Placental cis-eQTL analysis identifies preeclampsia-dependent genetic regulation at promoters

Yazgeldi Gunaydin, G.; Leinonen, J.; Ezer, S.; Kajantie, E.; Kivinen, K.; Heinonen, S.; Pouta, A.; FINNPEC Group,; Laivuori, H.; Wedenoja, S.; Kere, J.; Katayama, S.

doi:10.64898/2026.10.05.756656

bioRxiv · 10.64898/2026.10.05.756656

Placental cis-eQTL analysis identifies preeclampsia-dependent genetic regulation at promoters

Yazgeldi Gunaydin, G.·Leinonen, J.·Ezer, S.·Kajantie, E.·Kivinen, K.·Heinonen, S.·Pouta, A.·FINNPEC Group,·Laivuori, H.·Wedenoja, S.·Kere, J.·Katayama, S.

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Abstract

Background: Preeclampsia (PE) is a hypertensive pregnancy disorder with contributions from both maternal and fetal genetic factors, but how both genomes regulate placental transcription remains incompletely understood. Results: We analyzed placental 5'-end RNA sequencing data from 59 pregnancies in the FINNPEC cohort and performed separate maternal and fetal cis-eQTL analyses using gene-level expression and promoter-level expression defined as Transcript Far 5' Ends (TFE). Genotype-by-PE interaction models were used to identify genetic effects that differ according to PE status. No gene-level interaction eQTLs remained significant after multiple-testing correction, although suggestive signals included LILRB2 in the maternal and LPCAT3 in the fetal analyses. In contrast, we identified two significant syntenic promoter-level interaction eQTLs: rs12504642-TFE61820 at the FHDC1 locus in the maternal analysis and rs1557150-TFE9032 at the PPIAP31 locus in the fetal analysis. Conclusion: These findings suggest that PE-dependent genetic interaction effects may be detectable at specific transcript promoter regions even when they are not captured at annotated gene levels.

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Yazgeldi Gunaydin, G., Leinonen, J., Ezer, S., Kajantie, E., Kivinen, K., Heinonen, S., Pouta, A., FINNPEC Group,, Laivuori, H., Wedenoja, S., Kere, J., Katayama, S.. 2026-10-07. Placental cis-eQTL analysis identifies preeclampsia-dependent genetic regulation at promoters. https://doi.org/10.64898/2026.10.05.756656

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