Cancer epigenetics


Student project opportunities

 
Development of a novel strategy using engineered peptides to selectively sensitise metastatic breast cancers to chemotherapy agents

Research area: cancer targeted therapies
Chief supervisor:  Associate Professor Pilar Blancafort
Other supervisors: Dr Anabel Sorolla
Project suitable for:  Honours, Masters  and PhD   
Essential qualifications:  molecular and cell biology experience
Start date:  available immediately

Project outline 
This project focuses on generating novel targeted therapies for triple negative breast cancers. Triple negative breast cancers are responsible for most of the deaths related to breast cancer in Australia and in the world. These cancers do not express oestrogen receptor alpha, progesterone receptor and epidermal growth factor receptor 2, targets typically exploited in the clinic. They belong to the basal-like subtype breast cancer, comprising 15% of all breast cancers. In the metastatic setting they are highly resistant to chemotherapy. DNA-damaging agents used in chemotherapy, lacking target selectivity have generalized side effects. Thus, there is an urgent need to develop novel, more specific and targeted molecular approaches to treat this lethal disease.

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 - pilar.blancafort@uwa.edu.au
Dr Anabel Sorolla -  anabel.sorollabardaji@uwa.edu.au

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Engineering the cancer epigenome and targeting metastatic behaviour using CRISPR/Cas9

Research area: cancer targeted therapies
Chief supervisor:  Associate Professor Pilar Blancafort
Other supervisors: Dr Anabel Sorolla
Project suitable for:  Honours , Masters  and PhD   
Essential qualifications:  cell biology experience
Start date:  available immediately

Project outline 
Cancer is one of the major causes of death in Australia. For decades, the origin of cancer was attributed to genetic mutations. However, their involvement in gene regulation and cancer has illuminated the prospect of novel therapies. Epigenetic marks are heritable covalent modifications in the DNA or associated proteins.  Epigenetic modifications provide the mechanisms by which a cell “knows” and “remembers” which genetic information to read and which to ignore. Epigenetic modifications include DNA methylation and modifications in the proteins that the DNA is wrapped around. Abnormal epigenetic modifications are frequently observed in cancer. In contrast to genetic mutations, epigenetic modifications are reversible and this can be used to restore the normal state of gene expression in the cancer. In this proposal, we aim to reverse the epigenetic modifications of key breast cancer drivers. We propose the development novel and more selective technologies able to stably suppress the genes that cause breast cancer and breast cancer spread.

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 - pilar.blancafort@uwa.edu.au

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Discovery and characterisation of new oncogenic drivers in breast cancer

Research area:  cancer 
Chief supervisor:  Associate Professor Pilar Blancafort
Project suitable for:  Masters and PhD   
Essential qualifications:  A good background of cellular and molecular biology
Start date:  available immediately

Project outline 

Breast cancer is a heterogeneous disease comprising different subtypes associated with distinct portraits of gene expression, patterns of clinical behaviour and responses to therapy.  Importantly, with the advent of the recent sequencing of thousands of breast cancers a novel subgroup of hormone receptor positive breast cancer was discovered (IntClust2) linked with the second worst prognosis after the HER2-enriched group. The hallmark of these tumours is an amplification in chromosome 11 including new oncogenes of uncharacterised function linked with poor outcome. The project involves the development of CRISPR/Cas9 technology in patient-derived cell lines to assess the role of these putative drivers in metastases and endocrine resistance. The result of this work will define biomarkers to help distinguish the hormone receptor positive tumours at risk of relapse and guide the design of novel precision therapeutics to target these cancer drivers.


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 - pilar.blancafort@uwa.edu.au

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