Identification of common variants influencing risk of the tauopathy progressive supranuclear palsy

Progressive supranuclear palsy (PSP) is a movement disorder with prominent tau neuropathology. Brain diseases with abnormal tau deposits are called tauopathies, the most common of which is Alzheimer's disease. Environmental causes of tauopathies include repetitive head trauma associated with some sports. To identify common genetic variation contributing to risk for tauopathies, we carried out a genome-wide association study of 1,114 individuals with PSP (cases) and 3,247 controls (stage 1) followed by a second stage in which we genotyped 1,051 cases and 3,560 controls for the stage 1 SNPs that yielded P ≤ 10(-3). We found significant previously unidentified signals (P < 5 × 10(-8)) associated with PSP risk at STX6, EIF2AK3 and MOBP. We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT brain expression. The genes implicated encode proteins for vesicle-membrane fusion at the Golgi-endosomal interface, for the endoplasmic reticulum unfolded protein response and for a myelin structural component.     

Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion

Prior studies have identified recurrent oncogenic mutations in colorectal adenocarcinoma and have surveyed exons of protein-coding genes for mutations in 11 affected individuals. Here we report whole-genome sequencing from nine individuals with colorectal cancer, including primary colorectal tumors and matched adjacent non-tumor tissues, at an average of 30.7× and 31.9× coverage, respectively. We identify an average of 75 somatic rearrangements per tumor, including complex networks of translocations between pairs of chromosomes. Eleven rearrangements encode predicted in-frame fusion proteins, including a fusion of VTI1A and TCF7L2 found in 3 out of 97 colorectal cancers. Although TCF7L2 encodes TCF4, which cooperates with β-catenin in colorectal carcinogenesis, the fusion lacks the TCF4 β-catenin-binding domain. We found a colorectal carcinoma cell line harboring the fusion gene to be dependent on VTI1A-TCF7L2 for anchorage-independent growth using RNA interference-mediated knockdown. This study shows previously unidentified levels of genomic rearrangements in colorectal carcinoma that can lead to essential gene fusions and other oncogenic events.     

Xlr3b is a new imprinted candidate for X-linked parent-of-origin effects on cognitive function in mice

Imprinted genes show differential expression between maternal and paternal alleles as a consequence of epigenetic modification that can result in 'parent-of-origin' effects on phenotypic traits. There is increasing evidence from mouse and human studies that imprinted genes may influence behavior and cognitive functioning. Previous work in girls with Turner syndrome (45,XO) has suggested that there are X-linked parent-of-origin effects on brain development and cognitive functioning, although the interpretation of these data in terms of imprinted gene effects has been questioned. We used a 39,XO mouse model to examine the influence of the parental origin of the X chromosome on cognitive behaviors and expression of X-linked genes in brain. Our findings confirm the existence of X-linked imprinted effects on cognitive processes and identify a new maternally expressed imprinted gene candidate on the X chromosome, Xlr3b, which may be of importance in mediating the behavioral effects.     

Missense mutations interfere with VEGFR-3 signalling in primary lymphoedema

Primary lymphoedema is a rare, autosomal dominant disorder that leads to a disabling and disfiguring swelling of the extremities and, when untreated, tends to worsen with time. Here we link primary human lymphoedema to the FLT4 locus, encoding vascular endothelial growth factor receptor-3 (VEGFR-3), in several families. All disease-associated alleles analysed had missense mutations and encoded proteins with an inactive tyrosine kinase, preventing downstream gene activation. Our study establishes that VEGFR-3 is important for normal lymphatic vascular function and that mutations interfering with VEGFR-3 signal transduction are a cause of primary lymphoedema.     

BRCA1 regulates the G2/M checkpoint by activating Chk1 kinase upon DNA damage

The breast cancer tumor-suppressor gene, BRCA1, encodes a protein with a BRCT domain-a motif that is found in many proteins that are implicated in DNA damage response and in genome stability. Phosphorylation of BRCA1 by the DNA damage-response proteins ATM, ATR and hCds1/Chk2 changes in response to DNA damage and at replication-block checkpoints. Although cells that lack BRCA1 have an abnormal response to DNA damage, the exact role of BRCA1 in this process has remained unclear. Here we show that BRCA1 is essential for activating the Chk1 kinase that regulates DNA damage-induced G2/M arrest. Thus, BRCA1 controls the expression, phosphorylation and cellular localization of Cdc25C and Cdc2/cyclin B kinase-proteins that are crucial for the G2/M transition. We show that BRCA1 regulates the expression of both Wee1 kinase, an inhibitor of Cdc2/cyclin B kinase, and the 14-3-3 family of proteins that sequesters phosphorylated Cdc25C and Cdc2/cyclin B kinase in the cytoplasm. We conclude that BRCA1 regulates key effectors that control the G2/M checkpoint and is therefore involved in regulating the onset of mitosis.     

Kanab ambersnail and other terrestrial snails in south central Utah

Surveys for succineid snails were conducted to improve genetic and geographical information for the endangered Kanab ambersnail ( Oxyloma haydeni kanabensis Pilsbry) and related taxa within the Succineidae. Surveys were carried out in the Bureau of Land Management Kanab District, at the Grand Staircase Escalante National Monument, on 3 private holdings, and along Highways 89, 12, and 14, all in south central Utah. A population of Kanab ambersnails was known to exist in the region; other populations of Oxyloma were discovered in primarily seep-fed wetlands in Kanab Creek and in tributaries of and wetlands along the Virgin, Sevier, and Escalante rivers in Kane, Garfield, and Piute counties. None of the newly discovered populations was identified as Kanab ambersnail on the basis of anatomical evidence, although one was at the type locale for that species. We list other snail species encountered and discuss the status of the Kanab ambersnail in light of recent genetic research.     

Experimental manipulations of fertile islands and nurse plant effects in the Mojave Desert, USA

In a mixed desert shrub community we removed and added shrub canopies to examine above- and belowground influences of 3 species of shrubs on islands of soil fertility and the survival of transplanted Ambrosia dumosa seedlings. Soils sampled under shrubs in the wet season had higher pH, water content, organic matter, and both total and mineralizable nitrogen than soils in adjacent open areas, confirming a widely established pattern in arid lands. However, we also found species differences in soil parameters. Soils under Coleogyne ramosissima had highest pH, soils under A. dumosa had highest water content and nitrogen mineralization rates, and soils under Larrea tridentata had lowest water content. Soils sampled under shrubs in the dry season, 7 months after experimental shrub removal, maintained higher organic matter and total and mineralizable nitrogen content than adjacent open soils, but pH and water were altered by shrub manipulations. Species differences persisted only in soil water levels ( A. dumosa soils were driest). Over a 1-year period, transplanted A. dumosa seedlings had highest survivorship in shrub removal and open treatments and died most rapidly under control shrubs of all 3 species, suggesting that shrubs had a strong negative effect on seedling survival, even in the presence of higher organic matter, nutrients, and (initially) higher water content of fertile islands. Our results suggest that nurse plants and islands of soil fertility have the potential to facilitate growth of other species by nutrient additions, but that the net effect of nurse plants can be negative due to shading and/or root competition.