CANCER EPIGENETICS

The objective of this work is to create and characterise novel therapies for triple negative breast cancers. We propose the generation of interference peptides (iPeps), which are synthetic peptides engineered from oncogenic transcription factors over-expressed in these breast cancers. The iPeps carry cell penetration and nuclear localization sequences that mediate a rapid internalisation of the peptide through the cell and nuclear membranes. In addition, the iPeps are engineered with residues essential for protein-protein interactions and DNA-binding derived from the endogenous oncogenic transcription factor. Thus, the iPeps are designed to compete with the endogenous transcription factor by sequestering the binding partners necessary for transcriptional and DNA binding activity.

Herein, we will deploy this novel interference peptide technology to inhibit toncogenic transcription factors overexpressed in nearly half of the triple negative breast cancers and has a role in maintaining their oncogenic capability. In addition, we propose a highly innovative approach to physically link the iPep with small molecules like Doxorubicin and pro-drugs like platinum IV, to localise them specifically in the nucleus of the cancer cells. We hypothesise that the iPeps will act as “guides” for the chemotherapeutic drugs, directing them into the nucleus to induce DNA damage. These iPeps should increase the selectivity and the kinetics of uptake of the small molecule, and decrease the dose of the small molecule that is required for anti-cancer activity, thereby reducing the toxicity related to chemotherapy. In this project we will make use of both triple negative breast cancer cell lines and different breast cancer animal models (mice). In the long run, we hope to translate this intervention to patients and contribute eliminate the mortality associated with metastatic breast cancer, particularly for triple negative cancers.

Reading about interference peptides
Novel role of Engrailed 1 as a prosurvival transcription factor in basal-like breast cancer and engineering of interference peptides block its oncogenic function. Beltran AS, Graves LM, Blancafort P. Oncogene. 2013 Oct 21. doi: 10.1038/onc.2013.422. PMID: 24141779
Sensitizing basal-like breast cancer to chemotherapy using nanoparticles conjugated with interference peptide. Sorolla A, Ho D, Wang E, Evans CW, Ormonde CF, Rashwan R, Singh R, Iyer KS, Blancafort P. Nanoscale. 2016 Apr 28;8(17):9343-53. doi: 10.1039/c5nr08331a.

Contact
Associate Professor Pilar Blancafort – [email protected]
Dr Anabel Sorolla – [email protected]

The comprehensive genome-wide maps of epigenetic modifications in cancer revealed the deep involvement of epigenetics in cancer; in the majority of cancers, tumor suppressor genes are more frequently inactivated by epigenetic mutations than by genetic mutations1. Importantly, some of the key drivers in cancer cannot be targeted by current therapies. In this regard, we chose key oncogenic drivers often overexpressed in aggressive breast cancers: SOX2, MYC, KRAS, C11ORF67 and FOXM1. We aim to develop epigenomic tools to precisely re-write the specific epigenetic modifications controlling the expression of these oncogenes. We propose the generation of programmable DNA-binding proteins that ferry epigenome-modifers to stably silence these key targets. In our lab, the oncogene SOX2 was successfully methylated and down-regulated by zinc finger proteins (ZFPs) fused to the catalytic domain of DNA methyltransferase 3A (DNMT3A)2. Recently, we also induced DNA methylation on the Estrogen Receptor Receptor-α in cancer using a ZFP linked to a DNA methylatransferase3. In this project, we propose the construction of a sequence specific DNA-binding domain engineered from another state-of-the art technology, the bacterial Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) combined with an epigenetic silencing domain. The advantage of CRISPR system is that it is a protein-RNA complex in which the information to bind the target gene is provided by a guide RNA. The protein component of CRISPRs will be linked to novel combinations of epigenetic modifiers promoting long lasting chromatin condensation and gene silencing to establish both DNA and histone methylation and chromatin condensation. The outcomes of this research are novel proteins able to catalyse local reconfiguration of the chromatin state to permanently suppress oncogenic gene expression. Thus, this work will be highly transformative by providing long lasting strategies to suppress breast cancer growth.

Objective: To develop novel epigenome editing proteins (epiCRISPRs) to selectively inhibit oncogenic drivers of aggressive breast cancers. We hypothesise that the induction of epigenetic silencing in these key oncogenic drivers lead to a long lasting oncogenic silencing.

Aim1. Develop novel epigenome reprogramming tools to edit the epigenetic pattern of the targeted oncogenes (MYC, FOXM1, ZFN703, SOX2, KRAS, C11Orf67). By examining different epigenetic modifiers we will determine the epigenetic marks that “fine tune” and maximize the silencing effect.

Aim2. Determine the capacity of epiCRISPR to promote long lasting phenotypic changes e.g. inhibition of cell growth, suppression cell invasion and increased cell death in combination with chemotherapy agents.

Reading
Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer. Stolzenburg S, Beltran AS, Swift-Scanlan T, Rivenbark AG, Rashwan R, Blancafort P.
Oncogene. 2015 Oct;34(43):5427-35. doi: 10.1038/onc.2014.470. Epub 2015 Feb 16.

Contact
Associate Professor Pilar Blancafort – [email protected]

Reading:
Curtis C, Shah SP, Chin SF, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature. 2012 Jun 21;486(7403):346-52. PubMed PMID: 22522925. Pubmed Central PMCID: 3440846. Epub 2012/04/24. eng.

Contact
Associate Professor Pilar Blancafort – [email protected]