De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas

Introduction: The SOX gene family consists of twenty transcription factors that play a pivotal role in cell fate and differentiation during the development of many organ systems. Within these SRY-related (SOX) genes is a highly conserved high mobility group (HMG) domain that has been shown to be critical for DNA binding and bending, nuclear trafficking, and protein-protein interactions. Mutations within this transcription factor family have been associated with rare congenital disorders, known as SOXopathies. These mutations are commonly de novo, heterozygous and inactivating, and exhibit gene haploinsufficiency. Of these twenty transcription factors, SOX6 is known to be involved in chondrocyte differentiation and development of the central nervous system. Although there have been reports of SOX6 variants causing adult pathological conditions, there has yet to be a well-established association between SOX6 variants and a developmental syndrome. Objectives: The objective of this study was to use clinical and genetic data to examine SOX6 mutations found in 19 individuals demonstrating developmental delay and to test the transcriptional activity of the 4 missense variants in vitro to determine if SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy. Methods: Nineteen individuals were identified as carriers of SOX6 variants, confirmed by molecular karyotyping, whole-exome sequencing, or whole-genome sequencing. Clinical pathogenicity was predicted and assessed in silico and in vitro. Expression plasmids for SOX6 missense variants were generated by PCR mutagenesis. The four missense variants generated were: p.Trp161Cys, p.Met605Thr, p.Trp639Arg, and p.Ser746Leu, with p.Met605Thr and p.Trp639Arg located within the HMG domain. For reporter assays, HEK293 cells were transfected in triplicate cultures with 3.5 µL ViaFect Transfection Reagent and a total of 1000ng of DNA. SOX6 intracellular localization was tested by transfecting either HEK293 or COS-1 cells and cytoplasmic and nuclear extracts were prepared for Western Blot analysis. Whole cell extracts transfected with respective WT-SOX6 or variant plasmid were also prepared for a dimerization assay. SOX6’s ability to bind DNA was also tested in an electrophoretic mobility shift assay (EMSA). Results: Study cohort consisted of 19 individuals from 17 unrelated families originating in Belgium, Canada, France, Germany, the Netherlands, Slovenia, the UK, and the US. These individuals shared milestone delays and intellectual disability, and exhibited abnormalities including mild dysmorphism, craniosynostosis, and osteochondromas. Immunoblots of nuclear and cytoplasmic extracts showed all variants were efficiently expressed however p.Met605Thr and p.Trp639Arg were not translocated or retained into the nucleus as efficiently as WT-SOX6 and the other two missense variants. The EMSA showed that proteins outside of the HMG domain behaved like WT-SOX6, but p.Met605Thr and p.Trp639Arg failed to bind the DNA probe. Reporter assay activity showed that the two variants outside of the HMG domain p.Trp161Cys and p.Ser746Leu displayed similar or slightly higher activity compared to WT-SOX6 while the two variants p.Met605Thr and p.Trp639Arg showed diminished reporter activity. Conclusions: These findings provide evidence that SOX6 variants cause a SOXopathy, which has been designated in Online Mendelian Inheritance in Man (OMIM) as #618971 Tolchin-Le Caignec syndrome (TOLCAS)

Comprehensive resequence analysis of a 97 kb region of chromosome 10q11.2 containing the MSMB gene associated with prostate cancer

Genome-wide association studies of prostate cancer have identified single nucleotide polymorphism (SNP) markers in a region of chromosome 10q11.2, harboring the microseminoprotein-β (MSMB) gene. Both the gene product of MSMB, the prostate secretory protein 94 (PSP94) and its binding protein (PSPBP), have been previously investigated as serum biomarkers for prostate cancer progression. Recent functional work has shown that different alleles of the significantly associated SNP in the promoter of MSMB found to be associated with prostate cancer risk, rs10993994, can influence its expression in tumors and in vitro studies. Since it is plausible that additional variants in this region contribute to the risk of prostate cancer, we have used next-generation sequencing technology to resequence a ~97-kb region that includes the area surrounding MSMB (chr10: 51,168,025–51,265,101) in 36 prostate cancer cases, 26 controls of European origin, and 8 unrelated CEPH individuals in order to identify additional variants to investigate in functional studies. We identified 241 novel polymorphisms within this region, including 142 in the 51-kb block of linkage disequilibrium (LD) that contains rs10993994 and the proximal promoter of MSMB. No sites were observed to be polymorphic within the exons of MSMB

The p12 Domain Is Unstructured in a Murine Leukemia Virus p12-CAN Gag Construct

The Gag polyproteins of gammaretroviruses contain a conserved p12 domain between MA and CA that plays critical roles in virus assembly, reverse transcription and nuclear integration. Here we show using nuclear magnetic resonance, that p12 is unstructured in a Moloney murine leukemia virus (MMLV) Gag fragment that includes the N-terminal domain of CA (p12-CAN). Furthermore, no long range interactions were observed between the domains, as has been previously predicted. Flexibility appears to be a common feature of Gag “late” domains required for virus release during budding. Residues near the N-terminus of CAN that form a β-hairpin in the mature CA protein are unfolded in p12-CAN, consistent with proposals that hairpin formation helps trigger capsid assembly

Skill metrics for confronting global upper ocean ecosystem-biogeochemistry models against field and remote sensing data

Author Posting. © Elsevier B.V., 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Journal of Marine Systems 76 (2009): 95-112, doi:10.1016/j.jmarsys.2008.05.015.We present a generalized framework for assessing the skill of global upper ocean ecosystem-biogeochemical models against in-situ field data and satellite observations. We illustrate the approach utilizing a multi-decade (1979-2004) hindcast experiment conducted with the Community Climate System Model (CCSM-3) ocean carbon model. The CCSM-3 ocean carbon model incorporates a multi-nutrient, multi-phytoplankton functional group ecosystem module coupled with a carbon, oxygen, nitrogen, phosphorus, silicon, and iron biogeochemistry module embedded in a global, threedimensional ocean general circulation model. The model is forced with physical climate forcing from atmospheric reanalysis and satellite data products and time-varying atmospheric dust deposition. Data-based skill metrics are used to evaluate the simulated time-mean spatial patterns, seasonal cycle amplitude and phase, and subannual to interannual variability. Evaluation data include: sea surface temperature and mixed layer depth; satellite derived surface ocean chlorophyll, primary productivity, phytoplankton growth rate and carbon biomass; large-scale climatologies of surface nutrients, pCO2, and air-sea CO2 and O2 flux; and time-series data from the Joint Global Ocean Flux Study (JGOFS). Where the data is sufficient, we construct quantitative skill metrics using: model-data residuals, time-space correlation, root mean square error, and Taylor diagrams.This work was supported in part by grants from the NSF/ONR National Ocean Partnership Program (N000140210370), the NASA Ocean Biology and Biogeochemistry Program (NNX07AL80G), and the NSF Center for Microbial Oceanography Research and Education (C-MORE)

Challenges and Prospects in Ocean Circulation Models

We revisit the challenges and prospects for ocean circulation models following Griffies et al. (2010). Over the past decade, ocean circulation models evolved through improved understanding, numerics, spatial discretization, grid configurations, parameterizations, data assimilation, environmental monitoring, and process-level observations and modeling. Important large scale applications over the last decade are simulations of the Southern Ocean, the Meridional Overturning Circulation and its variability, and regional sea level change. Submesoscale variability is now routinely resolved in process models and permitted in a few global models, and submesoscale effects are parameterized in most global models. The scales where nonhydrostatic effects become important are beginning to be resolved in regional and process models. Coupling to sea ice, ice shelves, and high-resolution atmospheric models has stimulated new ideas and driven improvements in numerics. Observations have provided insight into turbulence and mixing around the globe and its consequences are assessed through perturbed physics models. Relatedly, parameterizations of the mixing and overturning processes in boundary layers and the ocean interior have improved. New diagnostics being used for evaluating models alongside present and novel observations are briefly referenced. The overall goal is summarizing new developments in ocean modeling, including: how new and existing observations can be used, what modeling challenges remain, and how simulations can be used to support observations.Peer reviewe

Characterizing Associations and SNP-Environment Interactions for GWAS-Identified Prostate Cancer Risk Markers—Results from BPC3

Genome-wide association studies (GWAS) have identified multiple single nucleotide polymorphisms (SNPs) associated with prostate cancer risk. However, whether these associations can be consistently replicated, vary with disease aggressiveness (tumor stage and grade) and/or interact with non-genetic potential risk factors or other SNPs is unknown. We therefore genotyped 39 SNPs from regions identified by several prostate cancer GWAS in 10,501 prostate cancer cases and 10,831 controls from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3). We replicated 36 out of 39 SNPs (P-values ranging from 0.01 to 10−28). Two SNPs located near KLK3 associated with PSA levels showed differential association with Gleason grade (rs2735839, P = 0.0001 and rs266849, P = 0.0004; case-only test), where the alleles associated with decreasing PSA levels were inversely associated with low-grade (as defined by Gleason grade <8) tumors but positively associated with high-grade tumors. No other SNP showed differential associations according to disease stage or grade. We observed no effect modification by SNP for association with age at diagnosis, family history of prostate cancer, diabetes, BMI, height, smoking or alcohol intake. Moreover, we found no evidence of pair-wise SNP-SNP interactions. While these SNPs represent new independent risk factors for prostate cancer, we saw little evidence for effect modification by other SNPs or by the environmental factors examined

Comprehensive Evaluation of One-Carbon Metabolism Pathway Gene Variants and Renal Cell Cancer Risk

Folate and one-carbon metabolism are linked to cancer risk through their integral role in DNA synthesis and methylation. Variation in one-carbon metabolism genes, particularly MTHFR, has been associated with risk of a number of cancers in epidemiologic studies, but little is known regarding renal cancer.Tag single nucleotide polymorphisms (SNPs) selected to produce high genomic coverage of 13 gene regions of one-carbon metabolism (ALDH1L1, BHMT, CBS, FOLR1, MTHFR, MTR, MTRR, SHMT1, SLC19A1, TYMS) and the closely associated glutathione synthesis pathway (CTH, GGH, GSS) were genotyped for 777 renal cell carcinoma (RCC) cases and 1,035 controls in the Central and Eastern European Renal Cancer case-control study. Associations of individual SNPs (n = 163) with RCC risk were calculated using unconditional logistic regression adjusted for age, sex and study center. Minimum p-value permutation (Min-P) tests were used to identify gene regions associated with risk, and haplotypes were evaluated within these genes.The strongest associations with RCC risk were observed for SLC19A1 (P(min-P) = 0.03) and MTHFR (P(min-P) = 0.13). A haplotype consisting of four SNPs in SLC19A1 (rs12483553, rs2838950, rs2838951, and rs17004785) was associated with a 37% increased risk (p = 0.02), and exploratory stratified analysis suggested the association was only significant among those in the lowest tertile of vegetable intake.To our knowledge, this is the first study to comprehensively examine variation in one-carbon metabolism genes in relation to RCC risk. We identified a novel association with SLC19A1, which is important for transport of folate into cells. Replication in other populations is required to confirm these findings

Short Telomeres Initiate Telomere Recombination in Primary and Tumor Cells

Human tumors that lack telomerase maintain telomeres by alternative lengthening mechanisms. Tumors can also form in telomerase-deficient mice; however, the genetic mechanism responsible for tumor growth without telomerase is unknown. In yeast, several different recombination pathways maintain telomeres in the absence of telomerase—some result in telomere maintenance with minimal effects on telomere length. To examine non-telomerase mechanisms for telomere maintenance in mammalian cells, we used primary cells and lymphomas from telomerase-deficient mice (mTR−/− and Eμmyc+mTR−/−) and CAST/EiJ mouse embryonic fibroblast cells. These cells were analyzed using pq-ratio analysis, telomere length distribution outliers, CO-FISH, Q-FISH, and multicolor FISH to detect subtelomeric recombination. Telomere length was maintained during long-term growth in vivo and in vitro. Long telomeres, characteristic of human ALT cells, were not observed in either late passage or mTR−/− tumor cells; instead, we observed only minimal changes in telomere length. Telomere length variation and subtelomeric recombination were frequent in cells with short telomeres, indicating that length maintenance is due to telomeric recombination. We also detected telomere length changes in primary mTR−/− cells that had short telomeres. Using mouse mTR+/− and human hTERT+/− primary cells with short telomeres, we found frequent length changes indicative of recombination. We conclude that telomere maintenance by non-telomerase mechanisms, including recombination, occurs in primary cells and is initiated by short telomeres, even in the presence of telomerase. Most intriguing, our data indicate that some non-telomerase telomere maintenance mechanisms occur without a significant increase in telomere length

Cytoskeleton as an Emerging Target of Anthrax Toxins

Bacillus anthracis, the agent of anthrax, has gained virulence through its exotoxins produced by vegetative bacilli and is composed of three components forming lethal toxin (LT) and edema toxin (ET). So far, little is known about the effects of these toxins on the eukaryotic cytoskeleton. Here, we provide an overview on the general effects of toxin upon the cytoskeleton architecture. Thus, we shall discuss how anthrax toxins interact with their receptors and may disrupt the interface between extracellular matrix and the cytoskeleton. We then analyze what toxin molecular effects on cytoskeleton have been described, before discussing how the cytoskeleton may help the pathogen to corrupt general cell processes such as phagocytosis or vascular integrity

Rapid decline of the CO2 buffering capacity in the North Sea and implications for the North Atlantic Ocean

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 21 (2007): GB4001, doi:10.1029/2006GB002825.New observations from the North Sea, a NW European shelf sea, show that between 2001 and 2005 the CO2 partial pressure (pCO2) in surface waters rose by 22 μatm, thus faster than atmospheric pCO2, which in the same period rose approximately 11 μatm. The surprisingly rapid decline in air-sea partial pressure difference (ΔpCO2) is primarily a response to an elevated water column inventory of dissolved inorganic carbon (DIC), which, in turn, reflects mostly anthropogenic CO2 input rather than natural interannual variability. The resulting decline in the buffering capacity of the inorganic carbonate system (increasing Revelle factor) sets up a theoretically predicted feedback loop whereby the invasion of anthropogenic CO2 reduces the ocean's ability to uptake additional CO2. Model simulations for the North Atlantic Ocean and thermodynamic principles reveal that this feedback should be stronger, at present, in colder midlatitude and subpolar waters because of the lower present-day buffer capacity and elevated DIC levels driven either by northward advected surface water and/or excess local air-sea CO2 uptake. This buffer capacity feedback mechanism helps to explain at least part of the observed trend of decreasing air-sea ΔpCO2 over time as reported in several other recent North Atlantic studies.S. Doney and I. Lima were supported by NSF/ONR NOPP (N000140210370) and NASA (NNG05GG30G)