Cellular reprogramming and ageing

The state of the transcription factor (TF) network defines cellular identity due to regulatory control over gene expression and its influence on the epigenetic landscape.  
 
Ageing is the greatest risk factor for most degenerative diseases but meaningful interventions targeting the process itself, to move the focus away from merely treating its symptoms, are missing. On a cellular level, functional decline appears to have a largely non-genetic or epigenetic basis, since age-compromised cells can be reprogrammed towards a pluripotent state (iPS technology) and then used to generate young and healthy mice (e.g., PMID 28224997; PMID 23476050). Despite a growing appreciation, we still do not understand how age-related epigenetic changes drive cellular dysfunction hindering development of effective strategies for mitigating functional cellular decline in ageing.
 
To gain a deep understanding about the age-altered TF network and enable strategies to directly improve it (without any form of pluripotency induction), the lab investigates (among other things) how the TF-network is reshaped by age in major mammalian cell types at base pair resolution through multiomics strategies and functionally tests the effects of reinforcing or destabilising factors/factor combinations with age-altered activity using model systems.  

M Naval-Sanchez, N Deshpande, M Tran, J Zhang, M Alhomrani, W Alsanie, Q Nguyen, CM Nefzger#. Benchmarking of ATAC Sequencing Data From BGI’s Low-Cost DNBSEQ-G400 Instrument for Identification of Open and Occupied Chromatin Regions. FRONTIERS IN MOLECULAR BIOSCIENCE. 9: 900323.
doi: 10.3389/fmolb

Nefzger CM, Jardé T, Srivastava A, Schroeder J, Rossello FJ, Horvay K, Prasko M, Paynter JM, Chen J, Weng CF, Sun YBY, Liu X, Chan E, Deshpande N, Chen X, Li YJ, Pflueger J, Engel RM, Knaupp AS, Tsyganov K, Nilsson SK, Lister R, Rackham OJL, Abud HE, Polo JM. Intestinal stem cell aging signature reveals a reprogramming strategy to enhance regenerative potential. NPJ REGENERATIVE MEDICINE 2022 Jun 16;7(1):31.
doi: 10.1038/s41536-022-00226-7.PMID: 35710627

Sun X, Cao B, Naval-Sanchez M, Pham T, Sun YBY, Williams B, Heazlewood SY, Deshpande N, Li J, Kraus F, Rae J, Nguyen Q, Yari H, Schröder J, Heazlewood CK, Fulton M, Hatwell-Humble J, Das Gupta K, Kapetanovic R, Chen X, Sweet MJ, Parton RG, Ryan MT, Polo JM, Nefzger CM# and Nilsson SK#. Nicotinamide riboside attenuates age-associated metaboic and functional changes in hematopietic stem cells.  NATURE COMMUNICATIONS. 2021 May 11;12(1):2665. doi: 10.1038/s41467-021-22863-0. 

Liu X, Ouyang JF, Rossello FJ, Tan JP, Davidson KC, Valdes DS, Schröder J, Sun YBY, Chen J, Knaupp AS, Sun G, Chy HS, Huang Z, Pflueger J, Firas J, Tano V, Buckberry S, Paynter JM, Larcombe MR, Poppe D, Choo XY, O'Brien CM, Pastor WA, Chen D, Leichter AL, Naeem H, Tripathi P, Das PP, Grubman A, Powell DR, Laslett AL, David L, Nilsson SK, Clark AT, Lister R, Nefzger CM, Martelotto LG, Rackham OJL, Polo JM. Reprogramming roadmap reveals route to human induced trophoblast stem cells. NATURE. 2020 Oct;586(7827):101-107. doi: 10.1038/s41586-020-2734-6. Epub 2020 Sep 16.

Jardé T, Chan WH, Rossello FJ, Kaur Kahlon T, Theocharous M, Kurian Arackal T, Flores T, Giraud M, Richards E, Chan E, Kerr G, Engel RM, Prasko M, Donoghue JF, Abe SI, Phesse TJ, Nefzger CM, McMurrick PJ, Powell DR, Daly RJ, Polo JM, Abud HE. Mesenchymal Niche-Derived Neuregulin-1 Drives Intestinal Stem Cell Proliferation and Regeneration of Damaged Epithelium. CELL STEM CELL. 2020 Oct 1;27(4):646-662.e7. doi: 10.1016/j.stem.2020.06.021. Epub 2020 Jul 20.

Joseph Chen*, Christian M. Nefzger*#, Fernando J. Rossello, Yu B.Y. Sun, Sue Mei Lim, Xiaodong Liu, Suzan de Boer Anja S. Knaupp, Jinhua Li, Kathryn C. Davidson, Jose M. Polo#, Tiziano Barberi#. Fine tuning of canonical Wnt stimulation enhances differentiation of pluripotent stem cells independent of β-catenin-mediated TCF signaling. STEM CELLS. 2018 Jun;36(6):822-833. doi: 10.1002/stem.2794. Epub 2018 Feb 14.

Pflueger C, Tan D, Swain T, Nguyen T, Pflueger J, Nefzger CM, Polo JM, Ford E, Lister R. A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. GENOME RESEARCH. 2018 Aug;28(8):1193-1206. doi: 10.1101/gr.233049.117. Epub 2018 Jun 15.

Christian M. Nefzger*, Fernando J. Rossello*, Joseph Chen, Xiaodong Liu, Anja S. Knaupp, Jaber Firas, Jacob M. Paynter, Jahnvi Pflueger, Sam Buckberry, Sue Mei Lim, Brenda Williams, Sara Alaei, Keshav Faye-Chauhan, Enrico Petreto, Susan K. Nilsson, Ryan Lister, Mirana Ramialison, David R. Powel, Owen J.L. Rackham# and Jose M. Polo#. Cell type of origin dictates the route to pluripotency. CELL REPORTS. 2017 Dec 5;21(10):2649-2660. DOI: 10.1016/j.celrep.2017.11.029.

Anja S. Knaupp, Sam Buckberry, Jahnvi Pflueger, Sue Mei Lim, Ethan Ford, Michael R. Larcombe, Fernando J. Rossello, Alex de Mendoza, Sara Alaei, Jaber Firas, Melissa L. Holmes, Christian M. Nefzger, Ryan Lister# and Jose M. Polo#. Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming. CELL STEM CELL. 2017 Dec 7;21(6):834-845.e6. DOI: 10.1016/j.stem.2017.11.007.

Liu X*, Nefzger CM*, Rossello FJ, Chen J, Knaupp AS, Firas J, Ford E, Pflueger J, Paynter JM, Chy HS, O’Brien CM, Huang C, Mishra K, Hodgson-Garms M, Jansz N, Williams SM, Blewitt ME, Nilsson SK, Schittenhelm RB, Laslett AL, Lister R, Polo JM#. Comprehensive characterization of distinct states of human naïve pluripotency generated by reprogramming. NATURE METHODS, 2017 Nov;14(11):1055-1062. DOI: 10.1038/nmeth.4436.

Nefzger CM, Polo JM#. DEAD-Box RNA Binding Protein: Not a Black-Box during reprogramming. CELL STEM CELL. 2017 Apr 6;20(4):419-420. DOI: 10.1016/j.stem.2017.03.006

Alaei S, Knaupp AS, Lim SM, Chen J, Holmes ML, Änkö ML, Nefzger CM# and Polo JM#. An improved reprogrammable mouse model harboring the reverse tetracycline-controlled transcriptional transactivator 3. STEM CELL RESEARCH. 2016 Jul;17(1):49-53. DOI: 10.1016/j.scr.2016.05.008.

Nefzger CM*, Jarde T*, Horvay K, Knaupp AS, Rosello FJ, Chen J, Powel DR, Abud HE#, Polo JM#. A versatile strategy for isolating a highly enriched population of intestinal stem cells. STEM CELL REPORTS. 2016 Mar 8;6(3):321-9. DOI: 10.1016/j.stemcr.2016.01.014.

Owen J.L. Rackham*, Jaber Firas*, Hai Fang, Matt E. Oates, Melissa Holmes, Anja Knaupp, the fantom consortium, Harukazu Suzuki, Christian M Nefzger, Carsten O. Daub, Jay W. Shin,Enrico Petretto, Alistair R.R. Forrest, Yoshihide Hayashizaki, Jose M. Polo#, Julian Gough#. Mogrify: An Atlas for Direct Reprogramming Between Human Cell Types. NATURE GENETICS. 2016. 2016 Mar;48(3):331-5. DOI: 10.1038/ng.3487.

Firas J*, Liu X*, Nefzger CM# and Polo JM#. GM-CSF and MEF-conditioned media support feeder-free reprogramming of mouse granulocytes to iPS cells. DIFFERENTIATION. 2014 Jun;87(5):193-9. DOI: 10.1016/j.diff.2014.05.003.

Polo JM*, Anderssen E*, Walsh RM, Schwarz BA, Nefzger CM, Lim SM, Borkent M, Apostolou E, Alaei S, Cloutier J, Bar-Nur O, Cheloufi S, Stadtfeld M, Figueroa ME, Robinton D, Natesan S, Melnick A, Zhu J, Ramaswamy S#, Hochedlinger K#. A molecular roadmap of reprogramming somatic cells into iPS cells. CELL. 2012 Dec 21;151(7):1617-32. DOI: 10.1016/j.cell.2012.11.039.

Nefzger CM*, Su CT*, Fabb SR, Hartley BJ, Beh SJ, Zeng WR, Haynes JM#, Pouton CW#. Lmx1a allows context-specific isolation of progenitors of GABAergic or dopaminergic neurons during neural differentiation of embryonic stem cells. STEM CELLS. 2012 Jul;30(7):1349-61. DOI: 10.1002/stem.1105.


Khaira SK*, Nefzger CM*, Beh SJ, Pouton CW#, Haynes JM#. Midbrain and forebrain patterning delivers immunocytochemically and functionally similar populations of neuropeptide Y containing GABAergic neurons. NEUROCHEMISTRY INTERNATIONAL. 2011 Sep;59(3):413-20. DOI: 10.1016/j.neuint.2011.02.016. 
 

Nefzger CM, Haynes JM#, Pouton CW#. Directed Expression of Gata2, Mash1 and Foxa2 synergise to induce the serotonergic neuron phenotype during in vitro differentiation of embryonic stem cells. STEM CELLS. 2011 Jun;29(6):928-39. DOI: 10.1002/stem.640. 
 

 

CI Nefzger was appointed as Group Leader at IMB/UQ in 2019. He has a strong publication record; 44 papers with collectively >2,800 citations (11 as first/co-first, 8 as corresponding author). His past studies transformed our understanding about iPSC generation, including the associated rewiring of the TF network (e.g. Nefzger et al. CELL REPORTS 2017; Liu and Nefzger et al. NATURE METHODS 2017; Alaei, ..., Nefzger# and Polo#, STEM CELL RESEARCH 2016; Firas,…, Nefzger# and Polo#, DIFFERENTIATION 2014; Polo et al. CELL 2012; collectively >900 citations). Leveraging knowledge about cell identity, his research has characterised other cell state transitions and pioneered novel conversions for clinically relevant cell types via new differentiation & transdifferentiation paradigms (e.g., Chen and Nefzger et al. STEM CELLS 2018; Rackham et al. NATURE GENETICS 2017; Nefzger et al. STEM CELLS 2011; collectively >700 citations). A new paradigm to derive dopaminergic neuron progenitors from PSCs (Nefzger et al. STEM CELLS, 2012), is now on track for clinical translation in a Parkinson’s disease context (PMID:31641054). In the ageing field, his work has recently demonstrated that age-intervention strategies based on NAD precursors (Sun et al., 2021, corresponding author publication, NATURE COMMUNICATIONS) only result in partial restoration of a young HSC state (e.g., no correction of the myeloid differentiation bias). Therefore, his laboratory has started a research programme in 2019 to investigate TF based strategies to directly correct the age-rewired molecular landscape by identifying and testing TFs that underpin differences between the young and the aged state.

CI Nefzger has been awarded >$3,7 million (~1,7 million as CIA) in research funding, beyond this he is supported by a generous start-up package from his host institute. Prestigious oral presentations (7 int., 16 national) include speaker invitations (e.g., ComBio 2016, 2017) and selected oral presentations at the leading international (ISSCR 2018, Cell Press Symposia 2018) and national meetings (ASSCR 2011-2018, best ERC presentation award in 2016). CI Nefzger is an elected committee member of the Australian Society for Stem Cell Research (nationally leading organisation) and is currently co-organising the society’s annual meeting (Nov 2021). He was lead organiser of the successful ASSCR ECR symposium in QLD (Jan 2021), promoting emerging researchers and has co-organised the regional NSW and Victoria symposia (May and June 2021 respectively). He has been serving on the NHRMC (Australia’s primary government funding source for medical research)’s Ideas grant panel (2019, 2020, 2021 and now 2022) and on institutional ERC grant review panels. Due to his longstanding expertise in viral gene delivery, he is co-director of the University of Queensland’s viral vector core to promote innovations in the area of adenoviral, adeno associated virus and lentiviral gene delivery for both in vivo and in intro applications.

We collaborate nationally and internationally, and across research fields.
Collaborators include:

• Quan Nguyen, IMB, University of Queensland, Brisbane, Australia
• Jess Mar, AIBN, University of Queensland
• Susie Nilsson, CSIRO, Melbourne, Australia
• Helen Abud, Monash University, Melbourne, Australia
• Ryan Lister, University of Western Australia, Perth, Australia

2022-2023 Innovations connection grant, Australian Government, academic lead CI

2022 MGI DNBSEQ MPS Research Grant (Spatial context for aged cells with altered epigenetic landscape)

2022-2025 NHMRC Ideas Grant (sole CI, APP2013574) – Reinforcing the cell identity network to improve the function of aged cells.

2020-2021 Genome Innovation Hub external project (Innovation of single cell multiome assays, UQ, sole CI)

2021-2022 Innovations connection grant, Australian Government, academic lead CI

2021-2022 TAIF University funding scheme, Saudi Arabia, Co-CI

2021-2022 TAIF University funding scheme, Saudi Arabia, Co-CI

2018-2022 NHMRC Project Grant (sole CI, APP1146623) - Generation of somatic stem cells by direct reprogramming