of the Murzikhinsky II burial ground, which is located near the village of Alekseevskoye (Tatarstan) in the mouth of the Kama River. The data we obtained do not exclude that the Early Eneolithic Upper Volga Culture has local Mesolithic roots, which indicates the long-term preservation of the oldest gene pool of Europe in the central part of the Russian Plain.

To date, only 10 of the more than 30 fur colours that had been observed in American mink (Neogale vison) have been linked to specific genes. The Royal pastel fur colour is part of a large family of brownish colours that are quite similar to one another, making breeding and selecting processes more difficult. Here we carried out whole-genome sequencing of five American minks with Royal pastel (b/b) phenotypes originating from two distinct mink populations. We identified an insertion of endogenous retroviral element type 1 (ERV1) into the first intron of the gene encoding the HPS3 protein, which regulates the trafficking of tyrosinase-containing vesicles to maturing melanosomes. With Cas9-targeted nanopore sequencing, we reconstructed the full-length sequence of the 11.7 Kb ERV1 insertion and observed hypermethylation that spread to the HPS3 gene promoter region. These findings highlight the role of HPS3 in the formation of melanosomes and melanin, as well as the genetic process regulating the intensity and spectrum of hair colour. Moreover, in mink breeding projects, these data are also useful for tracking economically important fur qualities.

In domesticated sable population, after almost 100 years of selective breeding, individuals with colored fur began to be recorded. In particular, in the offspring of a pair of sables with black coat color, a puppy with pastel coat color was identified. In the TYRP1 gene that determines this sable coat color, single nucleotide insertion was determined, and the trait inheritance mode was recessive. In 2022, in this population, puppies with white coat color were born simultaneously to the representatives of two sable lines. In most mammalian species, albinism is caused by the mutations in the TYR gene, which encodes the tyrosinase enzyme. In the present study, the sable TYR gene was analyzed as a functional candidate gene for albinism. Sequence analysis of the TYR gene coding region and splicing sites did not reveal any differences of white sables from standard colored sables, which suggested that the studied phenotype was caused by genetic variants in other genes.

The MAOA gene is a widely known regulator of aggressive behavior among humans and animals. Here, we analyze the genetic variability of the MAOA gene and its promoter region in a noncanonical behavioral model of American mink ( Neogale vison ). Significant genetic variations among animals with aggressive behavior are not observed, which suggests the presence of genetic and/or epigenetic variations in other systems involved in the regulation of aggression in this model.

Alzheimer’s disease (AD) is linked to toxic Aβ plaques in the brain and activation of innate responses. Recent findings however suggest that the disease may also depend on the adaptive immunity, as B cells exacerbate and CD8+ T cells limit AD-like pathology in mouse models of amyloidosis. Here, by artificially blocking or augmenting CD8+ T cells in the brain of 5xFAD mice, we provide evidence that AD-like pathology is promoted by pathogenic, proinflammatory cytokines and exhaustion markers expressing CXCR6+ CD39+CD73+/- CD8+ TRM-like cells. The CD8+ T cells appear to act by targeting disease associated microglia (DAM), as we find them in tight complexes with microglia around Aβ plaques in the brain of mice and humans with AD. We also report that these CD8+ T cells are induced by B cells in the periphery, further underscoring the pathogenic importance of the adaptive immunity in AD. We propose that CD8+ T cells and B cells should be considered as therapeutic targets for control of AD, as their ablation at the onset of AD is sufficient to decrease CD8+ T cells in the brain and block the amyloidosis-linked neurodegeneration.

Археологические и палеоантропологические материалы средневековых могильников Русского Севера уже несколько десятилетий служат важнейшим источником для изучения славяно-финского взаимодействия и процессов интеграции в состав Древнерусского государства обширных территорий между волжско-северодвинским водоразделом и Белым морем. Геномный анализ образцов костной ткани из этих могильников до сих пор не производился. В качестве первых материалов для такого анализа были отобраны образцы из средневекового могильника Минино на Кубенском озере. Исследовано одно необычное погребение, где были совместно захоронены подросток предположительно мужского пола и лесной хорь (Mustela (Putorius) putorius L.). Проведен геномный анализ человека и животного. По его результатам определена принадлежность исследованного индивида мужскому полу. Филогеографический анализ полной последовательности митохондриальной ДНК (мтДНК) человека показал: данная митохондриальная линия характерна для восточнославянских популяций, что предполагает его славянские, а не финно-угорские, корни и согласуется с археологическими данными. Митохондриальная последовательность животного из погребения соответствует мтДНК современных лесных хорьков, отличных от современной группы одомашненных хорьков. Проведенное исследование предоставляет свидетельство присутствия индивидов славянского происхождения на территории Русского Севера во втор. пол. XII - нач. XIII в. и открывает неизвестные стороны повседневной жизни средневекового населения. Archaeological materials and paleoanthropological remains from medieval cemeteries in the Russian North have been a major source of information for studying Slavic-Finnic relationships and integration of vast areas between the Volga and North Dvina watershed and the White Sea into Medieval Russia for several decades. Genomic analysis of bone tissue samples from these cemeteries has not been conducted yet. Samples from Minino, which is a medieval cemetery at the Kubenskoe Lake, were the first to be selected for this analysis. The grave from this cemetery subjected to the analysis is unusual. An adolescent, presumably, a male, was buried together with a forest polecat (Mustela (Putorius) putorius L.). We performed a genomic analysis of the human and the animal and found that the individual was a male. The phylogeographic analysis of the full mitochondrial DNA (mtDNA) sequence shows that this mitochondrial lineage is characteristic of Eastern Slavic populations, thus suggesting Slavic rather than Finno-Ugric ancestry of the individual which is consistent with archaeological data. The mitochondrial sequence of the animal from the grave is consistent with mtDNA of modern forest polecats distinct from the modern group of domesticated polecats. This study provides evidence that individuals of Slavic ancestry lived in the Russian North in the second half of the 12th - early 13th centuries. It also reveals unknown facts about everyday life of the medieval people.

Effective molecular diagnosis of congenital diseases hinges on comprehensive genomic analysis, traditionally reliant on various methodologies specific to each variant type—whole exome or genome sequencing for single nucleotide variants (SNVs), array CGH for copy-number variants (CNVs), and microscopy for structural variants (SVs). We introduce a novel, integrative approach combining exome sequencing with chromosome conformation capture, termed Exo-C. This method enables the concurrent identification of SNVs in clinically relevant genes and SVs across the genome and allows analysis of heterozygous and mosaic carriers. Enhanced with targeted long-read sequencing, Exo-C evolves into a cost-efficient solution capable of resolving complex SVs at base-pair accuracy. Through several case studies, we demonstrate how Exo-C’s multifaceted application can effectively uncover diverse causative variants and elucidate disease mechanisms in patients with rare disorders. ### Competing Interest Statement The authors have declared no competing interest.

The clusterin (CLU) rs11136000 CC genotype is a probable risk factor for Alzheimer’s disease (AD). CLU, also known as the apolipoprotein J gene, shares certain properties with the apolipoprotein E (APOE) gene with a well-established relationship with AD. This study aimed to determine whether the electrophysiological patterns of brain activation during the letter fluency task (LFT) depend on CLU genotypes in adults without dementia. Previous studies have shown that LFT performance involves activation of the frontal cortex. We examined EEG alpha1 and alpha2 band desynchronization in the frontal regions during the LFT in 94 nondemented individuals stratified by CLU (rs11136000) genotype. Starting at 30 years of age, CLU CC carriers exhibited more pronounced task-related alpha2 desynchronization than CLU CT&TT carriers in the absence of any differences in LFT performance. In CLU CC carriers, alpha2 desynchronization was significantly correlated with age. Increased task-related activation in individuals at genetic risk for AD may reflect greater “effort” to perform the task and/or neuronal hyperexcitability. The results show that the CLU genotype is associated with neuronal hyperactivation in the frontal cortex during cognitive tasks performances in nondemented individuals, suggesting systematic vulnerability of LFT related cognitive networks in people carrying unfavorable CLU alleles.

GAB2 rs2373115 genotype increases the risk of Alzheimer’s (AD) and vascular (VD) diseases (Reiman et al., 2007; Lambert et al., 2013; Kondreddy et al., 2021). EEG reactivity to hyperventilation (HV) depends on hypocapnia-induced cerebral vasoconstriction, which may be impaired in subjects with preclinical AD and VD. EEG differences in the carriers of GAB2 genotype in nondemented adults remain unknown. The study was aimed to determine the possible effect of GAB2 rs2373115 genotype on resting EEG and EEG reactivity to HV in non-demented adults during aging. The enrolled cohort included 151 healthy volunteers, age range 20-80 years, stratified by GAB2 rs2373115 genotype. Informed written consent was obtained from all participants. All subjects underwent a neurological examination and cognitive screening. The significance of the differences between the EEG in different subgroups was estimated using ANOVA in the general linear model. APOE and sex was included in the analysis as covariates. In the entire sample the presence of GAB2 C allele was associated with higher alpha2 relative power in resting EEG, with more pronounced differences in the right parietal area. EEG reactivity to HV decreased with aging, and the decrease was more pronounced in the carriers of GAB2 C allele. Under HV the older GAB2 AC&CC carriers as compared with the older GAB2 AA carriers had lower theta power. The HV reactivity of blood pressure and heart rate was decreased in aging to a greater extend in the GAB2 C allele carriers than in the homozygous GAB2 AA individuals. The results show that GAB2 genotype is associated with alpha2 relative power difference in non-demented adults. Reduced EEG and vascular reactivity to HV in the older GAB2 C allele carriers indicates altered cerebrovascular reactivity to hypocapnia and suggests that vascular factors can mediate GAB2-related AD susceptibility. The study was supported by Russian Science Foundation (Project N 22-15-00448, Project N 19-75-30039 genotyping) and the National Institutes of Health, United States (grant R01AG054712 to ER statistical analysis).

Schizophrenia is a mental disorder, the hereditary nature of which has been confirmed by numerous studies. Currently, more than a hundred genetic loci associated with schizophrenia have been described, and rare variants in genes and chromosomal rearrangements associated with familial cases of the disease have also been identified. However, it is not always possible to determine the hereditary nature of the pathology, many cases of schizophrenia are sporadic, and the genetic cause of such cases remains unknown. By using whole-genome-sequencing data for three family trios from Russia with sporadic cases of schizophrenia, we search for rare potentially pathogenic variants in the coding and regulatory loci of the genome, including de novo and compound mutations. The polygenic risk of schizophrenia is also assessed using common polymorphic markers. As a result of the analysis, the genetic heterogeneity of sporadic forms of schizophrenia is shown, as well as the potential role of rare substitutions in genes associated with the metabolism of glutamate and inositol phosphate in sporadic cases of schizophrenia.

Metabotropic glutamate receptor 1 (mGluR1) plays a crucial role in slow excitatory postsynaptic conductance, synapse formation, synaptic plasticity, and motor control. The GRM1 gene is expressed mainly in the brain, with the highest expression in the cerebellum. Mutations in the GRM1 gene have previously been known to cause autosomal recessive and autosomal dominant spinocerebellar ataxias. In this study, whole-exome sequencing of a patient from a family of Azerbaijani origin with a diagnosis of congenital cerebellar ataxia was performed, and a new homozygous missense mutation in the GRM1 gene was identified. The mutation leads to the homozygous amino acid substitution of p.Thr824Arg in an evolutionarily highly conserved region encoding the transmembrane domain 7, which is critical for ligand binding and modulating of receptor activity. This is the first report in which a mutation has been identified in the last transmembrane domain of the mGluR1, causing a congenital autosomal recessive form of cerebellar ataxia with no obvious intellectual disability. Additionally, we summarized all known presumable pathogenic genetic variants in the GRM1 gene to date. We demonstrated that multiple rare variants in the GRM1 underlie a broad diversity of clinical neurological and behavioral phenotypes depending on the nature and protein topology of the mutation.

With the recent development of long-read sequencing technologies, it is now possible for the first time to read a complete gapless sequence of the human genome. The result was the first T2T (telomere-to-telomere) genomic assembly, published by an international consortium of scientists in 2022. The most significant contribution of the new assembly were the centromeric regions consisting of highly repetitive satellite DNA. In this review, we will briefly list the major achievements of the T2T consortium related to centromeres and take a closer look at the unexpected findings of cytogenetic magnitude that analysis of first assembled human centromeres has brought, such as the “split” centromeres of chromosomes 3 and 4, mega-inversion in the active centromere array of chromosome 1, haplotypic epialleles in the centromere of X chromosome and the macro-repeats found in several centromeres.