Anatomy, Physiology and Human Biology

Cancer and Cancer Targeted Therapies

Further Information

Contact a supervisor for detailed information on student research projects

Associate professor Pilar Blancafort

Associate Professor Pilar Blancafort

The School of Anatomy, Physiology and Human Biology offers a diverse range of student research topics.

Each project will take place in the Cancer Epigenetics Laboratory at the Perkins institute of Medical Research.

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

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 the oncogenic transcription factor SOX2 which is 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 overexpressing SOX2. 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 near future, we expect to translate this intervention to patients in clinical trials. At the end we hope to 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
Project is suitable for

Honours, Masters, PhD

Supervisor
A/Prof Pilar Blancafort
Supervisor
Dr. Anabel Sorolla
Essential qualifications

Cell Biology Experience.

For Honours: An appropriate undergraduate degree with  a minimum weighted average of 65% in the level 3 subjects that comprise the relevant major from an approved institution. Applicants will be assessed on a case-by-case basis.

For Masters or PhD:An appropriate Honours degree  or equivalent research experience from an approved institution. Applicants will be assessed on a case-by-case basis.
 
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Engineering the cancer epigenome and targeting metastatic behaviour using CRISPR/Cas9

Project outline

Overview- 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:
  • Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer. Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Qian H, Strahl BD, Blancafort P. Nucleic Acids Res. 2012 Aug;40(14):6725-40. Epub 2012 May 4. PMID: 22561374 Related citations
  • Epigenetic reprogramming of cancer cells via targeted DNA methylation. Rivenbark AG, Stolzenburg S, Beltran AS, Yuan X, Rots MG, Strahl BD, Blancafort P. Epigenetics. 2012 Apr;7(4):350-60. doi: 10.4161/epi.19507. Epub 2012 Apr 1. PMID: 22419067
Project is suitable for
Honours, Masters, PhD
Supervisor
A/Prof Pilar Blancafort
Supervisor
Dr. Anabel Sorolla
Essential qualifications
Cell Biology Experience.


For Honours: An appropriate undergraduate degree with  a minimum weighted average of 65% in the level 3 subjects that comprise the relevant major from an approved institution. Applicants will be assessed on a case-by-case basis.

For Masters or PhD: An appropriate Honours degree  or equivalent research experience from an approved institution. Applicants will be assessed on a case-by-case basis.

 
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Epigenetic characterization of metastatic cells able to colonise and remodel the bone

Project outline

Metastasis is a devastating problem in cancer and often the reason why tumor cells become resistant to treatment and kill the patient. Despite decades of study, little is known about the molecular basis as to why cells leave their niche, float into blood to reach other organs and colonize target organs. Recently, patient-specific blood circulating tumor cells (CTCs) have been isolated, which harbour a high degree of heterogeneity, as only a few cells are believed to successfully home to the target organs. Moreover, the study of these infrequent early events of colonization has been limited by our lack of model systems to image single CTCs. In patients, metastases are typically detected in late stages after the cells underwent often few years of dormancy and remain seeded but not seen. The aim is development of a 3D microengineered environment that would allow us to study at single cell resolution, the cellular, molecular, and epigenetic determinants of bone colonization of patient-derived CTCs.

Development of a novel microfluidics chip: The outcome of this project is the generation of a novel technology to detect CTCs and cultured breast cancer cells with the capacity to home to the bone. The isolation of these cells will be of high clinical significance to discover early determinants of metastasis, which can help to design novel therapeutics to inhibit breast cancer metastasis.

Methods: Chips will be coated with extracellular matrix proteins and populated by osteoclasts and osteoblast cells (Fig1). Devices will be next populated with human bone marrow. After the Chips are successfully populated, fluorescently labelled breast tumor cells will be injected into a microfluidics input port. Selected cells able to colonize the bone will be imaged to visualize the captured bone-tropic cells, which will be next isolated for gene expression/epigenetic studies. Finally, clinically relevant CTCs isolated from breast cancer patients will be tested.

Gene expression/epigenetic studies: gene expression and epigenetics pattern (DNA methylation and histone modifications) of colonized cells to bone will be assessed using RNA-seq and chromatin immunoprecipitation/DNA methylation assays. The results of this study will reveal early transcriptional and epigenetic determinants, which can be used as prognosis signatures for breast cancer metastasis in the bone.

The eligible student will study the metastasis and will be expert at local- and genome-wide Chromatin immunoprecipitation (ChIP), DNA methylation assays as well as gene expression analysis.

  Useful reference:

  • Sieh et al., Bone 63(2014) 121-131
Project is suitable for

Masters, PhD

Supervisor
A/Prof Pilar Blancafort
Supervisor
Dr. Fahimeh Falahi
Essential qualifications

A good background of cellular and molecular biology.

For Honours: An appropriate undergraduate degree with  a minimum weighted average of 65% in the level 3 subjects that comprise the relevant major from an approved institution. Applicants will be assessed on a case-by-case basis.

For Masters or PhD: An appropriate Honours degree  or equivalent research experience from an approved institution. Applicants will be assessed on a case-by-case basis.

 
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