Identification of genes contributing to preterm birth: insights from genetic, transcriptomic, and epigenetic analyses

Preterm birth (PTB) is a global public health problem that has significant adverse effects on neonatal mortality and morbidity. Progress in understanding the pathological mechanisms underlying PTB has been greatly hampered by the complex and polygenic nature of the disease. As a result, a multifaceted approach may hold promise for identifying true causal factors. The main objective of this thesis is to identify genes that play a role in the etiology of PTB using experimental data derived from different molecular levels (genome, transcriptome, and epigenome). To achieve this goal, we performed association studies using a candidate gene approach to identify genetic factors contributing to PTB. Our analysis of genetic variants in three OXT pathway genes (oxytocin (OXT), oxytocin receptor (OXTR), and leucyl/cystinyl aminopeptidase (LNPEP)) revealed several common polymorphisms in LNPEP that show significant association with prematurity. Large-scale sequence analysis of the OXTR gene identified several novel rare coding variants that might be of etiologic importance. Our results suggest that these variants, in aggregate, appear to make some contribution to susceptibility to PTB. We also examined the gene expression profiles in the human placenta to identify, at the transcriptomic level, candidate genes for PTB. Using splicing-sensitive microarray and deep sequencing technologies, we identified transcriptome signatures that differ between term (with and without labor) and preterm placental tissues and between placental and other human tissues. The transcriptome data were analyzed not only at the gene-level, but also at the exon-level, enabling the detection of alternative splicing events. The exon-level analysis revealed more frequent disruption of alternative splicing in preterm than term placental tissues, indicating that alternative splicing may represent one possible mechanism contributing to PTB. Our study at the epigenomic level was pursued through investigation of placental DNA methylation profiles. We, using a genome-wide approach, detected a panel of genes showing labor- and gestational age-associated methylation differences. Selected genes were validated using bisulfite sequencing and methylation-specific PCR. SLC30A3, a validated differentially methylated gene between term labor and preterm labor amnion tissues, for instance, may potentially play a role in the pathogenesis of PTB. Taken together, this thesis work provides a valuable source of novel candidate genes for PTB, and future research using integrative systems biology approaches may shed light on the molecular mechanisms underlying this complex, heterogeneous disease.