Time course analysis of large-scale gene expression in incised muscle using correspondence analysis. Time course analysis of large-scale gene expression in incised muscle using correspondence analysis

The time course of wound healing or the estimation of wound age is one of the most important research subjects in forensic pathology. In this study, we obtained microarray data of incision injury samples of mouse skeletal muscle at 3 different time points post-injury (6, 12, and 24 h). To visualize the time course fluctuation in gene expression on a plot, and to examine large-scale data using various analytical methods, correspondence analysis (CA) was carried out on microarray data that was converted to a matrix (data type is fold change (FC) values) consisting of data of each time point (columns) by each gene (rows) as variables. Genes were successfully clustered based on the magnitude relationship of FC values of 3 time series with a CA plot, which effectively visualizes the data of time course experiments. Overall design: Pathogen-free 8-week-old male BALB/c mice were divided into 4 groups (control, 6, 12, and 24 h after injury: n=4 each). After nasal anesthesia of mice with isoflurane, the skin on the dorsal side of the left hind limb was shaved, and about a 1-cm incision was made on the skin using sterile straight stainless-steel scissors. Then, a 5 mm incision was made in the biceps femoris muscle, and then the skin incision was closed using a silk suture. At 6, 12, and 24 h after injury, a 3-mm thick injured muscle tissue sample (about 30 mg) with the injury in the center was excised. As a control sample, biceps femoris muscle was collected from an uninjured mouse that was euthanized without making the injury.

伤口愈合的时间进程或损伤时间推断是法医病理学领域最为重要的研究课题之一。本研究获取了小鼠骨骼肌切割损伤后3个不同时间点（伤后6、12、24小时）的微阵列（microarray）数据。为实现基因表达时间进程波动的绘图可视化，并借助多种分析方法对大规模数据进行考察，我们将微阵列数据转换为以基因为行、各时间点为列的变量矩阵（数据类型为倍数变化（fold change, FC）值），并对该矩阵开展了对应分析（correspondence analysis, CA）。研究成功基于3个时间序列的FC值大小关系，通过CA绘图完成了基因聚类，该方法可有效实现时间进程实验数据的可视化。实验设计：选取无特定病原体（Pathogen-free）8周龄雄性BALB/c小鼠，随机分为4组：对照组、伤后6小时组、伤后12小时组、伤后24小时组，每组n=4。以异氟烷（isoflurane）对小鼠进行鼻内麻醉后，剃除左侧后肢背侧皮肤，使用无菌直头不锈钢剪刀在皮肤上制作约1cm的切口。随后在股二头肌（biceps femoris muscle）上制作5mm的切口，再以丝线缝合皮肤切口。分别于伤后6、12、24小时，切取以损伤部位为中心的3mm厚损伤肌组织样本（重量约30mg）。对照组样本则取自未实施造模手术、直接安乐死的小鼠的股二头肌。