May 5, 2022 / Oncology

A single cell multiomic map reveals regulatory landscape of gynecologic tumors

Jeanene Swanson

Ovarian cancer is the most deadly of cancers of the female reproductive system, afflicting not only the ovaries, but the fallopian tubes and primary peritoneal cavity as well (1). However, despite the severity, it is often ignored and its research underfunded (2). On May 8, World Ovarian Cancer Day aims to bring awareness to this disease in an effort to increase funding for research into treatments and cures.

Cancer cells often repurpose regulatory elements that are located throughout the human genome to activate genes that allow tumors to grow faster and resist therapy (3). Increasing our understanding of the mechanisms that drive transcriptional programs in cancer cells will not only help better define the regulatory logic of these cells, but will also uncover sources of intratumoral heterogeneity that drives some types of treatment resistance.

In a recent Nature Oncology webinar sponsored by 10x Genomics, Hector Franco, PhD, and his lab at the University of North Carolina at Chapel Hill School of Medicine discussed their recent publication that made use of single cell tools to probe deeper into the non-coding genomic regions of ovarian and endometrial cancer cells. In this work, he and his team combined single cell transcriptomic and epigenomic profiling of human ovarian and endometrial tumors to reveal novel insights into the molecular underpinnings of gynecologic cancers (4).

Hector Franco, PhD, Assistant Professor, Department of Genetics, University of North Carolina at Chapel Hill School of Medicine
Hector Franco, PhD, Assistant Professor, Department of Genetics, University of North Carolina at Chapel Hill School of Medicine

Matched single cell datasets create a human gynecologic cancer map

Dr. Franco and team used Chromium Single Cell Gene Expression and Chromium Single Cell ATAC to perform single cell RNA-sequencing (scRNA-seq) and scATAC-seq on cells isolated from 11 human ovarian and endometrial tumors, unveiling complex heterogeneity. Pairing scRNA-seq data with scATAC-seq data, they were able to identify cancer-specific and clinically relevant distal regulatory elements and reveal that differential transcription factor (TF) activity is what partially drives intratumor heterogeneity.

Their method used “large-scale peak-to-gene linkage analysis” and a “robust empirical false discovery rate (eFDR) procedure for determining statistically significant peak-to-gene associations in single-cell data” to characterize cancer cell–specific distal regulatory elements and the genes that they up-regulated in cancer cell populations. For example, they found that RHEB, a regulator of the mTOR pathway, which is a hallmark cancer pathway, was significantly up-regulated in a subcluster of endometrioid ovarian cancer cells of one patient. This subcluster also showed enrichment for the mTOR pathway gene signature. These data suggest that distal regulatory elements are “rewired” when a cell becomes malignant, the authors write.

Linking distal elements to transcription factors in tumors

After identifying critical distal elements, Dr. Franco and team used a previously published method called Total Functional Score of Enhancer Elements (TFSEE) to predict what TFs are enriched at active distal elements within specific cancer cells (5). When they performed the TFSEE analysis on 11 malignant cell-type subclusters, they discovered differences in TF activity  among tumor subclones, which may offer insight into intratumoral heterogeneity.

Identifying regulatory elements drives discovery of novel therapies

Taken together, paired dataset analysis of gene expression and chromatin accessibility at the single cell level demonstrated that tumor cells rewire regulatory elements that then drive hallmark cancer pathways. Moreover, cancer cells from the same patient can differ in terms of chromatin accessibility linked to transcriptional activity, which provides new insight into the downstream effects of intratumoral heterogeneity. By examining both scRNA-seq and scATAC-seq data, researchers were able to access levels of resolution previously hidden by bulk genomic techniques, revealing epigenetic events that may underlie tumor biology and pointing to regulatory elements that drive hallmark cancer pathways and represent potential avenues for the development of novel targeted therapies and improved patient outcomes.

Watch the on-demand webinar to gain further insight into how these tools can help your own single cell cancer research.


  3. Corces MR, et al. The chromatin accessibility landscape of primary human cancers. Science 362: eaav1898 (2018). doi: 10.1126/science.aav1898
  4. Regner MJ, et al. A multi-omic single-cell landscape of human gynecologic malignancies. Mol Cell 81: 4924–4941.e10 (2021). doi: 10.1016/j.molcel.2021.10.013
  5. Malladi VS, et al. Total functional score of enhancer elements identifies lineage-specific enhancers that drive differentiation of pancreatic cells. Bioinform Biol Insights 14: 1177932220938063 (2020). doi: 10.1177/1177932220938063