Turner Lab research
About Professor Stephen Turner
Professor Stephen Turner is currently a NHMRC Principal Research Fellow and Head of the Department of Microbiology, Monash University. He was awarded his PhD in Viral Immunology from Monash University in 1997. He completed postdoctoral training with Dr Janet Ruby (University of Melbourne) studying pox viral pathogenesis, and then with Nobel Laureate, Professor Peter Doherty (St Jude Children’s Research Hospital, USA) studying influenza virus-specific T cell immunity. He returned to the University of Melbourne in 2002, was awarded an NHMRC RD Wright Fellowship in 2005 establishing his own research group. He was awarded a Pfizer Australia Senior Research Fellowship in 2007, an ARC Future Fellowship in 2012, and is currently CIA on an NHMRC program grant that focuses on T cell immunity to influenza. His research interests utilize a combination of structural biology, genomics, systems biology, recombinant viral technology and cellular immunology to examine molecular factors that impact T cell responses to virus infection.
Our laboratory aims to identify novel transcriptional and epigenetic pathways and regulatory elements that regulate virus-specific killer T cell differentiation, function and the establishment of immunological memory. Such analysis will lead to the identification of molecular immune correlates of protective immunity that will serve to better understand how optimal immunity is generated. Further, this information will contribute to improvement of immunotherapies for infection (vaccines), autoimmune disease and cancer therapy. We use a multidisciplinary approach that includes the application of multiple next generation sequencing applications (RNA-seq, ChiP-seq, ATAC-seq, and HiC), small molecule inhibitor treatment of epigenetic and transcriptional regulators, novel transgenic and gene deficient mouse models, viral models of immunity and advanced bioinformatics.
1. The role of chromatin modifying enzymes in regulating virus-specific T cell differentiation.
Infection triggers large-scale changes in the phenotype and function of T cells that are critical for immune clearance, yet the gene regulatory mechanisms that control these changes are largely unknown. A mechanism for We have recently demonstrated that upon naïve, virus-specific CD8+ T cell activation, large-scale but focused changes in post-translational modifications occur at CD8+ T cell lineage-specific gene promoters (Russ et al., Immunity, 2014) and transcriptional enhancers (Russ et al., Cell Reports, 2017). Importantly, the particular dynamics of histone PTM loss and gain at these regulatory regions identified functionally distinct classes of genes and provided a basis for the coordinated regulation of CTL differentiation. The timed expression of specific enzymes capable of driving the addition or removal of histone PTMs is a key factor in chromatin dynamics and gene regulation. We have a number of projects that focus on gene deficient models, siRNA knockdown and use of chemical inhibitors that are used to probe how blocking histone modifying enzyme function impacts killer T cell responses to infection.
This figure shows that an enzyme called KDM6B, a histone demethylase, is significantly and rapidly upregulated upon naive T cell activation.
2. Understanding how changes in higher order genome structure impacts virus-specific T cell immunity
A wonder of cell biology is how the mammalian is able to condense and package almost 2 meters of DNA into the very compact space within the nucleus. To do this, cells compact and then arrange their genetic information via formation of a DNA/histone protein complex called chromatin. Chromatin then forms long fibres that can then be folded onto itself to form chromosomes. As cells differentiate, there are changes in the folding patterns of chromatin that result changes in DNA accessibility, and formation of close contacts between regulatory elements (termed transcriptional enhancers) and specific target genes. In this way, cells are able to ensure appropriate gene expression profiles at distinct stages of differentiation. This project uses a combination of high throughput sequencing and chromosomal conformation capture (termed HiC), with high resolution imaging (STORM) to both map and visualise changes in the spatial organisation of chromatin and associated interactions at various stages of virus-specific T cell differentiation. When combined with other data we have generated (eg ATAC-seq, ChIP-seq for histone PTMs and transcription factors), we can identify the key regulatory elements, their target genes and potential TF binding to those sites important for regulating optimal T cell responses to infection.
3. How does CD4+ T cell help contribute to programming effective virus-specific CD8+ T cell immunity.
It is well accepted that the activation of CD4+ T helper (TH) cells is key for ensuring the maturation of protective humoral and cellular immunity following immune challenge. Even so, when it comes to generating effective cytotoxic T lymphocyte CD8+ responses in naïve individuals the need, or otherwise, for CD4+ T cell involvement is highly dependent on the nature of the immune challenge. In the case of influenza infection, while CD4+ T cell-independent primary CD8+ T cell responses can be readily induced, the establishment of functional influenza-specific CD8+ T cell memory requires a concurrent CD4+ T cell response. This project aims to explore what the defect in unhelped memory T cells is by examining transcriptional, epigenetic and metabolic differences compared to memory IAV-specific. Further, this project will examine whether novel vaccine strategies can be employed to overcome CD4+ T cell deficiency to generate robust IAV-specific T cell immunity.
4. The role of transcription factors in regulating optimal virus-specific T cell function.
Naive T cell activation results in a program of proliferation and differentiation that is associated with wholesale changes in epigenetic and transcriptional profiles, that in turn, alter cellular function and phenotype. The changes to chromatin structure associated with dynamic addition and removal of histone PTMs serves to prime the DNA for transcription factor binding. It has long been appreciated that the CD8+ T cell differentiation is underpinned by the appropriate temporal expression of key transcription factors such as T-BET (encoded by Tbx21), BLIMP1 (encoded by Prdm1) and EOMESODERMIN (encoded by eomes). Interestingly, despite the importance of such TFs in driving CD8+ T cell differentiation, the precise mechanism of action is unclear. Our own analysis of the transcription factor binding sites at dynamically regulated chromatin regions suggest that CD8+ T cell differentiation involves a combination of TFs working together to shape the chromatin landscape. This project uses a combination of ChIP-seq (for TF and histone PTMs), computational biology and gene deficient mice to examine the precise role of particular TFs, and determine their mechanism of action for generation of optimal T cell immunity.
5. Understanding how single cell heterogeneity contributes to the generation of optimal T cell immunity
There is currently much debate around how the distinct memory T cells arise and whether they represent distinct subsets or are part of a spectrum of differentiation. A greater understanding of the factors required for memory T cell generation and that promote the generation of distinct memory T cell subsets has the potential to vastly improve both current and novel vaccination approaches. Using a combination of next-generation sequencing of total mRNA (RNA-seq) and our murine model of IAV infection, we have generated a comprehensive transcriptomic analysis of the mRNA transcriptional signatures on bulk populations of naïve, effector and memory IAV-specific CD8+ T populations. This analysis demonstrated that each T cell subset is distinguished by it’s own unique transcriptional signature. However, this approach does not determine whether the observed differences in gene expression that defined each T cell subset was in fact uniform across the total subset, or reflected transcriptional heterogeneity within only a proportion of the population being analysed. An approach to get around this issue is to use single cell biology approaches (such as single cell RNA sequencing, or single cell ATAC-seq) to examine the true heterogeneity of individual T cells at a population level. This project uses the 10x chromium platform for scRNA-seq, our mouse models of infection, and the development of novel computational biology approaches to dissect at an unparalleled level of resolution the unique transcripional signatures evident in single IAV specific cells at different stages of differentiation. Moreover, we can use this approach to examine the impact of gene deficiency, novel vaccine strategies, or chemical inhibition of enzyme function to assess outcome on IAV-specific T cell quality.
Visit Professor Turner's Monash research profile to see a full listing of current projects.
Cytotoxic T cell immunity to virus infection
Cytotoxic T cells (also known as killer T cells) are the immune system’s hitmen. As the name suggests, their primary role is to identify and kill cells of the body that have been infected with intracellular pathogens (such as viruses), or that have become cancerous. One aspect of our research program examines the factors that enable the acquisition and maintenance of this killing capacity.
The formation of immunological killer T cell memory
A cardinal feature of killer T cell immunity is the ability to establish a pool of long-lived cells once a viral infection has been controlled. This "immunological memory" ensures that if infected a second time, that the immune response is swift and effective providing protection against secondary infection. Our lab uses a variety of approaches to study factors that contribute to killer T cell memory, and to evaluate novel vaccine strategies designed to promote immunological memory.
Epigenetic and transcriptional regulation of optimal killer T cell immunity
Infection triggers large-scale changes in the phenotype and function of killer T cells that are critical for immune function, yet the gene regulatory mechanisms that control these changes are largely unknown. Our lab uses cutting edge technologies to interrogate changes in the biochemical and spatial characteristics of the genome interactions within virus-specific killer T cells, and how this impacts gene transcriptional signatures associated with optimal virus-specific killer T cell responses.
We utilise a combination of cellular immunology (eg in vitro T cell culture, flow cytometry, functional assessment), virus infection models (influenza A virus, IAV; Lymphocytic choriomeningitits virus, LCMV), transgenic and gene deficient mouse models, and high through put sequencing based technologies (RNA-seq, single cell RNA-seq, ATAC-seq, single cell ATAC-seq, ChIP-seq and HiC) to assess phenotypic, functional and molecular characteristics of virus-specific T cell populations (immature, naive, effector and memory T cells subsets).
Influenza A virus infection of mice
LCMV infection of mice
Genetically modified organisms
We collaborate with many scientists and research organisations around the world. Some of our more significant national and international collaborators are listed below. Click on the map to see the details for each of these collaborators (dive into specific publications and outputs by clicking on the dots).
Professor Sudha Rao, Canberra University
Professor Nicole La Gruta, Monash University
Professor Joachim Schultze, Bonn University, Germany
Professor Philippe Collas, University of Oslo, Norway
Professor Ananda Goldrath, University of California, San Diego, USA
Professor Kees Murre, University of California, San Diego, USA
Professor Jamie Rossjohn, Monash University
Professor Colby Zaph, Monash University
Associate Professor Kim Good-Jacobson, Monash University
Professor Sammy Bedoui, Melbourne University
Professor Eric Morand, School of Clinical Sciences, Monash University
Professor Paul Hertzog, Centre for Innate Immunity and Infectious Disease, Hudson Institute for Medical Research
Student research projects
The Turner Lab offers a variety of Honours, Masters and PhD projects for students interested in joining our group. There are also a number of short term research opportunities available.
Please visit Supervisor Connect to explore the projects currently available in the Turner Lab.