Small scale transcript expression profile of Human first trimester placental villi analyzed by a custom-tailored cDNA array.

Human placental trophoblastic mass grows rapidly between 4 and 8 weeks of gestation making it highly vulnerable to external and internal challenges, however, there has been no reported study exploring the developmental molecular characteristics in human first trimester placental villi. In the present study, transcript expressions of human placental villi of normal pregnancies during 6 (n=6), 7 (n=6) and 8 (n=6) weeks of gestation using custom-tailored cDNA-based expression arrays for -400 annotated human gene products were examined. Unsupervised and supervised analyses of expression data revealed that 386 (95%) genes were overtly involved in the first trimester placental villi, and these genes segregated into three clusters specifically corresponding to 6-, 7- and 8-weeks of gestation in principal component analysis. Bayesian prediction analysis based on relative expression levels of genes studied identified that expression patterns in 15 samples out of 18 samples showed concordance with high (0.8-1.0) confidence measures with the chronological age of the placenta, however, two samples collected during 7-weeks of gestation and one sample collected during 8-weeks of gestation were predicted to be 6-weeks sample with confidence measures between 0.6 and 0.5. Unsupervised hierarchical clustering analysis segregated the samples into two major branches; while one of them was composed of five 7-weeks samples only, the second major branch had three sub-branches: one of them was exclusively composed of three 8-week samples only, while other two sub-branches were mainly composed of 6-weeks samples. K-means clustering analysis identified four optimal clusters of genes depending on the similarity of their relative expression for the set of genes studied across all the samples. Gene ontology (GO) based functional classifications of genes in K-means clusters revealed that the overall putative functions of co-regulated gene clusters were mutually comparable, however, specific genes related to ion homeostasis, metabolism, and VEGF activity specifically clustered in 8-weeks samples. Analysis of relative gene expression during in 6-8 week placental villi revealed that a large number of gene products were over represented by their either up-regulation (70 genes: approximately 18%) or down regulation (53 genes; approximately 14%) between 6 and 8 weeks villi samples and these genes are reportedly involved in biological processes like regulation of cell growth and proliferation, anti-apoptosis, angiogenesis, immune and inflammatory responses, extracellular matrix remodeling and multicellular organismal development involving almost all cellular components and molecular functions like signal transduction activity, transcription factor activity, nucleotide and protein binding, ion (especially calcium and zinc) binding and growth receptor activities. Interestingly, four genes (oxytocin receptor, tenascin C, TNF-R1 and retinol binding protein 1) showed differential regulation in human placental villi during 6-8 weeks of gestation, suggestive of an underlying network of regulation involving these factors in the developing placenta. To our knowledge, this is the first report indicating that these genes are involved in the early stage development of human placenta.