Index and biological spectrum of human DNase I hypersensitive sites.

DNase I hypersensitive sites (DHSs) are generic markers of regulatory DNA1-5 and contain genetic variations associated with diseases and phenotypic traits6-8. We created high-resolution maps of DHSs from 733 human biosamples encompassing 438 cell and tissue types and states, and integrated these to delineate and numerically index approximately 3.6 million DHSs within the human genome sequence, providing a common coordinate system for regulatory DNA. Here we show that these maps highly resolve the cis-regulatory compartment of the human genome, which encodes unexpectedly diverse cell- and tissue-selective regulatory programs at very high density. These programs can be captured comprehensively by a simple vocabulary that enables the assignment to each DHS of a regulatory barcode that encapsulates its tissue manifestations, and global annotation of protein-coding and non-coding RNA genes in a manner orthogonal to gene expression. Finally, we show that sharply resolved DHSs markedly enhance the genetic association and heritability signals of diseases and traits. Rather than being confined to a small number of distal elements or promoters, we find that genetic signals converge on congruently regulated sets of DHSs that decorate entire gene bodies. Together, our results create a universal, extensible coordinate system and vocabulary for human regulatory DNA marked by DHSs, and provide a new global perspective on the architecture of human gene regulation.

Global reference mapping of human transcription factor footprints.

Combinatorial binding of transcription factors to regulatory DNA underpins gene regulation in all organisms. Genetic variation in regulatory regions has been connected with diseases and diverse phenotypic traits1, but it remains challenging to distinguish variants that affect regulatory function2. Genomic DNase I footprinting enables the quantitative, nucleotide-resolution delineation of sites of transcription factor occupancy within native chromatin3-6. However, only a small fraction of such sites have been precisely resolved on the human genome sequence6. Here, to enable comprehensive mapping of transcription factor footprints, we produced high-density DNase I cleavage maps from 243 human cell and tissue types and states and integrated these data to delineate about 4.5 million compact genomic elements that encode transcription factor occupancy at nucleotide resolution. We map the fine-scale structure within about 1.6 million DNase I-hypersensitive sites and show that the overwhelming majority are populated by well-spaced sites of single transcription factor-DNA interaction. Cell-context-dependent cis-regulation is chiefly executed by wholesale modulation of accessibility at regulatory DNA rather than by differential transcription factor occupancy within accessible elements. We also show that the enrichment of genetic variants associated with diseases or phenotypic traits in regulatory regions1,7 is almost entirely attributable to variants within footprints, and that functional variants that affect transcription factor occupancy are nearly evenly partitioned between loss- and gain-of-function alleles. Unexpectedly, we find increased density of human genetic variation within transcription factor footprints, revealing an unappreciated driver of cis-regulatory evolution. Our results provide a framework for both global and nucleotide-precision analyses of gene regulatory mechanisms and functional genetic variation.

Mesh versus non-mesh for inguinal and femoral hernia repair.

BACKGROUND: This is an update of a Cochrane Review first published in 2001.Hernias are protrusions of all or part of an organ through the body wall that normally contains it. Groin hernias include inguinal (96%) and femoral (4%) hernias, and are often symptomatic with discomfort. They are extremely common, with an estimated lifetime risk in men of 27%. Occasionally they may present as emergencies with complications such as bowel incarceration, obstruction and strangulation. The definitive treatment of all hernias is surgical repair, inguinal hernia repair being one of the most common surgical procedures performed. Mesh (hernioplasty) and the traditional non-mesh repairs (herniorrhaphy) are commonly used, with an increasing preference towards mesh repairs in high-income countries. OBJECTIVES: To evaluate the benefits and harms of different inguinal and femoral hernia repair techniques in adults, specifically comparing closure with mesh versus without mesh. Outcomes include hernia recurrence, complications (including neurovascular or visceral injury, haematoma, seroma, testicular injury, infection, postoperative pain), mortality, duration of operation, postoperative hospital stay and time to return to activities of daily living. SEARCH METHODS: We searched the following databases on 9 May 2018: Cochrane Colorectal Cancer Group Specialized Register, Cochrane Central Register of Controlled Trials (Issue 1), Ovid MEDLINE (from 1950), Ovid Embase (from 1974) and Web of Science (from 1900). Furthermore, we checked the WHO International Clinical Trials Registry Platform (ICTRP) and ClinicalTrials.gov for trials. We applied no language or publication restrictions. We also searched the reference lists of included trials and review articles. SELECTION CRITERIA: We included randomised controlled trials of mesh compared to non-mesh inguinal or femoral hernia repairs in adults over the age of 18 years. DATA COLLECTION AND ANALYSIS: We used standard methodological procedures expected by Cochrane. Where available, we collected information on adverse effects. We presented dichotomous data as risk ratios, and where possible we calculated the number needed to treat for an additional beneficial outcome (NNTB). We presented continuous data as mean difference. Analysis of missing data was based on intention-to-treat principles, and we assessed heterogeneity using an evaluation of clinical and methodological diversity, Chi2 test and I2 statistic. We used GRADE to assess the quality of evidence for each outcome. MAIN RESULTS: We included 25 studies (6293 participants) in this review. All included studies specified inguinal hernias, and two studies reported that femoral hernias were included.Mesh repair probably reduces the risk of hernia recurrence compared to non-mesh repair (21 studies, 5575 participants; RR 0.46, 95% CI 0.26 to 0.80, I2 = 44%, moderate-quality evidence). In absolute numbers, one hernia recurrence was prevented for every 46 mesh repairs compared with non-mesh repairs. Twenty-four studies (6293 participants) assessed a wide range of complications with varying follow-up times. Neurovascular and visceral injuries were more common in non-mesh repair groups (RR 0.61, 95% CI 0.49 to 0.76, I2 = 0%, NNTB = 22, high-quality evidence). Wound infection was found slightly more commonly in the mesh group (20 studies, 4540 participants; RR 1.29, 95% CI 0.89 to 1.86, I2 = 0%, NNTB = 200, low-quality evidence). Mesh repair reduced the risk of haematoma compared to non-mesh repair (15 studies, 3773 participants; RR 0.88, 95% CI 0.68 to 1.13, I2 = 0%, NNTB = 143, low-quality evidence). Seromas probably occur more frequently with mesh repair than with non-mesh repair (14 studies, 2640 participants; RR 1.63, 95% CI 1.03 to 2.59, I2 = 0%, NNTB = 72, moderate-quality evidence), as does wound swelling (two studies, 388 participants; RR 4.56, 95% CI 1.02 to 20.48, I2 = 33%, NNTB = 72, moderate-quality evidence). The comparative effect on wound dehiscence is uncertain due to wide confidence intervals (two studies, 329 participants; RR 0.55, 95% CI 0.12 to 2.48, I2 = 37% NNTB = 77, low-quality evidence). Testicular complications showed nearly equivocal results; they probably occurred slightly more often in the mesh group however the confidence interval around the effect was wide (14 studies, 3741 participants; RR 1.06, 95% CI 0.63 to 1.76, I2 = 0%, NNTB = 2000, low-quality evidence). Mesh reduced the risk of postoperative urinary retention compared to non-mesh (eight studies, 1539 participants; RR 0.53, 95% CI 0.38 to 0.73, I2 = 56%, NNTB = 16, moderate-quality evidence).Postoperative and chronic pain could not be compared due to variations in measurement methods and follow-up time (low-quality evidence).No deaths occurred during the follow-up periods reported in the seven studies (2546 participants) reporting this outcome (high-quality evidence).The average operating time was longer for non-mesh repairs by a mean of 4 minutes 22 seconds, despite wide variation across the studies regarding size and direction of effect, thus this result is uncertain (20 studies, 4148 participants; 95% CI -6.85 to -1.60, I2= 97%, very low-quality evidence). Hospital stay may be shorter with mesh repair, by 0.6 days (12 studies, 2966 participants; 95% CI -0.86 to -0.34, I2 = 98%, low-quality evidence), and participants undergoing mesh repairs may return to normal activities of daily living a mean of 2.87 days sooner than those with non-mesh repair (10 studies, 3183 participants; 95% CI -4.42 to -1.32, I2 = 96%, low-quality evidence), although the results of both these outcomes are also limited by wide variation in the size and direction of effect across the studies. AUTHORS' CONCLUSIONS: Mesh and non-mesh repairs are effective surgical approaches in treating hernias, each demonstrating benefits in different areas. Compared to non-mesh repairs, mesh repairs probably reduce the rate of hernia recurrence, and reduce visceral or neurovascular injuries, making mesh repair a common repair approach. Mesh repairs may result in a reduced length of hospital stay and time to return to activities of daily living, but these results are uncertain due to variation in the results of the studies. Non-mesh repair is less likely to cause seroma formation and has been favoured in low-income countries due to low cost and reduced availability of mesh materials. Risk of bias in the included studies was low to moderate and generally handled well by study authors, with attention to details of allocation, blinding, attrition and reporting.

Mitral valve surgery and coronary artery bypass grafting for moderate-to-severe ischemic mitral regurgitation: Meta-analysis of clinical and echocardiographic outcomes.

OBJECTIVE: This meta-analysis was conducted to compare clinical and echocardiographic outcomes following isolated coronary artery bypass grafting (CABG) versus CABG and mitral valve (MV) surgery in patients with moderate-to-severe ischemic mitral regurgitation (IMR). METHODS: Seven databases were systematically searched to identify relevant studies. For eligibility, studies were required to report on the primary endpoint of perioperative or late mortality. Data were analyzed according to predefined clinical endpoints. RESULTS: Four randomized controlled trials (RCTs) (n = 505) and 15 observational studies (OS) (n = 3785) met the criteria for inclusion. Compared with isolated CABG, concomitant CABG and MV surgery was not associated with increased perioperative mortality (RCTs: relative risk [RR] 0.89, 95% confidence interval [CI], 0.26-3.02; OS: RR 1.40, 95% CI, 0.88-2.23). CABG and MV surgery was associated with significantly lower incidence of moderate-to-severe MR at follow-up (RCTs: RR 0.16, 95% CI, 0.04-0.75; OS: RR 0.20, 95% CI, 0.09-0.48). Late mortality was similar between the surgical approaches in RCTs (hazard ratio [HR] 1.20, 95% CI, 0.57-2.53) and OS (HR 0.99, 95% CI, 0.81-1.21). There were no significant differences in echocardiographic outcomes. These results remained consistent in subgroup analyses restricted to patients with strictly moderate IMR. CONCLUSIONS: In patients with moderate-to-severe IMR, the addition of MV surgery to CABG was not associated with increased perioperative mortality. Although concomitant MV surgery reduced recurrence of moderate-to-severe MR at follow-up, this was not associated with a reduction in late mortality. Larger trials with longer follow-up duration are required to further assess long-term survival and freedom from reintervention.

A systematic review and meta-analysis of multidetector computed tomography in the assessment of coronary artery bypass grafts.

PURPOSE: The present meta-analysis aimed to compare the diagnostic accuracy of more recent computed tomography coronary angiography (CTCA) with invasive coronary angiography (ICA) in the assessment of graft patency after coronary artery bypass graft surgery (CABG). MATERIAL AND METHODS: A systematic review was performed using nine electronic databases from their dates of inception to July 2015. Predefined inclusion criteria included studies reporting on comparative outcomes using ≥64 slice multidetector computed tomography (MDCT) and ICA. The primary endpoints included graft occlusion and significant graft stenosis ≥50%. Secondary analyses included the comparison of arterial versus venous graft conduits, and the use of different MDCT techniques. RESULTS: Thirty-one studies were identified according to selection criteria, involving 1975 patients with 5364 assessed grafts. Combined assessment of stenosis and occlusion for all grafts demonstrated a sensitivity of 96.1% [95% confidence interval (CI) 94.3-97.4%] and specificity of 96.3% (95% CI 95.1-97.3%). CTCA assessment of venous grafts demonstrated higher sensitivity compared to arterial grafts, when testing for both occlusion and stenosis (97.6% vs 89.2%, p=0.004). CONCLUSION: Results of this study demonstrated that CTCA had a relatively high pooled sensitivity, specificity and negative predictive value compared to ICA. However, patient baseline characteristics varied between studies, and the results should be interpreted with caution. Nonetheless, our results indicate that CTCA should be recognized as an accurate and non-invasive investigation for graft patency in symptomatic patients after CABG.

A meta-analysis of mitral valve repair versus replacement for ischemic mitral regurgitation.

BACKGROUND: The development of ischemic mitral regurgitation (IMR) portends a poor prognosis and is associated with adverse long-term outcomes. Although both mitral valve repair (MVr) and mitral valve replacement (MVR) have been performed in the surgical management of IMR, there remains uncertainty regarding the optimal approach. The aim of the present study was to meta-analyze these two procedures, with mortality as the primary endpoint. METHODS: Seven databases were systematically searched for studies reporting peri-operative or late mortality following MVr and MVR for IMR. Data were independently extracted by two reviewers and meta-analyzed according to pre-defined study selection criteria and clinical endpoints. RESULTS: Overall, 22 observational studies (n=3,815 patients) and one randomized controlled trial (n=251) were included. Meta-analysis demonstrated significantly reduced peri-operative mortality [relative risk (RR) 0.61; 95% confidence intervals (CI), 0.47-0.77; I(2)=0%; P<0.001] and late mortality (RR, 0.78; 95% CI, 0.67-0.92; I(2)=0%; P=0.002) following MVr. This finding was more pronounced in studies with longer follow-up beyond 3 years. At latest follow-up, recurrence of at least moderate mitral regurgitation (MR) was higher following MVr (RR, 5.21; 95% CI, 2.66-10.22; I(2)=46%; P<0.001) but the incidence of mitral valve re-operations were similar. CONCLUSIONS: In the present meta-analysis, MVr was associated with reduced peri-operative and late mortality compared to MVR, despite an increased recurrence of at least moderate MR at follow-up. However, these findings must be considered within the context of the differing patient characteristics that may affect allocation to MVr or MVR. Larger prospective studies are warranted to further compare long-term survival and freedom from re-intervention.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

The basic body plan and major physiological axes have been highly conserved during mammalian evolution, yet only a small fraction of the human genome sequence appears to be subject to evolutionary constraint. To quantify cis- versus trans-acting contributions to mammalian regulatory evolution, we performed genomic DNase I footprinting of the mouse genome across 25 cell and tissue types, collectively defining ∼8.6 million transcription factor (TF) occupancy sites at nucleotide resolution. Here we show that mouse TF footprints conjointly encode a regulatory lexicon that is ∼95% similar with that derived from human TF footprints. However, only ∼20% of mouse TF footprints have human orthologues. Despite substantial turnover of the cis-regulatory landscape, nearly half of all pairwise regulatory interactions connecting mouse TF genes have been maintained in orthologous human cell types through evolutionary innovation of TF recognition sequences. Furthermore, the higher-level organization of mouse TF-to-TF connections into cellular network architectures is nearly identical with human. Our results indicate that evolutionary selection on mammalian gene regulation is targeted chiefly at the level of trans-regulatory circuitry, enabling and potentiating cis-regulatory plasticity.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

To study the evolutionary dynamics of regulatory DNA, we mapped >1.3 million deoxyribonuclease I-hypersensitive sites (DHSs) in 45 mouse cell and tissue types, and systematically compared these with human DHS maps from orthologous compartments. We found that the mouse and human genomes have undergone extensive cis-regulatory rewiring that combines branch-specific evolutionary innovation and loss with widespread repurposing of conserved DHSs to alternative cell fates, and that this process is mediated by turnover of transcription factor (TF) recognition elements. Despite pervasive evolutionary remodeling of the location and content of individual cis-regulatory regions, within orthologous mouse and human cell types the global fraction of regulatory DNA bases encoding recognition sites for each TF has been strictly conserved. Our findings provide new insights into the evolutionary forces shaping mammalian regulatory DNA landscapes.

The accessible chromatin landscape of the human genome.

DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned the discovery of all classes of cis-regulatory elements including enhancers, promoters, insulators, silencers and locus control regions. Here we present the first extensive map of human DHSs identified through genome-wide profiling in 125 diverse cell and tissue types. We identify ∼2.9 million DHSs that encompass virtually all known experimentally validated cis-regulatory sequences and expose a vast trove of novel elements, most with highly cell-selective regulation. Annotating these elements using ENCODE data reveals novel relationships between chromatin accessibility, transcription, DNA methylation and regulatory factor occupancy patterns. We connect ∼580,000 distal DHSs with their target promoters, revealing systematic pairing of different classes of distal DHSs and specific promoter types. Patterning of chromatin accessibility at many regulatory regions is organized with dozens to hundreds of co-activated elements, and the transcellular DNase I sensitivity pattern at a given region can predict cell-type-specific functional behaviours. The DHS landscape shows signatures of recent functional evolutionary constraint. However, the DHS compartment in pluripotent and immortalized cells exhibits higher mutation rates than that in highly differentiated cells, exposing an unexpected link between chromatin accessibility, proliferative potential and patterns of human variation.

An expansive human regulatory lexicon encoded in transcription factor footprints.

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting across 41 diverse cell and tissue types, we detected 45 million transcription factor occupancy events within regulatory regions, representing differential binding to 8.4 million distinct short sequence elements. Here we show that this small genomic sequence compartment, roughly twice the size of the exome, encodes an expansive repertoire of conserved recognition sequences for DNA-binding proteins that nearly doubles the size of the human cis-regulatory lexicon. We find that genetic variants affecting allelic chromatin states are concentrated in footprints, and that these elements are preferentially sheltered from DNA methylation. High-resolution DNase I cleavage patterns mirror nucleotide-level evolutionary conservation and track the crystallographic topography of protein-DNA interfaces, indicating that transcription factor structure has been evolutionarily imprinted on the human genome sequence. We identify a stereotyped 50-base-pair footprint that precisely defines the site of transcript origination within thousands of human promoters. Finally, we describe a large collection of novel regulatory factor recognition motifs that are highly conserved in both sequence and function, and exhibit cell-selective occupancy patterns that closely parallel major regulators of development, differentiation and pluripotency.