Skin immune atlas, now available in 3D

Defences mapped in time and space

Researcher available for interview Wednesday 6 August 2014Centenary Logo

Researchers at the Centenary Institute in Sydney have developed the first 3D model of the distribution of immune cells in living mammalian skin.

“It takes us from something like a paper map to Google Street View,” says the study’s lead author Dr Philip Tong.

“We knew all of these cells were there, but not how many of them and where.  Now we can dive right in and we see that some types of immune cells are evenly distributed, while others clump in strategic locations.”

The resulting ‘Atlas’, recently posted online by the highly ranked Journal of Investigative Dermatology,  provides the basis for understanding an immune response at a particular site of the skin. It helps explain how the same challenge—for example, injecting the same vaccine or drug—to different areas of the skin can generate a different immune response.

The study found that some immune cells in mice skin, such as the infection-detecting dendritic cells, are evenly distributed throughout the skin, while others, such as the inflammatory mast cells, only occur at certain depths or regions where they can have most impact—in this case close to blood vessels. In mice, there were more of the immune system foot soldiers known as T cells in the skin on the back than in the other areas.

Also, the proportions of the different types of immune cells changed over time. A surprise finding of the study was that in older mice greater numbers of the first-strike gamma-delta T cells were displayed.  Whilst as expected alpha-beta T cells—which contain the cells involved in recognising past infections—were also increased.

While the study was not geared to interpret human disease, it should allow a better understanding of what goes on in the mouse models used to study disease mechanisms. “This is a baseline study. But it has wide implications for any study involving the immune response of skin,” says Dr Tong.

Dr Philip Tong

Dr Philip Tong

The work could also open the way to similar ‘maps’ of the human immune system, allowing finer diagnosis and better-targeted treatments for skin infections.

The next step, Dr Tong says, will be to expand the work to human skin, and also to incorporate further features, such as nerves and the drainage or lymphatic system.

Dr Tong is a dermatologist in training and undertaking his PhD at the Centenary Institute as the Dean’s Fellow in Dermatology at the University of Sydney Medical School. He is supervised by the papers’ senior author and Head of Centenary’s Immune Imaging Research Group, Professor Wolfgang Weninger. They worked on the project with colleagues at the University of Sydney, the Royal Prince Alfred Hospital and the University of South Australia.

The researchers exploited a technology known as intravital multiphoton microscopy, which allows monitoring of immune cells at different depths in living tissue. They also used transgenic mice with fluorescently-labelled immune cells of different colours so they could be picked out by the microscope. This allowed the team to survey the deployment of the immune cells in four areas of skin—on the ear, the tail, the back and the footpad—in mice of different ages. The microscope observations were combined with information on the numbers of each type of immune cell encountered using a technology called flow cytometry.

“This study shows the enormous value of Centenary’s research and its close links both with Sydney University and the Royal Alfred Hospital,” the Institute’s Executive Director, Professor Mathew Vadas AO says. “Dr Tong is one of a group of young clinician researchers who can see the potential for their studies to assist in the clinic and drive them towards improving patient care in dermatology”.

Media contacts:

Philip Tong, Centenary Institute, on 0430 796 512 or

Toni Stevens, Science in Public, on 0401 763 130 or


Background Information


The skin immune atlas: three-dimensional analysis of cutaneous leukocyte subsets by in vivo microscopy

Site-specific differences in skin response to pathogens and in the course of cutaneous inflammatory diseases are well appreciated. The composition and localization of cutaneous leukocytes has been studied extensively using histology and flow cytometry. However, the precise three-dimensional (3D) distribution of distinct immune cell subsets within skin at different body sites requires visualization of intact living skin. We used intravital multiphoton microscopy in transgenic reporter mice in combination with quantitative flow cytometry to generate a 3D immune cell atlas of mouse skin. The 3D location of innate and adaptive immune cells and site-specific differences in the densities of macrophages, T cells and mast cells at four defined sites (ear, back, footpad, tail) is presented. The combinatorial approach further demonstrates an as yet unreported age-dependent expansion of dermal gamma-delta T cells. Localization of dermal immune cells relative to anatomical structures was also determined. While dendritic cells were dispersed homogeneously within the dermis, mast cells preferentially localized to the perivascular space. Finally, we show the functional relevance of site-specific mast cell disparities using the passive cutaneous anaphylaxis model. These approaches are applicable to assessing immune cell variations and potential functional consequences in the setting of infection as well as the pathogenesis of inflammatory skin conditions.

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About the Immune Imaging Group

The Immune Imaging research program comprises four groups whose common feature is that they all employ similar technology – multiphoton microscopes – which can be used to track immune events as they occur in living tissue. This novel imaging approach provides a new way of studying fundamental questions about how the immune system defends us against microbes and cancer cells. Studies of targeted treatments and vaccines also help us understand their mode of action so we can improve therapeutic strategies for patients.

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About the Centenary Institute

The Centenary Institute is an independent leader in medical research seeking improved treatments and cures for cancer, cardiovascular and infectious diseases. We are working to discover new prevention, early diagnosis and treatment options to enable each generation to live longer, healthier lives than the one before. Centenary’s affiliation with the RPA Hospital and the University of Sydney means that our discoveries can be quickly applied to the fight against disease in the clinic.

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Immune ‘atlas” shows distribution of T cells, (in green) surrounding blood vessels (blue) in the skin.

Skin immune atlas shows how T cells (shown in green) interact with the skin’s blood vessels (in blue)

Mast cells are sentinel immune cells that can be found in all organs of the body and protect us agains worms and other parasites but are also involved in asthma and allergy. Shown here is a 3D representation of mast cells (green) distributed evenly throughout the skin, with blood vessels shown in red.

3D immune atlas shows mast cells (in green) distributed evenly throughout the skin, with blood vessels shown in red. Mast cells are sentinel immune cells that can be found in all organs of the body and protect us against worms and other parasites but are also involved in asthma and allergy.

Mast cells (green) distributed evenly throughout the skin, with blood vessels shown in red and the collagen matrix depicted in blue.

Mast cells (green) distributed evenly throughout the skin, with blood vessels shown in red and the collagen matrix depicted in blue.