Lack of Wdr13 Gene in Mice Leads to Enhanced Pancreatic Beta Cell Proliferation, Hyperinsulinemia and Mild Obesity

WD-repeat proteins are very diverse, yet these are structurally related proteins that participate in a wide range of cellular functions. WDR13, a member of this family, is conserved from fishes to humans and localizes into the nucleus. To understand the in vivo function(s) of Wdr13 gene, we have created and characterized a mutant mouse strain lacking this gene. The mutant mice had higher serum insulin levels and increased pancreatic islet mass as a result of enhanced beta cell proliferation. While a known cell cycle inhibitor, p21, was downregulated in the mutant islets, over expression of WDR13 in the pancreatic beta cell line (MIN6) resulted in upregulation of p21, accompanied by retardation of cell proliferation. We suggest that WDR13 is a novel negative regulator of the pancreatic beta cell proliferation. Given the higher insulin levels and better glucose clearance in Wdr13 gene deficient mice, we propose that this protein may be a potential candidate drug target for ameliorating impaired glucose metabolism in diabetes

Analysis of Tp53 Codon 72 Polymorphisms, Tp53 Mutations, and HPV Infection in Cutaneous Squamous Cell Carcinomas

Non-melanoma skin cancers are one of the most common human malignancies accounting for 2-3% of tumors in the US and represent a significant health burden. Epidemiology studies have implicated Tp53 mutations triggered by UV exposure, and human papilloma virus (HPV) infection to be significant causes of non-melanoma skin cancer. However, the relationship between Tp53 and cutaneous HPV infection is not well understood in skin cancers. In this study we assessed the association of HPV infection and Tp53 polymorphisms and mutations in lesional specimens with squamous cell carcinomas.We studied 55 cases of histologically confirmed cutaneous squamous cell carcinoma and 41 controls for the presence of HPV infection and Tp53 genotype (mutations and polymorphism).We found an increased number of Tp53 mutations in the squamous cell carcinoma samples compared with perilesional or control samples. There was increased frequency of homozygous Tp53-72R polymorphism in cases with squamous cell carcinomas, while the Tp53-72P allele (Tp53-72R/P and Tp53-72P/P) was more frequent in normal control samples. Carcinoma samples positive for HPV showed a decreased frequency of Tp53 mutations compared to those without HPV infection. In addition, carcinoma samples with a Tp53-72P allele showed an increased incidence of Tp53 mutations in comparison carcinomas samples homozygous for Tp53-72R.These studies suggest there are two separate pathways (HPV infection and Tp53 mutation) leading to cutaneous squamous cell carcinomas stratified by the Tp53 codon-72 polymorphism. The presence of a Tp53-72P allele is protective against cutaneous squamous cell carcinoma, and carcinoma specimens with Tp53-72P are more likely to have Tp53 mutations. In contrast Tp53-72R is a significant risk factor for cutaneous squamous cell carcinoma and is frequently associated with HPV infection instead of Tp53 mutations. Heterozygosity for Tp53-72R/P is protective against squamous cell carcinomas, possibly reflecting a requirement for both HPV infection and Tp53 mutations

Errors in RNA-Seq quantification affect genes of relevance to human disease

BACKGROUND: RNA-Seq has emerged as the standard for measuring gene expression and is an important technique often used in studies of human disease. Gene expression quantification involves comparison of the sequenced reads to a known genomic or transcriptomic reference. The accuracy of that quantification relies on there being enough unique information in the reads to enable bioinformatics tools to accurately assign the reads to the correct gene. RESULTS: We apply 12 common methods to estimate gene expression from RNA-Seq data and show that there are hundreds of genes whose expression is underestimated by one or more of those methods. Many of these genes have been implicated in human disease, and we describe their roles. We go on to propose a two-stage analysis of RNA-Seq data in which multi-mapped or ambiguous reads can instead be uniquely assigned to groups of genes. We apply this method to a recently published mouse cancer study, and demonstrate that we can extract relevant biological signal from data that would otherwise have been discarded. CONCLUSIONS: For hundreds of genes in the human genome, RNA-Seq is unable to measure expression accurately. These genes are enriched for gene families, and many of them have been implicated in human disease. We show that it is possible to use data that may otherwise have been discarded to measure group-level expression, and that such data contains biologically relevant information. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0734-x) contains supplementary material, which is available to authorized users

X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4−/− mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases

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Un gen importante controla el mimetismo y la cripsis en mariposas y polillas.

The wing patterns of butterflies and moths (Lepidoptera) are diverse and striking examples of evolutionary diversification by natural selection1,2. Lepidopteran wing colour patterns are a key innovation, consisting of arrays of coloured scales. We still lack a general understanding of how these patterns are controlled and whether this control shows any commonality across the 160,000 moth and 17,000 butterfly species. Here, we use fine-scale mapping with population genomics and gene expression analyses to identify a gene, cortex, that regulates pattern switches in multiple species across the mimetic radiation in Heliconius butterflies. cortex belongs to a fast-evolving subfamily of the otherwise highly conserved fizzy family of cell-cycle regulators3, suggesting that it probably regulates pigmentation patterning by regulating scale cell development. In parallel with findings in the peppered moth (Biston betularia)4, our results suggest that this mechanism is common within Lepidoptera and that cortex has become a major target for natural selection acting on colour and pattern variation in this group of insects

IL-17C^-/- and IL-17RE^-/- mice are resistant to systemic candidiasis.

<p><b>A-C.</b> IL-17RE^-/- and IL-17RE^+/+ littermate controls were subjected to systemic candidiasis by tail vein injection of 2x10⁵ C. albicans strain SC5314 (IL-17RE^+/+ n = 11; IL-17RE^-/-, n = 13; IL-17C^+/+; n = 10; IL-17C^-/- n = 11). Mice were evaluated daily and time to sacrifice is presented. ns., not significant. Data are representative of 2 independent experiments. <b>C-D.</b> IL-17RE^-/- mice (n = 7) and IL-17C^-/- (n = 5) mice were injected with 1x10⁵ cells C. albicans as in panel A. WT littermates (IL-17C^+/+, n = 4 and IL-17RE^+/+, n = 5) and IL-17RA^-/- mice (n = 5) served as controls. ns., not significant. Data are representative of one independent experiment. <b>E.</b> Weight change assessments were made in all cohorts after infection with 2x10⁵ C. albicans cells, and presented as a percentage of starting weight. <b>F.</b> Kidneys were harvested from each cohort on day 2 after systeic infection and qperformed for the indicated genes. *p<0.05 by ANOVA and post-hoc Tukey’s test. <b>G.</b> Indicated tissue types were harvested on day 2 and tissue fungal burdens determined. Each data point represents one mouse. (IL-17RE^+/+ Sham, n = 3; IL-17RE^-/- Sham, n = 2; IL-17RE^+/+ n = 9; IL-17RE^-/- n = 10). Pooled data from two independent experiments is shown.</p

IL-17C^-/- and IL-17RE^-/- mice are resistant to oropharyngeal candidiasis.

<p><b>A.</b> WT and IL-17RA^-/- mice (n = 3 per group) were subjected to OPC and IL-17C transcript levels assessed by qPCR. *p<0.05 with error bars indicating SEM. <b>B.</b> OPC was induced in the indicated mice (IL-17C^-/- Sham, n = 2; IL-17RE^-/- Sham, n = 2; Infected: IL-17C^+/+ n = 9; IL-17RE^+/+, n = 6; IL-17C^-/-, n = 9; IL-17RE^-/-, n = 6; IL-17RA^-/- n = 7). Tongue was harvested on day 5, and CFU enumerated 48 h later by plating serial dilutions on YPD agar. Data presented as the geometric mean of CFU. Each data point represents one mouse, and the graph depicts pooled data from two independent experiments (n = 2 for each sham-infected cohort and n≥6 total for each Candida-infected cohort). *p<0.0001 by Mann Whitney U test. <b>C.</b> Weight loss was assessed daily and is presented as a percentage of starting weight. Error bars indicate SEM. <b>D.</b> Indicated mice (n = 3 per group) were subjected to OPC and qPCR performed for Defb3 and Lcn2 genes on day 2. *p<0.05 by ANOVA and post-hoc Tukey’s test. Error bars indicate SEM.</p

IL-17RE^-/- mice are resistant to cutaneous candidiasis.

<p><b>A.</b> The indicated mice were subjected to dermal candidiasis by subcutaneous injection with C. albicans strain CAF2-1 hyphae (IL-17RE^+/+ Sham, n = 6; Infected: IL-17RC^-/-, n = 5; C57BL/6 WT, n = 4; IL-17RE^+/+, n = 21; IL-17RE^-/-, n = 19). The percent of mice positive for lesions over time is presented. *p<0.01 compared to WT by a Log-rank (Mantel Cox) test. Graph depicts pooled data from two independent experiments. <b>B.</b> Ulceration (left panels) and nodule formation (right panels) are depicted in WT, IL-17RE^-/- and IL-17RC^-/- mice on days 4 and 6. Data are representative of two independent experiments.</p