DOI: 10.5281/zenodo.15384723
title: Multiplexed imaging mass cytometry reveals tumor-immune microenvironment dependent hormone receptor expression in adult type ovarian granulosa cell tumors

description: All data supporting the publication: Khlebus E.Y., et al. "Multiplexed imaging mass cytometry reveals tumor-immune microenvironment dependent hormone receptor expression in adult type ovarian granulosa cell tumors." (2025)

Abstract: Adult-type granulosa cell tumors (AGCTs) are rare ovarian tumors with few effective treatments for recurrent disease. To elucidate spatial features and cellular interactions within the AGCT tumor microenvironment (TME), we applied imaging mass cytometry (IMC) using a 34-marker panel on 130 regions from 24 AGCT samples, profiling over 900,000 single cells. Analysis confirmed the immune “cold” phenotype of AGCTs and showed higher macrophage abundance in recurrent compared to primary tumors. We observed substantial heterogeneity in tissue architecture across samples, including variable presence of FOXL2+ cells embedded in collagen-rich regions (FOXL2+COL1A1+ cells). Based on TME composition, we defined two AGCT subtypes: AGCT-1 and AGCT-2 with distinct FOXL2+ cell distributions, differences in progesterone receptor (PR) expression, and unique transcriptomic profiles. Our findings highlight the role of macrophages, Foxl2+ subpopulations, and extracellular matrix (ECM) in AGCT progression and suggest AGCT subtype-specific vulnerabilities that could inform personalized therapies for this rare malignancy.

Dataset includes:



 Clinical characteristics by patient.xlsx: This table contains clinical characteristics of Adult-type Granulosa Cell Tumor (AGCT) cohort, including primary/recurrent condition status; age, stage and tumor size at diagnosis, anatomical tumor site, menopause status.

IMC-images_Raw_OME-TIFF: This folder contains raw OME.TIFF files with all markers and summary files per ROI. The file names related to Sample IDs from clinical table (described above). IMC images were exported from original MCD files using MCD Viewer via File → Export, selecting the format OME-TIFF (16-bit) and setting Page to Multi to retain all imaging channels. This preserved the multiplexed channel structure in a single OME-TIFF file, with each channel stored as a separate page in the TIFF.

H&E_Images: This collection contains histopathology H&E images for each sample.

ROIs_Selection: Images of individual samples showing where the ROIs for each sample are collected.

Output_Data: This folder contains AGCT_All-Cells.csv, AGCT_Images-Stats.csv, and Columns_Description.docx.



AGCT_All-Cells.csv contains information for each cell identified through IMC image analysis, including cell coordinates within each IMC image, biomarker intensity data within cells, morphological parameters, and proliferation status.

AGCT_Images-Stats.csv includes data for each IMC image, such as the total number of cells per image, areas of segmented regions, and the mean signal intensities of collagen, estrogen receptor, and progesterone receptor in those regions.

Columns_Description.docx provides descriptions for each column in the two aforementioned tables.




Please note that in the IMC dataset, the following channels are blank:



80Ar, 101Ru, 102Ru, 103Rh, 120Sn, 127I, 131Xe, 134Xe, 138Ba, 208Pb


The same AGCT samples were also previously described and analyzed in the following two studies:





Hillman RT, et al. KMT2D/MLL2 inactivation is associated with recurrence in adult-type granulosa cell tumors of the ovary. Nat Commun. Nature Publishing Group; 2018;9:1–7.




Khlebus EY, et al. Comparative Tumor Microenvironment Analysis of Primary and Recurrent Ovarian Granulosa Cell Tumors. Mol Cancer Res. AACR; 2023;21:483–94.



The whole-exome sequencing data for the same AGCT samples have been deposited with the European Genome-phenome Archive (EGA) under access code EGAS00001002833. RNA-seq data are available through the EGAS00001006478.