Defining a Registry of Candidate Regulatory Elements to Interpret Disease Associated Genetic Variation

Over the last decade there has been a great effort to annotate noncoding regions of the genome, particularly those that regulate gene expression. These regulatory elements contain binding sites for transcription factors (TF), which interact with one another and transcriptional machinery to initiate, enhance, or repress gene expression. The Encyclopedia of DNA Elements (ENCODE) consortium has generated thousands of epigenomic datasets, such as DNase-seq and ChIP-seq experiments, with the goal of defining such regions. By integrating these assays, we developed the Registry of candidate Regulatory Elements (cREs), a collection of putative regulatory regions across human and mouse. In total, we identified over 1.3M human and 400k mouse cREs each annotated with cell-type specific signatures (e.g. promoter-like, enhancer-like) in over 400 human and 100 mouse biosamples. We then demonstrated the biological utility of these regions by analyzing cell type enrichments for genetic variants reported by genome wide association studies (GWAS). To search and visualize these cREs, we developed the online database SCREEN (search candidate regulatory elements by ENCODE). After defining cREs, we next sought to determine their potential gene targets. To compare target gene prediction methods, we developed a comprehensive benchmark of enhancer-gene links by curating ChIA-PET, Hi-C and eQTL datasets. We then used this benchmark to evaluate unsupervised linking approaches such as the correlation of epigenomic signal. We determined that these methods have low overall performance and do not outperform simply selecting the closest gene. We then developed a supervised Random Forest model which had notably better performance than unsupervised methods. We demonstrated that this model can be applied across cell types and can be used to predict target genes for GWAS associated variants. Finally, we used the registry of cREs to annotate variants associated with psychiatric disorders. We found that these psych SNPs are enriched in cREs active in brain tissue and likely target genes involved in neural development pathways. We also demonstrated that psych SNPs overlap binding sites for TFs involved in neural and immune pathways. Finally, by identifying psych SNPs with allele imbalance in chromatin accessibility, we highlighted specific cases of psych SNPs altering TF binding motifs resulting in the disruption of TF binding. Overall, we demonstrated our collection of putative regulatory regions, the Registry of cREs, can be used to understand the potential biological function of noncoding variation and develop hypotheses for future testing

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression(1). The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community

Syndemics and the PrEP Cascade: Results from a Sample of Young Latino Men Who Have Sex with Men.

Young Latino men who have sex with men (MSM) are a highly vulnerable population for HIV infection. Pre-exposure prophylaxis (PrEP) is a novel biomedical HIV prevention tool that may aid in reducing the disparity in HIV incidence among Latino MSM. However, PrEP use is disproportionally low among Latino MSM and, therefore, identifying barriers along the PrEP continuum of care (the "PrEP cascade") would provide insight into how to best deploy PrEP interventions. Syndemics theory is a prominent framework employed in HIV prevention; however, to date, no known studies have applied this theory to PrEP. Thus, the aim of the current study was to explore the association between syndemics and the PrEP cascade, including the degree to which psychosocial and structural syndemic constructs are related to the PrEP cascade. Participants were 151 young Latino MSM (M age = 24 years; SD = 3) residing in San Diego, California, who completed a battery of online self-report measures. Results indicated high levels of syndemic indicators and varying levels of engagement across the PrEP cascade. As syndemic indicators increased, the odds of engagement across the PrEP cascade were significantly lowered. Psychosocial and structural syndemic factors accounted for unique variance in the PrEP cascade. Results highlight the need for combination interventions that address both psychosocial and structural barriers to PrEP use and persistence among young Latino MSM

Factorbook: an Updated Catalog of Transcription Factor Motifs and Candidate Regulatory Motif Sites [preprint]

The human genome contains roughly 1,600 transcription factors (TFs) (1), DNA-binding proteins recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX (2), and in vivo, using techniques including ChIP-seq (3, 4). We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog derived from thousands of ENCODE Phase II and III ChIP-seq experiments and HT-SELEX experiments; this motif catalog is integrated with the ENCODE registry of candidate cis-regulatory elements to annotate a comprehensive collection of genome-wide candidate TF binding sites. The database also offers novel tools for applying the motif models within machine learning frameworks and using these models for integrative analysis, including annotation of variants and disease and trait heritability. We will continue to expand the resource as ENCODE Phase IV data are released

TCR hypervariable regions expressed by T cells that respond to effective tumor vaccines

A major goal of immunotherapy for cancer is the activation of T cell responses against tumor-associated antigens (TAAs). One important strategy for improving antitumor immunity is vaccination with peptide variants of TAAs. Understanding the mechanisms underlying the expansion of T cells that respond to the native tumor antigen is an important step in developing effective peptide-variant vaccines. Using an immunogenic mouse colon cancer model, we compare the binding properties and the TCR genes expressed by T cells elicited by peptide variants that elicit variable antitumor immunity directly ex vivo. The steady-state affinity of the natural tumor antigen for the T cells responding to effective peptide vaccines was higher relative to ineffective peptides, consistent with their improved function. Ex vivo analysis showed that T cells responding to the effective peptides expressed a CDR3β motif, which was also shared by T cells responding to the natural antigen and not those responding to the less effective peptide vaccines. Importantly, these data demonstrate that peptide vaccines can expand T cells that naturally respond to tumor antigens, resulting in more effective antitumor immunity. Future immunotherapies may require similar stringent analysis of the responding T cells to select optimal peptides as vaccine candidates. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00262-012-1217-5) contains supplementary material, which is available to authorized users

Predictors of Depression Among Older African American Cancer Patients

Depression is becoming an increasing concern in cancer patients because of its impact on quality of life. Although risk factors of having depression have been examined in the literature, there has been no research examining these factors in older African American cancer patients

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers

Enhancers are distal cis-regulatory elements that modulate gene expression. They are depleted of nucleosomes and enriched in specific histone modifications; thus, calling DNase-seq and histone mark ChIP-seq peaks can predict enhancers. We evaluated nine peak-calling algorithms for predicting enhancers validated by transgenic mouse assays. DNase and H3K27ac peaks were consistently more predictive than H3K4me1/2/3 and H3K9ac peaks. DFilter and Hotspot2 were the best DNase peak callers, while HOMER, MUSIC, MACS2, DFilter and F-seq were the best H3K27ac peak callers. We observed that the differential DNase or H3K27ac signals between two distant tissues increased the area under the precision-recall curve (PR-AUC) of DNase peaks by 17.5-166.7% and that of H3K27ac peaks by 7.1-22.2%. We further improved this differential signal method using multiple contrast tissues. Evaluated using a blind test, the differential H3K27ac signal method substantially improved PR-AUC from 0.48 to 0.75 for predicting heart enhancers. We further validated our approach using postnatal retina and cerebral cortex enhancers identified by massively parallel reporter assays, and observed improvements for both tissues. In summary, we compared nine peak callers and devised a superior method for predicting tissue-specific mouse developmental enhancers by reranking the called peaks

Perceptions of Support Among Older African American Cancer Survivors

To explore the perceived social support needs among older adult African American cancer survivors

The Lantern Vol. 54, No. 2, Spring 1988

• Burning the Christmas Guests • A Song in Time • I Ask a Question • As If Raggedy Anne • One Man\u27s Escape • Gypsy Caravan • Apartment 14B • The College Inferno • Somewhere Under Manhattan • Trumped • Sunday • In Quest of Creativity • Imperfect Healing • The Game • The Hunger • Peanuts on the Beach • Battlefield Prom • Confessions of the Untrained Eye • Animal Attraction • Street Lamps • Hey, Old Man • In Search of Self-Actualization • Cousin Joe Bob\u27s First Visit to Pulsationshttps://digitalcommons.ursinus.edu/lantern/1132/thumbnail.jp

Preclinical Safety, Tolerability, Pharmacokinetics, Pharmacodynamics, and Antifungal Activity of Liposomal Amphotericin B

The improved safety profile and antifungal efficacy of liposomal amphotericin B (LAmB) compared to conventional amphotericin B deoxycholate (DAmB) is due to several factors including, its chemical composition, rigorous manufacturing standards, and ability to target and transit through the fungal cell wall. Numerous preclinical studies have shown that LAmB administered intravenously distributes to tissues frequently infected by fungi at levels above the minimum inhibitory concentration (MIC) for many fungi. These concentrations can be maintained from one day to a few weeks, depending upon the tissue. Tissue accumulation is dose-dependent with drug clearance occurring most rapidly from the brain and slowest from the liver and spleen. LAmB localizes in lung epithelial lining fluid, within liver and splenic macrophages and in kidney distal tubules. LAmB has been used successfully in therapeutic and prophylactic animal models to treat many different fungal pathogens, significantly increasin