Stem Cell Biology & Neurodegenerative Disease

Project areas

Research focus

Pluripotent stem cell derived neurons expressing green fluorescent protein (under the control of LMX1A promoters) and counter labelled with antibodies to a non-specific neuronal marker (β3 tubulin, in white) and a marker of nuclei (blue). These cells were isolated using green fluorescence activated cell sort 15 days before immunolabeling. While many remain green, it is clear that some are not. We are currently investigating how neurons respond to their extracellular environment in health and disease.

Stem cells can self-renew indefinitely and, being pluripotent, they can develop into any cell type present in the adult. Much of the focus of stem cell biology is directed at the specification of particular cellular phenotypes (neurons, cardiomyocytes, blood, etc.) for use in cell replacement therapies, drug screening and disease modelling.

My research is largely focussed on the development of models of neuropsychiatric and neurodegenerative diseases. The first step in this model development program is defining conditions that permit the generation of specific cell types (for example, A9 or A10 midbrain dopaminergic neurons), the second step is defining conditions that reflect the environment associated with disease. This simple approach enables us to track the progression of healthy cells to unhealthy states. Understanding disease pathology enables us to efficiently direct studies toward new therapeutic targets.

The Stem Cell Group at MIPS has generated a number of embryonic stem cell reporter lines enabling the identification of particular neurons in culture. The development of these reporter lines underlies our core interest in developing human stem cell based models of human disease; however, these fluorescent reporter lines have a broader significance and we have used them to facilitate (i) the identification of conditions conducive to the enrichment of specific neural phenotypes, (ii) the characterization of neurons in culture and (iii) the development of models of neurodegeneration and neuropsychiatric disease.

For a general overview of our work, watch the Stem Cell Group video here

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Key publications

Daniel, P., Filiz, G., Brown, D., Christie, M., Waring, P., Zhang, Y., Haynes, J.M., Pouton, CW., Flanagan, D., Vincan, E., Johns, T., Montgomery, M., Phillips, W., Mantamadiotis, T. (2018). PI3K Activation In Neural Stem Cells Drives Tumorigenesis Which Can Be Suppressed By Targeting CREB. Neuro-oncology, 20(10):1344-1355.

Haynes, J.M., Selby, J.N., Vandekolk, T.H., Abad, I.P.L., Ho, J.K., Lieuw, W., Leach, K., Savige, J., Saini, S., Fisher, C.L., Ricardo, S.D.  (2018). Alport syndrome patient derived podocyte-like cells show impaired potassium channel activity. Journal of Pharmacology and Experimental Therapeutics, 367(2):335-347.

Zhu, C., Rodda, A.F., Truong, V.X.  Shi, Y., Zhou, K., Haynes, J.M., Wang, B., Cook, W.D., Forsythe J.S. (2018) Increased cardiomyocyte alignment and intracellular calcium transients using micropatterned and drug-releasing poly(glycerol sebacate) elastomers. ACS Biomaterials Science & Engineering 4(7):2494-2504.

Anderson, D.J., Kaplan, D.I., Bell, K.M., Koutsis, K., Haynes, J.M., Mills, R., Phelan, D., Arasaratnam, D., Qian, E.L., Labonne, T., Ng, E., Davis, R.P., Cassini, S., Hudson, J.E., Porello, E.R., Costa, M.W., Raffii, A., Curl, C.L., Delbridge, L.M., Harvey, R.P., Oshlack, A., Cheung, M.M., Pedersen, R.A., Mummery, C.L., Petrou, S., Elefanty, A.G., Stanley, E.G., & Elliott, D.A. (2018)NKX2-5 regulates human cardiomyogenesis via a HEY2 -dependent transcriptional network.  Nature Communications 9(1):1373.

Evans, M.A., Lim R., Kim, H.A., Chu H.X., Gardiner-Mann, C.V. Taylor, K.W.E., Chan, C.T., Brait, V.H., Lee, S., Dinh, Q.N., Vinh, A., Phan, T.G., Srikanth, V.K., Arumugam, T.V., Fann, D.Y., Luting, P., Hunt, C.P.J., Pouton, Haynes, J.M., Kwan W., Teo, L., Bourne, J.A, Neumann, S., Young, S., Gowing, E.K., Drummond, G.R., Clarkson, A.N., Wallace, E.M., Sobey, C.G., Broughton B.R.S. (2018). Acute or delayed systemic administration of human amnion epithelial cells improves outcome after stroke.  Stroke. 49(3):700-709.

Alsanie, W.F., Niclis, J.C., Hunt, C.P.,  De Luzy, I.R., Penna, V., Bye, C.R., Pouton, C.W. Haynes, J., Firas, J., Thompson, L.H., Parish, C.L. (2017). Specification of murine ground state pluripotent stem cells to regional neuronal populations.  Scientific Reports. 7(1):16001.

Niclis, J., Gantner, C., Alsanie, W., McDougall, S., Bye, C., Elefanty, A., Stanley, E., Haynes, J.M., Pouton, C.W.P. Thompson, L., Parish, C. (2017). A PITX3-EGFP Reporter Line Reveals Connectivity of Dopamine and Non-dopamine Neuronal Subtypes in Grafts Generated from Human Embryonic Stem Cells. Stem Cell Reports. 9(3):868-882.

Haynes, J.M., & Halliwell, R.F. (2017) Editorial: The Potential of Stem Cells for 21st Century Neuroscience II. Neurochem Int. 106:1-2.

Hunt, C.P.J., Pouton, C.W. & Haynes, J.M. (2017) Differentiation and characterization of human DARPP32 cortical neurons from embryonic stem cells. Neurochem Int. 106:3-13.

Niclis, J., Gantner, C., Alsanie, W., McDougall, S., Bye, C., Elefanty, A., Stanley, E., Haynes, J.M., Pouton, C.W.P. Thompson, L., Parish, C. (2017).  Efficiently Specified Ventral Midbrain Dopamine Neurons From Human Pluripotent Stem Cells Under Xeno-Free Conditions Restore Motor Deficits in Parkinsonian Rodents. Stem Cells Translational Medicine. Stem Cells Transl Med. 6(3):937-948.

Lagerqvist, E.L., Finnin, B.A, Elliott, D.A., Anderson, D.J., Wu, S., Pouton, C.W. & Haynes, J.M. (2015) Comparing mouse and human pluripotent stem cell derived cardiac cells: both systems have advantages for pharmacological and toxicological screening. J Pharm Meth Tox. 74:17-25.

Watmuff, B., Hartley, B.J., Hunt, C.P.J, Fabb, S.A., Pouton, C.W. & Haynes, J.M. (2015).  Human pluripotent stem cell derived midbrain PITX3eGFP/w neurons: a versatile tool for pharmacological screening and neurodegenerative modelling.  Frontiers in Cellular Neuroscience.  9:104.

Chan, L.J., Bulitta, J.B., Williams, C.C., Ascher, D., Haynes, J.M., McLeod, V.M., Porter, C.J.H., Kaminskas, L.M. (2015) PEGylation does not significantly change the initial intravenous or subcutaneous pharmacokinetics or lymphatic exposure of trastuzumab in rats, but increases plasma clearance after subcutaneous administration.  Molecular Pharmaceutics 12(3):794-809.

Kaminskas, L., McLeod, V., Ascher, D., Ryan, G., Jones, S., Haynes, J.M., Trevaskis, N., Chan, L., Sloan, E., Finnin, B., Williamson, M., Velkov, T., Williams, E., Kelly, B., Owen, D., Porter, C. (2015) Methotrexate-conjugated PEGylated dendrimers show differential patterns of deposition and activity in tumour-burdened lymph nodes after intravenous and subcutaneous administration in rats.  Molecular Pharmaceutics 12(2):432-43.

Tsang, K.M.C., Annabi, N., Zhou, K., Ercole, F., Karst, D. Haynes, J.M., Evans, R.A., Thissen, H., Khademhosseini, A. & Forsythe, J.S. (2014) Facile One-step Micropatterning Using Photodegradable Gelatin Methacrylate Hydrogels for Improved Cardiomyocyte Organization and Alignment. Advanced Functional Materials. 25(6):977–986.

Skelton, R.J.P., Costa M., Anderson D.J. Bruveris F., Finnin B.A., Koutsis K., Arasaratnam D., White A.J., Rafii A., Ng E.S., Elefanty A.G., Stanley E.G., Pouton C.W., Haynes J.M., Ardehali R., Davis R.P., Mummery C.L. & Elliott D.A. (2014). SIRPA, VCAM1 and CD34 identify discrete lineages during early human cardiovascular development.  Stem Cell Res. 13(1):172-9.

Kaminskas, L. McLeod, V.M. Ryan, G.M., Kelly, B.D., Haynes, J.M., Williamson, M. Thienthong, N., Owen, D.J., Porter, C.J. (2014).  Pulmonary administration of a doxorubicin-conjugated dendrimer enhances exposure of lung metastases to drug and improves cancer therapy, Journal of Controlled Release. 183:18-26.

Hartley, B.J., Fabb, S.A., Finnin, B.A.L., Haynes, J.M., Pouton, C.W. (2014). Zinc-finger Nuclease Enhanced Gene Targeting in Human Pluripotent Stem Cells. J Vis Exp. 90:e51764.

Hunt, C.P.J., Watmuff, B., Hartley, B.J., Pouton C.W. & Haynes, J.M. (2014) Genetic reporter cell lines: tools for stem cell biology and drug discovery. 'Neural Stem Cell Assays' Ed: Kaur, N and Vermuri, M C,  John Wiley & Sons.

Hartley, B.J., Watmuff, B., Hunt, C.P.J., Haynes, J.M. & Pouton, C.W. (2014) In vitro differentiation of pluripotent stem cells towards either forebrain GABAergic or midbrain dopaminergic neurons. 'Neural Stem Cell Assays' Ed:  Kaur, N and Vermuri, M C, John Wiley & Sons.

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Neurodegenerative modelling

  • Mathew Blurton-Jones (University of California, Irvine)
  • Jon Niclis,  Clare Parish, Lachlan Thompson (Florey Institute)
  • Professor Colin Pouton (MIPS)

Other projects

  • Sharon Ricardo (Faculty MNHS, Monash University)
  • John Forsythe (Monash Engineering)
  • Carmel O'Brien (CSIRO)
  • David Elliott (MCRI)

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Lab members

Current students

  • Teresa Vandekolk (PhD, Characterisation and functional biology of microglia derived in vitro from human embryonic stem cells)
  • Adele Quaran (PhD, Role of gangliosides in regulating the activity of glial derived neurotrophic factor).
  • Enubi Kwak (PhD, Deriving human microglia and their interaction with neurons and astrocytes).
  • Alita Aguiar (PhD, Stem cell derived neuronal models: A tool for understanding schizophrenia and for drug discovery).
  • Shanti Sibuea (PhD, Directing A9 and A10 differentiation from pluripotent stem cells).
  • Horatio Sicilia (PhD, Understanding the role of neuroinflammatory mediators in regulating neuronal function).
  • James Selby (PhD, Assessing the bioactivity of microbiome-produced metabolites of tyrosine upon stem cell derived dopaminergic neurons).

Former student members

  • Durgesh Tiwari (PhD, Investigating the effect of stem cell based therapy in murine models of Alzheimer’s disease, awarded 2015).
  • Brad Watmuff (PhD, Functional development of mouse and human stem cell derived dopaminergic neurons, 2014).
  • Wendy Rong Zeng (PhD, Neural induction and multipotency in mouse embryonic stem cells, 2014).
  • Benjamin Finnin (PhD, Developing embryonic stem cells derived cardiomyocytes as tools for pharmacology and toxicology, 2014).
  • Cameron Hunt (PhD, Regulating development of mouse embryonic stem cells using small molecules, 2014).
  • Pankaj Gulati (PhD, Influence of the extracellular matrix on the in vitro differentiation of mouse embryonic stem cells into neurons, 2014).
  • Rhys Bellinge (MSc, Generation of Mouse Embryonic Stem Cell Reporter Lines to Identify Developmental Stages during Induction of Dopaminergic Neurons, 2013).
  • Brigham Hartley (PhD, Defining conditions required for the derivation of midbrain dopaminergic neurons from embryonic stem cells, 2013).
  • Angela Xie (PhD, A biological study of growth and development in the mouse prostate, 2013).
  • Colin Su (PhD, Investigating the development of midbrain dopaminergic neurons using mouse embryonic stem cell reporter lines, 2012).
  • Victoria Oliver (PhD, Regulation of intracellular calcium by androgens in stromal cells cultured from the human prostate, 2012).
  • Ebba Louise Lagerqvist (PhD, Functional characterisation of cardiomyocytes derived from mouse and human embryonic stem cells, 2011).
  • Christian Nefzger (PhD, Neural differentiation of murine embryonic stem cells with a focus on serotonergic neuron differentiation, 2009).
  • Simer Khaira (PhD, Characterisation of GABAergic neurons derived from mouse embryonic stem cells, 2009).
  • Anna Cook (PhD, Prostatic stroma cell function: modulation of contractility and viability by cGMP-dependent  protein kinases, 2004).
  • Ashley Preston (PhD, α1-Adrenoceptor responses in human cultured prostatic stromal cells: modulation by adenosine and steroid sex hormones, 2003).

Former staff members

  • Nathalie Touchon-Danguy
  • Warren Raye
  • Hady Warden
  • Joan Ho

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  • 2018-2021  Monash University/Fraunhofer Institute for Molecular Biology and Applied Ecology. ICON Collaboration-Tracing health impacts of natural and added nutrients in foods – approach for next-generation validation of the function of foods. Bennett, Bucking, Kotthoff, McCaffrey, Robinson, & Haynes.
  • 2018  International Networks of Excellence Scheme (Monash University). Molecular modelling of Alzheimer’s Disease. Polo, Grubmann, Pouton & Haynes.
  • 2018-2019  Yulgilbar Alzheimer’s Research Program & Stem Cells Australia. Use of hESC-derived models to identify new therapeutic targets for treatment of neurodegenerative diseases. Pouton & Haynes.
  • 2015-2018  NHMRC. Optimizing the differentiation and expansion of microglial progenitors from human pluripotent stem cells for the study and treatment of neurological disease. Pouton & Haynes.
  • 2017  Alport Foundation of Australia. Dysregulation of focal adhesion kinase in Alport Syndrome patients.  Haynes & Ricardo.
  • 2014-2016  ARC Control of cell fate decisions in neurogenesis: use of embryonic stem cells to investigate key signalling systems and gene expression programs. Pouton & Haynes.
  • 2014  Using induced pluripotent stem cell-derived podocytes to create an in vitro model of Alport syndrome.
  • 2010-2013  California Institute of Regenerative Medicine (CIRM)/Victorian Government Stem Cell Alliance. (DIIRD funding). "Developmental Candidates" for Cell-Based Therapies for Parkinson's Disease (PD).

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