Technical note: Use of laser capture microdissection for the localization of tissue-specific global gene expression in rumen papillae

Gene expression profiling of bovine rumen tissue has provided insight into dietary regulation of rumen epithelial function. However, most studies have relied on a heterogeneous sample with multiple tissue and cell types. The objective of this study was to use laser capture microdissection to characterize RNA expression profiling of epithelial and connective tissues of rumen papillae. Papillae were biopsied from 3 lactating dairy cows, frozen in cryomolds, cut into sections, stained, and dehydrated, and epithelial and connective cells were collected using laser capture microdissection. Total RNA was isolated from epithelial and connective tissue and global gene expression was assessed using the Affymetrix GeneChip Bovine Gene 1.0 ST array (Affymetrix, Santa Clara, CA). Data preprocessing was conducted using the robust multi-array average method, and detection of differentially expressed genes (DEG) was determined using ANOVA. The model included the fixed effect of tissue, and a Benjamini-Hochberg false discovery rate of 0.1 was applied to DEG. We found 382 DEG between epithelial and connective tissues. Analysis of these DEG using Ingenuity Pathway Analysis (Redwood City, CA) found that epithelial and connective tissues in rumen papillae expressed distinct RNA profiles (signatures). The epithelial signature was enriched with RNA encoding tight junction and metabolic genes, whereas connective signatures were enriched with RNA encoding proteins involved in cell structure and extracellular matrix composition. The molecular functions enriched within the top networks between the 2 tissues from the Ingenuity Pathway Analysis included connective tissue disorders, dermatological diseases and conditions, gastrointestinal disease, tissue morphology, and tissue development. In summary, it is possible to use laser capture microdissection for the localization of tissue-specific global gene expression in rumen papillae. This approach may be useful to improve the accuracy and interpretation of molecular measurements in future studies.