Professor Aleksandra Filipovska PhD


Laboratory Head, Professor Aleksandra FilipovskaMitochondrial Medicine and Biology
E:   aleksandra.filipovska@uwa.edu.au
T:   +61 8 6151 0736

Profile

Aleksandra Filipovska received her PhD in 2002 from the University of Otago, New Zealand. From 2003-2005 she was a NZ Foundation for Research, Science and Technology Fellow at the MRC Mitochondrial Biology Unit in Cambridge, the United Kingdom. In 2006 she relocated to Australia as a NHMRC Howard Florey Fellow and established her research group at the Harry Perkins Institute for Medical Research. She was an Australian Research Council Future Fellow from 2009 to 2014 and currently she is a NHMRC Senior Research Fellow and Research Professor at The University of Western Australia. Her research interests are in the regulation of mitochondrial gene expression by RNA-binding proteins in health and disease. In addition her research group uses next generation technologies to identify pathogenic mutations in mitochondrial genes that cause mitochondrial disease in genetically isolated populations.

Research overview - mitochondria and their role in health and disease
Mitochondria are microscopic, energy producing machines that are found in all human cells. Mitochondria are essential for the normal function and survival of all eukaryotic cells. Mitochondria contain a small set of genes that must work properly to make the energy our bodies require for health. Given their central role in providing energy for cells it is not surprising that mitochondrial dysfunction is involved in neurodegenerative disorders, diabetes, and cancer. Despite their importance the regulation of gene expression in mammalian mitochondria remains poorly understood. Defects in the expression of mitochondrial genes cause debilitating diseases for which there are no cures currently. We investigate RNA-binding proteins that regulate the stability, expression and translation of mitochondrial genes. We investigate the genetic causes of diseases caused by mitochondrial dysfunction and analyse the molecular mechanisms that cause pathology in the diseases. As well as unraveling the mysteries of mitochondrial genetics and biology we are interested in the development of gene therapy approaches and therapeutics to combat mitochondrial dysfunction in disease.

Research projects:

1. Mitochondrial RNA-binding proteins and their role in mitochondrial gene expression
Mitochondria play a fundamental role in cell and energy metabolism and consequently mitochondrial dysfunction can lead to severe multi-system disorders with wide range of clinical presentations that commonly include neurodegeneration, muscle defects and exercise intolerance. To understand these conditions better and identify therapeutic targets it is necessary to understand how gene expression is regulated within mitochondria, as some of the most significant gaps in our knowledge of mitochondrial function and disease are in the regulation of mitochondrial gene expression. Links between transcription and translation in mammalian mitochondria are not well understood.

Mitochondrial mRNAs

Fig 1.

Mitochondrial mRNAs are transcribed as part of long primary transcripts that generally encompass the entire mtDNA, therefore the ratios of the 11 mammalian mitochondrial mRNAs and their proteins are controlled post-transcriptionally.

Little is known about how these 11 mRNAs are regulated in mammalian mitochondria. This is particularly important since tissue-, cell- and disease-specific variations in expression of mitochondrial RNAs has been observed, but cannot be explained at present. The basic components and mechanisms of transcription have recently been discovered, however the control of mRNA processing, translation and stability remains unclear. 

We are interested in identifying mammalian mitochondrial RNA-binding proteins and investigating their role in RNA metabolism in cells. Discovery of proteins and the RNAs they bind may shed light on the regulation of gene expression in mammalian mitochondria. In addition, we are developing new methods for the identification of mitochondrial RNAs bound by the mitochondrial RNA-binding proteins that may regulate their expression in health and in disease

 

2. Identification of mutations that cause mitochondrial disease
Mitochondrial diseases are progressive and debilitating multi-system disorders that occur as a result of mutations in nuclear or  mitochondrial genes with no known cures to date. The clinical heterogeneity in mitochondrial disorders is complemented by genetic heterogeneity, where mutations in mitochondrial or nuclear genes cause similar phenotypes thus complicating mutation identification. We use next generation technologies to identify mutations in DNA from patients that suffer from mitochondrial diseases to identify the mutations that cause these diseases. We use patient cells to investigate how mutations in mitochondrial genes cause the molecular changes that cause mitochondrial and cellular dysfunction that leads to the disease pathology.

3. Characterizing the pathology of mitochondrial diseases
Mitochondrial diseases are progressive and debilitating multi-system disorders that occur as a result of mutations in nuclear or mitochondrial genes at a frequency of up to 1 in 4,000 live births with no known cure. Mutations in nuclear genes that code for mitochondrial proteins have been found to cause a range of diseases including mitochondrial diseases that have the same pathologies to those observed in patients with mutations in mtDNA.

Our group works towards developing several animal models of mitochondrial disease and we investigate the effects of mitochondrial dysfunction in different tissues. Furthermore we are investigating how specific proteins regulate gene expression and how lack of these genes can cause the disease pathology. Our goal is to understand the molecular mechanisms underlying mitochondrial disease and provide new avenues for therapeutic interventions. Furthermore we are developing treatments for our established models of mitochondrial disease by synthesising specific small molecule drugs or repurposing of already available drugs.

4. Development of new technologies to investigate mitochondrial gene expression
We are developing new next generation technologies and analytical methods to investigate mitochondrial transcripts, their processing, translation and the role of mitochondrial RNA-binding proteins in cell and mouse models of disease. Furthermore we create new assays and arrays to identify the RNA targets of mitochondrial RNA-binding proteins and modulate mitochondrial gene expression.

Selected publications

  1. Liu, G., Mercer, T.R., Shearwood, A.-M.J., Siira, S.J., Hibbs, M.E., Mattick, J.S., Rackham, O. and Filipovska, A. (2013) Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting. Cell Reports 5(3):839-48. [NCBI PubMed Entry]
  2. Richman, T.R., Ermer, J.A., Davies, S.M., Perks, K.L., Viola, H.M., Shearwood, A.-M.J., Hool, L.C., Rackham, O. and Filipovska, A. (2015) Mutation in MRPS34 compromises protein synthesis and causes mitochondrial dysfunction. PLOS Genetics 10.1371/journal.pgen.1005089. [NCBI PubMed Entry]
  3. Small, I.D., Rackham O. and Filipovska, A. (2013) Organelle transcriptomes: innovations on a prokaryotic blueprint. Current Opinions in Microbiology 16(5):652-8. [NCBI PubMed Entry]
  4. Coquille, S. *, Filipovska, A.*, Chia, T., Rajappa, L., Lingford, J.P., Razif, M.F., Thore, S. and Rackham, O. (2015) An artificial PPR scaffold for programmable RNA recognition. Nature Communications 5:5729. doi: 10.1038/ncomms6729. [NCBI PubMed Entry] *co-first authors 
  5. Richman, T.R., Davies, S.M.K., Shearwood, A-M.J., Ermer, J.A., Scott, L.H., Hibbs, M.E., Rackham, O. and Filipovska, A. (2014) A bifunctional protein regulates mitochondrial protein synthesis. Nucleic Acids Research 42(9): 5483-94. [NCBI PubMed Entry]
  6. Rackham, O., Shearwood, A.-M.J., Mercer, T.R., Davies, S.M.K., Mattick, J.S. and Filipovska, A. (2011) Long non-coding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA 17(12): 2085-93. [NCBI PubMed Entry]
  7. Mercer, T.R., Neph, S., Crawford, J., Dinger, M.E., Smith, M.A., Shearwood, A.-M.J., Haugen, E., Bracken, C.P., Rackham, O., Stamatoyannopoulos, J.A., Filipovska, A.* and Mattick, J.S. (2011) The human mitochondrial transcriptome. Cell 146(4): 645-658. [NCBI PubMed Entry] *co-corresponding author
  8. Filipovska A., Razif M.F.M., Nygård K.K.A. and Rackham O. (2011) A universal code for RNA recognition by PUF proteins. Nature Chemical Biology 7(7): 425-7. [NCBI PubMed Entry]
  9. Lopez Sanchez, M.I.G., Mercer, T.R., Davies, S.M., Shearwood, A.-M.J., Nygård, K.K.A., Richman, T.R., Mattick, J.S., Rackham, O. and Filipovska, A. (2011) RNA processing in human mitochondria. Cell Cycle 10(17): 1-13. [NCBI PubMed Entry]
  10. Rackham O., Davies, S.M.K., Shearwood, A.-M.J., Hamilton, K.L., Whelan, J. and Filipovska, A. Pentatricopeptide repeat domain protein 1 lowers the levels of mitochondrial leucine tRNAs in cells (2009) Nucleic Acids Research 37(17):5859-67. [NCBI PubMed Entry]
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