ABSTRACT:To gain insight into specific gene expression in the gastrointestinal (GI) tract of preterm infants, we adapted a method to isolate exfoliated epithelial cells. Gastric residual fluid aspirates (n ϭ 89) or stool samples (n ϭ 10) were collected from 96 neonates (gestational age, 24 -36 wk). Cells were characterized by microscopic observation, cytokeratin-18 immunodetection, and expression of transcripts. The human origin of cellular DNA was confirmed by amplification of specific X and Y chromosome sequences. Isolation yielded 100 -500 cells per sample for gastric aspirates (n ϭ 8) and 10 -20 cells for fecal samples (n ϭ 5). Epithelial origin was confirmed by immunodetection of cytokeratin 18. Analyses of reverse transcribed products, using two independent methods, from 15 gastric fluid and two stool samples showed that 18S-rRNA and transcripts of beta-actin, glyceraldehyde-3-phosphate dehydrogenase (gapdh), and period1 were in quantities corresponding to at least 10 cells. On 59 aspirates, we found beta-actin transcripts (all but one), cytokeratin 18 (eight positive of eight samples), SLC26-A7-1 ( I nvestigation of gene expression in the gastrointestinal (GI) tract commonly relies on the analysis of tissue biopsies. The performance of tissue biopsies, however, is unethical in human neonates. Exfoliated or sloughed cells are naturally lost by mammals in their environment and have been used as surrogates for target cells to predict the response to bioactive food components (1) or to detect biomarkers of cancer in children with inflammatory bowel disease (2) and cancer in adults (3). Yet, the feasibility of this approach has not been assessed for the exploration of neonatal GI tract.Our aims were to determine the feasibility of this approach in human infants and assess the number, quality, and lineage of cells exfoliated that can be recovered from gastric and intestinal lumen in premature infants and to evaluate whether these cells can be used to measure the expression of specific genes of interest in a "noninvasive" fashion and thus serve as surrogates for true invasive tissue biopsy specimens. The ability to use exfoliated cells instead of biopsy or autopsy material would be highly useful to evaluate disease biomarkers in therapeutics and to explore GI functional maturation (4). We have chosen to assay clock genes as well because (1) these genes are believed to be ubiquitous in somatic cells of mammals and may be modulated in the GI tract by food intake (5) and (2) we detected the expression of these genes in cells from intestinal biopsy specimens obtained in adults in earlier studies (6). To our knowledge, even though the ability of feeding to induce and synchronize the expression of these genes has been extensively studied in peripheral tissues in laboratory rodents (7), this has not been explored in human infants, whether full term or preterm. In newborn rats, a common animal model used in neonatology (8), breast-feeding was shown to alter the circadian rhythm of the clock in the liver, with the beginn...