Oviductal vs. ovarian epithelial transformation yields very different tumor phenotypes in Apc fl/fl;Pten fl/fl mice. Mus musculus

We treated 6-8 week old mice that had floxed alleles of both Apc and Pten (for both alleles in each case) that also carry an Ovgp1-iCre-ERT2 transgene, with one of two treatments; a third group received neither treatment. The Ovgp1-iCre-ERT2 expresses Cre recombinase fused to a tamoxifen-inducible fragment of the estrogen receptor, in tissues where the Ovgp1 gene (oviductal glycoprotein 1) is expressed, which is almost exclusively in mouse oviductal epithelium (equivalent to human fallopian tube epithelium = FTE). Treating the mice with tamoxifen permits the Cre recombinase to enter the cell nucleus and inactivate the Apc and Pten genes. Six of the mice were treated with intraperitoneal injection of tamoxifen (0.1g/kg of body weight) dissolved in corn oil on days 1 and 3 and developed oviductal tumors (OdT) yielding 6 of the samples. Four mice (yielding 5 samples) were instead injected with 50 million plaque-forming units of replication-incompetent AdCre into both ovarian bursal cavities on day 1, which inactivated Apc and Pten in the ovarian surface epithelium (OSE), and lead to ovarian tumors (OT). Ovaries were also harvested from four untreated 6-8 week old mice with the same genotype, with two ovaries from each mouse comprising one control sample. RNA was purified from tumor or normal tissue, and targets for Affymetrix arrays synthesized from the mRNAs. We used Affymetrix Mouse Gene 2.1 ST arrays, which hold 41345 probe-sets, but we largely analyzed just those 25216 probe-sets that were mapped to Entrez gene IDs. Raw data was processed with Robust Multi-array Average algorithm (RMA). Data is log2-transformed transcript abundance estimates. We fit a one-way ANOVA model to the three groups of samples. We supply a supplementary excel workbook that holds the same data as the data matrix file, but also holds the probe-set annotation at the time we analyzed the data, and some simple statistical calculations, which select subsets of the probe-sets as differentially expressed. Consumers should consider obtaining more up-to-date probe-set annotation for the array platform. We also provide supplementary excel files that show our simple analysis of GSE6008, which consists of 99 human ovarian tumor samples of 4 types, and 4 normal ovary samples, where we fit an ANOVA model to the 5 groups. In yet another supplementary file we show the correlation between each human tumor and mouse tumor, where we correlate the difference in log2-transformed values of each tumor from the average of the normals for the same species, for just those genes that were 1-to-1 best homologs according to build 68 of NCBI's Homologene, in order to see how much the human tumors resemble the mouse tumors. Overall design: Six oviductal tumor samples from 6 mice with conditional knockout of Apc and Pten driven by an Ovgp1-iCre-ERT2 transgene , 5 ovarian tumor samples from 4 mice with conditional knockout of Apc and Pten driven by injection of AdCre into both ovarian bursal cavities, and 4 normal ovary samples from 4 mice.

我们对同时携带Apc与Pten两个等位基因的floxed等位基因（即两个等位基因均经flox修饰）且带有Ovgp1-iCre-ERT2转基因的6-8周龄小鼠施以两种处理之一，另有第三组小鼠不接受任何处理。Ovgp1-iCre-ERT2可在表达Ovgp1基因（输卵管糖蛋白1，oviductal glycoprotein 1）的组织中，表达与雌激素受体他莫昔芬诱导型片段融合的Cre重组酶；而Ovgp1基因几乎仅在小鼠输卵管上皮（对应人类输卵管上皮，fallopian tube epithelium, FTE）中表达。对小鼠施以他莫昔芬处理可使Cre重组酶进入细胞核并灭活Apc与Pten基因。其中6只小鼠于第1天和第3天通过腹腔注射溶于玉米油的他莫昔芬（剂量为0.1g/kg体重），最终形成输卵管肿瘤（OdT），共获得6份样本。另有4只小鼠（共获得5份样本）于第1天向双侧卵巢囊腔注射5000万噬斑形成单位的复制缺陷型AdCre，该处理可在卵巢表面上皮（ovarian surface epithelium, OSE）中灭活Apc与Pten基因，并诱发卵巢肿瘤（OT）。我们还从4只同基因型的未处理6-8周龄小鼠中获取卵巢，每只小鼠的2个卵巢组成1份对照样本，共获得4份正常卵巢样本。从肿瘤或正常组织中纯化核糖核酸（RNA），并以mRNA为模板合成Affymetrix芯片的杂交靶标。我们使用的Affymetrix小鼠基因2.1 ST芯片包含41345个探针组，但主要分析了其中25216个已映射至Entrez基因ID的探针组。原始数据采用稳健多数组平均算法（Robust Multi-array Average, RMA）进行处理，数据为log₂转换后的转录本丰度估计值。我们对三组样本拟合了单因素方差分析（one-way ANOVA）模型。我们提供了一份补充Excel工作簿，其中包含与数据矩阵文件完全一致的数据集，同时收录了我们分析时的探针组注释信息与部分简单统计计算结果，该部分可筛选出差异表达的探针组子集。使用者可考虑获取该芯片平台更新版本的探针组注释信息。此外，我们还提供了针对GSE6008数据集的简单分析补充Excel文件：该数据集包含99份分为4种类型的人类卵巢肿瘤样本与4份正常卵巢样本，我们针对这5组样本拟合了方差分析模型。在另一补充文件中，我们展示了各人类肿瘤与小鼠肿瘤之间的相关性：我们仅针对NCBI Homologene数据库第68版中鉴定的一对一最佳同源基因，计算各肿瘤相对于同物种正常样本平均值的log₂转换值之差的相关性，以此评估人类肿瘤与小鼠肿瘤的相似程度。本数据集的整体实验设计如下：6份输卵管肿瘤样本，来自6只通过Ovgp1-iCre-ERT2转基因介导的Apc与Pten条件性敲除小鼠；5份卵巢肿瘤样本，来自4只通过向双侧卵巢囊腔注射AdCre介导的Apc与Pten条件性敲除小鼠；以及4份正常卵巢样本，来自4只同基因型未处理小鼠。