Single-Cell Integration of Chromatin Accessibility and Transcriptomics Reveals Regulatory Networks in Ovarian Tumor-Infiltrating Adaptive NK Cells

Sun, Y.; Wan, M.; Kolbeinsdottir, S.; Wang, K.; Khare, S.; Gultekin, O.; Salehi, S.; Lehti, K.; Dasgupta, R.; Foukakis, T.; Enge, M.; Sarhan, D.

doi:10.1101/2025.09.13.676040

bioRxiv · 10.1101/2025.09.13.676040

Single-Cell Integration of Chromatin Accessibility and Transcriptomics Reveals Regulatory Networks in Ovarian Tumor-Infiltrating Adaptive NK Cells

Sun, Y.·Wan, M.·Kolbeinsdottir, S.·Wang, K.·Khare, S.·Gultekin, O.·Salehi, S.·Lehti, K.·Dasgupta, R.·Foukakis, T.·Enge, M.·Sarhan, D.

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Abstract

Natural killer (NK) cells are traditionally recognized for their rapid, non-specific responses against virus-infected or malignantly transformed cells, functioning as key effectors of innate immunity. However, a distinct subset known as adaptive NK (aNK) cells has been shown to acquire memory-like properties following viral infections, indicating their capacity for antigen-specific immune recall. Intriguingly, aNK cells have also been identified within the tumor microenvironment, where they can mediate tumor-specific recall responses. Yet, the regulatory mechanisms governing their function in tumor-infiltrating aNK cells remain largely undefined. In this study, we integrated publicly available multiomics datasets from ovarian cancer, including single-cell chromatin accessibility (scATAC-seq) and single-cell RNA sequencing (scRNA-seq), to identify chromatin-accessible regions and construct transcription factors (TF)-gene regulatory networks. To validate and extend these findings, we performed Smart-seq3 on NK cells isolated from ovarian tumors and applied SCENIC analysis to identify TF-driven gene regulation. By integrating results from both analyses, we identified PRDM1 and STAT2 as key TFs, along with their downstream targets CRCP and MTFP1, specifically enriched in tumor-infiltrating aNK cells. The expression levels of CRCP and MTFP1 positively correlated with NK cell infiltration in ovarian cancer tissues, suggesting their potential functions in supporting tumor-specific NK cell memory responses. In addition, external validation using data from the PROMIX clinical trial demonstrated that PRDM1 and STAT2 expression levels are positively associated with both overall survival and aNK cell-associated transcriptional features. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/676040v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@6df026org.highwire.dtl.DTLVardef@1b16dc8org.highwire.dtl.DTLVardef@19e916borg.highwire.dtl.DTLVardef@15d431a_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Sun, Y., Wan, M., Kolbeinsdottir, S., Wang, K., Khare, S., Gultekin, O., Salehi, S., Lehti, K., Dasgupta, R., Foukakis, T., Enge, M., Sarhan, D.. 2025-09-15. Single-Cell Integration of Chromatin Accessibility and Transcriptomics Reveals Regulatory Networks in Ovarian Tumor-Infiltrating Adaptive NK Cells. https://doi.org/10.1101/2025.09.13.676040

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