Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance

BACKGROUND

Monocytes are key mediators of innate immunity to infection, undergoing profound and dynamic changes in epigenetic state and immune function which are broadly protective but may be dysregulated in disease. Here, we aimed to advance understanding of epigenetic regulation following innate immune activation, acutely and in endotoxin tolerant states.

METHODS

We exposed human primary monocytes from healthy donors (n = 6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2 h) and two models of endotoxin tolerance: repeated stimulations (6 + 6 h) and prolonged exposure to endotoxin (24 h). Another subset of monocytes was left untreated (naïve). We identified context-specific regulatory elements based on epigenetic signatures for chromatin accessibility (ATAC-seq) and regulatory non-coding RNAs from total RNA sequencing.

RESULTS

We present an atlas of differential gene expression for endotoxin and interferon response, identifying widespread context specific changes. Across assayed states, only 24-29% of genes showing differential exon usage are also differential at the gene level. Overall, 19.9% (6,884 of 34,616) of repeatedly observed ATAC peaks were differential in at least one condition, the majority upregulated on stimulation and located in distal regions (64.1% vs 45.9% of non-differential peaks) within which sequences were less conserved than non-differential peaks. We identified enhancer-derived RNA signatures specific to different monocyte states that correlated with chromatin accessibility changes. The endotoxin tolerance models showed distinct chromatin accessibility and transcriptomic signatures, with integrated analysis identifying genes and pathways involved in the inflammatory response, detoxification, metabolism and wound healing. We leveraged eQTL mapping for the same monocyte activation states to link potential enhancers with specific genes, identifying 1,946 unique differential ATAC peaks with 1,340 expression associated genes. We further use this to inform understanding of reported GWAS, for example involving FCHO1 and coronary artery disease.

CONCLUSION

This study reports context-specific regulatory elements based on transcriptomic profiling and epigenetic signatures for enhancer-derived RNAs and chromatin accessibility in immune tolerant monocyte states, and demonstrates the informativeness of linking such elements and eQTL to inform future mechanistic studies aimed at defining therapeutic targets of immunosuppression and diseases.

Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis

Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis characterized by enthesitis of the spine and sacroiliac joints. Genome-wide association studies (GWASs) have revealed more than 100 genetic associations whose functional effects remain largely unresolved. Here, we present a comprehensive transcriptomic and epigenomic map of disease-relevant blood immune cell subsets from AS patients and healthy controls. We find that, while CD14⁺ monocytes and CD4⁺ and CD8⁺ T cells show disease-specific differences at the RNA level, epigenomic differences are only apparent upon multi-omics integration. The latter reveals enrichment at disease-associated loci in monocytes. We link putative functional SNPs to genes using high-resolution Capture-C at 10 loci, including PTGER4 and ETS1, and show how disease-specific functional genomic data can be integrated with GWASs to enhance therapeutic target discovery. This study combines epigenetic and transcriptional analysis with GWASs to identify disease-relevant cell types and gene regulation of likely pathogenic relevance and prioritize drug targets.

Identification of 19 new risk loci and potential regulatory mechanisms influencing susceptibility to testicular germ cell tumor

Genome-wide association studies (GWAS) have transformed understanding of susceptibility to testicular germ cell tumors (TGCTs), but much of the heritability remains unexplained. Here we report a new GWAS, a meta-analysis with previous GWAS and a replication series, totaling 7,319 TGCT cases and 23,082 controls. We identify 19 new TGCT risk loci, roughly doubling the number of known TGCT risk loci to 44. By performing in situ Hi-C in TGCT cells, we provide evidence for a network of physical interactions among all 44 TGCT risk SNPs and candidate causal genes. Our findings implicate widespread disruption of developmental transcriptional regulators as a basis of TGCT susceptibility, consistent with failed primordial germ cell differentiation as an initiating step in oncogenesis. Defective microtubule assembly and dysregulation of KIT-MAPK signaling also feature as recurrently disrupted pathways. Our findings support a polygenic model of risk and provide insight into the biological basis of TGCT.

Genetic Predisposition to Chronic Lymphocytic Leukemia Is Mediated by a BMF Super-Enhancer Polymorphism

Chronic lymphocytic leukemia (CLL) is an adult B cell malignancy. Genome-wide association studies show that variation at 15q15.1 influences CLL risk. We deciphered the causal variant at 15q15.1 and the mechanism by which it influences tumorigenesis. We imputed all possible genotypes across the locus and then mapped highly associated SNPs to areas of chromatin accessibility, evolutionary conservation, and transcription factor binding. SNP rs539846 C>A, the most highly associated variant (p = 1.42 × 10⁻¹³, odds ratio = 1.35), localizes to a super-enhancer defined by extensive histone H3 lysine 27 acetylation in intron 3 of B cell lymphoma 2 (BCL2)-modifying factor (BMF). The rs539846-A risk allele alters a conserved RELA-binding motif, disrupts RELA binding, and is associated with decreased BMF expression in CLL. These findings are consistent with rs539846 influencing CLL susceptibility through differential RELA binding, with direct modulation of BMF expression impacting on anti-apoptotic BCL2, a hallmark of oncogenic dependency in CLL.

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SNP rs539846 underlies 15q15.1 association with chronic lymphocytic leukemia

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rs539846 resides in a B cell super-enhancer, disrupting a conserved RELA-binding site

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The rs539846 risk allele (A) reduces enhancer activity and RELA binding in CLL

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rs539846-A confers lower BMF expression

Genome-wide association study identifies multiple susceptibility loci for multiple myeloma

Multiple myeloma (MM) is a plasma cell malignancy with a significant heritable basis. Genome-wide association studies have transformed our understanding of MM predisposition, but individual studies have had limited power to discover risk loci. Here we perform a meta-analysis of these GWAS, add a new GWAS and perform replication analyses resulting in 9,866 cases and 239,188 controls. We confirm all nine known risk loci and discover eight new loci at 6p22.3 (rs34229995, P=1.31 × 10(-8)), 6q21 (rs9372120, P=9.09 × 10(-15)), 7q36.1 (rs7781265, P=9.71 × 10(-9)), 8q24.21 (rs1948915, P=4.20 × 10(-11)), 9p21.3 (rs2811710, P=1.72 × 10(-13)), 10p12.1 (rs2790457, P=1.77 × 10(-8)), 16q23.1 (rs7193541, P=5.00 × 10(-12)) and 20q13.13 (rs6066835, P=1.36 × 10(-13)), which localize in or near to JARID2, ATG5, SMARCD3, CCAT1, CDKN2A, WAC, RFWD3 and PREX1. These findings provide additional support for a polygenic model of MM and insight into the biological basis of tumour development.

Cytochrome P450 Allele CYP3A7*1C Associates with Adverse Outcomes in Chronic Lymphocytic Leukemia, Breast, and Lung Cancer

CYP3A enzymes metabolize endogenous hormones and chemotherapeutic agents used to treat cancer, thereby potentially affecting drug effectiveness. Here, we refined the genetic basis underlying the functional effects of a CYP3A haplotype on urinary estrone glucuronide (E1G) levels and tested for an association between CYP3A genotype and outcome in patients with chronic lymphocytic leukemia (CLL), breast, or lung cancers. The most significantly associated SNP was rs45446698, an SNP that tags the CYP3A7*1C allele; this SNP was associated with a 54% decrease in urinary E1G levels. Genotyping this SNP in 1,008 breast cancer, 1,128 lung cancer, and 347 CLL patients, we found that rs45446698 was associated with breast cancer mortality (HR, 1.74; P = 0.03), all-cause mortality in lung cancer patients (HR, 1.43; P = 0.009), and CLL progression (HR, 1.62; P = 0.03). We also found borderline evidence of a statistical interaction between the CYP3A7*1C allele, treatment of patients with a cytotoxic agent that is a CYP3A substrate, and clinical outcome (Pinteraction = 0.06). The CYP3A7*1C allele, which results in adult expression of the fetal CYP3A7 gene, is likely to be the functional allele influencing levels of circulating endogenous sex hormones and outcome in these various malignancies. Further studies confirming these associations and determining the mechanism by which CYP3A7*1C influences outcome are required. One possibility is that standard chemotherapy regimens that include CYP3A substrates may not be optimal for the approximately 8% of cancer patients who are CYP3A7*1C carriers.

Capture Hi-C identifies the chromatin interactome of colorectal cancer risk loci

Multiple regulatory elements distant from their targets on the linear genome can influence the expression of a single gene through chromatin looping. Chromosome conformation capture implemented in Hi-C allows for genome-wide agnostic characterization of chromatin contacts. However, detection of functional enhancer-promoter interactions is precluded by its effective resolution that is determined by both restriction fragmentation and sensitivity of the experiment. Here we develop a capture Hi-C (cHi-C) approach to allow an agnostic characterization of these physical interactions on a genome-wide scale. Single-nucleotide polymorphisms associated with complex diseases often reside within regulatory elements and exert effects through long-range regulation of gene expression. Applying this cHi-C approach to 14 colorectal cancer risk loci allows us to identify key long-range chromatin interactions in cis and trans involving these loci.

Abstract 407: Targeted Hi-C and integrative analyses reveal functionality of colorectal cancer risk loci

Genetic risk factors identified by genome-wide association studies (GWAS) are thought to function through allele-specific regulation of gene expression. Long-range chromatin looping interactions, as revealed by chromosome conformation capture (3C)-based techniques, bring risk variants into spatial proximity with loci otherwise distal on the linear genome. Hi-C, using next generation sequencing (NGS), allows for genome-wide agnostic characterization of chromatin contacts, however, detection of functional enhancer-promoter interactions is precluded by its limited resolution. Here we apply Targeted Hi-C, a novel technique combining the unbiased coverage of Hi-C with target sequence capture to identify functional chromatin interactions for 15 colorectal cancer risk loci at high resolution. We depicted the CRC risk interactome as a set of generic highly significant genome-wide interactions, predominantly overlaying the strongest risk association signals. Integrative analyses involving profiles for epigenetic marks, evolutionary conservation and transcription factor binding, revealed regulatory function of long-range chromatin interactions. At the 8q24.21 risk locus, we could extend a previously reported contact between rs6983267 and the MYC promoter to a network of interactions involving CCAT1 (colorectal cancer associated transcript 1). At other risk loci, our data supports the central role of TERC, BMP4, GREM1, BMP2, SMAD7 and in CRC pathogenesis. Additionally, distal to the risk loci we identified contacts with the genes such as TRPS1, TPO, ETS1, VEZT and RAN, previously implicated in cancer and mutated in CRC. Our results demonstrate the capability of high resolution chromatin interaction analyses in conjunction with combinatorial integrative analyses to decipher disease risk loci.

Citation Format: Roland Jäger, Gabriele Migliorini, Marc Henrion, Nicola Whiffin, Laura Broome, Nicola Dryden, Takashi Nagano, Stefan Schoenfelder, Peter Fraser, Olivia Fletcher, Richard Houlston. Targeted Hi-C and integrative analyses reveal functionality of colorectal cancer risk loci. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 407. doi:10.1158/1538-7445.AM2014-407

visPIG--a web tool for producing multi-region, multi-track, multi-scale plots of genetic data

We present VISual Plotting Interface for Genetics (visPIG; http://vispig.icr.ac.uk), a web application to produce multi-track, multi-scale, multi-region plots of genetic data. visPIG has been designed to allow users not well versed with mathematical software packages and/or programming languages such as R, Matlab®, Python, etc., to integrate data from multiple sources for interpretation and to easily create publication-ready figures. While web tools such as the UCSC Genome Browser or the WashU Epigenome Browser allow custom data uploads, such tools are primarily designed for data exploration. This is also true for the desktop-run Integrative Genomics Viewer (IGV). Other locally run data visualisation software such as Circos require significant computer skills of the user. The visPIG web application is a menu-based interface that allows users to upload custom data tracks and set track-specific parameters. Figures can be downloaded as PDF or PNG files. For sensitive data, the underlying R code can also be downloaded and run locally. visPIG is multi-track: it can display many different data types (e.g association, functional annotation, intensity, interaction, heat map data,…). It also allows annotation of genes and other custom features in the plotted region(s). Data tracks can be plotted individually or on a single figure. visPIG is multi-region: it supports plotting multiple regions, be they kilo- or megabases apart or even on different chromosomes. Finally, visPIG is multi-scale: a sub-region of particular interest can be 'zoomed' in. We describe the various features of visPIG and illustrate its utility with examples. visPIG is freely available through http://vispig.icr.ac.uk under a GNU General Public License (GPLv3).

Variation at 10p12.2 and 10p14 influences risk of childhood B-cell acute lymphoblastic leukemia and phenotype

Acute lymphoblastic leukemia (ALL) is the major pediatric cancer diagnosed in economically developed countries with B-cell precursor (BCP)-ALL, accounting for approximately 70% of ALL. Recent genome-wide association studies (GWAS) have provided the first unambiguous evidence for common inherited susceptibility to BCP-ALL, identifying susceptibility loci at 7p12.2, 9p21.3, 10q21.2, and 14q11.2. To identify additional BCP-ALL susceptibility loci, we conducted a GWAS and performed a meta-analysis with a published GWAS totaling 1658 cases and 4723 controls, with validation in 1449 cases and 1488 controls. Combined analysis identified novel loci mapping to 10p12.2 (rs10828317, odds ratio [OR] = 1.23; P = 2.30 × 10(-9)) and 10p14 marked by rs3824662 (OR = 1.31; P = 8.62 × 10(-12)). The single nucleotide polymorphism rs10828317 is responsible for the N215S polymorphism in exon 7 of PIP4K2A, and rs3824662 localizes to intron 3 of the transcription factor and putative tumor suppressor gene GATA3. The rs10828317 association was shown to be specifically associated with hyperdiploid ALL, whereas the rs3824662-associated risk was confined to nonhyperdiploid non-TEL-AML1 + ALL. The risk allele of rs3824662 was correlated with older age at diagnosis (P < .001) and significantly worse event-free survivorship (P < .0001). These findings provide further insights into the genetic and biological basis of inherited genetic susceptibility to BCP-ALL and the influence of constitutional genotype on disease development.

Laparoscopic resection of colorectal cancer: matched comparison in elderly and younger patients

BACKGROUND

Several studies have addressed the issue of the feasibility of laparoscopic colorectal surgery in elderly patients, usually by choosing an arbitrary cut-off age limit, and retrospectively evaluating patient outcomes. The aim of this study was to assess the effects of age on the outcome of laparoscopic colorectal surgery for cancer in a single department, by comparing younger and older patients, matched by ASA score and type of operation.

METHODS

The perioperative outcome of patients ≥75 years old who underwent laparoscopic colorectal surgery for cancer between June 2005 and January 2009 were compared with findings in younger patients, matched by ASA score and type of operation.

RESULTS

The study included 100 patients, fifty <75 years old (Group A) and fifty ≥75 (Group B) years old. There were 18 right hemicolectomies, 16 left hemicolectomies, 4 anterior resections, 9 low anterior resections, 2 Miles' operations and 1 segmental resection in each group. We observed a significantly higher overall morbidity rate among elderly patients than among younger patients (24 vs. 8%).

CONCLUSIONS

Short-term results after laparoscopic colorectal surgery for cancer in patients ≥75 years old reveal that they have higher postoperative risk compared to their younger counterparts, even when matched by ASA score and type of operation. It suggests that although advanced age, per se, is not a contraindication, it is a risk for patients who undergo laparoscopic colorectal surgery for cancer. This surgery in elderly patients should be performed by experienced surgeons in specialized centers to keep postoperative risk to a minimum.

Finite-connectivity spin-glass phase diagrams and low-density parity check codes

We obtain phase diagrams of regular and irregular finite-connectivity spin glasses. Contact is first established between properties of the phase diagram and the performance of low-density parity check (LDPC) codes within the replica symmetric (RS) ansatz. We then study the location of the dynamical and critical transition points of these systems within the one step replica symmetry breaking theory (RSB), extending similar calculations that have been performed in the past for the Bethe spin-glass problem. We observe that the location of the dynamical transition line does change within the RSB theory, in comparison with the results obtained in the RS case. For LDPC decoding of messages transmitted over the binary erasure channel we find, at zero temperature and rate , an RS critical transition point at while the critical RSB transition point is located at , to be compared with the corresponding Shannon bound . For the binary symmetric channel we show that the low temperature reentrant behavior of the dynamical transition line, observed within the RS ansatz, changes its location when the RSB ansatz is employed; the dynamical transition point occurs at higher values of the channel noise. Possible practical implications to improve the performance of the state-of-the-art error correcting codes are discussed.

Self-generated disorder and structural glass formation in homopolymer globules

We have investigated the interrelation between spin glasses and structural glasses. Spin glasses in this case are p-spin interaction spin glasses (at p>2) or Potts glasses that contain quenched disorder, whereas the structural glasses are here exemplified by a homopolymeric globule, which can be viewed as a liquid of connected units on a nanoscale. It is argued that the homopolymeric globule problem can be mapped onto a disorder field theoretical model whose effective Hamiltonian resembles the corresponding one for the spin glass model. In this sense the disorder in the globule is self-generated (in contrast to spin glasses) and can be related to competing interactions (virial coefficients of different signs) and the chain connectivity. The work is aimed at giving a quantitative description of this analogy. We have investigated in the mean-field approximation the phase diagram of the homopolymeric globule where the transition line from the liquid to glassy globule is treated in terms of the replica symmetry breaking paradigm. The configurational entropy temperature dependence is also discussed.

Patient-administered tampon-collected genital cells in the assessment of Chlamydia trachomatis infection using polymerase chain reaction

BACKGROUND

Diagnosis of genital Chlamydia trachomatis infection in women traditionally requires a speculum examination to collect endocervical cells, followed by cell culture. This method is time consuming, requires stringent transport conditions, and is technically demanding.

GOALS

To compare tampons as a patient-administered collection method followed by detection with polymerase chain reaction (PCR) with the traditional endocervical swab culture followed by cell culture detection.

STUDY DESIGN

At the emergency department of a hospital for obstetrics and gynecology, 1,000 consecutive women with symptoms suggestive of infection with C. trachomatis were tested for C. trachomatis infection by PCR on both tampon (PCR-T) and swab (PCR-S) specimen and by culture of the swab specimen.

RESULTS

Seventeen PCR-T and 16 PCR-S specimens were positive; 16 endocervical specimens were positive by culture, and 14 of the endocervical samples were positive by the three methods. Sixty-one PCR-S samples were inadequate as shown by the lack of amplification of the beta-globin gene segment, indicating poor collection of specimens by endocervical swab for chlamydial testing.

CONCLUSIONS

Tampon specimens collected for PCR detection provided an easy and sensitive method of detection of C. trachomatis and overcame the obstacle of endocervical sampling and subsequent stringent transport requirements of culture.

[Acute psychosis. Clinical contribution]

In a vast survey of clinical cases Authors have considered 50 specific cases of acute psychosis corresponding to the following criteria: first stage, lack of organic and caused by drugs disorders, lack of visible affective symptoms. Different social and personal situations have been considered as well as the initial symptoms and the characteristics of the clinical picture. These variations have been correlated to the result and the course of the illness and attention has been drawn to the importance of adaptation before illness, presence of stress elements, very acute initial symptoms, oneiric characteristics of the clinical picture on the positive course. In a further diagnosis only 20 of these cases can be attributed to the schizophreniform disorder and among these 20 the majority develop with relapses, consequences and emotional damages.

[Study of acute psychoses. I. The problem of acute psychoses: nosographic classification]

Survey of the first admitted patients for nonorganic and nonaffective acute psychotic decompensation in an Inpatient Treatment Unit, as a part of a Mental HealthCenter, in a General Hospital. Preliminarily the Authors review the concept of "acute psychosis" from Bleuler to Leonhard, Wyrsch, Lanfeldt, the bouffées delirantes of the French literature, the schizophreniform disorder of the DSM III R. The acute psychosis is "a carrefour state" where many types of acute events come together: schizophrenic, affective, reactive. Sometimes, but rarely, acute psychosis is a nosographic unit. This unit needs further evidence.

A case of complete testicular feminisation and 47,XXY karyotype

A very rare case of complete testicular feminisation with a 47,XXY sex chromosome complement is described. The X-chromatin is positive. The subject studied, who belongs to a family in which four other members have Morris's syndrome and have a 46,XY karyotype, is a perfect phenotypic female. The endocrine situation is unique and resembles, in part, that of subjects with Klinefelter's syndrome.