Whole Genome Sequencing of Turkish Genomes Reveals Functional Private Alleles and Impact of Genetic Interactions with Europe, Asia and Africa

Background Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×). Results We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency. Conclusion This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey

Involvement of TRAIL death receptors in human tumorigenesis and mechanisms of TRAIL-induced apoptosis signaling

When the membrane-incorporated homotrimeric TRAIL ligand binds its death receptors (DR), trimerized DR4 or DR5/KILLER, a death inducing signaling complex (DISC) is recruited, composed of the adaptor FADD and the cysteinyl proteases, pro-caspase 8 or 10. A DISC is not assembled when TRAIL interacts with its decoy receptors TRID, TRUNDD or OPG, which lack an essential cytoplasmic interaction motif, called the death domain (DD). The aggregation of initiator caspases facilitates their autocatalytic activation. The active enzymes cleave effector caspases 3, 6 and 7, which activate apoptotic endonucleases, CAD and EndoG, digesting genomic DNA into small pieces. Executioner caspases cleave other cellular components, packaging the cell into apoptotic bodies, rapidly phagocytized by macrophages or neighboring cells. TRAIL further amplifies signaling via the mitochondrion. Caspase 8 cleaves BID and truncated BID translocates to mitochondria, inducing cytochrome c release. Cytochrome c, the adaptor APAF-1 and the initiator pro-caspase 9 form the apoptosome holoenzyme, again activating the executioner caspase cascade. Cancer results from deregulated proliferation and/or inadequate cell death. We tested whether the putative tumor suppressor TRAIL-DR genes are targeted for inactivation during tumorigenesis and we find DR4 homozygously deleted in one cell line out of 141. FADU nasopharyngeal cancer cells are resistant to TRAIL but are rendered sensitive upon supplementation of DR4 cDNA. Clearly, in some cells DR4 is required and DR5/KILLER cannot compensate for it. Extrinsic and intrinsic death signaling cascades are also used differentially. We show that TRAIL signaling is dependent on caspase 9 in normal human hepatocytes and HCT116 colon cancer cells. Inhibition of caspase 9 protects hepatocytes and HCT116 from TRAIL, but not the mitochondria-independent death in SW480 colon cancer cells. These findings have a potential relevance and utility for the use of TRAIL as a cancer therapy in humans. Further studies suggest that the limiting difference between TRAIL-signaling in HCT116 and SW480 appears at the BID cleavage step, which is faster in HCT116 cells despite more efficient DISC assembly in SW480 cells. These differences between the two cell lines are also in agreement with the finding that heat shock exposure protects HCT116 but not SW480 cells from TRAIL