Prenatal Trace Metal Exposures and Genetic Variants Inform Birth Weight-related Placental Isoform Expression

Background: Placental gene expression patterns are increasingly recognized as functional targets associated with birth outcomes. However, studies to date do not capture transcript-level specification, an important resource for adaptive responses during fetal development. In this study, we conducted a genome-wide analysis to characterize differential transcript usage (DTU) in the placenta with respect to prenatal trace metal exposure, genetic variants, and birth weight. Methods: RNA sequencing was performed in placenta samples from the Rhode Island Child Health Study (n=199). A panel of essential and nonessential metals were measured in maternal toenails (Al, As, Cd, Cr, Cu, Fe, Mn, Mo, Ni, Pb, Sb, Se, Sn, U, V, Zn) and placenta (Ca, Cd, Co, Cu, Fe, K, Mg, Mn, Mo, Na, P, S, Se, Zn) using ICP-MS. DTU was assessed using the DRIMSeq R package to contrast infants small (SGA) and appropriate (AGA) for gestational age and infants above and below median trace metal exposure levels. Genetic variants that influence transcript usage were identified using the sQTLseeker R package. Results: We identified 82 genes demonstrating DTU in association with SGA status at an FDR < 0.05. Among the trace metals, placental transcript expression levels were most sensitive to Sn (n=377 genes) and Cd (n=73 genes) exposures measured in maternal toenails. Transcript proportions of LAMTOR4, a lysosome regulator implicated in neurodegenerative diseases, varied in association with SGA status, Sn and Cd levels measured in toenails, Ca levels measured in placenta, and genotypes across three local genetic variants (rs10231604, rs12878, and rs3736591). Discussion: We report a comprehensive genome-wide characterization of placental transcript usage and associations with prenatal trace metal exposure, genetic variants, and fetal growth restriction. These results highlight the utility of interrogating the transcriptome at transcript-level resolution to identify novel placental biomarkers of outcomes jointly impacted by genetic polymorphisms and environmental exposures.