PhD research at two world-class facilities

Sam in white research coat sitting in front of computer. Computer screen shows slide image of tissue.

Dr Sam Siljee first came to the GMRI as a summer student. He’ll now start his PhD study investigating early changes in lung cancer.

In October last year, we ran an article about former summer student Dr Sam Siljee investigating a new low-cost treatment for keloid disorder. Sam was recently awarded a PhD scholarship by Victoria University of Wellington (VUW) for his PhD research, which will be carried out at the GMRI and VUW.

Sam will investigate early changes in lung cancer using an emerging research method known as human organoids. Organoids are three-dimensional structures made from human cells that mimic the organs from which they originate. Research with organoids is becoming an increasingly important part of medical enquiry, and is now recognised as the gold-standard research method.

Using organoids to advance our research

Although not the most common cancer, lung cancer is the biggest cause of cancer deaths in New Zealand, with Māori and Pasifika having the worst outcomes. Although the sustained anti-smoking campaigns and other policies have reduced lung cancer caused by smoking, a large proportion of lung cancers are not smoking-related, especially in women.

Sam says organoids will allow him to observe early changes in lung cancer over time. This observation reveals stronger results than previous research techniques — static snapshots from formalin-fixed pieces of tissue and two-dimensional cell culture systems.

Organoids research places the GMRI at the forefront of scientific inquiry along with the international science community. We can get closer to observing disease processes happening in real time, and make findings that more accurately translate into improvements in health.

Traditionally in research, basic biology and early discovery of new treatments cannot use humans as testing systems.

‘Various other research models, such as testing on animals, have their advantages and disadvantages, but animals are fundamentally different to humans,’ Sam says.

‘The beauty of organoids is that they’re relatively complex structures consisting of different cell types. They’re three-dimensional, much more like the organs they represent, and mimic pathologies that researchers are studying.

‘Organoids are also very interesting in how they form themselves from a mix of cell types, or stem cells, when provided with the right environmental cues. This is just like in the developing human body.’

Sam will create organoids at the GMRI for his research

Sam will create two different types of organoids at the GMRI for his research — one that is submerged in cell culture media, the other on a membrane surface. Both organoids will have different types of functioning cells to mimic the system that keeps human lungs clean. These cells include those that secrete mucus and those that have beating hairs to sweep mucus along.

‘Strictly speaking, these are organoids of the airways (breathing tubes), rather than of the lungs themselves,’ Sam says.

Collaboration between two world-class research facilities

Sam will divide his research time between the GMRI and VUW’s world-class proteomics facilities at the School of Biological Sciences. This capability will allow Sam to study individual proteins and subtle changes to the structure of proteins, which is very important in the context of diseases. Sam’s supervisor at VUW, Dr Lifeng Peng, is a world expert in this area.

Sam says he feels incredibly fortunate to be working at both research facilities.

‘This opportunity gives me unrivalled access to dedicated cell culture facilities, state-of-the art automated immunohistochemical staining systems, and fluorescent microscopy using the sophisticated confocal microscope at the GMRI. It also gives me access to state-of-the art mass spectrometry and many other facilities at VUW,’ he says.

‘I’m lucky to have as my supervisors both Chief Scientist Dr Sean Hall and Dr Swee Tan at the GMRI, and Dr Lifeng Peng at VUW. I see this project very much as a collaboration between the GMRI and VUW.’

Explaining a few complex terms

To help understand some of the more complex terms related to Sam’s research, he’s provided some explanations.

Cell culture: The process in which we keep cells and organoids alive in highly controlled environments. Most of us take for granted what our bodies normally do to control the environment for our cells. With cell cultures, we monitor and control variables like temperature, humidity, carbon dioxide, acidity and nutrients as the cells are growing. We manipulate cells in special cabinets where we ensure the cells do not escape the lab and prevent inadvertent introduction of infections or foreign cells. We grow them in specialised incubators that have controlled temperature, moisture, and gases such as oxygen and carbon dioxide.

Staining: Most cells and tissues are naturally transparent, so we need to stain them with certain markers so that we can see them under the microscope. At the GMRI, we use specialised stains with antibodies that identify particular proteins of interest. The antibodies we use work like the molecules used by the immune system to target specific bacteria and other invading organisms. The state-of-the art automated staining system at the GMRI gives more reliable and consistent results and is more efficient, especially with higher sample volumes.

Fluorescent microscopy: The GMRI’s sophisticated confocal microscope is a specialised form of microscopy using lasers rather than a conventional light source. This process gives higher resolution (and therefore detail). Even more importantly, it allows us to investigate multiple markers simultaneously on the same slide — we’re able to label each marker with a different fluorescent colour, and separate out the colours for analysis.

Mass spectrometry: A complex and advanced technique where molecules are sorted by precise weight and charge. The world-class mass spectrometry system at VUW allows individual proteins to be detected and identified in a mixed sample. The real strength of this approach is that it allows researchers to take an unbiased observation of a complex biological sample — they can look at all the proteins present, rather than focusing only on a few markers that a scientist may choose to investigate.

Read about Sam’s first time as a summer student in 2015

Read about Sam’s investigations into a novel low-cost treatment for keloid disorder