Chancellery Research - Research Publications
Now showing items 1-12 of 482
MAIT cells regulate NK cell-mediated tumor immunity
(NATURE PORTFOLIO, 2021-08-06)
The function of MR1-restricted mucosal-associated invariant T (MAIT) cells in tumor immunity is unclear. Here we show that MAIT cell-deficient mice have enhanced NK cell-dependent control of metastatic B16F10 tumor growth relative to control mice. Analyses of this interplay in human tumor samples reveal that high expression of a MAIT cell gene signature negatively impacts the prognostic significance of NK cells. Paradoxically, pre-pulsing tumors with MAIT cell antigens, or activating MAIT cells in vivo, enhances anti-tumor immunity in B16F10 and E0771 mouse tumor models, including in the context of established metastasis. These effects are associated with enhanced NK cell responses and increased expression of both IFN-γ-dependent and inflammatory genes in NK cells. Importantly, activated human MAIT cells also promote the function of NK cells isolated from patient tumor samples. Our results thus describe an activation-dependent, MAIT cell-mediated regulation of NK cells, and suggest a potential therapeutic avenue for cancer treatment.
Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.
(Springer Science and Business Media LLC, 2020-01-24)
Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000 PPIs shows that this network is extensively rewired in cells expressing transforming levels of KRASG13D (mtKRAS). The factors driving PPIN rewiring are multifactorial including changes in protein expression and phosphorylation. Mathematical modelling also suggests that the binding dynamics of low and high affinity KRAS interactors contribute to rewiring. PPIN rewiring substantially alters the composition of protein complexes, signal flow, transcriptional regulation, and cellular phenotype. These changes are validated by targeted and global experimental analysis. Importantly, genetic alterations in the most extensively rewired PPIN nodes occur frequently in CRC and are prognostic of poor patient outcomes.
Francisella tularensis induces Th1 like MAIT cells conferring protection against systemic and local infection
(NATURE RESEARCH, 2021-07-16)
Mucosal-associated Invariant T (MAIT) cells are recognized for their antibacterial functions. The protective capacity of MAIT cells has been demonstrated in murine models of local infection, including in the lungs. Here we show that during systemic infection of mice with Francisella tularensis live vaccine strain results in evident MAIT cell expansion in the liver, lungs, kidney and spleen and peripheral blood. The responding MAIT cells manifest a polarised Th1-like MAIT-1 phenotype, including transcription factor and cytokine profile, and confer a critical role in controlling bacterial load. Post resolution of the primary infection, the expanded MAIT cells form stable memory-like MAIT-1 cell populations, suggesting a basis for vaccination. Indeed, a systemic vaccination with synthetic antigen 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil in combination with CpG adjuvant similarly boosts MAIT cells, and results in enhanced protection against both systemic and local infections with different bacteria. Our study highlights the potential utility of targeting MAIT cells to combat a range of bacterial pathogens.
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer-reviewed by leading experts in the field, making this an essential research companion.
Exercise serum increases GLUT4 in human adipocytes
NEW FINDINGS: What is the central question of this study? Do circulating factors mediate exercise-induced effects on adipose tissue GLUT4 expression? What is the main finding and its importance? Serum (10%) obtained from human volunteers immediately after a single exercise bout increased GLUT4 protein levels in human adipocytes in culture. This result suggests that circulating factors might mediate the effects of exercise on adipose tissue GLUT4 and prompts further effort to identify the specific factor(s) and tissue(s) of origin. ABSTRACT: In this study, we tested the hypothesis that circulating factors generated during exercise increase adipose tissue GLUT4 expression. Serum was obtained from eight healthy subjects before and after 60 min of cycling exercise, and primary adipocytes were cultured from stromal vascular fractions that were isolated from subcutaneous abdominal adipose tissue samples from one healthy, male volunteer. A 48 h exposure of human primary adipocytes to 10% serum obtained after exercise increased GLUT4 protein expression, on average, by 12% compared with exposure to 10% serum obtained at rest, before exercise. GLUT4 mRNA levels were increased after 12 h of exposure to exercise serum but were unchanged after 6 and 24 h of exposure. Our results suggest that circulating factors might mediate the effects of exercise on adipose tissue GLUT4 expression and encourage further efforts to identify the potential factor(s), tissue(s) of origin and physiological relevance.
Optic nerve tissue displacement during mild intraocular pressure elevation: its relationship to central corneal thickness and corneal hysteresis
PURPOSE: To determine the extent to which (1) optic nerve tissue is displaced following mild acute elevation of intraocular pressure, and (2) clinically accessible measures at the anterior eye can be used as a surrogate for such displacements. METHODS: We imaged the optic disc of 21 healthy subjects before and after intraocular pressure (IOP) elevation of ~10 mmHg delivered by ophthalmodynamometry. Steady-state tissue displacement during IOP elevation was assessed axially from OCT data, and laterally from SLO data. Recovery from IOP elevation was assessed by tracking a single vertical B-scan through the cup centre. Anatomical structures were demarcated by three masked clinicians to determine lateral shifts for temporal cup edge and central disc vessels, and axial shifts of disc surface and anterior lamina cribrosa. Spatial maps of deformation were constructed within the demarcated cup and disc to assess within-tissue displacement. Measured displacements were correlated with corneal hysteresis, corneal thickness, and IOP. RESULTS: The temporal cup edge moved more temporally with higher baseline IOP (R2 = 0.33, p = 0.006) and with lesser elevation of IOP (R2 = 0.43, p = 0.001); it moved more superiorly for thinner corneas (R2 = 0.35, p = 0.007). Thinner corneas also produced less within-cup deformation, relative to that of the disc (R2 = 0.39, p = 0.004). Axial displacement of the lamina and lateral displacement of vessels were often substantial (lamina 20 ± 15 μm, range 1-60 μm; vessels 37 ± 25 μm, range 2-102 μm) but did not correlate with measured parameters. Recovery from IOP elevation did not take more than 300-400 ms in any subject. CONCLUSIONS: Mild acute elevation of IOP produces large and rapidly reversible shifts in optic nerve tissue in young, healthy eyes. The resulting degree, direction and spatial distribution of cup movement are associated with IOP status and corneal thickness, but not corneal hysteresis.
An overview on the identification of MAIT cell antigens
Mucosal associated invariant T (MAIT) cells are restricted by the monomorphic MHC class I-like molecule, MHC-related protein-1 (MR1). Until 2012, the origin of the MAIT cell antigens (Ags) was unknown, although it was established that MAIT cells could be activated by a broad range of bacteria and yeasts, possibly suggesting a conserved Ag. Using a combination of protein chemistry, mass spectrometry, cellular biology, structural biology and small molecule chemistry, we discovered MR1 ligands derived from folic acid (vitamin B9) and from an intermediate in the microbial biosynthesis of riboflavin (vitamin B2). While the folate derivative 6-formylpterin generally inhibited MAIT cell activation, two riboflavin pathway derivatives, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil and 5-(2-oxoethylideneamino)-6-D-ribitylaminouracil, were potent MAIT cell agonists. Other intermediates and derivatives of riboflavin synthesis displayed weak or no MAIT cell activation. Collectively, these studies revealed that in addition to peptide and lipid-based Ags, small molecule natural product metabolites are also ligands that can activate T cells expressing αβ T-cell receptors, and here we recount this discovery.
Mucosal-associated invariant T cell receptor recognition of small molecules presented by MR1
The major histocompatibility complex (MHC) class-I related molecule MR1 is a monomorphic and evolutionary conserved antigen (Ag)-presenting molecule that shares the overall architecture of MHC-I and CD1 proteins. However, in contrast to MHC-I and the CD1 family that present peptides and lipids, respectively, MR1 specifically presents small organic molecules. During microbial infection of mammalian cells, MR1 captures and presents vitamin B precursors, derived from the microbial biosynthesis of riboflavin, on the surface of antigen-presenting cells. These MR1-Ag complexes are recognized by the mucosal-associated invariant T cell receptor (MAIT TCR), which subsequently leads to MAIT cell activation. Recently, MR1 was shown to trap chemical scaffolds including drug and drug-like molecules. Here, we review this metabolite Ag-presenting molecule and further define the key molecular interactions underlying the recognition and reactivity of MAIT TCRs to MR1 in an Ag-dependent manner.
Effects of compression garments on recovery following intermittent exercise
The objective of the study was to examine the effects of wearing compression garments for 24 h post-exercise on the biochemical, physical and perceived recovery of highly trained athletes. Eight field hockey players completed a match simulation exercise protocol on two occasions separated by 4 weeks after which lower-limb compression garments (CG) or loose pants (CON) were worn for 24 h. Blood was collected pre-exercise and 1, 24 and 48 h post-exercise for IL-6, IL-1β, TNF-α, CRP and CK. Blood lactate was monitored throughout exercise and for 30 min after. A 5 counter-movement jump (5CMJ) and squat jump were performed and perceived soreness rated at pre-exercise and 1, 24 and 48 h post-exercise. Perceived recovery was assessed post-exercise using a questionnaire related to exercise readiness. Repeated measures ANOVA was used to assess changes in blood, perceptual and physical responses to recovery. CK and CRP were significantly elevated 24 h post-exercise in both conditions (p < 0.05). No significant differences were observed for TNF-α, IL1-β, IL-6 between treatments (p > 0.05). Power and force production in the 5CMJ was reduced and perceived soreness was highest at 1 h post-exercise (p < 0.05). Perceived recovery was lowest at 1 h post-exercise in both conditions (p < 0.01), whilst overall, perceived recovery was greater when CG were worn (p < 0.005). None of the blood or physical markers of recovery indicates any benefit of wearing compression garments post-exercise. However, muscle soreness and perceived recovery indicators suggest a psychological benefit may exist.
The role of HLA genes in pharmacogenomics: unravelling HLA associated adverse drug reactions
Genetic polymorphism in the genes encoding the human leukocyte antigen (HLA) molecules enables presentation of a wide range peptide ligands thus maximising immune surveillance of pathogens. A consequence of the diversification of the HLA Ag-binding pocket is the enhanced opportunity for off-target binding of small drugs by HLA molecules, with subsequent immune reactivity. These potential off-target interactions are 'set up' to generate T cell-mediated adverse drug reactions even though the precise mechanisms of most HLA-drug interactions are still poorly understood. The association between abacavir hypersensitivity syndrome and HLA-B*57:01 is one exception that has been resolved at a molecular and mechanistic level. Here, we explore the road to understanding the interaction between abacavir and the HLA-B*57:01 molecule and review the current state of understanding of interactions between other drugs and HLA molecules implicated in adverse drug reactions, which appear to involve multiple mechanisms. The continued expansion of the pharmacopoeia generates an imperative to understand these interactions at the molecular level in order to prevent the continued burden on individuals and the health care system.
CO-llaborative VI-rtual D-esign: A Collaborative Autoethnography on Conducting Exclusively Online, Data-Led Collaborations in the Creative Industries
(SAGE PUBLICATIONS INC, 2021-08-24)
This collaborative autoethnographic story of #DataCreativities articulates data traces found within the rapid move online in education and creative sectors in Melbourne, Australia. As a result of the lockdowns imposed to combat the initial spread of COVID-19, this collaboratory began within the anxieties of 2020. #DataCreativities takes a data-related approach to understanding the fast-paced shift to making, learning, teaching, and living in a crisis through research and art. Twelve months on, we figure (out) our own data and practice. We ask: What does CO-llaborative VI-rtual D-esign look like, how can it be established, and how can it be sustained?
Explainable reinforcement learning through a causal lens
(Association for the Advancement of Artificial Intelligence (AAAI), 2020-01-01)
Prominent theories in cognitive science propose that humans understand and represent the knowledge of the world through causal relationships. In making sense of the world, we build causal models in our mind to encode cause-effect relations of events and use these to explain why new events happen by referring to counterfactuals — things that did not happen. In this paper, we use causal models to derive causal explanations of the behaviour of model-free reinforcement learning agents. We present an approach that learns a structural causal model during reinforcement learning and encodes causal relationships between variables of interest. This model is then used to generate explanations of behaviour based on counterfactual analysis of the causal model. We computationally evaluate the model in 6 domains and measure performance and task prediction accuracy. We report on a study with 120 participants who observe agents playing a real-time strategy game (Starcraft II) and then receive explanations of the agents' behaviour. We investigate: 1) participants' understanding gained by explanations through task prediction; 2) explanation satisfaction and 3) trust. Our results show that causal model explanations perform better on these measures compared to two other baseline explanation models.