North Asian population relationships in a global context.

Population genetic studies of North Asian ethnic groups have focused on genetic variation of sex chromosomes and mitochondria. Studies of the extensive variation available from autosomal variation have appeared infrequently. We focus on relationships among population samples using new North Asia microhaplotype data. We combined genotypes from our laboratory on 58 microhaplotypes, distributed across 18 autosomes, on 3945 individuals from 75 populations with corresponding data extracted for 26 populations from the Thousand Genomes consortium and for 22 populations from the GenomeAsia 100 K project. A total of 7107 individuals in 122 total populations are analyzed using STRUCTURE, Principal Component Analysis, and phylogenetic tree analyses. North Asia populations sampled in Mongolia include: Buryats, Mongolians, Altai Kazakhs, and Tsaatans. Available Siberians include samples of Yakut, Khanty, and Komi Zyriane. Analyses of all 122 populations confirm many known relationships and show that most populations from North Asia form a cluster distinct from all other groups. Refinement of analyses on smaller subsets of populations reinforces the distinctiveness of North Asia and shows that the North Asia cluster identifies a region that is ancestral to Native Americans.

Genetic relationships of Southwest Asian and Mediterranean populations.

The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMSE) together with Northern European populations form one of five "continental" groups of global populations in many analyses of population relationships. This region is of great anthropologic and forensic interest but relationships of large numbers of populations within the region have not been able to be cleanly resolved with autosomal genetic markers. To examine the genetic boundaries to the SWAMSE region and whether internal structure can be detected we have assembled data for a total of 151 separate autosomal genetic markers on populations in this region and other parts of the world for a global set of 95 populations. The markers include 83 ancestry informative SNPs as singletons and 68 microhaplotype loci defined by 204 SNPs. The 151 loci are ancestry informative on a global scale, identifying at least five biogeographic clusters. One of those clusters is a clear grouping of 37 populations containing the SWAMSE plus northern European populations to the exclusion of populations in South Central Asia and populations from farther East. A refined analysis of the 37 populations shows the northern European populations clustering separately from the SWAMSE populations. Within Southwest Asia the Samaritans and Shabaks are distinct outliers. The Yemenite Jews, Saudi, Kuwaiti, Palestinian Arabs, and Southern Tunisians cluster together loosely while the remaining populations from Northern Iraq, Mediterranean Europe, the Caucasus region, and Iran cluster in a more complex graded fashion. The majority of the SWAMSE populations from the mainland of Southwest Asia form a cluster with little internal structure reflecting a very complex history of endogamy and migrations. The set of 151 DNA polymorphisms not only distinguishes major geographical regions globally but can distinguish ancestry to a small degree within geographical regions such as SWAMSE. We discuss forensic characteristics of the polymorphisms and also identify those that rank highest by Rosenberg's In measure for the SWAMSE region populations and for the global set of populations analyzed. DATA AVAILABILITY: Genotypes on all 151 markers for all 3790 individuals typed in the Kidd Lab on the 72 Kidd lab populations have been deposited in the Zenodo archive and can be freely accessed at https://doi.org/10.5281/zenodo.4658892. Some of the data has been made public previously as supplemental files appended to publications. Data for the additional individuals included in the analyses was taken from already public datasets as indicated in the text.

Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs.

The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.

Mutational analysis of hMsh6 in Israeli HNPCC and HNPCC-like families.

Germline mutations in DNA mismatch repair (DNA-MMR) genes, mainly hMlh1 and hMsh2, underlie Hereditary Non-Polyposis Colorectal Cancer (HNPCC). Germline hMSH6 gene mutations have been reported in a small subset of HNPCC families. In the present study, ethnically diverse individuals with HNPCC and HNPCC-like features were genotyped for hMsh6 germline mutations using exon-specific PCR, DGGE, and DNA sequencing. The study encompassed 92 individuals representing 88 unrelated families who were previously analyzed for Msh2 and Mlh1 mutations: Jewish Ashkenazim (n = 44), non-Ashkenazim (n = 27), Israeli Moslem-Arab (n = 15), Druze (n=3), and Cypriot non-Jews (n = 3). Of the study population, 71 had colon cancer (CRC), mean age at diagnosis was 50.9+/-13.2 years (range 16-73 years), 5 had endometrial cancer (two with concurrent CRC), (mean 43.6+/-3.26 years, range 38-45 years), and unaffected individuals (n = 18) were first degree relatives within HNPCC families and were genotyped at a mean age of 48.3+/-11.7 years (range 30-69 years). Of the 92 individuals analyzed, none showed a truncating hMsh6 mutation, and 6 (6.6%) harbored one of three germline missense mutations: a previously reported one (V878A), and two novel mutations (V509A, S227I). The pathogenic significance of these three missense mutations is yet unclear. In addition, 5 polymorphisms were detected, 2 of which were novel. We conclude that the rate of pathogenic hMsh6 mutations in HNPCC families of Jewish and Mediterranean origin is low, and that mutations in other genes probably account for the phenotype in these families.

Generation of ligand-receptor alliances by "SEA" module-mediated cleavage of membrane-associated mucin proteins.

A mechanism is described whereby one and the same gene can encode both a receptor protein as well as its specific ligand. Generation of this receptor-ligand partnership is effected by proteolytic cleavage within a specific module located in a membrane resident protein. It is postulated here that the "SEA" module, found in a number of heavily O-linked glycosylated membrane-associated proteins, serves as a site for proteolytic cleavage. The subunits generated by proteolytic cleavage of the SEA module reassociate, and can subsequently elicit a signaling cascade. We hypothesize that all membrane resident proteins containing such a "SEA" module will undergo cleavage, thereby generating a receptor-ligand alliance. This requires that the protein subunits resulting from the proteolytic cleavage reassociate with each other in a highly specific fashion. The same SEA module that serves as the site for proteolytic cleavage, probably also contains the binding sites for reassociation of the resultant two subunits. More than one type of module can function as a site for proteolytic cleavage; this can occur not only in one-pass membrane proteins but also in 7-transmembrane proteins and other membrane-associated proteins. The proposal presented here is likely to have significant practical consequences. It could well lead to the rational design and identification of molecules that, by binding to one of the cleaved partners, will act either as agonists or antagonists, alter signal transduction and, hence, cellular behavior.

Surfactant protein D augments bacterial association but attenuates major histocompatibility complex class II presentation of bacterial antigens.

Surfactant protein D (SP-D) is a secreted pattern recognition molecule associated with lung surfactant and mediates the clearance of pathogens in multiple ways. SP-D is an established part of the innate immune system, but it also modulates the adaptive immune response by interacting with both antigen-presenting cells and T cells. In a previous study, antigen presentation by bone marrow-derived dendritic cells was enhanced by SP-D. As dendritic cell function varies depending on the tissue of origin, we extended these studies to antigen-presenting cells isolated from mouse lung. Flow cytometric studies showed that SP-D binds calcium dependently and specifically to lung CD11c-positive cells. Opsonization of fluorescently labeled Escherichia coli by SP-D enhanced uptake by lung dendritic cells. SP-D facilitated the association of E. coli and antigen-presenting cells by increasing the frequency of CD11+ cells associated with E. coli by up to 10-fold. In contrast to the effect on bone marrow-derived dendritic cells, SP-D decreased the antigen presentation of ovalbumin, expressed in E. coli, to ovalbumin-specific major histocompatibility complex class II-specific T-cell hybridomas by 30-50%. The reduction of antigen presentation did not depend on whether the dendritic cells were isolated from the lungs of nonstimulated mice or mice that had been exposed to LPS aerosols. Our results show that SP-D increases the opsonization of pathogens, but decreases the antigen presentation by lung dendritic cells, and thereby, potentially dampens the activation of T cells and an adaptive immune response against bacterial antigens--during both steady-state conditions and inflammation.