254: Gene expression network analysis in aneuploid human trophoblast progenitor cells (TBPC) reveals modular structures

Abstract

Eigengene network analysis enables the interpretation of relationships between gene transcripts according to cellular processes and pathways. Comparison of transcript products from aneuploid and normal trophoblast progenitor cell (TBPC) lines could improve the understanding of regulatory mechanisms of placental function in pregnancies associated with deficient placentation e.g., miscarriage, pre-eclampsia, IUGR. Three TBPC lines from each common human trisomies (Trisomy 13, 18, 21; n=9) and three age-matched euploid cell lines (n=3) were derived from placentas (gestational age 14-22 weeks) via methods described by Genbacev et al (Stem Cells 2011). Cells expressing the TBPC marker Integrin-α4 were isolated by fluorescent activated cell sorting. Ploidy of all cell lines was confirmed by karyotype. Eigengene network analysis of transcriptional profiles was used to identify differentially expressed genes. Top genes (n=2000) were selected that reflect the maximum average difference between trisomy and control while minimizing intra-group (control and each trisomy) variance. Karyotype stable lines derived from euploid, Trisomy 13, 18, and 21 placentas underwent microarray transcriptome analysis (Fig 1). Weighted gene co-expression networks were constructed and gene co-expression modules (n=7) were identified by average linkage hierarchical clustering (Zhang and Horvath, PMID: 16646834, 2005). These modules grouped densely interconnected genes and identified classes of over-represented patterns contrasting euploid and trisomic TBPCs. For example, module 1 identified 650 genes involved in collagen generation (COL1A1,3A1,5A1), epithelial-to-mesenchymal transition (VNT, ECM receptor interaction, LAMB2), invasion (TNF signaling), and immune privilege (HLG-A,B,C,E,F,G) (Fig 1). All of these are essential for normal placental growth and development (Fig. 1). Gene co-expression networks constructed from trisomic TBPC cell lines provide a systems-level view of underlying biological patterns involving common aneuploidies. Identified modules suggest novel candidate pathways that may contribute to abnormal TB function in complicated pregnancies, and warrant further functional investigation.