Data for: "Immune activation in the female genital tract: Expression profiles of soluble proteins in women at high risk for HIV infection" – User Guide

Permanent identifier

https://doi.org/10.17037/DATA.104

Data Creators

Suzanna C. Francis, Yanwen Hou, Kathy Baisley, Janneke van de Wijgert, Deborah Watson-Jones, Trong T. Ao, Carolina Herrera, Kaballa Maganja, Aura Andreasen, Saidi Kapiga, Gary R. Coulton,Richard J. Hayes, Robin J. Shattock

Description

An anonymised dataset containing details of a sub-study of 100 HIV-negative women in 2009. This sub-study was part of a microbicide feasibility study in North-West Tanzania that was carried out between 2008-2010. It contains information on sexual behaviour, vaginal practices, current contraception, STI symptoms, as well as results of a clinical and colposcopic examination.

Data collection methods

This study was nested within a 12 month microbicide feasibility study of 970 HIV-negative women aged 18–44 years working in bars, hotels, and other food and recreational facilities in the three towns of Geita, Shinyanga and Kahama in northwestern Tanzania from 2008-2010. Participants enrolled in the sub-study were followed up three times a week for 4 weeks (12 visits total). At enrolment, interviews were carried out to obtain information about sexual behaviour, vaginal practices, current contraception, and STI symptoms. On the first and last visit (visits 1 & 12), a clinical and colposcopic examination were performed; cervical and vaginal swabs were collected to test for vaginal pH and reproductive tract infections (Chlamydia trachomatis, Neisseria gonorrhoeae, Trichomonas vaginalis, bacterial vaginosis,  and yeast); and a CVL was obtained for the detection of Herpes simplex virus, types 1 and 2 (HSV), prostate-specific antigen (PSA) to measure seminal plasma exposure in the last 48 hours, soluble immune proteins, haemoglobin and white blood cells (WBCs). During visits 2 to 11, a shortened interview was conducted to obtain updated sexual behaviours and intravaginal practices. A brief clinical examination was performed to obtain vaginal swabs for testing vaginal pH, bacterial vaginosis and yeast, and a CVL for the detection of HSV, PSA, soluble immune proteins, haemoglobin and WBCs. Urine was collected at every visit to test for pregnancy and menstrual cycle phase. If a woman was menstruating, no genital samples were obtained on that visit. No blood samples were collected; however laboratory data from the main cohort on HSV antibody status, HIV status and syphilis results were available for the statistical analysis and methods have been reported in a previous study. Colposcopy was carried out by trained clinicians according to the CONRAD/WHO revised manual for the Standardization of Colposcopy for the Evaluation of Vaginal Products

Data analysis and preparation

We restricted the data set to “healthy visits” defined as visits without a positive STI test or reproductive tract infection. Visits were excluded from this dataset if results were positive for HSV shedding, vaginal yeast or bacterial vaginosis. In addition, all follow-up visits for women who tested positive at the first or last visit for C. trachomatis, N. gonorrhoeae, and T. vaginalis were excluded from this analysis.

CVL samples with analyte concentrations below the lower limit of quantification (LLOQ) of the assay were assigned a concentration of half the LLOQ. Those above the upper limit of quantification (ULOQ) were assigned values twice the ULOQ. Spearman’s rank correlation coefficient was calculated for each of the analytes within a Luminex panel to look for evidence of cross-reactivity.

The proportion of samples with concentration above the LLOQ, and the median and range of concentrations above the LLOQ, were calculated for each analyte. Since most analytes showed skewed distribution, concentrations were log10 transformed. To characterize the variation of the analytes over time between and within women, we used mixed-effects linear regression to estimate the ICC of each log-transformed value; variance components were estimated using residual maximum likelihood. The ICC was calculated as σB2/ (σB2 + σW2), where σB2 is the between-women variance and σW2 is the within-woman variance. An ICC of 0 implies that observations from the same woman are no more similar to each other than they are to observations from different women. An ICC of 1 implies that all observations from the same woman are identical, so that the variation is due to between-woman differences. We also explored the effects of the dilution factor of the CVL by ICC.

We examined the association of analytes concentrations with the following exposures: menstrual cycle stage, hormonal contraception (reported use of combined oral contraceptive [COC] or injectable depot medroxyprogesterone acetate [DMPA]), seminal plasma, reported vaginal practices, cervical ectopy, colposcopic findings, and vaginal pH. Since detailed clinical examinations were only done at Visits 1 and 12, ectopy and colposcopy results were not available at other time points. To explore the association with the exposures of interest, we used mixed-effect linear regression for analytes with concentration >85% above LLOQ, or logistic regression with random effects for analytes with concentration ≤85% above LLOQ.

For the analysis, PSA was categorised into three levels: no PSA detected; low positive (<4ng/ml); and high positive (≥4ng/ml). Neutrophil counts were categorised into the following levels per 100 WBCs: no cells, 1–10 cells, 11–50 cells, >50 cells, and lymphocytes were analysed as presence/ absence. Vaginal pH results were categorised into the following levels:  3.6-4.1 (normal pH); 4.4-4.7 (high normal pH); and 5.0 and above (abnormal pH).

For each of the analyses of intravaginal cleansing with soap, intravaginal cleansing with cloth, and intravaginal insertion (i.e. the insertion of pulverized herbs or detergents), we compared samples from visits in which women reported the specific intravaginal practice to visits in which no cleansing or cleansing with fingers and water only was reported. We excluded visits in which women reported insertion of prescribed medications (e.g. treatment for candidiasis), leaving all but two women inserting detergents.

In the multivariable analysis, we considered age, reported sex in the past 3 days, and the presence of haemoglobin in the CVL as a priori confounders based on a conceptual model. For menstrual cycle phase, hormonal contraceptive use, intravaginal practices, clinical cervical ectopy, colposcopic abnormalities, and vaginal pH we controlled for the effects of age, reported sexual intercourse in the past three days and presence of haemoglobin; for PSA we controlled for age and presence of haemoglobin.

Additional information

This dataset cannot be made available through the repository due to ethical restrictions. Interested researchers may submit request for de-identified data to Saidi.Kapiga@lshtm.ac.uk.

Quality controls

All positive tests for N. gonorrhoeae were confirmed using specific primers to the 16S DNA coding region in PCR in-house assays.

We measured PSA at every visit using a quantitative PSA ELISA Kit (Calbiotech, Inc, Spring Valley, CA, USA) for the detection of PSA in human serum for cancer detection. A random selection of CVL supernatant aliquots were shipped to the Institute of Tropical Medicine in Antwerp, Belgium for evaluation against the SERATEC PSA Semiquant (Göttingen, Germany). The SERATEC test is a semi-quantitative chromatographic immunoassay also originally developed for human serum for cancer detection, and subsequently validated for the detection of PSA in vaginal fluid for professional forensic purposes with a sensitivity and specificity of 100% . The Calbiotech test was found to be 70% sensitive and 100% specific for PSA in the cervical vaginal lavages against SERATEC when combining low positive (<4ng/ml) and negative values.

Geographic regions

Geita, Shinyanga and Kahama in northwestern Tanzania

Key dates

• Date collected: 2008 - 2010
• Date published: 24 November 2015

Population

100 HIV-negative women living in North-West Tanzania

Privacy

Personal identifiers were removed prior to analysis.

Ethics

All study procedures were approved by the ethics committees of the London School of Hygiene and Tropical Medicine and the Medical Research Coordinating Committee of the Tanzanian National Institute for Medical Research. All participants received detailed information about the study to ensure that they understood why the study was being carried out and what the study involved. Informed consent was obtained by signature if literate, or thumb-printed and witnessed (if illiterate) prior to their participation in the study.

Keywords

Cytokines, Chemokines, HIV, Microbicides, Vaccines, Sub-Saharan

Language of written material

English

Project information

Financial support for the Biomarkers Project was provided by the European and Developing Countries Clinical Trials Partnership (project code: CT_ct_05_32070_002), the European Combined Highly Active Retroviral Microbicides (CHAARM-FP7 - Grant agreement n°242135 -www.chaarm.eu), the International Partnership for Microbicides, the Medical Research Council (MRC) and Department for International Development (DFID) with S.C. Francis (G1002369), R.J. Hayes and K. Baisley (G0700837) receiving MRC & DFID support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Creators

Copyright holders

• London School of Hygiene & Tropical Medicine, London, United Kingdom
• St George's, University of London, London, United Kingdom
• University of Liverpool, Liverpool, United Kingdom
• Imperial College London, London, United Kingdom
• National Institute for Medical Research

File description