Methods for Joint Normalization and Comparison of Hi-C data

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing individual Hi-C datasets, but little work has been done on developing joint normalization methods for comparing two or more Hi-C datasets. To make full use of Hi-C data, joint normalization and statistical comparison techniques are needed to carry out experiments to identify regions where chromatin structure differs between conditions. We develop methods for the joint normalization and comparison of two Hi-C datasets, which we then extended to more complex experimental designs. Our normalization method is novel in that it makes use of the distance-dependent nature of chromatin interactions. Our modification of the Minus vs. Average (MA) plot to the Minus vs. Distance (MD) plot allows for a nonparametric data-driven normalization technique using loess smoothing. Additionally, we present a simple statistical method using Z-scores for detecting differentially interacting regions between two datasets. Our initial method was published as the Bioconductor R package HiCcompare [http://bioconductor.org/packages/HiCcompare/](http://bioconductor.org/packages/HiCcompare/). We then further extended our normalization and comparison method for use in complex Hi-C experiments with more than two datasets and optional covariates. We extended the normalization method to jointly normalize any number of Hi-C datasets by using a cyclic loess procedure on the MD plot. The cyclic loess normalization technique can remove between dataset biases efficiently and effectively even when several datasets are analyzed at one time. Our comparison method implements a generalized linear model-based approach for comparing complex Hi-C experiments, which may have more than two groups and additional covariates. The extended methods are also available as a Bioconductor R package [http://bioconductor.org/packages/multiHiCcompare/](http://bioconductor.org/packages/multiHiCcompare/). Finally, we demonstrate the use of HiCcompare and multiHiCcompare in several test cases on real data in addition to comparing them to other similar methods (https://doi.org/10.1002/cpbi.76)

Hip contact forces in asymptomatic total hip replacement patients differ from normal healthy individuals: implications for preclinical testing

BACKGROUND Preclinical durability testing of hip replacement implants is standardised by ISO-14242-1 (2002) which is based on historical inverse dynamics analysis using data obtained from a small sample of normal healthy individuals. It has not been established whether loading cycles derived from normal healthy individuals are representative of loading cycles occurring in patients following total hip replacement. METHODS Hip joint kinematics and hip contact forces derived from multibody modelling of forces during normal walking were obtained for 15 asymptomatic total hip replacement patients and compared to 38 normal healthy individuals and to the ISO standard for pre-clinical testing. FINDINGS Hip kinematics in the total hip replacement patients were comparable to the ISO data and the hip contact force in the normal healthy group was also comparable to the ISO cycles. Hip contact forces derived from the asymptomatic total hip replacement patients were comparable for the first part of the stance period but exhibited 30% lower peak loads at toe-off. INTERPRETATION Although the ISO standard provides a representative kinematic cycle, the findings call into question whether the hip joint contact forces in the ISO standard are representative of those occurring in the joint following total hip replacement

Relapse after withdrawal from anti-TNF therapy for inflammatory bowel disease: an observational study, plus systematic review and meta-analysis.

Infliximab and adalimumab have established roles in inflammatory bowel disease (IBD) therapy. UK regulators mandate reassessment after 12 months' anti-TNF therapy for IBD, with consideration of treatment withdrawal. There is a need for more data to establish the relapse rates following treatment cessation.This article is freely available via Open Access. Click on the 'Additional Link' above to access the full-text from the publisher's site.Publishe

International genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.

Primary biliary cirrhosis (PBC) is a classical autoimmune liver disease for which effective immunomodulatory therapy is lacking. Here we perform meta-analyses of discovery data sets from genome-wide association studies of European subjects (n=2,764 cases and 10,475 controls) followed by validation genotyping in an independent cohort (n=3,716 cases and 4,261 controls). We discover and validate six previously unknown risk loci for PBC (Pcombined<5 × 10(-8)) and used pathway analysis to identify JAK-STAT/IL12/IL27 signalling and cytokine-cytokine pathways, for which relevant therapies exist

Firearm availability and police shootings of citizens: a city level analysis of fatal and injurious shootings in California and Florida

Abstract Background A growing body of research has found a link between firearm availability and police shootings of citizens across place. The problem, however, is that the previous studies on the topic tend to suffer from several limitations: a near exclusive focus on citizen fatalities, units of analysis at the state or county levels, and a variety of proxy measures tapping into community-level firearm access. The current study set out to address these issues by examining the relationship between different forms of firearm availability and both fatal and nonfatal injurious police shootings of citizens at the city level. Methods More specifically, it merged The Trace’s “Missing Pieces” measures of guns reported lost and stolen to police as well as licensed firearms dealers across jurisdictions from the Bureau of Alcohol, Tobacco, Firearms, and Explosives as proxies for firearm availability with data on police shootings of citizens in California and Florida from California’s URSUS system and the Tampa Bay Times’ “Why Cops Shoot” database, respectively. Negative binomial regression analyses were performed on a sample of 253 cities across the two states and a sub-sample of cities with licensed firearms dealers. Results Findings uncovered a small positive association between rates of federally licensed guns stores and the number citizens shot by police as well as police shooting incidents while controlling for several community-level measures (e.g., concentrated disadvantage, gun homicide rates). Rates of guns lost or reported stolen were generally not significantly associated with the outcome measures in the multivariate models. Conclusions Firearm availability is a significant correlate of police shootings. Pooled counts of both citizens shot by police and police shooting incidents are heightened in jurisdictions with higher rates of licensed gun dealers, which may be due to the fact that all firearms sold in the USA first make their way to the public through these mechanisms. Such licensed gun dealers must be appropriately monitored and audited to reduce illicit behavior and prevent firearms from making their way into secondary markets. Addressing access to firearms can be meaningful for a host of gun-related morbidity and mortality outcomes, including police shootings of citizens

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

Abstract Background Changes in spatial chromatin interactions are now emerging as a unifying mechanism orchestrating the regulation of gene expression. Hi-C sequencing technology allows insight into chromatin interactions on a genome-wide scale. However, Hi-C data contains many DNA sequence- and technology-driven biases. These biases prevent effective comparison of chromatin interactions aimed at identifying genomic regions differentially interacting between, e.g., disease-normal states or different cell types. Several methods have been developed for normalizing individual Hi-C datasets. However, they fail to account for biases between two or more Hi-C datasets, hindering comparative analysis of chromatin interactions. Results We developed a simple and effective method, HiCcompare, for the joint normalization and differential analysis of multiple Hi-C datasets. The method introduces a distance-centric analysis and visualization of the differences between two Hi-C datasets on a single plot that allows for a data-driven normalization of biases using locally weighted linear regression (loess). HiCcompare outperforms methods for normalizing individual Hi-C datasets and methods for differential analysis (diffHiC, FIND) in detecting a priori known chromatin interaction differences while preserving the detection of genomic structures, such as A/B compartments. Conclusions HiCcompare is able to remove between-dataset bias present in Hi-C matrices. It also provides a user-friendly tool to allow the scientific community to perform direct comparisons between the growing number of pre-processed Hi-C datasets available at online repositories. HiCcompare is freely available as a Bioconductor R package https://bioconductor.org/packages/HiCcompare/

Proteomic analysis of enriched microsomal fractions from GS-NS0 murine myeloma cells with varying secreted recombinant monoclonal antibody productivities

The folding, transport and modification of recombinant proteins in the constitutive secretory pathway of eukaryotic cell expression systems are reported to be a bottleneck in their production. We have utilised a proteomic approach to investigate the processes catalysed by proteins constituting the secretory pathway to further our understanding of those processes involved in high-level antibody secretion. We used GS-NS0 cell populations differing in qmAb to prepare enriched microsome fractions from each cell population at mid-exponential growth phase. These were analysed by 2-D PAGE to characterise the microsome protein component and test the hypothesis that bottlenecks in recombinant protein synthesis exist in these compartments, which are alleviated in high producers by the up-regulation of key secretory pathway proteins. Proteins whose abundance changed in a statistically significant manner with increasing qmAb were involved in a range of cellular functions: energy metabolism, mAb folding/assembly, cytoskeletal organisation and protein turnover. Amongst these were BiP and PDI, chaperones resident in the ER that interact with nascent immunoglobulins during their folding/assembly. However, our results suggest that there are diverse mechanisms by which these cells achieve qmAb. The results imply that cell-engineering strategies for improving qmAb should target proteins associated with altered functional phenotype identified in this study

CHAC1 inactivation is effective to preserve muscle glutathione but is insufficient to protect against muscle wasting in cachexia.

Muscle wasting is one of the main characteristics of cachexia associated with cancer and other chronic diseases and is often exacerbated by antineoplastic agents. Increased oxidative stress is associated with muscle wasting, along with depletion of glutathione, the most abundant endogenous antioxidant. Therefore, boosting endogenous glutathione has been proposed as a therapeutic strategy to prevent muscle wasting. Here, we tested this hypothesis by inactivating CHAC1, an intracellular glutathione degradation enzyme. We found CHAC1 expression is increased under multiple muscle wasting conditions in animal models, including fasting, cancer cachexia, and chemotherapy. The elevation of muscle Chac1 expression is associated with reduced glutathione level. CHAC1 inhibition via CRSPR/Cas9 mediated knock-in of an enzyme inactivating mutation demonstrates a novel strategy to preserve muscle glutathione levels under wasting conditions but fails to prevent muscle wasting in mice. These results suggest that preserving intracellular glutathione level alone may not be sufficient to prevent cancer or chemotherapy induced muscle wasting