Longitudinal plasma proteomics along a menstrual cycle highlights the regulatory effect of sex hormones on inflammatory and cardiometabolic circuits.

Sex hormones exert widespread effects on immune, metabolic, and cardiovascular physiology, yet their systemic impact in healthy women remains poorly characterised due to the scarcity of longitudinal molecular data across the menstrual cycle. Here, we carried out the first longitudinal, high-throughput plasma proteomics analysis of the menstrual cycle. We profiled 159 naturally cycling women from the Women4Health cohort, integrating plasma levels of 2,453 circulating proteins, 5 sex hormones, and 10 serum cardiometabolic phenotypes across four menstrual phases, enabling high-resolution mapping of dynamic proteomic changes. We identified 43 proteins differentially abundant across phases and hundreds associated with sex hormones and cardiometabolic phenotypes. These included proteins involved in extracellular matrix remodelling, immune regulation and hormone metabolism, such as beta-glucuronidase, previously described mainly as part of the microbial estrobolome and here for the first time identified in plasma. To investigate directional relationships, leveraging longitudinal measurements, we applied a cross-lagged structural equation modelling framework and validated its robustness through extensive simulations. With this approach we recovered expected links such as progesterone-mediated regulation of PROK1, as well as novel connections, including those linking IGFBP1 to both hormone and lipid levels. Many of the identified proteins have established causal roles in complex diseases. Our study provides the first proteomic atlas of the menstrual cycle and reveals mechanistic pathways underlying sex-hormone-driven regulation of inflammatory and cardiometabolic circuits.