Associate Professor Pilar Blancafort BSc, PhD

Pilar Blancafort

Laboratory Head, Cancer Epigenetics
T: + 61 8 6151 0990

Associate Professor Pilar Blancafort completed her Bachelor of Science at the University of Barcelona, and her PhD at the University of Montreal in the field of Biochemistry in 1999. She pursued her postdoctoral studies at the Scripps Research Institute, California in the field of genome-engineering . In 2005, she established her own laboratory at the University of North Carolina, as Assistant Professor and later as tenured Associate Professor in 2011.  In 2012, Professor Blancafort moved her laboratory at the University of Western Australia.   In 2014, she joined the Perkins as Head of the Laboratory in Cancer Epigenetics.   Pilar is a specialist in genome engineering and gene targeting and her laboratory has pioneered the development of engineered DNA binding proteins to modulate the epigenetic state of cancer cells and delivery strategies for tumor targeting in pre-clinical studies. She has received several awards, including awards from the Department of Defense Breast Cancer Program, American Lung Association, several cancer nanotechnology awards, NCI/NIH awards, a Cancer Council of Western Australia Research Fellowship and a ARC Future Fellowship and a National Breast Cancer Novel Concept award.

Research overview
The Blancafort laboratory focuses on the development of novel approaches to target cancers that are currently refractory to treatment and associated to poor outcome, such as triple negative breast cancers and ovarian cancers. At present, there are no targeted approaches to combat these tumors with chemotherapy and radiation the only treatment options. The laboratory generates novel functionalised molecules able to specifically target these tumors with minimal toxicity to normal cells. Our emphasis is in advanced stage metastatic tumors, which quasi invariably develop resistance. Ultimately we wish to revert the behavior of metastatic cells by sensitizing these treatment resistant tumors to chemotherapy regimes.

Nanoparticle delivery


Delivery of nanoparticles into tumors to promote gene silencing
and sensitize 
cancer cells to chemotherapy

Recently, the genomes of thousands of cancer patients have been resolved at single base pair resolution, which has delineated the aberrant landscape of mutations, deletions and copy number amplifications that characterize the intrinsic subtypes of cancers. By integrating this information with cancer transcriptomes and DNA methylomes, a discrete number of genomic loci involved in cancer initiation and metastatic progression have been identified. Major cancer drivers include molecules such as transcription factors (e.g MYC) and small GTPases (e.g KRAS) for which there is currently no small molecule specific inhibitors. In addition, the cancer genome project has identified other elusive targets not involved in proliferative capacity, but in residual disease, drug resistance and in tumor-stromal interactions.

With this integrated knowledge of the cancer genome we have developed novel precision molecular medicine strategies to selectively revert or reprogram the aberrant gene expression and epigenetic state of prospective cancer drivers in breast and ovarian tumors. We deployed state of the art molecular biology and structural biology approaches to engineer a novel generation of sequence-specific DNA-binding molecules with the capacity to recognize the cancer genome with single locus selectivity.

Structure of a transactivator like effector (TALE) DNA binding domain in complex with DNA.

These engineered DNA-binding domains (DBDs, for example made of zinc fingers, transactivator-like effector TALEs and RNA guides: CRISPR/dCas9) are designed to bind promoters, enhancers and other regulatory regions controlling the expression of the targeted loci. These DBDs are linked to effector domains able to modify and edit chromatin, for example by inducing DNA methylation or by promoting irreversible DNA damage in specific oncogenic loci. The active proteins and small peptide variants are encapsulated using nanoparticles to target the delivery of our agents in breast and ovarian cancer models. The nanoparticles incorporate both targeted ligands for tumor targeting, imaging modalities, which allow the in vivo detection of the particles using MRI and other approaches.

The outcomes of our research are the generation of novel state of the art nanoparticles for short-term clinical trials for the treatment of fatal diseases, such as metastatic ovarian cancer, and the discovery of novel therapeutic agents for these malignancies.

Engineering of arrays of zinc finger domains binding DNA.



Research projects

  • Genome and epigenome engineering using artificial DNA-binding proteins: Zinc fingers, TALEs, CRISPR/dCas9
  • Engineering of novel sequence-specific methyl-DNA binding proteins
  • Interference peptide technology to target cancer
  • Nanotechnology and tumor targeting


  1. Beltran A.S., Graves, L.M., Blancafort, P. Novel role of Engrailed 1 as pro-survival factor in basal-like breast cancer and engineering of interference peptides to block its oncogenic function. Oncogene. 2013 Oct 21. doi:10.1038/onc.2013.422. [NCBI PubMed Entry]
  2. Prabhakaran, P., Hassiotou, F., Blancafort, P., Filgueira, L. Cisplatin induces differentiation of breast cancer cells. Front Oncol. (2013) Jun 3;3:134. doi: 10.3389/fonc.2013.00134. [NCBI PubMed Entry].
  3. Hassioutou, F. Hepworth, A. Beltran, AS. Mathews, M. Stuebe, A. Hartmann, P. Filgueira, L. and Blancafort, P. Expression of the pluripotency transcription factor OCT4 in the normal and aberrant mammary gland. Front Oncol. (2013) Apr 11;3:79. doi:10.3389/fonc.2013. [NCBI PubMed Entry]
  4. Van der Gun BTF, Huisman C.,  Stolzenburg S., Kazemier HG, Ruiters, MHJ., Blancafort, P. Rots MG (2013),  Bidirectional modulation of endogenous EpCAM expression to unravel its function in ovarian cancer.BJC. In Press.[NCBI PubMed Entry]
  5. Juárez-Moreno K, Erices R, Beltran AS, Stolzenburg S, Cuello-Fredes M, Owen, GI, Qian H, Blancafort P (2013). Breaking through an epigenetic wall: Re-activation of OCT4 by KRAB-containing designer zinc finger transcription factors. Epigenetics. Jan 11;8(2). [Epub ahead of print]PMID: 23314702 [NCBI PubMed Entry]
  6.  Wang Y, Su H-h, Yang Y, Zhang L, Blancafort P, Huang L. Systemic Delivery of Modified mRNA Encoding Herpes Simplex Virus 1 Thymidine Kinase for Targeted Cancer Gene Therapy. Molecular Therapy. (2012); Dec 11. doi: 10.1038/mt.2012.250. [NCBI PubMed Entry]
  7. Blancafort P, Jin J, Frye S (2012). Writing and re-writing the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacology Minireview. Available on line [NCBI PubMed Entry]
  8. Hassiotou F, Beltran A, Chetwynd E, Stuebe AM, Twigger AJ, Metzger P, Trengove N, Tat Lai C, Filgueira L, Blancafort P, Hartmann PE. Breastmilk is a Novel Source of Stem Cells with Multi-Lineage Differentiation Potential. Stem Cells. (2012) Aug 3. doi: 10.1002/stem.1188. [NCBI PubMed Entry]
  9. Stolzenburg S, Rots MG, Beltran AS, Rivenbark AS, Yuan X, Strahl BS, Blancafort P (2012) Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer. Nucleic Acids Research. (2012); 40:6725-40. [NCBI PubMed Entry] Significance: This paper was selected for the Highlights of the Journal (and the cover), which comprises 5% of the papers based on innovation and scientific excellence.
  10. Lara H, Wang Y, Beltran AS, Juarez-Moreno K, Yuan X, Kato S, Leisewitz AV, Cuello-Fredes M, Licea AF, Connolly DC, Huang L, Blancafort P. Targeting serous epithelial ovarian cancer with designer zinc finger transcription factors. J Biol Chem. (2012); 287:29873-86. [NCBI PubMed Entry]
  11. Rivenbark AG, Beltran AS, Yuan X, Rots MG, Strahl BD, Blancafort P. Epigenetic Reprogramming of Cancer Cells via Targeted DNA Methylation. Epigenetics (2012); 7:350-60. [NCBI PubMed Entry]
  12. Huang X, Narayanaswamy R, Fenn K, Szpakowski S, Sasaki C, Costa J, Blancafort P, Lizardi PM. Sequence-Specific Biosensors Report Drug-Induced Changes in Epigenetic Silencing in Living Cells. DNA Cell Biol. (2012) Feb 7. [NCBI PubMed Entry]
  13. Beltran, A and Blancafort, P. Reactivation of Maspin in Non-Small Cell Lung Carcinoma cells (NSCLC) by Artificial Transcription Factors (ATFs). Epigenetics. 2011 Feb 20;6(2). [NCBI PubMed Entry]
  14. Beltran, A. S., Russo, A, Lara, H, Fan, C, Lizardi, P. M, Blancafort, P. Suppression of breast tumor growth and metastasis by an engineered transcription factor. PLoS One. 2011. 6: 9 e24595 [NCBI PubMed Entry]
  15. Beltran AS, Rivenbark AG, Richardson BT, Yuan X, Quian H, Hunt JP, Zimmerman E, Graves LM, Blancafort P. Generation of tumor-initiating cells by exogenous delivery of OCT4 transcription factor. Breast Cancer Res. 2011 Sep 27;13(5):R94 [NCBI PubMed Entry]
  16. Beltran, A., Blancafort, P.  Remodeling genomes with Artificial Transcription Factors and chromatin remodeling drugs. Zinc Finger Protocols. Humana Press. Methods Mol Biol. 2010;649: 163-82. [NCBI PubMed Entry]
  17. Beltran, A., Sun, X., Lizardi,PM,  Blancafort, P. Reprogramming epigenetic silencing: Artificial Transcription Factors synergize with chromatin remodeling drugs to re-activate the tumor suppressor mammary serine protease inhibitor maspin. Mol Cancer Ther. 2008;7:1080-90. [NCBI PubMed Entry]
  18. Blancafort P, Beltran AS. Rational Design, Selection and Specificity of Artificial Transcription Factors (ATFs): The Influence of Chromatin in Target Gene Regulation. Comb Chem High Throughput Screen. (2008);11:146-58.[NCBI PubMed Entry]
  19. Blancafort, P., Tschan, M.P., Edrmann, D., Barbas III, C.F. Modulation of drug resistance by artificial transcription factors. Mol Cancer Ther. (2008); 7:688-97. [NCBI PubMed Entry]
  20. Beltran, A., Parikh, S., Liu, Y., Cuevas, BD, Johnson GL, Fustcher, BW and Blancafort, P. Reactivation of a dormant tumor suppressor by designed transcription factors. Oncogene. (2007);26:2791-8. [NCBI PubMed Entry]
  21. Beltran, A., Liu, Y., Parikh, S., Brenda, T., and Blancafort, P. Interrogating genomes with combinatorial transcription factor libraries: asking zinc finger questions. Assay Drug Dev Technol. (2006); 4:317-331 [NCBI PubMed Entry]
  22. Dreier, B., Fuller, R.P, Segal, D.J., Lund, C., Blancafort, P., Huber, A., Koksch, B., and Barbas, C.F.III. Development of zinc finger domains for recognition of the 5’-CNN-3’ family DNA sequences and their use in the construction of artificial transcription factors. J. Biol. Chem. (2005); 280: 35588-97.[NCBI PubMed Entry]
  23. Blancafort, P., Chen, E., Gonzalez, B., Bergquist, S., Zijlstra, A., Guthy, D., Brachat, A., Brakenhoff, R., Quigley, J., Edrmann, D., and Barbas C.F.III. Genetic reprogramming of tumor cells by zinc finger transcription factors. Proc. Natl. Acad. Sci. (2005); 102:11716-21. [NCBI PubMed Entry]
  24. Magnenat, L., Blancafort, P. and Barbas III, C.F. In vivo library selection and designed affinity manuration of polydactyl zinc finger transcription factors for ICAM–1 gene regulation. J. Mol. Biol. (2004); 341:635-49.[NCBI PubMed Entry]
  25. Blancafort, P, Segal, D.J., and Barbas III, C.F. Designing transcription factor architectures for drug design. Mol Pharmacol. (2004); 66:1361-71. [NCBI PubMed Entry]
  26. Lund, C.V, Blancafort, P., Popkov, M. and Barbas III, C.F. Promoter-targeted Phage Display Selections with Preassembled Synthetic Zinc Finger Libraries for Endogenous Gene Regulation. J.Mol. Biol. (2004); 340:599-613.[NCBI PubMed Entry]
  27. Blancafort,P., Magnenat, L. and Barbas III, C.F. Scanning the human genome with combinatorial transcription factor libraries. Nat Biotechnol. (2003);21:269-74. [NCBI PubMed Entry]
  28. Segal, D.J., Beerli R.R, Blancafort, P., Dreider, B., Effertz, K., Huber, A., Koksch, B., Magnenat, L., Valente, D., and Barbas III., C.F. (2003). Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins. Biochemistry. 2003; 42:2137-48.[NCBI PubMed Entry]
  29. Blancafort, P., Klinck, R., Steinberg, S., Scott, J.K. and Cedergren, R. The recognition of a non-canonical base pair by a zinc finger protein. Chem Biol. (1999); 6:585-97.[NCBI PubMed Entry]
  30. Blancafort, P., Ferbeyre, G., Sariol, C., and Cedergren, R. Pol I-driven integrative expression vectors for yeast. Journal of Biotechnology (1997);56:41-7 [NCBI PubMed Entry]
  31. Ferbeyre, G., Bratty, J., Blancafort, P., and Cedergren, R. (1995). Yeast as a model for hammerhead ribozyme action. Yeast, 11:15-48A.


  • Blancafort, P. and Barbas III, C.F. "Zinc finger libraries". International Patent Application Serial No. PCT/US03/03705 (2001).
  • Blancafort P, Beltran AS. “Interference Peptides, ipeps. Provisional patent submitted.

Books and Chapters

  1. Blancafort P, Juárez-Moreno K, Stolzenburg S, Beltran AS (2011). Engineering Transcription Factors in Breast Cancer Stem Cells, Breast Cancer - Carcinogenesis, Cell Growth and Signalling Pathways, Mehmet Gunduz and Esra Gunduz (Ed.), ISBN: 978-953-307-714-7, InTech, DOI: 10.5772/23788. Available from:
  2. Hassiotou F., Geddes D., Blancafort P., Filgueira L., Hartmann P.E. (2013). Breastmilk stem cells: Recent advances and future prospects. IN: Regenerative medicine using redundant abdominal fat and menstrual blood. Niranjan Bhattacharya, Phillip Stubblefield (eds.), Springer Verlag International (In press - expected publication date: September 2013).
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