The unknown immune system and other news from the Imaging Centre of Excellence

ARC Centre of Excellence for Advanced Molecular Imaging, Bulletins

Posted on behalf of James Whisstock, Director Imaging CoE

It’s now less than three weeks until Aidan Byrne, the CEO of the ARC, officially launches the Centre of Excellence for Advanced Molecular Imaging on Wednesday 15 October.

It’ll be a grand occasion. I hope you can come to the ceremony at Monash which will be followed by a tour of the facilities. Then there will be lunch at the Australian Synchrotron, an afternoon symposium on our research, and the Centre’s first Annual General Meeting.

But why do we need to spend $39 million on advanced molecular imaging? Fundamentally we need to able to better understand the workings of our immune system and how it fights disease, and sometimes over-reacts.

This month’s newsletter highlights the work of our immunologists and the critical role they are playing in developing tomorrow’s more subtle approach to medical treatment.  When you read the profiles of Chief Investigators Bill Heath and Dale Godfrey from the University of Melbourne, you’ll see their future work depends fundamentally on advanced molecular imaging.

The studies of Bill’s group on resident memory T cells and the dendritic cells which capture and present antigens to the immune system have changed our understanding of the way the whole immune system functions. Dale charts the little known area of innate-like T cells which are activated not by the traditional protein antigens, but by lipids and vitamins. He and his group have been working at the very edges of technology, sorting out the different subgroups of these cells.

By drawing on the microscopy and X-ray crystallography expertise and technology available through the Centre, both hope to be able to go much further by observing interactions at the molecular level—Bill, of dendritic cells, and Dale, of innate-like T cells.

They will need access to facilities of the highest quality and I’ve just visited two of them. I met our partners at the Deutsches Elektronen-Synchrotron in Hamburg, where the European X-ray Free-Electron Laser facility is being constructed. And I visited our colleagues at the University of Warwick, who are experts in combining optical and electron microscopy.  These are remarkable facilities which, together with the Australian Synchrotron and ANSTO, will deliver for the Centre.

But we’re also working at the other end of the financial scale with the $2 microscope. Our Associate Investigator Steve Lee of the Australian National University and Tri Phan at Sydney’s Garvan Institute have won the ANSTO Eureka Prize for Innovative Use of Technology for their plastic droplet lens that can convert a smartphone into a useful and powerful microscope. The technology they have developed may well form the basis for implantable lenses that can be used in future imaging work in the Centre.

This kind of ingenuity and innovation augurs well for the success of the Centre.

In this newsletter we:

Please feel free to share this newsletter with interested colleagues, and do of course let me know if you do not want to receive future issues.

James Whisstock
Director, Australian Research Council Centre of Excellence in Advanced Molecular Imaging
Professor, Department of Biochemistry and Molecular Biology, Monash University

In search of the unknown immune system

Looking in from outside many people, even doctors, tend to assume we have a reasonable knowledge of the immune system.

“The whole basis for my work,” says immunologist and Imaging Centre of Excellence Chief Investigator Dale Godfrey, “is that our understanding of the immune system is very incomplete. We still don’t know about many of the immune system cell types that are operating during disease—infection, cancer, allergies and autoimmune conditions. And we are right at the very limits of what technology will allow us to do.”

Every innovation that allows researchers to see cells and their components more clearly is a step forward, says Professor Godfrey, a National Health and Medical Research Council Senior Principal Research Fellow in the Department of Microbiology and Immunology of the University of Melbourne and current President of the Australasian Society for Immunology. “That’s why the Centre will be really helpful.”

So far in immunology, he says, the major focus has been on T cells which respond to that protein fragments or peptides presented by major histocompatibility complex (MHC) molecules. This is not surprising, because they comprise the overwhelming bulk of known T cells. But another significant group of between 5% and 20% of T cells, the innate-like T cells, respond to lipid and vitamin fragments presented by CD1 and MR1 molecules. And these are much less well known.

These innate-like T cells tend to be early responders to infection and disease. They begin to act within hours, rather than days, Dale says, and can shape the environment in which the protein-based adaptive immune system plays its part. There are many different subgroups of innate-like T cells, but they are difficult to identify and isolate. In fact, he says, we only know more than a little about two of the subgroups—natural killer T cells (NKT cells) and mucosal-associated invariant T cells (MAIT cells). He and his group have set themselves the not inconsiderable task of identifying and studying all of these innate T cell types.

And that work is based around the development of tetramers, compounds which bind to multiple receptors on T cells. Once an efficient tetramer has
been developed for a particular subgroup of innate-like T cells, the cells themselves can be isolated and fluorescently tagged and followed, to determine where they are likely to be found both in healthy people and in those with particular disease conditions. Then, the researchers have a chance of studying several other characteristics, including the molecules with which each subgroup interacts, and where and how the T cells develop.

Dale’s group has already made progress in discovering new antigens for known innate-like T cells, and in collaboration with Chief Investigator Jamie Rossjohn’s group and that of Prof James McCluskey at the University of Melbourne, they are making fruitful progress in studying MAIT cells, as has been detailed in previous newsletters.

The advent of the Centre now provides them with access to technology and colleagues to support their quest. For instance, chemist and Chief Investigator David Fairlie and others are able to produce new lipid antigens for them to test; Deputy Director and microscopist Kat Gaus and Chief Investigator Bill Heath (see profile below) can provide access to techniques which allow them to observe what’s happening in individual cells and even with individual molecules; Chief Investigator Jamie Rossjohn and Associate Investigators Stefanie Gras and Michelle Dunstone can target atomic interactions using x-ray crystallography, and Chief Investigator Harry Quiney and the researchers at the La Trobe node are studying ways of pushing the boundaries of detection using the latest technological developments, including X-ray free electron lasers.

And there are international collaborations with high profile chemists, such as Professor Amy Howell at the University of Connecticut and Professor Del Besra at the University of Birmingham, and immunologist Dr Branch Moody at Harvard.

“We are working at the fundamental level of understanding the immune system—and, while it can be very frustrating, it’s really exciting when we manage to identify and isolate a new population of immune cells.”

Taking advantage of disease to study immunity

If you ask Bill Heath what he does, he’ll tell you he works on infectious diseases, particularly malaria and Herpes simplex, the virus that causes cold sores. But that’s only half the answer. Bill’s actually an immunologist, who uses these infectious diseases to study how the immune system functions.

Almost all his research life Bill has been probing the interactions of the major players of the adaptive immune system, the T cells and the dendritic cells that present to them the antigens that trigger their activation. “How is the immune response initiated? What happens to immune cells over the course of time? How do the remaining immune cells respond to infection in the future?” Infectious diseases provide him with a stage on which he can study these questions, as well as the potential for clinical application of what he learns.

As a Chief Investigator of the Imaging Centre of Excellence, he will now have access to technology and collaborators that can allow him to see what happens directly. One practical outcome could be the development of more effective vaccines.

For the past five years, Bill’s research group at the University of Melbourne, in close collaboration with that of Frank Carbone, has been involved in changing the view of how the immune system’s foot soldiers, the T cells,  “remember” an infection—so they can fight it more efficiently if it recurs. Once sent into action, T cells proliferate rapidly to destroy the microorganisms causing an infection. When the crisis is over, a much reduced garrison of “memory” T cells remains to cope next time round. Vaccines work by prodding the immune system to generate these memory T cells, typically by initiating an easily overcome infection.

It used to be thought that all memory T cells circulated around the body to be on hand if the same microorganism attempted to reinvade. Bill’s group has found that a previously unrecognised group of memory T cells remains at the site of the original infection or can be localised within specific organs. These resident memory T cells are located at the coal-face where reinfections are likely to occur and are able to mount a stronger response when it happens. So, if a vaccine was able to target development of resident memory T cells, it would be more effective.

Malaria grows in the liver. In collaboration with other researchers at the Centre, Bill would like to develop imaging techniques to check if the malaria parasite induces anti-malaria resident memory T cells in the liver—and if so, how it would be possible to boost them, improving protection against the disease.

Bill is also interested is sorting out the world of dendritic cells. These cells were first described more than 100 years ago. Their critical role in triggering an immune reaction by presenting antigens to T cells, however, has only been unravelled since the 1970s. But the story is much more complex than that. It turns out that there is not just one form of dendritic cell, there are as many as seven distinct subgroups, each with a specific job. One subgroup, for instance, lives in the skin and grabs foreign protein material from that area and takes it to the nearest lymph node (where T cells are). Another subgroup lives permanently in the spleen monitoring the bloodstream.

Some of the subgroups are difficult to find and distinguish. So, Bill and his colleagues have been searching for marker compounds that will designate each of them. Not only that, but they are hoping to use the markers as targets for antigens, developing antibodies that will allow them to target antigens to the dendritic cell subgroups directly with vaccines.

One of the marker molecules they have found, known as clec9A, is a receptor for F-actin, a protein polymer that forms filaments. It is unusual in that dendritic cells carrying clec9A present not only to T cells, but also to the other major group of immune cells, the B cells. Bill and his team are interested in the mechanics of this interaction between T, B and dendritic cells, and are hoping to collaborate with colleagues in the Centre to develop techniques to enable them to observe this interaction unfolding. A significant difficulty is that it all happens deep inside the tissue of the spleen, which is hard to penetrate by microscopy. So the researchers will have to develop probes to get in there.

Another dendritic marker with which Bill’s group has been working is Dec205. It binds to CpG oligonucleotides, synthetic compounds that mimic bacterial and viral DNA and can be used to boost the impact of cancer vaccines. The researchers would like to determine to what Dec205 binds naturally. They think they may be able to do so by drawing on the X-ray crystallography expertise present in the Centre.

From smartphone microscope to probing cells

Congratulations to Associate Investigator Dr Woei Ming (Steve) Lee from ANU and his colleague Dr Tri Phan of Sydney’s Garvan Institute for winning the ANSTO Eureka Prize for Innovative Use of Technology. They developed a technique of using gravity to shape a polymer lens that can convert a smartphone into a microscope which can resolve structures smaller than a human red blood cell. And the technology is directly relevant to the work of the Imaging Centre of Excellence

As the process is inexpensive, it opens up the possibility for biologists to adapt it to form implantable lenses for observing cellular interactions deep inside the body’s organs, Steve says.

Not only is the fabrication simple and direct, but the materials are so cheap, that the lenses are effectively disposable. What’s more, the polymer bases can be varied to produce lenses with different characteristics and resolving power.

“Initially we will probably use bio-compatible lenses, which can then be implanted into different organs,” Steve says. “But in a second stage we would like to explore other polymers for forming special lenses inside the body itself that can withstand considerable wear and tear.”

Cementing the Centre’s international links

The level of scientific achievement and research capabilities encompassed by the Imaging Centre of Excellence are viewed very favourably in Europe. That’s what Centre Director James Whisstock and Chief Operating Officer, Manoj Sridhar found on a recent visit to the Centre’s partner organisations, the Deutches Elektronen-Synchrotron (DESY) in Hamburg and the University of Warwick in Coventry.

“People we met were very impressed and very keen to work with us,” Manoj says. “They had a feel for the unique things we are doing by putting together different capabilities from atomic high energy instruments through to light microscopy to address immunology.”

Beam Tunnel at the European Xfel

At DESY Manoj and James met with Partner Investigator, high energy physicist Dr Henry Chapman and research staff to have a look at progress on the $1.5 billion European X-ray free electron laser (XFEL) facility. It involves a 3.5 kilometre linear accelerator, five metres in diameter running 12 metres underground. And when it opens at the end of 2016, it will be of higher energy and shorter pulse duration that world’s current largest accelerator at Stanford University. “It’s massive—truly a world class facility,” Manoj says.

The plan is to have jointly-funded Centre staff at DESY to facilitate a strong collaborative relationship between Centre and DESY researchers. In addition, staff, mainly from the La Trobe and Melbourne nodes, will be going over there on short exchanges.

At the University of Warwick, Partner Investigator Professor John Davey and his team are experts in combining and correlating light and electron microscopy. “They can move samples smoothly between one environment the other, referencing the position in each microscope.” The university also has excellent capabilities in 3D printing which may prove useful.

James and Manoj also visited the Kennispark Innovation Campus of Twente University in the Netherlands where they spoke to Dr Kees Eijkel, a member of the Centre’s Scientific Advisory Committee. “They take student innovation out of the University and drive it to commercialisation,” says Manoj, “and they do it very, very well.” The Centre is looking at how it might replicate their experience.

And while in the Netherlands, Manoj travelled to Eindhoven to renew links with FEI Company, the company that built the Centre’s new flagship Titan Krios cryo-electron microscope. The Krios, along with other complementary microscopes that are part of the Clive and Vera Ramaciotti Centre for Structural Cryo-Electron Microscopy, arrived at Monash University on 22 September and will now be installed, tested and commissioned over the next few months. The Centre is looking forward to establishing closer links with FEI as we get this facility fully operational.

The work of the Centre forges ahead

From physics through chemistry to molecular biology and many points in between, in the past couple of months the researchers of the Imaging Centre of Excellence have been busy publishing their findings. They have released at least seven papers.

Chief Investigator Jamie Rossjohn from Monash University has been involved in a couple of papers. On 18 August, he and Associate Investigator Michelle Dunstone, also from Monash, published in the Journal of Biological Chemistry with American and Australian colleagues, a study of how the cellular chemical environment impacts antigen presentation. Read the abstract here. Then, in mid-September Jamie and post-doctoral research fellow Julian Vivian were among a large international group contributing to a paper which appeared in Nature Genetics linking the treatment of inflammatory bowel disease in patients with certain immune system gene variants with an increase in the risk of developing pancreatitis. Read the abstract here.

Meanwhile, Chief Investigator David Fairlie of the University of Queensland was last author on two papers published in September with university colleagues. One, in the Journal of the American Chemical Society, reports how a nitrogen or sulfur atom in a carbon ring compound can change the shape of a small molecule to activate or block an immunologically important protein on the surface of the human immune cells known as macrophages. Read the abstract here. The other, in the British Journal of Pharmacology, shows that an experimental drug that activates most signalling pathways linked to G protein coupled receptors on cell surfaces at the same time actually blocks an important pathway associated with inflammatory diseases.  Read the abstract here.

Centre Director James Whisstock, Associate Investigator Michelle Dunstone and PhD student Cyril Reboul put forward a new model for pore formation by the perforin-like cholesterol-dependent cytolysins in PLoS Computational Biology in late August. Read the article here. And, Chief Investigator Bill Heath in mid-August contributed with colleagues from the University of Melbourne and ANU to a paper published in PLoS Pathogens. Their study shows how the body regulates its immune response to chronic Herpes simplex virus skin infection. Read the article here.

The two Chief Investigators from La Trobe University, Keith Nugent and Brian Abbey, together with Partner Investigator Andrew Peele of the Australian Synchrotron released a paper on 5 September to do with a microscopy technique they have used, Fresnel coherent diffractive imaging tomography. The article is open access in the New Journal of Physics. Read the article here.

Taking the Centre’s message to the world

The Imaging Centre of Excellence is certainly getting out there on the hustings and broadcasting what it is doing. In September and October there are or have been at least 13 lectures, seminars or talks presented by Centre researchers in seven different countries.

Director James Whisstock, for instance, gave a seminar on perforin-like proteins at partner institution, the University of Warwick in the UK on 2 September, and followed it on 7 September with a paper on the cleavage of a growth factor in Drosophila at the XIVth International Symposium on Proteinases, Inhibitors and Biological Control in Slovenia. In mid-October, he will be presenting on a different aspect of fly development at the Garvan Institute in Sydney.

Meanwhile, members of Chief Investigator Jamie Rossjohn’s laboratory have also been busy. Early in September, post-doctoral fellow Richard Birkinshaw spoke at the University of Southampton in the UK on how vitamin B metabolites prime innate T cell responses, while on 12 September another post doc, Richard Berry was at the NK2014 meeting in Hannover, Germany talking about viral immunoevasins. Late in the month, PhD student Stephen Scally was at the ComBio 2014 conference in Canberra describing the molecular basis for the association between the HLA-DRB1 allele and rheumatoid arthritis. Between 7 and 10 October, Associate Investigator Stephanie Gras will be attending a crystallography meeting in Grenoble, France and telling them about the molecular basis of T cell antigen recognition.

From the La Trobe University node, on 6 September Chief Investigator Brian Abbey was at an Advanced Photon Source synchrotron workshop near Chicago speaking about opportunities for X-ray imaging at diffraction limited storage rings. And Chief Investigator Keith Nugent travelled to the 20th Users’ Meeting & Workshops at the National Synchrotron Radiation Research Center in Taiwan to talk about coherent diffractive imaging and partial coherence on 11 September.

From the University of Melbourne node, Chief Investigator Dale Godfrey dashed to James Cook University in Townsville on 12 September to introduce the growing family of innate-like T cells, and Chief Investigator Bill Heath will talk on malaria immunity at a one-day symposium at the University of Melbourne on 24 October.

And from the Monash University node, on 17 September Associate Investigator Michelle Dunstone spoke at the 8th Asia Oceania Forum for Synchrotron Radiation Research in Hsinchu, Taiwan on pore formation in a perforin-like proteins. She will also present on advanced molecular imaging of pore-forming toxins at Monash on 23 October.

PhD top-up scholarships in biology, chemistry and physics

Help us transform immunology and microscopy

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  • The University of New South Wales
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Over 40 top-up scholarships will be awarded between 2014 and 2020.

The Centre aims to provide an unprecedented understanding of how immunity works and to pioneer the next generation of imaging at the atomic, molecular, cellular and whole animal levels.

The Centre’s PhD program offers:

  • biology, chemistry and physics projects
  • exceptional interdisciplinary projects
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