Validation of genes with a putative role in the pathophysiology of endometriosis and adenomyosis by using NanoString
Description
An RNA-Seq discovery study using endometrial samples (19 controls, 8 ovarian, 4 deep-infiltrating endometriosis, and 6 adenomyosis) identified differentially expressed genes. In the discovery study, four candidates (GADD45G, PJA2, GGT8P, and HSPA1A) correctly distinguished between disease and controls (accuracy=0.86). Eleven phenotypic characteristics (e.g. dysmenorrhea and hypermenorrhea) were used in combination with gene expression data to generate hybrid classifiers and the predictive power increased (accuracy=0.977). The validation by Nanostring (n=285) showed an accuracy=0.5 when using solely genetic data and an accuracy=0.72 with a combination of genetic and phenotypic data. Only women between 18 and 49 years old were included. A complete clinical history review was done to exclude patients with heritable diseases or with viral infections, such as HIV, VHB, and VHC. The control, endometriosis, and adenomyosis groups were women who went to the clinic because they had gynecological symptoms such as pelvic pain, hypermenorrhea, or dysmenorrhea. Thus, an endometrial biopsy was taken for histological analysis. Women presenting only one specific type of endometriosis and/or adenomyosis were included, for example, patients with endometriosis suffered only from ovarian endometriosis (OE) or deep infiltrating endometriosis (DIE) exclusively. Collected samples were selected from women without history of endometriosis or adenomyosis in the past seven to ten years from the collection of the biopsy. Endometriosis cases were proven by laparoscopy, and adenomyosis patients by laparoscopy and/or TVUS. Women who were undergoing hormone treatment, such as oral contraceptives, were not excluded. In total, 285 blocks of formalin-fixed paraffin embedded (FFPE) endometrium, including endometriosis, adenomyosis, and control samples, were obtained retrospectively from the Pathological Anatomy Department of Vall d’Hebron University Hospital. These samples comprised 110 control, 58 OE, 60 DIE and 57 Adeno (adenomyosis) specimens. Samples were collected using a pipelle under an approved protocol after obtained written informed consent. Use of specimens was approved by the Ethics Committee of Vall d’Hebron Research Institute, Barcelona (Spain) under approval number PR(AMI)410/2016 on the 7th of July 2017 and all experiments were performed in accordance with relevant guidelines and regulations. The stage of menstrual cycle was determined by histological examination according to Noyes et al. This dataset includes the raw files from the Validation study by using a custom NanoString codeset (RCC files) (n=285), as well as the excel file with the normalized data for each gene studied and the housekeeping genes (and positive and negative controls from the manufacturer) and one excel file with the metadata of each of the 285 patients.