An <i>in vivo cis</i>-Regulatory Screen at the Type 2 Diabetes Associated <i>TCF7L2</i> Locus Identifies Multiple Tissue-Specific Enhancers

Genome-wide association studies (GWAS) have repeatedly shown an association between non-coding variants in the TCF7L2 locus and risk for type 2 diabetes (T2D), implicating a role for cis-regulatory variation within this locus in disease etiology. Supporting this hypothesis, we previously localized complex regulatory activity to the TCF7L2 T2D-associated interval using an in vivo bacterial artificial chromosome (BAC) enhancer-trapping reporter strategy. To follow-up on this broad initial survey of the TCF7L2 regulatory landscape, we performed a fine-mapping enhancer scan using in vivo mouse transgenic reporter assays. We functionally interrogated approximately 50% of the sequences within the T2D-associated interval, utilizing sequence conservation within this 92-kb interval to determine the regulatory potential of all evolutionary conserved sequences that exhibited conservation to the non-eutherian mammal opossum. Included in this study was a detailed functional interrogation of sequences spanning both protective and risk alleles of single nucleotide polymorphism (SNP) rs7903146, which has exhibited allele-specific enhancer function in pancreatic beta cells. Using these assays, we identified nine segments regulating various aspects of the TCF7L2 expression profile and that constitute nearly 70% of the sequences tested. These results highlight the regulatory complexity of this interval and support the notion that a TCF7L2 cis-regulatory disruption leads to T2D predisposition.</p

Brucellosis Control in Malta and Serbia: A One Health Evaluation

Brucellosis, also known as \u201cundulant fever\u201d or \u201cMalta fever\u201d, is a zoonotic infection caused by microorganisms belonging to Brucella, a genus of gram-negative coccobacilli that behave as facultative intracellular pathogens of ruminants, swine and other animals. Brucellosis is a threat to public health, hence identifying the optimal way of preventing disease spread is important. Under certain circumstances, integrated, multidisciplinary \u201cOne Health\u201d (OH) initiatives provide added value compared to unidisciplinary or conventional health initiatives. Conceptualizing and conducting evaluations of OH approaches may help facilitate decisions on resource allocation. This article historically describes and compares Malta's 1995\u20131997 with Serbia's 2004\u20132006 brucellosis control programmes and quantitatively assesses the extent to which they were compliant with a OH approach. For both case studies, we describe the OH initiative and the system within which it operates. Characteristic OH operations (i.e., thinking, planning, working) and supporting infrastructures (to allow sharing, learning and systemic organization) were evaluated. We scored the different aspects of these programmes, with values ranging from zero to one (1 = strong integration of OH). Malta demonstrated a higher OH index (0.54) and ratio (1.37) than Serbia (0.49 and 1.14 respectively). We conclude that context and timing are key to determining how, when and why a One Health approach should be applied. The adoption of a true OH approach that involved systemic organization, leadership clarity and transdisciplinary communication, collaboration, and co-ordination was essential to Malta's successful eradication of brucellosis after several failed attempts. In contrast, contextual factors in Serbia permitted the successful adoption of a primarily sectorial approach for short term control of brucellosis. However, while a fully-fledged transdisciplinary OH approach was not initially required, it is likely to be key to maintenance of brucellosis control in the medium and long term. Through these two case studies, we demonstrate that One Health initiatives should be applied at the right place, at the right time, with the right people and using the appropriate conditions/infrastructure. Lastly, OH evaluations should include economic assessments to identify optimal of resources in these situations, thereby justifying funding and political support required

Typology and Dynamics of Heavier Drinking Styles in Great Britain: 1978-2010.

AIMS: To identify a typology of heavier drinking styles in Great Britain and to identify socio-demographic trends in the typology over the period 1978-2010. METHODS: We applied multiple correspondence analysis and agglomerative hierarchical clustering to beverage-specific quantity-frequency measures of alcohol consumption in the repeated cross-sectional General Lifestyle Survey of Great Britain, 1978-2010. The cluster analysis focuses on the 60,043 adult respondents over this period reporting average drinking levels above the UK Government guidelines. We projected sex, age, income, education, socio-economic status and tobacco consumption variables onto the clusters to inspect socio-demographic trends in heavier drinking. RESULTS: We identified four stable clusters of heavier drinking: (a) high volume beer; (b) beer and spirit combination; (c) all beverage and (d) wine and spirit only. The socio-demographic characteristics of the clusters were distinct from both each other and the general population. However, all clusters had higher median incomes and higher smoking rates than the population. Increases in the prevalence of heavier drinking were driven by a 5-fold increase in the contribution of the female-dominated, wine and spirit only cluster. CONCLUSIONS: Recent changes in per capita alcohol consumption in Great Britain occurred within the context of a stable typology of heavier drinking styles and shifting socio-demographics. Identifying these trends is essential to better understand how drinking cultures develop over time and where potentially problematic drinking styles may emerge. Our findings suggest that careful attention to patterns and cultures of consumption is more important than relying on headline consumption data, for both understanding drinking behaviours and targeting interventions. SHORT SUMMARY: This analysis of alcohol consumption survey data identifies four styles of heavier drinking in Great Britain, which remain unchanged over the period 1978-2010. The socio-demographic characteristics of the drinking styles are distinct from both each other and the general population, with increased participation of female and older drinkers over time

Brucellosis Control in Malta and Serbia: A One Health Evaluation

Brucellosis, also known as “undulant fever” or “Malta fever”, is a zoonotic infection caused by microorganisms belonging to Brucella, a genus of gram-negative coccobacilli that behave as facultative intracellular pathogens of ruminants, swine and other animals. Brucellosis is a threat to public health, hence identifying the optimal way of preventing disease spread is important. Under certain circumstances, integrated, multidisciplinary “One Health” (OH) initiatives provide added value compared to unidisciplinary or conventional health initiatives. Conceptualizing and conducting evaluations of OH approaches may help facilitate decisions on resource allocation. This article historically describes and compares Malta's 1995–1997 with Serbia's 2004–2006 brucellosis control programmes and quantitatively assesses the extent to which they were compliant with a OH approach. For both case studies, we describe the OH initiative and the system within which it operates. Characteristic OH operations (i.e., thinking, planning, working) and supporting infrastructures (to allow sharing, learning and systemic organization) were evaluated. We scored the different aspects of these programmes, with values ranging from zero to one (1 = strong integration of OH). Malta demonstrated a higher OH index (0.54) and ratio (1.37) than Serbia (0.49 and 1.14 respectively). We conclude that context and timing are key to determining how, when and why a One Health approach should be applied. The adoption of a true OH approach that involved systemic organization, leadership clarity and transdisciplinary communication, collaboration, and co-ordination was essential to Malta's successful eradication of brucellosis after several failed attempts. In contrast, contextual factors in Serbia permitted the successful adoption of a primarily sectorial approach for short term control of brucellosis. However, while a fully-fledged transdisciplinary OH approach was not initially required, it is likely to be key to maintenance of brucellosis control in the medium and long term. Through these two case studies, we demonstrate that One Health initiatives should be applied at the right place, at the right time, with the right people and using the appropriate conditions/infrastructure. Lastly, OH evaluations should include economic assessments to identify optimal of resources in these situations, thereby justifying funding and political support required

An in vivo cis-Regulatory Screen at the Type 2 Diabetes Associated TCF7L2 Locus Identifies Multiple Tissue-Specific Enhancers

Genome-wide association studies (GWAS) have repeatedly shown an association between non-coding variants in the TCF7L2 locus and risk for type 2 diabetes (T2D), implicating a role for cis-regulatory variation within this locus in disease etiology. Supporting this hypothesis, we previously localized complex regulatory activity to the TCF7L2 T2D-associated interval using an in vivo bacterial artificial chromosome (BAC) enhancer-trapping reporter strategy. To follow-up on this broad initial survey of the TCF7L2 regulatory landscape, we performed a fine-mapping enhancer scan using in vivo mouse transgenic reporter assays. We functionally interrogated approximately 50% of the sequences within the T2D-associated interval, utilizing sequence conservation within this 92-kb interval to determine the regulatory potential of all evolutionary conserved sequences that exhibited conservation to the non-eutherian mammal opossum. Included in this study was a detailed functional interrogation of sequences spanning both protective and risk alleles of single nucleotide polymorphism (SNP) rs7903146, which has exhibited allele-specific enhancer function in pancreatic beta cells. Using these assays, we identified nine segments regulating various aspects of the TCF7L2 expression profile and that constitute nearly 70% of the sequences tested. These results highlight the regulatory complexity of this interval and support the notion that a TCF7L2 cis-regulatory disruption leads to T2D predisposition

Central tolerance shapes the neutralizing B cell repertoire against a persisting virus in its natural host

Viral mimicry of host cell structures has been postulated to curtail the B cell receptor (BCR) repertoire against persisting viruses through tolerance mechanisms. This concept awaits, however, experimental testing in a setting of natural virus–host relationship. We engineered mouse models expressing a monoclonal BCR specific for the envelope glycoprotein of lymphocytic choriomeningitis virus (LCMV), a naturally persisting mouse pathogen. When the heavy chain of the LCMV-neutralizing antibody KL25 was paired with its unmutated ancestor light chain, most B cells underwent receptor editing, a behavior reminiscent of autoreactive clones. In contrast, monoclonal B cells expressing the same heavy chain in conjunction with the hypermutated KL25 light chain did not undergo receptor editing but exhibited low levels of surface IgM, suggesting that light chain hypermutation had lessened KL25 autoreactivity. Upon viral challenge, these IgM $^{low}$ cells were not anergic but up-regulated IgM, participated in germinal center reactions, produced antiviral antibodies, and underwent immunoglobulin class switch as well as further affinity maturation. These studies on a persisting virus in its natural host species suggest that central tolerance mechanisms prune the protective antiviral B cell repertoire

Epigenetic activation of the FLT3 gene by ZNF384 fusion confers a therapeutic susceptibility in acute lymphoblastic leukemia.

FLT3 is an attractive therapeutic target in acute lymphoblastic leukemia (ALL) but the mechanism for its activation in this cancer is incompletely understood. Profiling global gene expression in large ALL cohorts, we identify over-expression of FLT3 in ZNF384-rearranged ALL, consistently across cases harboring different fusion partners with ZNF384. Mechanistically, we discover an intergenic enhancer element at the FLT3 locus that is exclusively activated in ZNF384-rearranged ALL, with the enhancer-promoter looping directly mediated by the fusion protein. There is also a global enrichment of active enhancers within ZNF384 binding sites across the genome in ZNF384-rearranged ALL cells. Downregulation of ZNF384 blunts FLT3 activation and decreases ALL cell sensitivity to FLT3 inhibitor gilteritinib in vitro. In patient-derived xenograft models of ZNF384-rearranged ALL, gilteritinib exhibits significant anti-leukemia efficacy as a monotherapy in vivo. Collectively, our results provide insights into FLT3 regulation in ALL and point to potential genomics-guided targeted therapy for this patient population

Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/ enhancer-binding protein beta binding sites

Transcription factors (TFs) bind to thousands of DNA sequences in mammalian genomes, but most of these binding events appear to have no direct effect on gene expression. It is unclear why only a subset of TF bound sites are actively involved in transcriptional regulation. Moreover, the key genomic features that accurately discriminate between active and inactive TF binding events remain ambiguous. Recent studies have identified promoter-distal RNA polymerase II (RNAP2) binding at enhancer elements, suggesting that these interactions may serve as a marker for active regulatory sequences. Despite these correlative analyses, a thorough functional validation of these genomic co-occupancies is still lacking. To characterize the gene regulatory activity of DNA sequences underlying promoter-distal TF binding events that co-occur with RNAP2 and TF sites devoid of RNAP2 occupancy using a functional reporter assay, we performed cis-regulatory element sequencing (CRE-seq). We tested more than 1000 promoter-distal CCAAT/enhancer-binding protein beta (CEBPB)-bound sites in HepG2 and K562 cells, and found that CEBPB-bound sites co-occurring with RNAP2 were more likely to exhibit enhancer activity. CEBPB-bound sites further maintained substantial cell-type specificity, indicating that local DNA sequence can accurately convey cell-type–specific regulatory information. By comparing our CRE-seq results to a comprehensive set of genome annotations, we identified a variety of genomic features that are strong predictors of regulatory element activity and cell-type–specific activity. Collectively, our functional assay results indicate that RNAP2 occupancy can be used as a key genomic marker that can distinguish active from inactive TF bound sites