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Genomics and immunology

The Genomics and Immunology Laboratory works in two general research areas. Firstly, we are interested in the molecular mechanisms that control immune cell development. The immune system is comprised a diverse range of cell types. Each has to be replenished continuously in appropriate numbers and with appropriate functional properties. This is to ensure that immunity to potential infections is maintained while inappropriate immune responses are suppressed. Any defect in the balance can result in susceptibility to infection or cancer, or the development of autoimmune disease. Secondly, we are interested in the biogenesis and function of non-coding RNAs. We study how these RNAs are transcribed and processed in order to generate functional molecules. We are also interested in understanding the regulation of the microRNA machinery.

Research Themes

Molecular control of T cell development

T cells are part of the adaptive immune system and comprise of several different lineages with distinct functions. These include CD8+ cytotoxic T cells that are responsible for destroying virus-infected or tumour cells, CD4+ helper T cells that are responsible for coordinating immune responses, Foxp3+ regulatory T cells that maintain immune homeostasis, and various innate-like T cells. T cells differentiate in the thymus from multipotent precursors and are dependent on highly controlled processes. While the overall T cell developmental pathway is reasonably well characterised, the molecular mechanisms that regulate the various checkpoints remain poorly understand. To gain a better understanding, we employ a range of next generation sequencing technologies, such as high throughput sequencing and single cell genomics. These allows us to more accurately track the process of T cell development as well as to identify the molecular pathways that are critical. Gene manipulation technologies then allow us to probe the requirement of identified pathways. Our goal is to understand how normal T cell development is controlled, and ultimately, how defects contribute to diseases of the immune system, such as autoimmunity and immunodeficiency.

Current projects:

1) The role of class II Coronins 
2) Single cell dissection of developmental checkpoints
3) MicroRNA networks
4) Transcriptional diversity during T cell development

Regulation of dendritic cell development and function by non-coding RNA pathways

Dendritic cells are specialised immune cells that function as a bridge between the innate and adaptive immune systems. The continually sample the environment for antigens. Upon activation, they migrate to secondary lymphoid organs where they interact with T cells and other lymphocytes to initiate a specific immune response. Thus, a functional dendritic cell must be able to 1) capture, process and present antigens to T cells; and 2) secrete immunomodulatory cytokines to drive the immune response of T cells and other lymphocytes. Our lab is interested understanding the role of non-coding RNA pathways in the regulation of these functions. In addition, we are interested how these pathway regulate the development of dendritic cells from precursors in the bone morrow.

Current projects:

1) MicroRNA control of TLR responses
2) Regulation of DC development by the microprocessor messenger RNA cleavage pathway

MicroRNA machinery

The biogenesis of most microRNAs is dependent on the RNase III enzymes Drosha and Dicer. However, it is now clear that some microRNAs can bypass the requirement of one or other enzyme. By comparing cells that lack either Drosha or Dicer, we have identified numerous non-canonical microRNAs that are independent of Drosha. Drosha-independent microRNAs were previously discovered in flies and worms. In these organisms, the biogenesis of Drosha-independent microRNAs requires the splicing machinery. In mammals, however, we find little evidence for a role of splicing. Alternate processing mechanism(s) must therefore be present in mammalian cells. We are interested in understanding how these non-canonical microRNAs are expressed in mammalian cells and whether they function like canonical microRNAs.

Drosha and Dicer can also directly regulate the stability of various RNA substrates, independent of their roles in microRNA biogenesis. In the case of Drosha, it can directly degrade certain messenger RNA targets. This occurs via recognition and cleavage of secondary stem-loop structures within the targets. Interestingly, this activity is largely restricted to stem/progenitor populations and is critical for safeguarding the multipotency of these cells. We are interested in understanding how this mRNA cleavage is regulated and ultimately why this mechanism is important for stem cells.

Current projects:

1) Regulation of microRNA microprocessor complex
2) Messenger RNA cleavage by RNase III enzymes
3) Biogenesis and function of non-canonical microRNAs

Honours and PhD Projects

Staff

  • Associate Professor Mark Chong
  • Dr Shayarana Gooneratne
  • Dr Lawrence Mok
  • Karen Gu
  • Jarrod Skinner
  • Emma Masterman
  • Sean Oh
  • Adrianna Liu
  • Matthew Andrews
  • Marco Montes de Oca
  • Qiwei Hu
  • Jenny Lam
  • Jenny Leong

Publication Highlights

1. Koay HF, Gherardin NA, Enders A, Loh L, Mackay LK, Russ BE, Nold-Petry C., Nold MF, Bedoui S, Chen Z, Corbett AJ, Eckle SBG, Meehan B, d'Udekem Y, Konstantinov I, Lappas M, Liu L, Goodnow CC, Fairlie DP, Rossjohn J, Chong MMW, Turner SJ, Kedzierska K, Berzins SP, Belz GT, McCluskey J, Uldrich AP, Godfrey DI & Pellicci DG (2016), Thymic precursors to the Mucosal-Associated Invariant T cell lineage, Nat Immunol, 17:1300-11.
2. Johanson TJ, Keown AA, Cmero M, Yeo JHC, Kumar A, Lew AM, Zhan Y & Chong MMW (2015), Drosha controls dendritic cell development by cleavage of messenger RNAs encoding inhibitors of myelopoiesis, Nat Immunol, 16:1134-41.
3. Yeo JHC, Skinner JPJ, Bird MJ, Formosa LE, Zhang JG, Kluck RM, Belz GT & Chong MMW (2015), A role for the mitochondrial protein Mrpl44 in maintaining OXPHOS capacity, PLoS One, 10: e0134326.
4. Kobayashi T, Papaioannou G, Mirzamohammadi F, Kozehmyakina E, Zhang M, Blelloch R & Chong MMW (2015), Early postnatal ablation of the microRNA-processing enzyme, Drosha, causes chondrocyte death and impairs the structural integrity of the articular cartilage, Osteoarthritis Cartilage, 23:1214-20.
5. Srivastava M, Duan G, Nadia K, Athanasopoulos V, Yeo JHC, Ose T, Hu D, Brown SHJ, Jergic S, Pratama S, Richards S, Verma A, Jones E, Heissmeyer V, Dixon N, Chong MMW*, Babon J* & Vinuesa CG* (2015), Roquin binds microRNA-146a and Argonaute 2 and regulates microRNA homeostasis, Nat Commun, 6:6253. * Co-senior authors
6. Johanson TM, Cmero M, Wettenhall J, Lew AM, Zhan Y & Chong MMW (2015), A microRNA expression atlas of mouse dendritic cell development, Immunol Cell Biol., 93: 480-5.
7. Skinner JP, Keown AA & Chong MMW (2014), The miR-17~92a cluster of microRNAs is required for the fitness of Foxp3+ regulatory T cells, PLoS One, 9:e88997.
8. Knuckles P, Vogt M, Lugert S, Milo M, Chong MMW, Hautbergue GM, Wilson SA, Littman DR & Taylor V (2012, Drosha regulates neurogenesis by controlling Neurogenin2 expression independent of microRNAs, Nat Neurosci, 15:962-9.
9. Kirigin FF, Lindstedt K, Sellars M, Ciofani M, Low SL, Jones L, Bell F, Pauli F, Bonneau R, Myers RM, Littman DR & Chong MMW (2012), Dynamic microRNA gene transcription and processing during T cell development, J Immunol, 188:3257-67.
10. Kaneko H, Dridi S, Tarallo V, Fowler BJ, Gelfrand BD, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Karikó K, Yoo JW, Lee D, Hadziahmetovic M, Song Y, Misra S, Chaudhuri G, Buaas FW, Braun RE, Hinton DR, Zhang Q, Grossniklaus HE, Provis JM, Madigan MC, Milam AH, Justice NL, Albuquerque RJC, Blandford AD, Bogdanovich S, Hirano Y, Witta J, Fuchs E, Littman DR, Ambati BK, Rudin CM, Chong MMW, Provost P, Kugel J, Goodrich JA, Dunaief JL, Baffi JZ & Ambati J (2011), DICER dysregulation induces cytotoxic Alu RNA accumulation in age-related macular degeneration, Nature, 471:325-30.