Matthew Regner, Kamila Wisniewska, Susana Garcia-Recio, Aatish Thennavan, Raul Mendez-Giraldez, Venkat S. Malladi, Gabrielle Hawkins, Joel S. Parker, Charles M. Perou, VIctoria L. Bae-Jump, Hector L. Franco. Molecular Cell. 2021.


Deconvolution of regulatory mechanisms that drive transcriptional programs in cancer cells is key to understanding tumor biology. Herein, we present matched transcriptome (scRNA-seq) and chromatin accessibility profiles (scATAC-seq) at single-cell resolution from human ovarian and endometrial tumors processed immediately following surgical resection. This dataset reveals the complex heterogeneity of these tumors and enabled us to quantitatively link variation in chromatin accessibility to gene expression. We show that malignant cells acquire previously unannotated regulatory elements to drive

hallmark cancer pathways. Moreover, malignant cells from within the same patients show substantial variation in chromatin accessibility linked to transcriptional output, highlighting the importance of intratumoral heterogeneity. Finally, we infer the malignant cell type-specific activity of transcription factors. By defining the regulatory logic of cancer cells, this work reveals an important reliance on oncogenic regulatory elements and highlights the ability of matched scRNAseq/scATACseq to uncover clinically relevant mechanisms of tumorigenesis in gynecologic cancers.

Michael R. Kelly, Kamila Wisniewska, Matthew J. Regner, Michael W. Lewis, Joel S. Parker, Hector L. Franco. Under Review. 2021.

Total Functional Score of Enhancer Elements Identifies Lineage-Specific Enhancers that Drive Differentiation of Pancreatic Cells

Venkat Malladi, Anusha Nagari, Hector Franco, W. Lee Kraus. Bioinformatics and Biology Insights. 2020 Jul 1; 14-20.

Transcriptional Control by Enhancers and Enhancer RNAs

Michael W. Lewis, Shen Li, Hector L. Franco. Transcription. 2019.

The regulation of gene expression is a fundamental cellular process and its misregulation is a key component of disease. Enhancers are one of the most salient regulatory elements in the genome and help orchestrate proper spatiotemporal gene expression during development, in homeosta- sis, and in response to signaling. Notably, molecular aberrations at enhancers, such as transloca- tions and single nucleotide polymorphisms, are emerging as an important source of human variation and susceptibility to disease. Herein we discuss emerging paradigms addressing how genes are regulated by enhancers, common features of active enhancers, and how non-coding enhancer RNAs (eRNAs) can direct gene expression programs that underlie cellular phenotypes. We survey the current evidence, which suggests that eRNAs can bind to transcription factors, mediate enhancer-promoter interactions, influence RNA Pol II elongation, and act as decoys for repressive cofactors. Furthermore, we discuss current methodologies for the identification of eRNAs and novel approaches to elucidate their functions.


Enhancer Transcription Reveals Subtype-Specific

Gene Expression Programs Controlling Breast Cancer Pathogenesis 

Hector L. Franco, Anusha Nagari, Venkat Malladi, Wenqian Li, Yuanxin Xi, Dana Richardson, Kaori Tanaka, Jing Li, Michelle C. Barton, Xiaobing Shi,  Khandan Keyomarsi, Mark T. Bedford, Wei Li, Sharon Y. R. Dent, W. Lee Kraus. Genome Research. 2018. 28: 159-170

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer


cell lines representing five major molecular subtypes of breast cancer, as well as two immortal- ized (“normal”) human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of en- hancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When ap- plied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.

Histone Modification Profiling in Breast Cancer Cell Lines Highlights Commonalities and Differences Among Subtypes

Yuanxin Xi, Wenqian Li, Kaori Tanaka, Kendra L. Allton, Dana Richardson, Jing Li, Hector L. Franco, Anusha Nagari, Venkat Malladi, Khandan Keyomarsi, Jianjun Shen, Mark T. Bedford, Xiaobing Shi, Michelle C. Barton, W. Lee Kraus, Wei Li, Sharon Y. R. Dent. BMC Genomics. 2018. 19:150 

Reciprocal Feedback between miR-181a and E2/ERα in Myometrium Enhances Inflammation Leading to Labor

Lu Gao, Gang Wang, Weina Liu, Holly Kinser, Hector L. Franco, Carole R. Mendelson. J. Clinical Endocrinology and Metabolism. 2016 Oct;101(10):3646-3656 

No Driver Behind the Wheel? Targeting Transcription as a Therapeutic Strategy in Cancer

Hector L. Franco, W. Lee Kraus. Cell. 2015. 163(1):28-30.

TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites to Alter the Breast Cancer Cell Transcriptome

Hector L. Franco, Anusha Nagari, W. Lee Kraus. Molecular Cell. 2015. 2;58(1):21-34.

The interplay between mitogenic and proinflamma- tory signaling pathways plays key roles in deter- mining the phenotypes and clinical outcomes of breast cancers. Using GRO-seq in MCF-7 cells, we defined the immediate transcriptional effects of crosstalk between estradiol (E2) and TNFa, identi- fying a large set of target genes whose expression is rapidly altered with combined E2 + TNFa treat- ment, but not with either agent alone. The pleiotropic effects on gene transcription in response to E2 + TNFa are orchestrated by extensive remodeling of the ERa enhancer landscape in an NF-kB- and FoxA1-dependent manner. In addition, expression of the de novo and synergistically regulated genes is strongly associated with clinical outcomes in breast cancers. Together, our genomic and molecu- lar analyses indicate that TNFa signaling, acting in pathways culminating in the redistribution of NF-kB and FoxA1 binding sites across the genome, creates latent ERa binding sites that underlie altered patterns of gene expression and clinically relevant cellular responses.


Interplay Between Inflammatory and Estrogen Signaling in Breast Cancer

Anusha Nagari, Hector L. Franco. Cytokine. 2015. 76(2):588-90.

Nonsense mutations of the bHLH transcription factor TWIST2 found in Setleis Syndrome patients cause dysregulation of periostin.

Hector L. Franco, Jose J. Casasnovas, Ruth G. Leon, Robert Friesel, Yongchao Ge, Robert J. Desnick,  Carmen L. Cadilla. Int Journal Biochemistry and Cell Biology. 2011. 43(10):1523-31

Redundant or separate entities; Roles of Twist1 and Twist2 as molecular switches during gene transcription.

Hector L. Franco, Jose Casasnovas, Jose R. Rodriguez Medina, Carmen L Cadilla. Nucleic Acids Research. 2010. 39(4):1177-86

Homozygous nonsense mutations in TWIST2 cause Setleis syndrome.

Turgut Tukel, Drazen Šošić, Lidah I. Al-Gazali, Mónica Erazo, Jose Casasnovas, Hector L. Franco, James A. Richardson, Eric N. Olson,2 Carmen L. Cadilla, Robert J. Desnick. American Journal of Human Genetics. 2010. 13;87(2):289-96