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Ectopic pregnancy is defined as a pregnancy implanted outside the uterus, and >98% implant in the Fallopian tube. It has a major clinical and socioeconomic impact worldwide. The diagnosis of ectopic pregnancy is often difficult and resource intensive owing to a lack of accurate biomarkers, and there is a need for improved medical management of ectopic pregnancy using new or adjuvant treatments. The aetiology of ectopic pregnancy is uncertain, but tubal implantation is probably due to retention of the embryo in the Fallopian tube owing to impaired embryo-tubal transport and alterations in the tubal microenvironment. This comprehensive review of the literature supporting current understanding of the endocrinology of Fallopian tube biology and tubal implantation focuses on genes expressed in the Fallopian tube regulated by oestrogen and progesterone and discusses their potential functions. It concludes with a discussion of how advances in this field are enabling the development of novel biomarkers and could lead to the identification of potential new treatments for ectopic pregnancy.