Mucosal effects of tenofovir 1% gel wane over longer-term use but retain pro-proliferative and type I/III interferon pathway signatures [MTN014_Vagina]

The nucleotide reverse transcriptase inhibitor (NRTI) tenofovir has been extensively tested as a topical preventative against vaginal and rectal HIV transmission. We sought to determine how use of this product affects gene expression. We used samples from MTN-014, a study of vaginal and rectal gel application. We obtained vaginal biopsies before treatment initiation and after two weeks of daily use of tenofovir 1% gel applied rectally or vaginally. We isolated RNA from vaginal biopsies preserved with RNAlater. Gene expression was measured from all three samples (three time points) from each participant. Gene expression was measured by Illumina HumanHT-12 v4 Expression BeadChips. Samples were paired with samples taken at baseline (pre-treatment) and after two weeks of daily gel use. Vaginal biopsies were preserved with RNAlater at -80 degrees C. Samples were not replicated on the arrays. During quality control assessment, two pairs of samples were determined by gene expression profiles to have been switched. In both cases, the pairs were physically adjacent during sample processing and the sample labeled “rectum” had gene expression consistent with vagina and vice versa. The two pairs are B11 (GSM8520898)/B12 (GSM8520862) and D10 (GSM8520864)/D11 (GSM8520894). The labeling has been corrected here so that the samples match their gene expression profiles.

核苷酸逆转录酶抑制剂（nucleotide reverse transcriptase inhibitor, NRTI）替诺福韦已被广泛应用于阴道及直肠HIV传播的局部预防研究。本研究旨在明确该产品的使用对基因表达的影响。我们使用了来自MTN-014研究的样本，该研究考察了阴道及直肠凝胶给药方案。我们在治疗开始前，以及每日使用1%替诺福韦凝胶（经直肠或阴道给药）两周后，获取阴道活检样本。我们从经RNAlater保存的阴道活检样本中提取RNA。对每位受试者的全部三个样本（对应三个时间点）进行基因表达量检测。基因表达量通过Illumina HumanHT-12 v4表达微珠芯片（Illumina HumanHT-12 v4 Expression BeadChips）进行测定。将样本与基线（治疗前）及每日使用凝胶两周后的样本进行配对分析。阴道活检样本经RNAlater保存后置于-80℃冰箱储存。所有样本未在芯片上进行重复检测。在质量控制评估环节，通过基因表达谱分析发现有两对样本存在标记混淆。两起案例中，混淆的样本在样本处理过程中物理位置相邻，且被标记为“直肠”的样本的基因表达谱符合阴道组织特征，反之亦然。该两对混淆样本分别为B11（GSM8520898）/B12（GSM8520862）以及D10（GSM8520864）/D11（GSM8520894）。本次数据已修正样本标记，使样本信息与其基因表达谱完全匹配。