Maternal plasma cell-free RNA as a predictor of early and late-onset preeclampsia throughout pregnancy

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Early- and late-onset preeclampsia (EOPE and LOPE) pose serious maternal-fetal risks, yet non-invasive early prediction remains challenging. In a prospective cohort of 9,586 pregnancies, we analyze trimester-specific plasma cell-free RNA (cfRNA) profiles from 42 EOPE and 43 LOPE cases versus 131 normotensive controls. Organ-specific transcriptomic shifts distinguish EOPE from LOPE. Predictive models based on cfRNA signatures identify EOPE up to 18.0 weeks before clinical onset in the first-trimester (T1) (AUC = 0.88), and 8.5 weeks in the second trimester (T2) (AUC = 0.89). LOPE is predicted 14.9 weeks in advance using T2 data (AUC = 0.90), while T1 performance is lower (AUC = 0.68). External validation confirms robust EOPE prediction (AUC = 0.87 at T1; 0.81 at T2) and acceptable LOPE performance (AUC = 0.63 at T1; AUC = 0.77 at T2). EOPE models are enriched for decidual transcripts, suggesting early maternal involvement; LOPE models reflect broader tissue contributions. These findings offer a path to early, non-invasive, subtype-specific preeclampsia risk stratification and prevention. Early- and late-onset preeclampsia pose serious maternal-fetal risks, yet non-invasive early prediction remains challenging. Here, the authors show that cfRNA signatures reveal distinct decidual and multiorgan signals, enabling accurate, externally validated prediction of both subtypes.