Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Deciphering the impact of genetic variants on gene regulation is fundamental to understanding human disease. Although gene regulation often involves long-range interactions, it is unknown to what extent non-coding genetic variants influence distal molecular phenotypes. Here, we integrate chromatin profiling for three histone marks in lymphoblastoid cell lines (LCLs) from 75 sequenced individuals with LCL-specific Hi-C and ChIA-PET-based chromatin contact maps to uncover one of the largest collections of local and distal histone quantitative trait loci (hQTLs). Distal QTLs are enriched within topologically associated domains and exhibit largely concordant variation of chromatin state coordinated by proximal and distal non-coding genetic variants. Histone QTLs are enriched for common variants associated with autoimmune diseases and enable identification of putative target genes of disease-associated variants from genome-wide association studies. These analyses provide insights into how genetic variation can affect human disease phenotypes by coordinated changes in chromatin at interacting regulatory elements.

A personalized decision aid for prostate cancer shared decision making.

BACKGROUND: A shared decision-making model is preferred for engaging prostate cancer patients in treatment decisions. However, the process of assessing an individual's preferences and values is challenging and not formalized. The purpose of this study is to develop an automated decision aid for patient-centric treatment decision-making using decision analysis, preference thresholds and value elicitations to maximize the compatibility between a patient's treatment expectations and outcome. METHODS: A template for patient-centric medical decision-making was constructed. The inputs included prostate cancer risk group, pre-treatment health state, treatment alternatives (primarily focused on radiation in this model), side effects (erectile dysfunction, urinary incontinence, nocturia and bowel incontinence), and treatment success (5-year freedom from biochemical failure). A linear additive value function was used to combine the values for each attribute (side effects, success and the alternatives) into a value for all prospects. The patient-reported toxicity probabilities were derived from phase II and III trials. The probabilities are conditioned on the starting state for each of the side effects. Toxicity matrices for erectile dysfunction, urinary incontinence, nocturia and bowel incontinence were created for the treatment alternatives. Toxicity probability thresholds were obtained by identifying the patient's maximum acceptable threshold for each of the side effects. Results are represented as a visual. R and Rstudio were used to perform analyses, and R Shiny for application creation. RESULTS: We developed a web-based decision aid. Based on preliminary use of the application, every treatment alternative could be the best choice for a decision maker with a particular set of preferences. This result implies that no treatment has determinist dominance over the remaining treatments and that a preference-based approach can help patients through their decision-making process, potentially affecting compliance with treatment, tolerance of side effects and satisfaction with the decision. CONCLUSIONS: We present a unique patient-centric prostate cancer treatment decision aid that systematically assesses and incorporates a patient's preferences and values to rank treatment options by likelihood of achieving the preferred outcome. This application enables the practice and study of personalized medicine. This model can be expanded to include additional inputs, such as genomics, as well as competing, concurrent or sequential therapies.

Genome-wide map of regulatory interactions in the human genome.

Increasing evidence suggests that interactions between regulatory genomic elements play an important role in regulating gene expression. We generated a genome-wide interaction map of regulatory elements in human cells (ENCODE tier 1 cells, K562, GM12878) using Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) experiments targeting six broadly distributed factors. Bound regions covered 80% of DNase I hypersensitive sites including 99.7% of TSS and 98% of enhancers. Correlating this map with ChIP-seq and RNA-seq data sets revealed cohesin, CTCF, and ZNF143 as key components of three-dimensional chromatin structure and revealed how the distal chromatin state affects gene transcription. Comparison of interactions between cell types revealed that enhancer-promoter interactions were highly cell-type-specific. Construction and comparison of distal and proximal regulatory networks revealed stark differences in structure and biological function. Proximal binding events are enriched at genes with housekeeping functions, while distal binding events interact with genes involved in dynamic biological processes including response to stimulus. This study reveals new mechanistic and functional insights into regulatory region organization in the nucleus.

Mango: a bias-correcting ChIA-PET analysis pipeline.

MOTIVATION: Chromatin Interaction Analysis by Paired-End Tag sequencing (ChIA-PET) is an established method for detecting genome-wide looping interactions at high resolution. Current ChIA-PET analysis software packages either fail to correct for non-specific interactions due to genomic proximity or only address a fraction of the steps required for data processing. We present Mango, a complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity. RESULTS: Comparison to the existing software packages, ChIA-PET Tool and ChiaSig revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly, Mango executes all steps required for processing ChIA-PET datasets, whereas ChiaSig only completes 20% of the required steps. Application of Mango to multiple available ChIA-PET datasets permitted the independent rediscovery of known trends in chromatin loops including enrichment of CTCF, RAD21, SMC3 and ZNF143 at the anchor regions of interactions and strong bias for convergent CTCF motifs. AVAILABILITY AND IMPLEMENTATION: Mango is open source and distributed through github at https://github.com/dphansti/mango. CONTACT: mpsnyder@standford.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Dentists' familiarity with tobacco cessation programs in dental settings in Iran.

OBJECTIVES: The current study assessed Iranian dentists' practice, knowledge, perceived barriers, and attitudes toward helping patients to quit. We hypothesized that Iranian dentists would have limited knowledge and awareness of tobacco cessation methods or of their important role in encouraging patients to quit. We expected the combination of quantitative and qualitative research to yield important insights regarding effective methods of engaging Iranian dentists in tobacco intervention. METHODS: From a list of registered dentists following an initial screening, we randomly selected a total of 1,000 dental practices in 10 randomly selected provinces. Following an initial letter describing the study, we mailed a questionnaire. For the qualitative part of the study, we used a convenience purposeful sampling of 16 dentists. RESULTS: Despite repeated contacts, only 35 percent of those contacted returned completed surveys. Key findings not only included generally positive attitudes toward tobacco cessation programs, but also identification of major barriers including concerns about patient resistance, lack of supportive organization, and opportunities for training. Dentists were far more likely to ask patients about smoking than to provide actual cessation support. Female dentists were more likely to ask patients. The qualitative interviews shed further light on barriers to intervention. CONCLUSIONS: Interpretation of the findings is limited by the relatively low response rate. However, despite identified barriers to intervention, we are encouraged by dentists' overall knowledge and interest in tobacco cessation services. We plan to use the current findings to inform development of continuing education programs and incorporation of tobacco cessation counseling into dental school curricula in Iran.

Molecular phylogeny and biogeography of the genus Acanthodactylus Fitzinger, 1834 (Reptilia: Lacertidae) in Iran, inferred from mtDNA Sequences.

Phylogenetic relationships of Iranian Acanthodactylus species were investigated using 1407 bp of mitochondrial DNA including 606 bp of cytochrome b and 801 bp of NADH dehydrogenase subunit 4 (ND4). Analyses done with maximum parsimony, maximum-likelihood, and Bayesian inference included 67 specimens from 27 geographically distinct localities in Iran. Our molecular results proposed three clear and geographically isolated clades by their phylogenetic positions and genetic differences. These three major clades are: (1) A. micropholis+ A. grandis+ A. khamirensis; (2) A. blanfordi+ A. schmidti+ Acanthodactylus sp1; (3) A. nilsoni+ A. boskianus + Acanthodactylus sp2. The phylogenetic analyses of the genus did not group A. grandis with the remaining species of the A. boskianus group and clustered it along with A. khamirensis within the A. micropholis group. In addition, phylogenetic results revealed a monophyletic status for A. schmidti and A. micropholis groups. Molecular clock approach indicated that the most recent divergence event splits A. micropholis from A. khamirensis about 2 MYA and results of dispersal-vicariance analyses showed that this diversification occurred by dispersal event rather than vicariance. Results of Reconstruct Ancestral State in Phylogenies (RASP) showed that Most Recent Common Ancestor (MRCA) of A. micropholis, A. blanfordi and A. sp1 originated in eastern Iran. The first diversification of the genus in Iran most likely occurred between 8.5-9 MYA corresponding with the hypothesis that the genus has entered Iran long after the complete uplifting of the Zagros Mts. (10-12 MYA) which limited its dispersal only to the Persian Gulf shores and western slopes of the Zagros Mts.

Apoptotic pathway induced by noscapine in human myelogenous leukemic cells.

It has been shown that noscapine, an opium-derived phthalideisoquinoline alkaloid that is currently being used as an oral antitussive drug, induces apoptosis in myeloid leukemia cells. The molecular mechanism responsible for the anticancer effects of noscapine is poorly understood. In the current study, the apoptotic effects of noscapine on two myeloid cell lines, apoptosis-proficient HL60 cells and apoptosis-resistant K562 cells, were analyzed. An increase in the activity of caspase-2, -3, -6, -8 and -9, poly(ADP ribose) polymerase cleavage, detection of phosphatidylserine on the outer layer of the cell membrane, nucleation of chromatin, and DNA fragmentation suggested the induction of apoptosis. Noscapine increased the Bax/Bcl-2 ratio with a significant decrease of Bcl-2 expression accompanied with Bcl-2 phosphorylation. Using an inhibitory approach, the activation of the caspase cascade involved in the noscapine-induced apoptosis was analyzed. We observed no inhibitory effect of the caspase-8 inhibitor on caspase-9 activity. In view of these results and taking into consideration that K562 cells are Fas-null, we suggested that caspase-8 is activated in a Fas-independent manner downstream of caspase-9. In conclusion, noscapine can induce apoptosis in both apoptosis-proficient and apoptosis-resistant leukemic cells, and it can be a novel candidate in the treatment of hematological malignancies.