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Most genome-wide association studies (GWAS) of complex traits are performed using models with additive allelic effects. Hundreds of loci associated with type 2 diabetes have been identified using this approach. Additive models, however, can miss loci with recessive effects, thereby leaving potentially important genes undiscovered. We conducted the largest GWAS meta-analysis using a recessive model for type 2 diabetes. Our discovery sample included 33,139 cases and 279,507 controls from seven European-ancestry cohorts including the UK Biobank. We identified 51 loci associated with type 2 diabetes, including five variants undetected by prior additive analyses. Two of the five had minor allele frequency less than 5% and were each associated with more than doubled risk in homozygous carriers. Using two additional cohorts, FinnGen and a Danish cohort, we replicated three of the variants, including one of the low-frequency variants, rs115018790, which had an odds ratio in homozygous carriers of 2.56 (95% CI 2.05-3.19, P=1´10-16) and a stronger effect in men than in women (interaction P=7´10-7). The signal was associated with multiple diabetes-related traits, with homozygous carriers showing a 10% decrease in LDL and a 20% increase in triglycerides, and colocalization analysis linked this signal to reduced expression of the nearby PELO gene. These results demonstrate that recessive models, when compared to GWAS using the additive approach, can identify novel loci, including large-effect variants with pathophysiological consequences relevant to type 2 diabetes.

ObjectiveMost genome-wide association studies (GWAS) of complex traits are performed using models with additive allelic effects. Hundreds of loci associated with type 2 diabetes have been identified using this approach. Additive models, however, can miss loci with recessive effects, thereby leaving potentially important genes undiscovered.Research Design and MethodsWe conducted the largest GWAS meta-analysis using a recessive model for type 2 diabetes. Our discovery sample included 33,139 cases and 279,507 controls from seven European-ancestry cohorts including the UK Biobank. We then used two additional cohorts, FinnGen and a Danish cohort, for replication. For the most significant recessive signal, we conducted a phenome-wide association study across hundreds of traits to make inferences about the pathophysiology underlying the increased risk seen in homozygous carriers.ResultsWe identified 51 loci associated with type 2 diabetes, including five variants with recessive effects undetected by prior additive analyses. Two of the five had minor allele frequency less than 5% and were each associated with more than doubled risk. We replicated three of the variants, including one of the low-frequency variants, rs115018790, which had an odds ratio in homozygous carriers of 2.56 (95% CI 2.05-3.19, P=1×10−16) and a stronger effect in men than in women (interaction P=7×10−7). Colocalization analysis linked this signal to reduced expression of the nearby PELO gene, and the signal was associated with multiple diabetes-related traits, with homozygous carriers showing a 10% decrease in LDL and a 20% increase in triglycerides.ConclusionsOur results demonstrate that recessive models, when compared to GWAS using the additive approach, can identify novel loci, including large-effect variants with pathophysiological consequences relevant to type 2 diabetes.

Familial Parkinson disease (PD) is associated with rare genetic mutations, but the etiology in most patients with sporadic (s)PD is largely unknown, and the basis for its progression to dementia (sPDD) is poorly characterized. We have identified that loss of IFNβ or IFNAR1, the receptor for IFNα/β, causes pathological and behavioral changes resembling PDD, prompting us to hypothesize that dysregulated genes in IFNβ-IFNAR signaling pathway predispose one to sPD. By transcriptomic analysis, we found defective neuronal IFNβ-IFNAR signaling, including particularly elevated PIAS2 associated with sPDD. With meta-analysis of GWASs, we identified sequence variants in IFNβ-IFNAR-related genes in sPD patients. Furthermore, sPDD patients expressed higher levels of PIAS2 mRNA and protein in neurons. To determine its function in brain, we overexpressed PIAS2 under a neuronal promoter, alone or with human α-synuclein, in the brains of mice, which caused motor and cognitive impairments and correlated with intraneuronal phosphorylated (p)α-synuclein accumulation and dopaminergic neuron loss. Ectopic expression of neuronal PIAS2 blocked mitophagy, increased the accumulation of senescent mitochondrial and oxidative stress, as evidenced by excessive oxDJ1 and 8OHdG, by inactivating ERK1/2-P53 signaling. Conversely, PIAS2 knockdown rescued the clinicopathological manifestations of PDD in Ifnb–/– mice on restoring mitochondrial homeostasis, oxidative stress, and pERK1/2-pP53 signaling. The regulation of JAK-STAT2-PIAS2 signaling was crucial for neurite outgrowth and neuronal survival and excitability and thus might prevent cognitive impairments. Our findings provide insights into the progression of sPD and dementia and have implications for new therapeutic approaches.

Tissue regeneration requires dynamic cellular adaptation to the wound environment. It is currently unclear how this is orchestrated at the cellular level and how cell fate is affected by severe tissue damage. Here we dissect cell fate transitions during colonic regeneration in a mouse dextran sulfate sodium (DSS) colitis model, and we demonstrate that the epithelium is transiently reprogrammed into a primitive state. This is characterized by de novo expression of fetal markers as well as suppression of markers for adult stem and differentiated cells. The fate change is orchestrated by remodeling the extracellular matrix (ECM), increased FAK/Src signaling, and ultimately YAP/TAZ activation. In a defined cell culture system recapitulating the extracellular matrix remodeling observed in vivo, we show that a collagen 3D matrix supplemented with Wnt ligands is sufficient to sustain endogenous YAP/TAZ and induce conversion of cell fate. This provides a simple model for tissue regeneration, implicating cellular reprogramming as an essential element. The mechanism that governs tissue regeneration following severe damage to the colonic epithelium remains poorly understood. Jensen and colleagues show that the colonic epithelium undergoes a profound reprogramming into a more primitive state with fetal-like properties. Moreover, they demonstrate that YAP and TAZ operate as essential mechano-sensors during tissue reprogramming.

Bovine mastitis is the most common and costly dairy cattle disease. Mastitis is most frequently caused by bacterial species, and to ensure optimal treatment and control strategies, proper quality assured diagnosis and identification of the causative agent is important. With the aim to assess the capacity to isolate and identify mastitis pathogens at veterinary clinics, an external quality assurance system (EQAS) was annually (from 2006 to 2011) provided for the identification of mastitis pathogens. This study presents the setup of the proficiency test and the obtained results that enabled the organizers to pinpoint areas for improvement and thereby to assist veterinary practices at strengthening their mastitis diagnostics. The proficiency test consisted of 15 milk samples spiked with a pure culture of a mastitis pathogen and distributed to veterinary practices for identification. Applying an internal quality control strain, i.e. including the same strain of Streptococcus agalactiae in all iterations of the proficiency test, served to gauge the bias caused by the year-to-year variation in the selection of test strains. A total of 73% of all uploaded results over the years were correct, with the internal quality control strain exhibiting a statistically significant ascending trend from 54% correct identifications in 2006 to 91% in 2011 ( p -value = 0.0082; n = 13). Even if specifics were not recorded as regards the laboratory methods employed at the veterinary clinics for identification of mastitis pathogens, the results from this study indicate that the practices’ application of basic biochemical analyses in this context could be optimized. In addition, dissemination of information on new methods and updated nomenclature appeared to be an area which future efforts with advantage could aim at.

We currently have limited knowledge of the involvement of long non-coding RNAs (lncRNAs) in normal cellular processes and pathologies. Here, we identify and characterize SNHG5 as a stable cytoplasmic lncRNA with up-regulated expression in colorectal cancer. Depletion of SNHG5 induces cell cycle arrest and apoptosis in vitro and limits tumour outgrowth in vivo, whereas SNHG5 overexpression counteracts oxaliplatin-induced apoptosis. Using an unbiased approach, we identify 121 transcript sites interacting with SNHG5 in the cytoplasm. Importantly, knockdown of key SNHG5 target transcripts, including SPATS2, induces apoptosis and thus mimics the effect seen following SNHG5 depletion. Mechanistically, we suggest that SNHG5 stabilizes the target transcripts by blocking their degradation by STAU1. Accordingly, depletion of STAU1 rescues the apoptosis induced after SNHG5 knockdown. Hence, we characterize SNHG5 as a lncRNA promoting tumour cell survival in colorectal cancer and delineate a novel mechanism in which a cytoplasmic lncRNA functions through blocking the action of STAU1., Several lncRNAs have been linked to cancer. Here, the authors identify SNHG5 as a long non-coding RNA promoting proliferation and survival of colorectal cancer cells by protecting specific mRNAs from STAU1-mediated degradation.

C4.4A is a modular glycolipid-anchored Ly6/uPAR/α-neurotoxin multidomain protein that exhibits a prominent membrane-associated expression in stratified squamous epithelia. C4.4A is also expressed in various solid cancer lesions, where high expression levels often are correlated to poor prognosis. Circumstantial evidence suggests a role for C4.4A in cell adhesion, migration and invasion, but a well-defined biological function is currently unknown. In the present study, we have generated and characterized the first C4.4A-deficient mouse line to gain insight into the functional significance of C4.4A in normal physiology and cancer progression. The unchallenged C4.4A-deficient mice were viable, fertile, born in a normal Mendelian distribution and, surprisingly, displayed normal development of squamous epithelia. The C4.4A-deficient mice were, nonetheless, significantly lighter than littermate controls predominantly due to differences in fat mass. Congenital C4.4A deficiency delayed migration of keratinocytes enclosing incisional skin wounds in male mice. In chemically induced bladder carcinomas, C4.4A deficiency attenuated the incidence of invasive lesions despite having no effect on total tumour burden. This new C4.4A-deficient mouse line provides a useful platform for future studies on functional aspects of C4.4A in tumour cell invasion in vivo.

Alterations in chromatin structure caused by deregulated epigenetic mechanisms collaborate with underlying genetic lesions to promote cancer. SMARCA4/BRG1, a core component of the SWI/SNF ATP-dependent chromatin-remodelling complex, has been implicated by its mutational spectrum as exerting a tumour-suppressor function in many solid tumours; recently however, it has been reported to sustain leukaemogenic transformation in MLL-rearranged leukaemia in mice. Here we further explore the role of SMARCA4 and the two SWI/SNF subunits SMARCD2/BAF60B and DPF2/BAF45D in leukaemia. We observed the selective requirement for these proteins for leukaemic cell expansion and self-renewal in-vitro as well as in leukaemia. Gene expression profiling in human cells of each of these three factors suggests that they have overlapping functions in leukaemia. The gene expression changes induced by loss of the three proteins demonstrate that they are required for the expression of haematopoietic stem cell associated genes but in contrast to previous results obtained in mouse cells, the three proteins are not required for the expression of c-MYC regulated genes.

Aim: To obtain an increased understanding of how the porcine lung pathogen Actinobacillus pleuropneumoniae (Ap) establish infection in the host. Understanding the means by which a pathogen establishes and maintains infection in the host organism is the first step towards controlling disease. Methods: The local in vivo genetic response of Ap during the early phase of infection in porcine lungs was detailed using pangenomic microarray analysis. The global transcriptional patterns of Ap serotype 2 and 6 isolated from lung tissue biopsies of 25 experimentally infected pigs were compared at four time points between 6 and 48 hours post infection. Results: We identified 310 genes (p

histology), circularity values increased up to 0.9. C57BL/6 enteroids showed a dose dependent increase in circularity in response to TNF (10-1000ng/ml) or IFN γ (1-100ng/ml) after 24 and 48 hours. Circularity did not however increase in Nfkb2-/enteroids to the same extent following these stimuli. C57BL/6 BMDCs or their CM or LPS alone did not induce an increase in the circularity of C57BL/6, Nfkb2 or Nfkb1-/enteroids. However, when stimulated with 1μg/ml LPS, C57BL/6 BMDCs and their CM induced a significant >2-fold increase in the circularity of C57BL/6 and Nfkb1-/enteroids. Nfkb2 derived enteroids showed no such increase. LPS stimulated BMDCs from Nfkb2-/mice were able to induce a significant increase in C57BL/6 enteroid circularity of a similar magnitude to C57BL/6 BMDCs. Conclusions:Circularity correlates well with cell death and shedding in murine enteroid culture. Deletion of Nfkb2 from intestinal epithelial cells prevents epithelial cell destruction in response to secreted immune cell factors. Therapeutics that specifically target NFKB2 signalling in intestinal epithelial cells may therefore prevent loss of intestinal barrier function and thus ameliorate intestinal inflammation.