1
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Taylor BD, Adekanmbi V, Zhang Y, Berenson A. The Impact of Neisseria gonorrhoeae Mono- and Coinfection on Adverse Pregnancy Outcomes. Open Forum Infect Dis 2023; 10:ofad220. [PMID: 37250177 PMCID: PMC10220503 DOI: 10.1093/ofid/ofad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/19/2023] [Indexed: 05/31/2023] Open
Abstract
Background Sexually transmitted infections (STIs) have recently been linked to hypertensive disorders of pregnancy (HDP). However, the impact of Neisseria gonorrhoeae on risk of HDP is not well understood. This study determined the impact of gonorrhea and gonorrhea coinfection on HDP and other adverse pregnancy outcomes in a population with a high screening rate and presumed treatment. Methods This retrospective study included 29 821 singleton births between 2016 and 2021. The STI testing results, demographic variables, and pregnancy outcomes were identified from electronic health records. The HDP were primary outcomes of interest including gestational hypertension, preeclampsia, and superimposed preeclampsia. We further examined preeclampsia subtypes defined by severe features and gestational age of delivery (term and preterm preeclampsia). Secondary outcomes included preterm premature rupture of membranes, chorioamnionitis, and preterm delivery. Logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs). Models were adjusted for maternal age, maternal race/ethnicity, and smoking. Results Gonorrhea screening occurred in 95% of the population. Gonorrhea increased the odds of preterm preeclampsia (adjusted OR [ORadj.], 1.95; 95% CI, 1.02-3.73) and preterm birth (ORadj., 1.78; 95% CI, 1.22-2.60). Furthermore, gonorrhea-chlamydia coinfection was associated with preterm birth (ORadj., 1.77; 95% CI, 1.03-3.04). However, results were similar when we examined gonorrhea monoinfection (ORadj., 1.76; 95% CI, 1.04-2.97). Conclusions Among a diverse population of pregnant individuals, gonorrhea increased odds of preterm preeclampsia and preterm delivery Further research is needed to determine the burden of STIs on HDP, including investigations into biological effects during pregnancy.
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Affiliation(s)
- Brandie DePaoli Taylor
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Population Health and Health Disparities, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Interdisciplinary Research in Women's Health, University of Texas Medical Branch, Galveston, Texas, USA
| | - Victor Adekanmbi
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Interdisciplinary Research in Women's Health, University of Texas Medical Branch, Galveston, Texas, USA
| | - Yuanyi Zhang
- Department of Biostatistics and Data Science, University of Texas Medical Branch, Galveston, Texas, USA
| | - Abbey Berenson
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Interdisciplinary Research in Women's Health, University of Texas Medical Branch, Galveston, Texas, USA
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2
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Zhong W, Kollipara A, Liu Y, Wang Y, O’Connell CM, Poston TB, Yount K, Wiesenfeld HC, Hillier SL, Li Y, Darville T, Zheng X. Genetic susceptibility loci for Chlamydia trachomatis endometrial infection influence expression of genes involved in T cell function, tryptophan metabolism and epithelial integrity. Front Immunol 2022; 13:1001255. [PMID: 36248887 PMCID: PMC9562917 DOI: 10.3389/fimmu.2022.1001255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Objectives Identify genetic loci of enhanced susceptibility to Chlamydial trachomatis (Ct) upper genital tract infection in women. Methods We performed an integrated analysis of DNA genotypes and blood-derived mRNA profiles from 200 Ct-exposed women to identify expression quantitative trait loci (eQTL) and determine their association with endometrial chlamydial infection using a mediation test. We further evaluated the effect of a lead eQTL on the expression of CD151 by immune cells from women with genotypes associated with low and high whole blood expression of CD151, respectively. Results We identified cis-eQTLs modulating mRNA expression of 81 genes (eGenes) associated with altered risk of ascending infection. In women with endometrial infection, eGenes involved in proinflammatory signaling were upregulated. Downregulated eGenes included genes involved in T cell functions pivotal for chlamydial control. eGenes encoding molecules linked to metabolism of tryptophan, an essential chlamydial nutrient, and formation of epithelial tight junctions were also downregulated in women with endometrial infection. A lead eSNP rs10902226 was identified regulating CD151, a tetrospanin molecule important for immune cell adhesion and migration and T cell proliferation. Further in vitro experiments showed that women with a CC genotype at rs10902226 had reduced rates of endometrial infection with increased CD151 expression in whole blood and T cells when compared to women with a GG genotype. Conclusions We discovered genetic variants associated with altered risk for Ct ascension. A lead eSNP for CD151 is a candidate genetic marker for enhanced CD4 T cell function and reduced susceptibility.
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Affiliation(s)
- Wujuan Zhong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Avinash Kollipara
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yutong Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yuhan Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Catherine M. O’Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Taylor B. Poston
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kacy Yount
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Harold C. Wiesenfeld
- The University of Pittsburgh School of Medicine and the Magee-Womens Research Institute, Pittsburgh, PA, United States
| | - Sharon L. Hillier
- The University of Pittsburgh School of Medicine and the Magee-Womens Research Institute, Pittsburgh, PA, United States
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Xiaojing Zheng, ; Toni Darville,
| | - Xiaojing Zheng
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- *Correspondence: Xiaojing Zheng, ; Toni Darville,
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3
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Whelan J, Ghoniem M, Médoc N, Apicella M, Beck E. Applying a novel approach to scoping review incorporating artificial intelligence: mapping the natural history of gonorrhoea. BMC Med Res Methodol 2021; 21:183. [PMID: 34488645 PMCID: PMC8418964 DOI: 10.1186/s12874-021-01367-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 08/02/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Systematic and scoping literature searches are increasingly resource intensive. We present the results of a scoping review which combines the use of a novel artificial-intelligence-(AI)-assisted Medline search tool with two other 'traditional' literature search methods. We illustrate this novel approach with a case study to identify and map the range of conditions (clinical presentations, complications, coinfections and health problems) associated with gonorrhoea infection. METHODS To fully characterize the range of health outcomes associated with gonorrhoea, we combined a high yield preliminary search with a traditional systematic search, then supplemented with the output of a novel AI-assisted Medline search tool based on natural language processing methods to identify eligible literature. RESULTS We identified 189 health conditions associated with gonorrhoea infection of which: 53 were identified through the initial 'high yield' search; 99 through the systematic search; and 124 through the AI-assisted search. These were extracted from 107 unique references and 21 International Statistical Classification of Diseases and Related Health Problems Ninth and Tenth Revision (ICD 9/10) or Read codes. Health conditions were mapped to the urogenital tract (n = 86), anorectal tract (n = 6) oropharyngeal tract (n = 5) and the eye (n = 14); and other conditions such as systemic (n = 61) and neonatal conditions (n = 7), psychosocial associations (n = 3), and co-infections (n = 7). The 107 unique references attained a Scottish Intercollegiate Guidelines Network (SIGN) score of ≥2++ (n = 2), 2+ (14 [13%]), 2- (30 [28%]) and 3 (45 [42%]), respectively. The remaining papers (n = 16) were reviews. CONCLUSIONS Through AI screening of Medline, we captured - titles, abstracts, case reports and case series related to rare but serious health conditions related to gonorrhoea infection. These outcomes might otherwise have been missed during a systematic search. The AI-assisted search provided a useful addition to traditional/manual literature searches especially when rapid results are required in an exploratory setting.
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Affiliation(s)
| | - Mohammad Ghoniem
- Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Nicolas Médoc
- Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
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4
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Hillier SL, Bernstein KT, Aral S. A Review of the Challenges and Complexities in the Diagnosis, Etiology, Epidemiology, and Pathogenesis of Pelvic Inflammatory Disease. J Infect Dis 2021; 224:S23-S28. [PMID: 34396398 PMCID: PMC8365114 DOI: 10.1093/infdis/jiab116] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pelvic inflammatory disease (PID) is a syndrome that causes substantial morbidity, including chronic pelvic pain, to women globally. While limited data are available from low- and middle-income countries, national databases from the United States and Europe suggest that PID incidence may be decreasing but the rate of decrease may differ by the etiologic cause. Recent studies of women with PID have reported that fewer than half of women receiving a diagnosis of PID have gonococcal or chlamydial infection, while Mycoplasma genitalium, respiratory pathogens, and the constellation of bacteria associated with bacterial vaginosis may account for a substantial fraction of PID cases. The clinical diagnosis of PID is nonspecific, creating an urgent need to develop noninvasive tests to diagnose PID. Advances in serologic testing for Chlamydia trachomatis and Neisseria gonorrhoeae could advance epidemiologic studies, while the development of vaccines against these sexually transmitted pathogens could affect incident PID and associated morbidity.
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Affiliation(s)
- Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh and the Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Kyle T Bernstein
- Centers for Disease Control and Prevention, Division of STD Prevention, Atlanta, Georgia, USA
| | - Sevgi Aral
- Centers for Disease Control and Prevention, Division of STD Prevention, Atlanta, Georgia, USA
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5
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Zheng X, Zhong W, O'Connell CM, Liu Y, Haggerty CL, Geisler WM, Anyalechi GE, Kirkcaldy RD, Wiesenfeld HC, Hillier SL, Steinkampf MP, Hammond KR, Fine J, Li Y, Darville T. Host Genetic Risk Factors for Chlamydia trachomatis-Related Infertility in Women. J Infect Dis 2021; 224:S64-S71. [PMID: 34396400 DOI: 10.1093/infdis/jiab149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
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.
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Affiliation(s)
- Xiaojing Zheng
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Wujuan Zhong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yutong Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Catherine L Haggerty
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - William M Geisler
- Departments of Medicine and Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Gloria E Anyalechi
- Centers for Disease Control and Prevention, Division of STD Prevention, Atlanta, Georgia, USA
| | - Robert D Kirkcaldy
- Centers for Disease Control and Prevention, Division of STD Prevention, Atlanta, Georgia, USA
| | - Harold C Wiesenfeld
- Department of Obstetrics, Gynecology and Reproductive Sciences, the University of Pittsburgh School of Medicine and the Magee-Womens Research Institute Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, the University of Pittsburgh School of Medicine and the Magee-Womens Research Institute Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | | | - Jason Fine
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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6
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Kersh EN, Geisler WM. A Commentary on Current Diagnostic Challenges and Research Needs for Evaluating Reproductive Sequelae of Sexually Transmitted Infections. J Infect Dis 2021; 224:S72-S74. [PMID: 34396409 PMCID: PMC8499708 DOI: 10.1093/infdis/jiaa798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Advancing the understanding of pelvic inflammatory disease (PID) requires access to advanced diagnostic approaches for evaluating reproductive sequelae of sexually transmitted infections (STIs). Current limitations of clinical criteria and advanced imaging technologies for diagnosing reproductive sequelae make diagnosis and surveillance of PID a challenge. We summarize and comment on major challenges in diagnostic evaluation of reproductive sequelae: limited point-of-care clinical diagnostic options for reproductive sequelae, economic and geographical obstacles to accessing state-of-the-art diagnostics, an expanding list of STIs that may cause reproductive sequelae and the complexities in evaluating them, and the need for coordinated research efforts to systematically evaluate biomarkers with gold-standard, well-defined specimens and associated clinical data. The future use of biomarkers in readily accessible mucosal or blood-derived specimens as a noninvasive approach to determining STI etiologies may be fruitful and requires more research. Biomarkers under consideration include cytokines, STI-specific antibody responses, and mRNA transcriptional profiles of inflammatory markers.
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Affiliation(s)
- Ellen N. Kersh
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA
| | - William M. Geisler
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
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7
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Darville T. Pelvic Inflammatory Disease Due to Neisseria gonorrhoeae and Chlamydia trachomatis: Immune Evasion Mechanisms and Pathogenic Disease Pathways. J Infect Dis 2021; 224:S39-S46. [PMID: 34396413 DOI: 10.1093/infdis/jiab031] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pelvic inflammatory disease (PID) results from ascension of sexually transmitted pathogens from the lower genital tract to the uterus and/or fallopian tubes in women, with potential spread to neighboring pelvic organs. Patients may present acutely with lower abdominal or pelvic pain and pelvic organ tenderness. Many have subtle symptoms or are asymptomatic and present later with tubal factor infertility, ectopic pregnancy, or chronic pelvic pain. Neisseria gonorrhoeae and Chlamydia trachomatis are the 2 most commonly recognized PID pathogens. Their ability to survive within host epithelial cells and neutrophils highlights a need for T-cell-mediated production of interferon γ in protection. Data indicate that for both pathogens, antibody can accelerate clearance by enhancing opsonophagocytosis and bacterial killing when interferon γ is present. A study of women with N. gonorrhoeae- and/or C. trachomatis-induced PID with histologic endometritis revealed activation of myeloid cell, cell death, and innate inflammatory pathways in conjunction with dampening of T-cell activation pathways. These findings are supported by multiple studies in mouse models of monoinfection with N. gonorrhoeae or Chlamydia spp. Both pathogens exert multiple mechanisms of immune evasion that benefit themselves and each other at the expense of the host. However, similarities in host immune mechanisms that defend against these 2 bacterial pathogens instill optimism for the prospects of a combined vaccine for prevention of PID and infections in both women and men.
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Affiliation(s)
- Toni Darville
- Departments of Pediatrics and Microbiology & Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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8
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de la Maza LM, Darville TL, Pal S. Chlamydia trachomatis vaccines for genital infections: where are we and how far is there to go? Expert Rev Vaccines 2021; 20:421-435. [PMID: 33682583 DOI: 10.1080/14760584.2021.1899817] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Chlamydia trachomatis is the most common sexually transmitted bacterial pathogen in the world. Antibiotic treatment does not prevent against reinfection and a vaccine is not yet available. AREAS COVERED We focus the review on the progress made of our understanding of the immunological responses required for a vaccine to elicit protection, and on the antigens, adjuvants, routes of immunization and delivery systems that have been tested in animal models. PubMed and Google Scholar were used to search publication on these topics for the last 5 years and recent Reviews were examined. EXPERT OPINION The first Phase 1 clinical trial of a C. trachomatis vaccine to protect against genital infections was successfully completed. We expect that, in the next five years, additional vaccine clinical trials will be implemented.
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Affiliation(s)
- Luis M de la Maza
- Department of Pathology and Laboratory Medicine Medical Sciences, I, Room D440 University of California, Irvine, California, USA
| | - Toni L Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sukumar Pal
- Department of Pathology and Laboratory Medicine Medical Sciences, I, Room D440 University of California, Irvine, California, USA
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9
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Zhong W, Darville T, Zheng X, Fine J, Li Y. Generalized multi-SNP mediation intersection-union test. Biometrics 2020; 78:364-375. [PMID: 33316078 DOI: 10.1111/biom.13418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/23/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022]
Abstract
To 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 the likelihood ratio test to detect mediation effect of multiple genetic variants via some mediator (e.g., 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 methods 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 methods. We believe our proposed methods 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.
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Affiliation(s)
- Wujuan Zhong
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xiaojing Zheng
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pediatrics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason Fine
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Statistics and Operations Research, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yun Li
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Computer Science, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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10
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Endocervical miRNA Expression Profiles in Women Positive for Chlamydia trachomatis with Clinical Signs and/or Symptoms Are Distinct from Those in Women Positive for Chlamydia trachomatis without Signs and Symptoms. Infect Immun 2020; 88:IAI.00057-20. [PMID: 32690634 DOI: 10.1128/iai.00057-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/10/2020] [Indexed: 12/26/2022] Open
Abstract
Chlamydia trachomatis is the leading cause of sexually transmitted infections that may progress to pelvic inflammatory disease and infertility. No effective vaccine exists for Chlamydia, nor are there biomarkers available that readily predict disease progression. In this cross-sectional pilot study, we recruited symptomatic and asymptomatic women with C. trachomatis (CT) infection and asymptomatic, uninfected control women from an urban sexually transmitted disease clinic to determine if there were differences in microRNA (miRNA) expression. Infected women with signs and/or symptoms (CTSS) have distinct miRNA profiles compared to asymptomatic infected women (CTNS). In the CTSS group, miR-142 and -147 showed 2.2- to 6.9-fold increases in expression. In the CTNS group, miR-449c, -6779, -519d, -449a, and -2467 showed 3.9- to 9.0-fold increases in expression. In the CTNS group, cyclins and cell cycle regulation and IL-17 pathways were likely downregulated, while the same signaling pathways were upregulated in the CTSS group. In addition, in the CTSS group, additional inflammatory pathways associated with TNFR1 and IL-8 appear to be upregulated. The miRNA expression patterns differ between CT-infected symptomatic and asymptomatic women, and these differences may warrant further study.
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11
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Dong L, Kollipara A, Darville T, Zou F, Zheng X. Semi-CAM: A semi-supervised deconvolution method for bulk transcriptomic data with partial marker gene information. Sci Rep 2020; 10:5434. [PMID: 32214192 PMCID: PMC7096458 DOI: 10.1038/s41598-020-62330-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/26/2020] [Indexed: 01/03/2023] Open
Abstract
Deconvolution of bulk transcriptomics data from mixed cell populations is vital to identify the cellular mechanism of complex diseases. Existing deconvolution approaches can be divided into two major groups: supervised and unsupervised methods. Supervised deconvolution methods use cell type-specific prior information including cell proportions, reference cell type-specific gene signatures, or marker genes for each cell type, which may not be available in practice. Unsupervised methods, such as non-negative matrix factorization (NMF) and Convex Analysis of Mixtures (CAM), in contrast, completely disregard prior information and thus are not efficient for data with partial cell type-specific information. In this paper, we propose a semi-supervised deconvolution method, semi-CAM, that extends CAM by utilizing marker information from partial cell types. Analysis of simulation and two benchmark data have demonstrated that semi-CAM outperforms CAM by yielding more accurate cell proportion estimations when markers from partial/all cell types are available. In addition, when markers from all cell types are available, semi-CAM achieves better or similar accuracy compared to the supervised method using signature genes, CIBERSORT, and the marker-based supervised methods semi-NMF and DSA. Furthermore, analysis of human chlamydia-infection data with bulk expression profiles from six cell types and prior marker information of only three cell types suggests that semi-CAM achieves more accurate cell proportion estimations than CAM.
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Affiliation(s)
- Li Dong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Avinash Kollipara
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Xiaojing Zheng
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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12
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Poston TB, Lee DE, Darville T, Zhong W, Dong L, O'Connell CM, Wiesenfeld HC, Hillier SL, Sempowski GD, Zheng X. Cervical Cytokines Associated With Chlamydia trachomatis Susceptibility and Protection. J Infect Dis 2020; 220:330-339. [PMID: 30820577 DOI: 10.1093/infdis/jiz087] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/26/2019] [Indexed: 01/05/2023] Open
Abstract
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.
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Affiliation(s)
- Taylor B Poston
- Department of Pediatrics, University of North Carolina at Chapel Hill
| | - De'Ashia E Lee
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill
| | - Wujuan Zhong
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | - Li Dong
- Department of Biostatistics, University of North Carolina at Chapel Hill
| | | | - Harold C Wiesenfeld
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine and the Magee-Womens Research Institute Pittsburgh, Pennsylvania
| | - Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine and the Magee-Womens Research Institute Pittsburgh, Pennsylvania
| | - Gregory D Sempowski
- Departments of Medicine and Pathology, Durham, North Carolina.,Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina
| | - Xiaojing Zheng
- Department of Pediatrics, University of North Carolina at Chapel Hill
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13
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Pathogenic Interplay Between Chlamydia trachomatis and Neisseria gonorrhoeae that Influences Management and Control Efforts—More Questions than Answers? CURRENT CLINICAL MICROBIOLOGY REPORTS 2019. [DOI: 10.1007/s40588-019-00125-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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14
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O'Connell CM, Brochu H, Girardi J, Harrell E, Jones A, Darville T, Seña AC, Peng X. Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis. MICROBIAL CELL 2019; 6:177-183. [PMID: 30854394 PMCID: PMC6402362 DOI: 10.15698/mic2019.03.672] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.
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Affiliation(s)
- Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hayden Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Jenna Girardi
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Erin Harrell
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Aiden Jones
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Arlene C Seña
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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15
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Zheng X, O'Connell CM, Zhong W, Poston TB, Wiesenfeld HC, Hillier SL, Trent M, Gaydos C, Tseng G, Taylor BD, Darville T. Gene Expression Signatures Can Aid Diagnosis of Sexually Transmitted Infection-Induced Endometritis in Women. Front Cell Infect Microbiol 2018; 8:307. [PMID: 30294592 PMCID: PMC6158555 DOI: 10.3389/fcimb.2018.00307] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/13/2018] [Indexed: 12/29/2022] Open
Abstract
Sexually transmitted infection (STI) of the upper reproductive tract can result in inflammation and infertility. A biomarker of STI-induced upper tract inflammation would be significant as many women are asymptomatic and delayed treatment increases risk of sequelae. Blood mRNA from 111 women from three cohorts was profiled using microarray. Unsupervised analysis revealed a transcriptional profile that distinguished 9 cases of STI-induced endometritis from 18 with cervical STI or uninfected controls. Using a hybrid feature selection algorithm we identified 21 genes that yielded maximal classification accuracy within our training dataset. Predictive accuracy was evaluated using an independent testing dataset of 5 cases and 10 controls. Sensitivity was evaluated in a separate test set of 12 women with asymptomatic STI-induced endometritis in whom cervical burden was determined by PCR; and specificity in an additional test set of 15 uninfected women with pelvic pain due to unknown cause. Disease module preservation was assessed in 42 women with a clinical diagnosis of pelvic inflammatory disease (PID). We also tested the ability of the biomarker to discriminate STI-induced endometritis from other diseases. The biomarker was 86.7% (13/15) accurate in correctly distinguishing cases from controls in the testing dataset. Sensitivity was 83.3% (5/6) in women with high cervical Chlamydia trachomatis burden and asymptomatic endometritis, but 0% (0/6) in women with low burden. Specificity in patients with non-STI-induced pelvic pain was 86.7% (13/15). Disease modules were preserved in all 8 biomarker predicted cases. The 21-gene biomarker was highly discriminatory for systemic infections, lupus, and appendicitis, but wrongly predicted tuberculosis as STI-induced endometritis in 52.4%. A 21-gene biomarker can identify asymptomatic women with STI-induced endometritis that places them at risk for chronic disease development and discriminate STI-induced endometritis from non-STI pelvic pain and other diseases.
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Affiliation(s)
- Xiaojing Zheng
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Wujuan Zhong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Taylor B Poston
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Harold C Wiesenfeld
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, PA, United States.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, Pittsburgh, PA, United States.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, United States
| | - Maria Trent
- Section on Adolescent Medicine, Department of Pediatrics, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Charlotte Gaydos
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brandie D Taylor
- Department of Epidemiology and Biostatistics, Texas A&M University, College Station, TX, United States
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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