Biological history of Homo sapiens populations living in Central and Eastern Europe

Archaeogenomis is a recently developed interdisciplinary research field that utilizes advanced molecular biology techniques, especially DNA sequencing, to study the history of biological species, including humans. Analyses of ancient genomes provide independent information about human ancestors and their migrations, allowing researchers to uncover history of mankind. Here, we present the fundamental principles of archaeogenomics and its application in the studies of biological history of the populations inhabiting central-east Europe

ENHO, RXRA, and LXRA polymorphisms and dyslipidaemia, related comorbidities and survival in haemodialysis patients

Abstract Background The energy homeostasis-associated gene (ENHO), retinoid X receptor alpha gene (RXRA), and liver X receptor alpha gene (LXRA) are involved in adipogenic/lipogenic regulation. We investigated whether single-nucleotide polymorphisms in these genes (ENHO rs2281997, rs72735260; RXRA rs749759, rs10776909, rs10881578; LXRA rs2279238, rs7120118, rs11039155) are associated with dyslipidaemia, related comorbidities and survival of haemodialysis (HD) patients also tested for T-helper (Th) cell interleukin genes (IL). Methods The study was carried out in 873 HD patients. Dyslipidaemia was diagnosed by the recommendations of the Kidney Disease Outcomes Quality Initiative (K/DOQI) guidelines (2003); atherogenic dyslipidaemia was referred to if the TG/HDL cholesterol ratio was equal to or higher than 3.8. Genotyping of ENHO SNPs, LXRA SNPs, and IL12A rs568408 was carried out using HRM analysis. RXRA SNPs, IL12B rs3212227, and IL18 rs360719 were genotyped using PCR-RFLP analysis. The circulating adropin concentration was determined in 126 patients by enzyme-linked immunosorbent assay. Survival probability was analysed using the Kaplan-Meier method in 440 patients followed through 7.5 years. Results Dyslipidaemia by K/DOQI was diagnosed in 459 patients (91% revealed hyper-LDL- cholesterolaemia), atherogenic dyslipidaemia was diagnosed in 454 patients, and 231 patients were free of dyslipidaemia by both criteria. The variant allele (T) of ENHO rs2281997 was associated with the hyper-LDL cholesterolaemic pattern of dyslipidaemia by K/DOQI. The frequency of atherogenic dyslipidaemia was lower in T-allele bearers than in CC-genotype patients. The rs2281997 T allele was associated with lower cardiovascular mortality in HD patients showing atherogenic dyslipidaemia. ENHO, RXRA, and LXRA showed epistatic interactions in dyslipidaemia. Circulating adropin was lower in atherogenic dyslipidaemia than in non-atherogenic conditions. RXRA rs10776909 was associated with myocardial infarction. Bearers of LXRA rs2279238, rs7120118 or rs11039155 minor alleles showed higher mortality. ENHO SNP positions fell within the same DNase 1 hypersensitivity site expressed in the Th1 cell line. Epistatic interactions occurred between rs2281997 and Th1 IL SNPs (rs360719, rs568408). Conclusions Atherogenic dyslipidaemia occurs in HD patients in whom ENHO encodes less adropin. ENHO, RXRA, and LXRA SNPs, separately or jointly, are associated with dyslipidaemia, myocardial infarction, and survival in HD patients. Differences in the availability of transcription binding sites may contribute to these associations

Genetic history of East-Central Europe in the first millennium CE

Abstract Background The appearance of Slavs in East-Central Europe has been the subject of an over 200-year debate driven by two conflicting hypotheses. The first assumes that Slavs came to the territory of contemporary Poland no earlier than the sixth century CE; the second postulates that they already inhabited this region in the Iron Age (IA). Testing either hypothesis is not trivial given that cremation of the dead was the prevailing custom in Central Europe from the late Bronze Age until the Middle Ages (MA). Results To address this problem, we determined the genetic makeup of representatives of the IA Wielbark- and MA Slav-associated cultures from the territory of present-day Poland. The study involved 474 individuals buried in 27 cemeteries. For 197 of them, genome-wide data were obtained. We found close genetic affinities between the IA Wielbark culture-associated individuals and contemporary to them and older northern European populations. Further, we observed that the IA individuals had genetic components which were indispensable to model the MA population. Conclusions The collected data suggest that the Wielbark culture-associated IA population was formed by immigrants from the north who entered the region of contemporary Poland most likely at the beginning of the first millennium CE and mixed with autochthons. The presented results are in line with the hypothesis that assumes the genetic continuation between IA and MA periods in East-Central Europe

From Alpha to Delta—Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland

In Poland, the first case of SARS-CoV-2 infection was confirmed in March 2020. Since then, many circulating virus lineages fueled rapid pandemic waves which inflicted a severe burden on the Polish healthcare system. Some of these lineages were associated with increased transmissibility and immune escape. Mutations in the viral spike protein, which is responsible for host cell recognition and serves as the primary target for neutralizing antibodies, are of particular importance. We investigated the molecular epidemiology of the SARS-CoV-2 clades circulating in Southern Poland from February 2021 to August 2021. The 921 whole-genome sequences were used for variant identification, spike mutation, and phylogenetic analyses. The Pango B.1.1.7 was the dominant variant (n = 730, 89.68%) from March 2021 to July 2021. In July 2021, the B.1.1.7 was displaced by the B.1.617.2 lineage with 66.66% in July 2021 and 92.3% in August 2021 frequencies, respectively. Moreover, our results were compared with the sequencing available on the GISAID platform for other regions of Poland, the Czech Republic, and Slovakia. The analysis showed that the dominant variant in the analyzed period was B.1.1.7 in all countries and Southern Poland (Silesia). Interestingly, B.1.1.7 was replaced by B.1.617.2 earlier in Southern Poland than in the rest of the country. Moreover, in the Czech Republic and Slovakia, AY lineages were predominant at that time, contrary to the Silesia region

W poszukiwaniu Piastów

The origin of the Piast dynasty is a matter of lively discussions and disputes. At least a few controversial hypotheses exist, but their credibility is difficult to assess due to the scarcity of written as well as material sources, especially from the time of Polish state formation. Life sciences, however, can support history and archeology. Application of genetic tests, used earlier mainly in forensic laboratories, enabled identification of the remains of King Richard III, the Romanov dynasty members and Nicolaus Copernicus. Contemporary DNA studies, based on next generation DNA sequencing, outreach the narrow area of known markers such as mitochondrial DNA (mtDNA) and selected regions of Y chromosome. Although ancient DNA (aDNA), extracted from remains, is usually highly degraded and contaminated with genetic material of microorganisms, there are methods which allow for the analysis of such material and retrieval of information about origin, kinship and some phenotypic features of an individual. Genetic studies of the Piast dynasty, a subject of our research project, have to deal with numerous difficulties. In or der to gain access to bone samples, we need to meet a number of formal requirements. Moreover, despite the existence of available abundant documentation on the Piast burials, the actual situation is not always consistent with the written sources. Our first experiences show how difficult it is to localize the remains, identify them and extract DNA of sufficient quality.The origin of the Piast dynasty is a matter of lively discussions and disputes. At least a few controversial hypotheses exist, but their credibility is difficult to assess due to the scarcity of written as well as material sources, especially from the time of Polish state formation. Life sciences, however, can support history and archeology. Application of genetic tests, used earlier mainly in forensic laboratories, enabled identification of the remains of King Richard III, the Romanov dynasty members and Nicolaus Copernicus. Contemporary DNA studies, based on next generation DNA sequencing, outreach the narrow area of known markers such as mitochondrial DNA (mtDNA) and selected regions of Y chromosome. Although ancient DNA (aDNA), extracted from remains, is usually highly degraded and contaminated with genetic material of microorganisms, there are methods which allow for the analysis of such material and retrieval of information about origin, kinship and some phenotypic features of an individual. Genetic studies of the Piast dynasty, a subject of our research project, have to deal with numerous difficulties. In or der to gain access to bone samples, we need to meet a number of formal requirements. Moreover, despite the existence of available abundant documentation on the Piast burials, the actual situation is not always consistent with the written sources. Our first experiences show how difficult it is to localize the remains, identify them and extract DNA of sufficient quality