Amy P. N. Skubitz

Ascites, the pathological accumulation of fluid in the peritoneal cavity, is common at diagnosis and with recurrence in high‐grade serous ovarian carcinoma (HGSOC). Higher volumes of ascites fluid are associated with greater likelihood of recurrent disease and poor prognosis. Due to its availability—volume and frequency—and its reflection of tumors and their microenvironments, ascites is a valuable resource for proteomic biomarker discovery. However, ascites has not been widely studied. Similar to plasma, relatively few proteins comprise the majority of the broad dynamic range of protein mass in ascites fluid, necessitating an enrichment or depletion strategy for proteomic sample preparation. ENRICH‐iST and ENRICHplus kits enrich low‐abundance proteins using paramagnetic beads. These enrichment strategies have not previously been validated for use with ascites fluid. Our goal was to evaluate the ENRICH‐iST and ENRICHplus kits using ascites fluid from HGSOC patients with differing extents of tumor resection during debulking surgery. This Dataset Brief describes the technical performance of these enrichment strategies based on DIA–MS proteome depth, reproducibility of identified proteins, Gene Ontology (GO) term enrichment (Biological Processes, Molecular Functions, and Cellular Components), and Human Protein Atlas‐based protein abundance ranking. ENRICHplus outperformed ENRICH‐iST by 1.4‐fold based on depth of proteome coverage. Relative to the total proteome coverage, ENRICH‐iST reduced the proportional contribution of the top 12 high‐abundance proteins more effectively than ENRICHplus, thereby increasing the representation of lower‐abundance proteins despite identifying fewer overall proteins. Analysis of the differential abundance of the proteins enriched from ascites fluid using these enrichment strategies could greatly facilitate HGSOC biomarker development.

Earlier detection is strongly associated with increased survival for women with ovarian cancer. Unfortunately, current screening strategies, employing serial serum or ultrasound assessments, lack adequate sensitivity and specificity for use in the low-prevalence general population. In contrast, screening for cervical cancer by Pap tests has been routinely performed for over 50 years. Since ovarian cancer cells have been observed in Pap tests, ovarian cancer protein biomarkers may also be present; yet Pap samples have not been rigorously examined for diagnostic proteins. Assessment of cervical effluent, as can be collected in a Pap test, has the potential to differentiate ovarian cancer cases from healthy controls, and thereby demonstrate that intra-abdominal pathology may be detected using this commonly acquired specimen. We hypothesize that proteins shed by ovarian cancer cells can be detected in the SurePath™ liquid-based Pap test fixative using mass spectrometry (MS)-based proteomics, making it possible to distinguish women with ovarian cancer from healthy women. Candidate ovarian cancer biomarkers were successfully identified in liquid-based Pap test samples from 20 cases of high grade serous ovarian cancer, 10 benign ovarian conditions, and 10 healthy control samples, by performing Tandem Mass Tag™ isobaric labeling, 2D liquid chromatography-MS/MS, and bioinformatics integration. Selected reaction monitoring (SRM) MS-based targeted proteomics was then performed using a panel of candidate biomarkers to quantify their abundance in an expanded patient cohort of 90 liquid-based Pap tests. A multi-protein classifier was developed using the SRM-MS data comprised of 6 proteins and achieving an AUC of 0.880 (95% CI: 0.738–0.989); sensitivity at 90% specificity was 0.800. This pilot study provides evidence that the cervical effluent collected in SurePath™ fixative from Pap tests has the potential to be used as a biospecimen for the detection of ovarian cancer proteins. Our long-term goal is to develop a noninvasive screening test that can be incorporated into a routine Pap test or a self-administered home test, so that women can be screened simultaneously for cervical and ovarian cancer. The online version contains supplementary material available at 10.1186/s12014-026-09610-7.

A: Comparison of serum estradiol levels vs BMI at baseline (pre-treatment) (p = 0.001). B: Serum estradiol vs BMI at surgery (post-treatment) (p = 0.0004) C: Change in serum estradiol vs BMI (p = 0.86)

Change in Ki-67 compared to change in steroid receptors

Comparison of clinicopathologic factors between participants who responded to exemestane (Ki-67 decrease) and did not respond to exemestane (Ki-67 increase)

Change in Ki-67 vs baseline steroid receptors

Changes in histologic diagnosis between baseline (pre-treatment) and surgery (post-treatment)

Comparison of change in Ki-67 with baseline (pre-treatment) serum estradiol level, p = 0.11

Purpose:To evaluate exemestane, an aromatase inhibitor, as a preventive intervention for endometrial cancer.Experimental Design:This is a multicenter, single-arm, “window of opportunity” pilot study of exemestane (25 mg daily for 21–42 days) in postmenopausal individuals undergoing hysterectomy for endometrial intraepithelial neoplasia (EIN) or low-grade endometrial cancer. The primary objective is to determine the change in proliferation, measured by Ki-67 expression, in pre- and posttreatment endometrial tissue specimens. Secondary outcomes include measurement of circulating serum estradiol and progesterone levels, pathologic response, tissue biomarkers, safety, and adverse effects.Results:Forty participants were accrued to the study. The mean body mass index was 40.3 (range, 22.8–60.5, SD = 9.8). Preoperative diagnoses included EIN (n = 11, 27.5%), grade 1 endometrial cancer (n = 26, 65%), and grade 2 endometrial cancer (n = 3, 7.5%). Median Ki-67 score decreased from 40.7% [IQR (33.9, 50.3)] at baseline to 18.1% [IQR (8.8, 31.8)] at surgery, representing a median absolute change from baseline of 20.4% [IQR (−29.9, −6.7), P < 0.001]. In a matched historic control cohort, participants also had a decrease in Ki-67 score with a median absolute change from baseline of −6.7% [IQR (−12.7, −1.3), P< 0.001]. However, the decrease in Ki-67 was greater in the study participants than the historic controls, with a median difference between the groups of −13.4% [IQR (−23.3, 6.9), P ≤ 0.01]. Both tissue estrogen receptor and progesterone receptor expression declined significantly with exemestane treatment (P < 0.001). However, serum estradiol levels did not change between baseline and after treatment (P = 0.16).Conclusions:In this pilot study, exemestane demonstrated antiproliferative effects in EIN and low-grade endometrial cancer. This agent warrants further evaluation for the prevention of endometrial cancer.

Supplementary Figure S1 from Pilot Study of Daily Exemestane in Women with Endometrial Intraepithelial Neoplasia or Low-Grade Endometrial Cancer