Solutrean hypothesis: genetics, the mammoth in the room

© 2014 Taylor & Francis. This is an Accepted Manuscript of an article published by Taylor & Francis Group in World Archaeology on 31/10/2014, available online: http://www.tandfonline.com/10.1080/00438243.2014.966273.The Solutrean Hypothesis for the origin of the Clovis archaeological culture has received numerous challenges and critiques. Oft-repeated contra-assertions, predominantly from archaeologists, range from: “NO genetic evidence”, to: it must have been either a sole Beringian or European origin, so Beringia wins, to: the troublesome fifth American mtDNA lineage “X2a” overlanded from West-Eurasia to Beringia, leaving no trace en-route, to: there is no evidence from the rest of the genome to parallel X2a. We refute these contra-assertions, detailing published contrary evidence, supporting a West-Eurasian origin for some Native American ancestors, mainly found in north-eastern America, in parallel to the majority arriving from Beringia. Specifically this includes mtDNA-X2a found in ancient and modern Native American populations, with no evidence to support migration of X2a through Siberia. Prima facie (i.e. under-researched) published evidence also exists for equivalent levels of West-Eurasian Y-chromosomes and autosomal markers in the same regions

The Multi-Epoch Nearby Cluster Survey: type Ia supernova rate measurement in z~0.1 clusters and the late-time delay time distribution

We describe the Multi-Epoch Nearby Cluster Survey (MENeaCS), designed to measure the cluster Type Ia supernova (SN Ia) rate in a sample of 57 X-ray selected galaxy clusters, with redshifts of 0.05 < z < 0.15. Utilizing our real time analysis pipeline, we spectroscopically confirmed twenty-three cluster SN Ia, four of which were intracluster events. Using our deep CFHT/Megacam imaging, we measured total stellar luminosities in each of our galaxy clusters, and we performed detailed supernova detection efficiency simulations. Bringing these ingredients together, we measure an overall cluster SN Ia rate within R_{200} (1 Mpc) of 0.042^{+0.012}_{-0.010}^{+0.010}_{-0.008} SNuM (0.049^{+0.016}_{-0.014}^{+0.005}_{-0.004} SNuM) and a SN Ia rate within red sequence galaxies of 0.041^{+0.015}_{-0.015}^{+0.005}_{-0.010} SNuM (0.041^{+0.019}_{-0.015}^{+0.005}_{-0.004} SNuM). The red sequence SN Ia rate is consistent with published rates in early type/elliptical galaxies in the `field'. Using our red sequence SN Ia rate, and other cluster SNe measurements in early type galaxies up to $z\sim1$, we derive the late time (>2 Gyr) delay time distribution (DTD) of SN Ia assuming a cluster early type galaxy star formation epoch of z_f=3. Assuming a power law form for the DTD, \Psi(t)\propto t^s, we find s=-1.62\pm0.54. This result is consistent with predictions for the double degenerate SN Ia progenitor scenario (s\sim-1), and is also in line with recent calculations for the double detonation explosion mechanism (s\sim-2). The most recent calculations of the single degenerate scenario delay time distribution predicts an order of magnitude drop off in SN Ia rate \sim 6-7 Gyr after stellar formation, and the observed cluster rates cannot rule this out.Comment: 35 pages, 14 figures, ApJ accepte

High-throughput screen using a single-cell tyrosine phosphatase assay reveals biologically active inhibitors of tyrosine phosphatase CD45

Many cellular signaling events are regulated by tyrosine phosphorylation and mediated by the opposing actions of protein tyrosine kinases and phosphatases. Protein tyrosine phosphatases are emerging as drug targets, but poor cell permeability of inhibitors has limited the development of drugs targeting these enzymes [Tautz L, et al. (2006) Expert Opin Ther Targets 10:157–177]. Here we developed a method to monitor tyrosine phosphatase activity at the single-cell level and applied it to the identification of cell-permeable inhibitors. The method takes advantage of the fluorogenic properties of phosphorylated coumaryl amino propionic acid (pCAP), an analog of phosphotyrosine, which can be incorporated into peptides. Once delivered into cells, pCAP peptides were dephosphorylated by protein tyrosine phosphatases, and the resulting cell fluorescence could be monitored by flow cytometry and high-content imaging. The robustness and sensitivity of the assay was validated using peptides preferentially dephosphorylated by CD45 and T-cell tyrosine phosphatase and available inhibitors of these two enzymes. The assay was applied to high-throughput screening for inhibitors of CD45, an important target for autoimmunity and infectious diseases [Hermiston ML, et al. (2003) Annu Rev Immunol 21:107–137]. We identified four CD45 inhibitors that showed activity in T cells and macrophages. These results indicate that our assay can be applied to primary screening for inhibitors of CD45 and of other protein tyrosine phosphatases to increase the yield of biologically active inhibitors

Antibody mediated targeting of the FGFR1c isoform increases glucose uptake in white and brown adipose tissue in male mice

The increased prevalence of obesity and its cardiometabolic implications demonstrates the imperative to identify novel therapeutic targets able to effect meaningful metabolic changes in this population. Antibody-mediated targeting of fibroblast growth factor receptor 1c isoform (FGFR1c) has been shown to ameliorate hyperglycaemia and protect from diet- and genetically-induced obesity in rodents and non-human primates. However, it is currently unknown which tissue(s) contribute to this glucose lowering effect. Thus, to elucidate this effect we treated euglycaemic mice with H7, a monoclonal antibody which selectively targets the FGFR1c isoform, and employed whole body positron emission computed tomography with a glucose tracer (18F-flurodeoxyglucose). Treatment with H7 increased basal glucose uptake in white and brown adipose tissues (WAT and BAT respectively), the brain and liver, but reduced it in the quadricep muscles. Consequentially, blood glucose was significantly reduced in response to treatment. Under insulin-stimulated conditions, the effects of H7 were maintained in WAT, BAT, liver and muscle. Treatment with H7 decreased triglyceride content and increased adipose triglyceride lipase content in white adipose tissue, whilst increasing activation of acetyl coenzyme A carboxylase, suggesting futile cycling of triglycerides, albeit favouring net hydrolysis. We demonstrated, in vitro, this is a direct effect of treatment in adipose tissue as basal cellular respiration and glucose uptake were increased in response to treatment. Taken together, these data suggest that antibody-mediated targeting of FGFR1c exerts its powerful glucose-lowering efficacy primarily due to increased glucose uptake in adipose tissue

Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease

Two Novel Susceptibility Loci for Prostate Cancer in Men of African Ancestry

Prostate cancer incidence is 1.6-fold higher in African Americans than in other populations. The risk factors that drive this disparity are unknown and potentially consist of social, environmental, and genetic influences. To investigate the genetic basis of prostate cancer in men of African ancestry, we performed a genome-wide association meta-analysis using two-sided statistical tests in 10 202 case subjects and 10 810 control subjects. We identified novel signals on chromosomes 13q34 and 22q12, with the risk-associated alleles found only in men of African ancestry (13q34: rs75823044, risk allele frequency = 2.2%, odds ratio [OR] = 1.55, 95% confidence interval [CI] = 1.37 to 1.76, P = 6.10 × 10−12; 22q12.1: rs78554043, risk allele frequency = 1.5%, OR = 1.62, 95% CI = 1.39 to 1.89, P = 7.50 × 10−10). At 13q34, the signal is located 5’ of the gene IRS2 and 3’ of a long noncoding RNA, while at 22q12 the candidate functional allele is a missense variant in the CHEK2 gene. These findings provide further support for the role of ancestry-specific germline variation in contributing to population differences in prostate cancer risk

Autoimmunity-Associated LYP-W620 Does Not Impair Thymic Negative Selection of Autoreactive T Cells.

A C1858T (R620W) variation in the PTPN22 gene encoding the tyrosine phosphatase LYP is a major risk factor for human autoimmunity. LYP is a known negative regulator of signaling through the T cell receptor (TCR), and murine Ptpn22 plays a role in thymic selection. However, the mechanism of action of the R620W variant in autoimmunity remains unclear. One model holds that LYP-W620 is a gain-of-function phosphatase that causes alterations in thymic negative selection and/or thymic output of regulatory T cells (Treg) through inhibition of thymic TCR signaling. To test this model, we generated mice in which the human LYP-W620 variant or its phosphatase-inactive mutant are expressed in developing thymocytes under control of the proximal Lck promoter. We found that LYP-W620 expression results in diminished thymocyte TCR signaling, thus modeling a "gain-of-function" of LYP at the signaling level. However, LYP-W620 transgenic mice display no alterations of thymic negative selection and no anomalies in thymic output of CD4(+)Foxp3(+) Treg were detected in these mice. Lck promoter-directed expression of the human transgene also causes no alteration in thymic repertoire or increase in disease severity in a model of rheumatoid arthritis, which depends on skewed thymic selection of CD4(+) T cells. Our data suggest that a gain-of-function of LYP is unlikely to increase risk of autoimmunity through alterations of thymic selection and that LYP likely acts in the periphery perhaps selectively in regulatory T cells or in another cell type to increase risk of autoimmunity

C-reactive protein, interleukin-6, and prostate cancer risk in men aged 65 years and older.

Inflammation is believed to play a role in prostate cancer (PCa) etiology, but it is unclear whether inflammatory markers C-reactive protein (CRP) and interleukin-6 (IL-6) associate with PCa risk in older men. Using Cox regression, we assessed the relationship between baseline concentrations of CRP and IL-6 and the subsequent PCa risk in the Cardiovascular Health Study, a population-based cohort study of mostly European American men of ages >64 years (n = 2,234; mean follow-up = 8.7 years; 215 incident PCa cases). We also tested associations between CRP and IL-6 tagSNPs and PCa risk, focusing on SNPs that are known to associate with circulating CRP and/or IL-6. Neither CRP nor IL-6 blood concentrations was associated with PCa risk. The C allele of IL-6 SNP rs1800795 (-174), a known functional variant, was associated with increased risk in a dominant model (HR = 1.44; 95% CI = 1.03-2.01; p = 0.03), but was not statistically significant after accounting for multiple tests (permutation p = 0.21). Our results suggest that circulating CRP and IL-6 do not influence PCa risk. SNPs at the CRP locus are not associated with PCa risk in this cohort, while the association between rs1800795 and PCa risk warrants further investigation

Synoviocyte-targeted therapy synergizes with TNF inhibition in arthritis reversal

Fibroblast-like synoviocytes (FLS) are joint-lining cells that promote rheumatoid arthritis (RA) pathology. Current disease-modifying antirheumatic agents (DMARDs) operate through systemic immunosuppression. FLS-targeted approaches could potentially be combined with DMARDs to improve control of RA without increasing immunosuppression. Here, we assessed the potential of immunoglobulin-like domains 1 and 2 (Ig1&2), a decoy protein that activates the receptor tyrosine phosphatase sigma (PTPRS) on FLS, for RA therapy. We report that PTPRS expression is enriched in synovial lining RA FLS and that Ig1&2 reduces migration of RA but not osteoarthritis FLS. Administration of an Fc-fusion Ig1&2 attenuated arthritis in mice without affecting innate or adaptive immunity. Furthermore, PTPRS was down-regulated in FLS by tumor necrosis factor (TNF) via a phosphatidylinositol 3-kinase–mediated pathway, and TNF inhibition enhanced PTPRS expression in arthritic joints. Combination of ineffective doses of TNF inhibitor and Fc-Ig1&2 reversed arthritis in mice, providing an example of synergy between FLS-targeted and immunosuppressive DMARD therapies.publishedVersio

A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci

Genome-wide association studies (GWAS) in European populations have identified genetic risk variants associated with multiple myeloma (MM)