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The Franco lab uses state-of-the-art single cell RNA-sequencing and single cell ATAC-sequencing to study the transcriptome and epigenome of breast and ovarian tumors collected directly from the clinic on the day of surgery. These single cell genomic techniques provide unprecedented resolution to reveal the complex cellular heterogeneity of these tumors and allows us to measure the complex cell-to-cell variation that affects tumor development and response to therapy. We also aim to  identify gene expression programs and the regulatory mechanisms that underlie these programs in order to discover novel therapeutic targets. Thus, deconvolution of the transcriptional and epigenetic pathways of the various cell types found within breast and ovarian tumors will lead to a better understanding of the drivers of tumorigenesis and suggest novel avenues for therapeutic intervention. 


Single Cell Genomics of Breast and Ovarian Tumors


The Roles of Non-Coding Enhancer RNAs in Gene Regulation

With the increasing feasibility of novel sequencing technologies used to analyze the transcriptome of a cell, it has become apparent that the human genome is pervasively transcribed and that the majority of transcription is not attributed to protein coding genes. Recently, transcription factor binding sites, known as enhancers, have been shown to be actively transcribed and produce non-coding RNA molecules known as enhancer RNAs (eRNAs). It has been suggested that the act of transcribing an enhancer may play a role in regulating several steps of gene activation, while the molecular functions of the eRNA transcripts themselves remain elusive.


We use Global Run-On Coupled Sequencing (GRO-seq) combined with additional genomic approaches to identify, annotate and study the roles of eRNAs across the cancer genome. GRO-seq is a novel tool that is uniquely suited to study non-coding RNAs because it is a direct measure of transcription and identifies the position and orientation of all actively transcribing RNA polymerases across the genome. 


An enhancer looping to a target gene promoter showing the production of both protein coding mRNAs and non-coding eRNAs. 


Genome browser visualization of a transcribed enhancer


TNFα signaling exposes latent estrogen receptor binding sites to alter the breast cancer cell transcriptome.

Franco et. al. Mol Cell (2015)


Formation of a latent ERα enhancer


FOXA1 Bound to DNA

Crosstalk between the endocrine and immune systems play key roles in determining the pheno-types and outcomes of hormone-dependent cancers. Inflammation is known to have a paradoxical effect on cancers, being able to both promote and inhibit the growth of tumors. Recent evidence suggests that inflammtion may play a role in acquired resistance to hormone therapies and is considered a risk factor for breast cancer.


In a recent publication, we uncovered an important mechanism linking inflammatory signaling to hormone -dependent cancers. We found that the pioneer transcription factor FoxA1, in response to proinflammatory cytokine TNFα, is driven to new sites across to genome to promote access to chromatin for the estrogen receptor (ERα). These newly formed ERα enhancers were found in compacted/latent regions of the genome and promoted the expression of a novel set of genes that resulted in altered cellular phenotypes and were predictive of clinical outcomes in breast cancer patients.


Based on these findings, we will continue to use proteomic, genomic and computational approaches to study how inflammatory cytokines alter endo-crine signaling in hormone-dependent cancers.

Crosstalk Between Proinflammatory Signaling and Endocrine Signaling in Hormone-dependent Cancers

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