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Harnessing the power of single-cell genomics technologies, single-cell Hi-C (scHi-C) and its derived technologies provide powerful tools to measure spatial proximity between regulatory elements and their target genes in individual cells. Using a global background model, we propose SnapHiC-G, a computational method to identify long-range enhancer-promoter interactions from scHi-C data. We applied SnapHiC-G to scHi-C datasets generated from mouse embryonic stem cells and human brain cortical cells and demonstrated that SnapHiC-G achieved high sensitivity in identifying long-range enhancer-promoter interactions. Moreover, SnapHiC-G can identify putative target genes for non-coding GWAS variants, and the genetic heritability of neuropsychiatric diseases is enriched for single nucleotide polymorphisms (SNPs) within SnapHiC-G-identified interactions in a cell-type-specific manner. In sum, SnapHiC-G is a powerful tool for characterizing cell-type-specific enhancer-promoter interactions from complex tissues and can facilitate the discovery of chromatin interactions important for gene regulation in biologically relevant cell types.

Background Chlamydia trachomatis (Ct) infection ascending to the upper genital tract can cause infertility. Direct association of genetic variants as contributors is challenging because infertility may not be diagnosed until years after infection. Investigating the intermediate trait of ascension bridges this gap. Methods We identified infertility genome-wide association study (GWAS) loci using deoxyribonucleic acid from Ct-seropositive cisgender women in a tubal factor infertility study and Ct-infected cisgender women from a longitudinal pelvic inflammatory disease cohort with known fertility status. Deoxyribonucleic acid and blood messenger ribonucleic acid from 2 additional female cohorts with active Ct infection and known endometrial infection status were used to investigate the impact of infertility single-nucleotide polymorphisms (SNPs) on Ct ascension. A statistical mediation test examined whether multiple infertility SNPs jointly influenced ascension risk by modulating expression of mediator genes. Results We identified 112 candidate infertility GWAS loci, and 31 associated with Ct ascension. The SNPs altered chlamydial ascension by modulating expression of 40 mediator genes. Mediator genes identified are involved in innate immune responses including type I interferon production, T-cell function, fibrosis, female reproductive tract health, and protein synthesis and degradation. Conclusions We identified Ct-related infertility loci and their potential functional effects on Ct ascension.

SummaryTo elucidate the molecular mechanisms underlying genetic variants identified from genome-wide association studies (GWAS) for a variety of phenotypic traits encompassing binary, continuous, count, and survival outcomes, we propose a novel and flexible method to test for mediation that can simultaneously accommodate multiple genetic variants and different types of outcome variables. Specifically, we employ the intersection-union test approach combined with likelihood ratio test to detect mediation effect of multiple genetic variants via some mediator (for example, the expression of a neighboring gene) on outcome. We fit high-dimensional generalized linear mixed models under the mediation framework, separately under the null and alternative hypothesis. We leverage Laplace approximation to compute the marginal likelihood of outcome and use coordinate descent algorithm to estimate corresponding parameters. Our extensive simulations demonstrate the validity of our proposed method and substantial, up to 97%, power gains over alternative methods. Applications to real data for the study of Chlamydia trachomatis infection further showcase advantages of our method. We believe our proposed method will be of value and general interest in this post-GWAS era to disentangle the potential causal mechanism from DNA to phenotype for new drug discovery and personalized medicine.

Background Chlamydia trachomatis can cause reproductive morbidities after ascending to the upper genital tract of women, and repeated infection can lead to worse disease. Data related to protective immune responses at the cervical mucosa that could limit chlamydial infection to the cervix and/or prevent reinfection inform vaccine approaches and biomarkers of risk. Methods We measured 48 cytokines in cervical secretions from women having chlamydial cervical infection alone (n = 92) or both cervical and endometrial infection (n = 68). Univariable regression identified cytokines associated with differential odds of endometrial infection and reinfection risk, and multivariable stepwise regression identified cytokine ratios associated with differential risk. Results Elevated interleukin (IL) 15/CXCL10 (odds ratio [OR], 0.55 [95% confidence interval {CI}, .37-.78]), IL-16/tumor necrosis factor-α (OR, 0.66 [95% CI, .45-.93]), and CXCL14/IL-17A (OR, 0.73 [95% CI, .54-.97]) cytokine ratios were significantly (P ≤ .05) associated with decreased odds of endometrial infection. A higher Flt-3L/IL-14 ratio was significantly (P = .001) associated with a decreased risk of reinfection (hazard ratio, 0.71 [95% CI, .58-.88]). Conclusions Cytokines involved in humoral, type I interferon, and T-helper (Th) 17 responses were associated with susceptibility to C. trachomatis, whereas cytokines involved in Th1 polarization, recruitment, and activation were associated with protection against ascension and reinfection.

BACKGROUND Ideal management of sexually transmitted infections (STI) may require risk markers for pathology or vaccine development. Previously, we identified common genetic variants associated with chlamydial pelvic inflammatory disease (PID) and reduced fecundity. As this explains only a proportion of the long-term morbidity risk, we used whole-exome sequencing to identify biological pathways that may be associated with STI-related infertility. METHODS We obtained stored DNA from 43 non-Hispanic black women with PID from the PID Evaluation and Clinical Health Study. Infertility was assessed at a mean of 84 months. Principal component analysis revealed no population stratification. Potential covariates did not significantly differ between groups. Sequencing kernel association test was used to examine associations between aggregates of variants on a single gene and infertility. The results from the sequencing kernel association test were used to choose "focus genes" (P < 0.01; n = 150) for subsequent Ingenuity Pathway Analysis to identify "gene sets" that are enriched in biologically relevant pathways. RESULTS Pathway analysis revealed that focus genes were enriched in canonical pathways including, IL-1 signaling, P2Y purinergic receptor signaling, and bone morphogenic protein signaling. CONCLUSIONS Focus genes were enriched in pathways that impact innate and adaptive immunity, protein kinase A activity, cellular growth, and DNA repair. These may alter host resistance or immunopathology after infection. Targeted sequencing of biological pathways identified in this study may provide insight into STI-related infertility.

Summary Tens of thousands of reproducibly identified GWAS (Genome-Wide Association Studies) variants, with the vast majority falling in non-coding regions resulting in no eventual protein products, call urgently for mechanistic interpretations. Although numerous methods exist, there are few, if any methods, for simultaneously testing the mediation effects of multiple correlated SNPs via some mediator (e.g. the expression of a gene in the neighborhood) on phenotypic outcome. We propose multi-SNP mediation intersection-union test (SMUT) to fill in this methodological gap. Our extensive simulations demonstrate the validity of SMUT as well as substantial, up to 92%, power gains over alternative methods. In addition, SMUT confirmed known mediators in a real dataset of Finns for plasma adiponectin level, which were missed by many alternative methods. We believe SMUT will become a useful tool to generate mechanistic hypotheses underlying GWAS variants, facilitating functional follow-up. Availability and implementation The R package SMUT is publicly available from CRAN at https://CRAN.R-project.org/package=SMUT. Supplementary information Supplementary data are available at Bioinformatics online.

Sexually transmitted infections with Chlamydia trachomatis and/or Neisseria gonorrhoeae and rates of pelvic inflammatory disease (PID) in women continue to rise, with reinfection being common because of poor adaptive immunity. Diagnosis remains imprecise, and pathogenesis data are derived primarily from monoinfection of mice with C. trachomatis or N. gonorrhoeae. By comparing blood mRNA responses of women with C. trachomatis– and/or N. gonorrhoeae–induced PID and histologic endometritis with those from women with C. trachomatis and/or N. gonorrhoeae infection limited to their cervix and asymptomatic uninfected women determined via microarray, we discovered important pathogenic mechanisms in PID and response differences that provide a pathway to biomarker discovery. Women with N. gonorrhoeae– and/or C. trachomatis–induced PID exhibit overexpression of myeloid cell genes and suppression of protein synthesis, mitochondrial oxidative phosphorylation, and T cell–specific genes. Coinfected women exhibited the greatest activation of cell death pathways and suppression of responses essential for adaptive immunity. Women solely infected with C. trachomatis expressed elevated levels of type I and type II IFN genes, and enhanced type I IFN–induced chemokines in cervical secretions were associated with ascension of C. trachomatis to the endometrium. Blood microarrays reveal discrete pathobiological endotypes in women with PID that are driven by pathogen invasion of the upper genital tract.

PROBLEM: Chlamydia infections in women can ascend to the upper genital tract, and repeated infections are common, placing women at risk for sequelae. The protective role of anti-chlamydia antibodies to surface exposed antigens in ascending and incident infection is unclear. METHOD OF STUDY: A whole-bacterial ELISA was used to quantify chlamydia-specific IgG and IgA in serum and cervical secretions of 151 high-risk women followed longitudinally. Correlations were determined between antibody and cervical burden and causal mediation analysis investigated the effect of antibody on ascension. We examined the relationship of antibody to incident infection using the marginal Cox model. RESULTS: Serum and cervical anti-chlamydia IgG and cervical IgA levels correlated inversely with cervical burden. While lower burden was associated with reduced ascension, causal mediation analysis revealed that the indirect effects of antibody mediated through reductions in bacterial burden were insufficient to prevent ascension. Analysis of women uninfected at enrollment revealed that serum and cervical anti-chlamydia IgG were associated with increased risk of incident infection; hazard ratio increased 3.6-fold (95% CI, 1.3 – 10.3), and 22.6-fold (95% CI, 3.1 – 165.2) with each unit of serum and cervical IgG, respectively. CONCLUSIONS: Although anti-chlamydia IgG and IgA correlated with reduced cervical chlamydia burden, they failed to prevent ascension and increased levels of anti-chlamydia IgG were associated with increased risk for incident infection.

BACKGROUND Natural infection induces partial immunity to Chlamydia trachomatis Identification of chlamydial antigens that induce interferon γ (IFN-) secretion by T cells from immune women could advance vaccine development. METHODS IFN-γ production by CD4+ and CD8+ peripheral blood T cells from 58 high-risk women was measured after coculture with antigen-presenting cells preincubated with recombinant Escherichia coli expressing a panel of 275 chlamydial antigens. Quantile median regression analysis was used to compare frequencies of IFN-γ responses in women with only cervical infection to those in women with endometrial infection and frequencies in women who remained uninfected for over 1 year to those in women who developed incident infection. Statistical methods were then used to identify proteins associated with protection. RESULTS A higher median frequency of CD8+ T-cell responses was detected in women with lower genital tract chlamydial infection, compared with those with upper genital tract chlamydial infection (13.8% vs 9.5%; P =04), but the CD4+ T-cell response frequencies were not different. Women who remained uninfected displayed a greater frequency of positive CD4+ T-cell responses (29% vs 18%; P < .0001), compared with women who had incident infection, while the frequencies of CD8+ T-cell responses did not differ. A subset of proteins involved in central metabolism, type III secretion, and protein synthesis were associated with protection. CONCLUSIONS Investigations in naturally exposed women reveal protective responses and identify chlamydial vaccine candidate antigens.

Background Chlamydia trachomatis (CT) is the leading bacterial sexually transmitted infection worldwide. CT can ascend to the upper reproductive tract in women, and cause tissue damage resulting in reproductive sequalae. Data from animal and human studies indicate a role for the Th1 cytokine, IFNγ, in protection from infection and disease. Methods We recruited 246 women at high risk for CT infection. Cervical swabs and endometrial biopsies were collected for detection of sexually transmitted pathogens, including CT, by nucleic acid amplification test (NAAT). Cervical secretions collected using cervical sponges were screened for 57 cytokines using multiplex bead arrays. Data were analyzed by logistic regression. Results 92 (37%) women were NAAT+ for CT in only their cervix and 69 (28%) women had CT infection detected at both their cervix and endometrium. Compared to women with endometrial infection, women with only cervical infection had higher levels of CX3CL1 (p Conclusions Th1-associated cytokines in cervical secretions are associated with limitation of infection to the cervix, whereas type I IFN-associated chemokines are associated with endometrial CT infection. These proteins may be used as biomarkers to identify women at increased risk for upper reproductive tract pathology and those who could benefit from enhanced screening.

Background. Chlamydia trachomatis genital tract infection is a major cause of female reproductive morbidity. Risk factors for ascending infection are unknown, and the role for antibody in protection is not well established. Methods. We recruited 225 women from urban outpatient clinics and followed them for a median of 12 months. We performed a cross-sectional analysis of serum anti-chlamydial immunoglobulin G (IgG), behavioral factors, and microbiological factors associated with endometrial infection at enrollment, and a longitudinal analysis of factors associated with incident infection. Results. Oral contraceptives (adjusted relative risk [RR], 2.02 [95% confidence interval {CI}, 1.38–2.97]) and gonorrhea (adjusted RR, 1.66 [95% CI, 1.07–2.60]) were associated with endometrial infection. Gonorrhea (adjusted hazard ratio [HR], 3.09 [95% CI, 1.41–6.78]), cervical infection at enrollment (adjusted HR, 2.33 [95% CI, 1.07–5.11]), and exposure to uncircumcised partners (adjusted HR, 2.65 [95% CI, 1.21–5.82]) or infected partners (adjusted HR, 4.99 [95% CI, 2.66–9.39]) significantly increased the risk of incident infection. Seropositivity was associated with a reduced cervical burden (P < .05) but no differences in rates of ascending infection (adjusted RR, 1.24 [95% CI, .71–2.19]) or incident infection (adjusted HR, 0.94 [95% CI, .52–1.69]). Conclusions. Serum anti-chlamydial IgG is not associated with a lowered rate of ascending or repeat infection. Identification of factors associated with ascending infection and increased risk of incident infection provide guidance for targeted screening of women at increased risk for sequelae.