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Mechanisms of cell fate choice upon therapeutic activation of p53

Led by Research Instructor Kelly Sullivan and Professional Research Assistant Amanda Hill, this project aims to identify genes that modulate the diverse cellular responses to biologically targeted therapies, with a focus on small molecule inhibitors of the p53-MDM2 interaction, such as Nutlin-3.

 

Using a genome-wide shRNA library, Kelly performed the first ‘Synthetic Lethal with Nutlin-3’ screens in human cells, which enabled the design of rational drug combinations that kill Nutlin-resistant cancer cells (see Sullivan et al, Nature Chemical Biology 2012). Using molecular and chemical biology Kelly then dissected the mechanisms underlying the synthetic lethal interactions identified in these screens (see Sullivan et al, Cell Cycle 2015).  Currently, he is expanding his screens to include numerous cancer types and additional targeted therapies in order to find novel therapeutic drug combinations.

Mechanisms of pleiotropy within the p53 gene network

 

Mechanisms of p53-dependent cell death

Led by Research Instructor Zdenek Andrysik and Professional Research Assistant Morgan MacBeth, this project aims to identify mechanisms and factors that regulate the p53 signaling cascade to drive alternative cell type -specific responses upon p53 activation. This highly collaborative project also involves other members of the lab who are studying the diverse responses of various cancer cell types to pharmacological inhibition of MDM2.

 

The team is using a suite of genomics approaches (e.g. ChIP-seq, GRO-seq, RNA-seq, Ribosome Profiling) to define how pleiotropy in the cellular response is generated. Our data suggest regulatory differences within the p53 gene network at multiple levels including binding of p53 to DNA, transcriptional activity, steady-state RNA, and translation.

Led by post-doc Chris Abraham, this project aims to elucidate mechanisms of action for the transcriptional repressor ΔNp63α in Squamous Cell Carcinomas (SCCs). Within the context of SCCs, ΔNp63α acts as an oncogene, driving uncontrolled cell proliferation while suppressing apoptosis. The molecular details of how ΔNp63α coordinates these hallmarks of cancer remain poorly understood.

 

Using cutting-edge functional genomics tools, Chris is working to identify the molecular mechanisms by which ΔNp63α promotes SCC progression. Given the heterogenity of these tumors in the clinic, he aims to illuminate ‘conserved’ versus ‘cell type-specific’ mechanisms driving uncontrolled SCC proliferation. These data will aid in identifying actionable drug targets and pathways for the treatment of ΔNp63α-driven SCCs.

The lab provides us with the means for self-expression and connectedness – each of us has an individual project, but we collaborate naturally.

 

These are our current projects:

Mechanistic studies of the p53 network.

 

A good portion of our research program focuses on p53, the most commonly mutated gene in human cancer. p53 is a transcription factor and a potent tumor suppressor. We want to understand how exactly p53 suppresses cancer development and to employ this knowledge to design effective p53-based cancer therapies. A key problem in this area is that p53 is a highly pleiotropic transcription factor that participates in very diverse cellular processes in a context-dependent fashion. Much of our research is aimed at understanding how pleiotropy is generated within the p53 network and how it could be tamed to drive cells into specific p53-dependent outcomes. 

Mechanisms of translational control within the p53 network

Led by Dr. Sara Zaccara in collaboration with the lab of Dr. Alberto Inga at the University of Trento, Italy, this project investigates how the protein translation machinery qualifies the p53 transcriptional program in a cell type-specific manner.

 

In the Inga lab, Sara employed genomics approaches to identify factors that modulate the translation of p53 target genes in response to diverse cellular contexts.

 

In collaboration with Research Instructor Matt Galbraith, Sara expanded her studies of translational control to cancer cell types of diverse tissue origin and is currently investigating the mechanism of action of specific miRNAs and RNA binding proteins that impact the quality of the p53 transcriptome.

Mechanistic studies of oncogenic transcription factors and their cofactors.

 

A significant fraction of our research program investigates DNA binding transcription factors and their transcriptional cofactors with known oncogenic activity, including the Mediator complex and the hypoxia inducible factors (HIFs). 

Mechanism of action of the Mediator CDK module

Led by Research Instructor Matt Galbraith, this project aims to define the mechanism by which the CDK module of the Mediator complex regulates gene expression in human cells.

 

Mediator is a critical regulator of RNAPII activity conserved from yeast to man, but its molecular mechanisms of action remain obscure.

Matt’s work has focused mainly on the role of the Mediator-associated kinase CDK8, a known oncoprotein in colorectal cancer, in control of RNAPII. His work led to the discovery that CDK8-Mediator is a critical co-activator Of the transcriptional program controlled by hypoxia-inducible transcription factors.

See Galbraith et al. Cell 2013.

 

Matt is currently employing a myriad of complementary approaches, from chemical genetics to functional genomics, to further investigate the mechanism of action of CDK8.

Functional specialization of the Mediator CDK module

Led by Research Instructor Matt Galbraith with Professional Research Assistant Elizabeth Bonner this project aims to investigate the functional specialization of the Mediator-associated kinases CDK8 and CDK19, as well as the auxiliary factors MED12/MED12L and MED13/MED13L.

 

Intriguingly, subunits of the CDK-module of Mediator have duplicated in vertebrates to create paralogous pairs with non-redundant functions, likely to accommodate the increased regulatory diversity seen in metazoans.

The team is using molecular biology and genomic approaches to characterize the specialized functions of the CDK8 and CDK19 kinases in human cells.

 

Likewise, we are using similar approaches to investigate the paralogous pairs MED12/MED12L and MED13/MED13L.

See Daniels et al. JPB 2013.

Mechanisms of gene expression control by hypoxia-inducible factors

Led by Research Instructor Matt Galbraith with Professional Research Assistant Elizabeth Bonner, this project aims to define the molecular mechanisms by which the hypoxia-inducible factors HIF1A and HIF2A control gene expression during conditions of low oxygen.

 

This project is focused on two major questions: (1) What are the mechanisms that generate cell type-specific gene expression programs upon HIF activation? (2) How does HIF1A employ CDK8-Mediator as a co-activator?

 

We are also investigating other HIF co-activators recently identified in collaboration with Dr. Pablo Wappner’s lab in Buenos Aires, Argentina.

See Dengler et al. CRMBB 2014

and Perez-Perri et al, 2016

Mechanisms of oncogenic transformation by p63

Functional genomics approaches for the study of trisomy 21.

 

A new area of interest for the lab has been stimulated by the establishment of the Linda Crnic Institute for Down Syndrome. Despite being the most common chromosomal aberration, much remains to be discovered about the molecular bases underlying the various pathologies associated with Down Syndrome. Our research aims to advance our understanding of how changes in gene expression and cell signaling contribute to the variable disease spectrum observed in people with Down Syndrome. 

Elucidation of the signaling cascades impacted by trisomy 21

Led by Instructor Kelly Sullivan and aided by Professional Research Assistants Amanda Hill and Hannah Lewis, this project aims to identify molecular mechanisms that enable cells from individuals with Down Syndrome to adapt to the burden of an extra copy of chromosome 21. This effort is a part of the Human Trisome Project, aimed at understanding why individuals with Down Syndrome are more susceptible to certain conditions such as Alzheimer’s Disease while they are protected from others, including many solid tissue-derived cancers.

 

Using a combination of RNA-seq and shRNA screens targeting all kinases, we have identified signaling nodes that differentially control the survival and proliferation of trisomy 21 relative to their disomic counterparts. Kelly and the team are currently working on understanding how these signaling nodes function differently in trisomy 21 cells.

 

See Sullivan et al, 2016

PROJECTS

Led by post-doc Anna Guarnieri and Professional Research Assistant Maddie Miller, this project aims to elucidate the mechanisms by which p53 elicits cell death in response to MDM2 inhibition. Despite considerable momentum with p53-based cancer therapies (e.g. Nutlin-3), their efficacy is currently limited by the heterogeneity of the p53 response, as most cancer cells undergo reversible cell cycle arrest rather than apoptosis.

 

Using pediatric cancer cell lines that are sensitive to Nutlin-3, Anna has conducted genome-wide screens with both shRNA and CRISPR libraries to identify genes required for p53-dependent cell death. Anna and Maddie are currently investigating the mechanisms of action of several of these genes with the goal of improving p53-based therapeutics.