Creating predictive tools for lung cancer and COVID-19

Using innovative new technologies, Dr Arutha Kulasinghe is developing an early lung cancer diagnostic, which could be used to predict lung along with head and neck cancer patients’ responsiveness to immunotherapies and targeted therapies.

In 2020, he also pivoted his research to include COVID-19, discovering a set of biomarkers, which could form the basis for a rapid COVID-19 test and help identify patients who will need critical care .

Based at the Translational Research Institute (TRI), the Queensland University of Technology NHMRC Early Career Researcher is working closely with clinicians and industry to ensure all his research delivers valuable solutions for improving patient care. Driven by his grandfather’s experience with colorectal cancer, Dr Kulasinghe believes in keeping the patient as the focal point for all his research.

“Making my research patient-centric is really important to me, so I work really closely with patients,” he says.

New diagnostic for lung cancer

Clinicians currently diagnose lung cancer from tumour biopsies. This is often an invasive procedure, and in many instances, not possible due to the location of the tumour.

To improve the diagnostic process in lung cancer, Dr Kulasinghe is developing a new liquid biopsy assay to detect and monitor non-small cell lung cancers (NSCLC), the most common form of lung cancer.

With initial funding from a 2018 TRI Spore grant, Dr Kulasinghe and his clinical collaborators were able to develop a new liquid biopsy-based test for the cancer, based on several biomarkers identified from patient blood samples. The test relies on analysing tumour material, including molecules and whole cells, which are found in body fluids such as blood.

According to Dr Kulasinghe, NSCLC cancer is usually diagnosed at very advanced stage. At this point, the patient prognosis is often poor, and the cancer has often spread to multiple organs.

“Our assay measures circulating tumour cells, tumour DNA and exosomes in the blood. It’s highly sensitive and can be used to analyse the cancer cells and pick up specific mutations, which may be targetable,” says Dr Kulasinghe.

“It may allow clinicians to identify the cancer before it spreads from the lungs and potentially before the tumour is large enough to do a tissue biopsy.

“In our laboratory-based study, we were able to predict the progression of non-small cell lung cancer in patients much earlier than imaging modalities, so we believe the assay has a potential value in predicting the longer-term clinical outcome and is worth testing in the clinic.

“More recently, we were able to pick up a rare small-cell lung cancer transformation by monitoring the patient over the course of therapy. In this case study, we could see the changes in mutational load in response to therapy and progression, possibly from residual, untreated disease.” [Read the paper]

Dr Kulasinghe is now working with clinicians from the Princess Alexandra Hospital, led by Professor Ken O’Byrne, and industry partner Agena Biosciences to develop the assay for a clinical trial running across several hospitals.

He says that without the TRI Spore Grant the research would not have progressed.

“The TRI Spore grant enabled me to interact closely with clinicians and industry partners to develop tools for unmet clinical needs – these collaborations are critical for early career researchers to progress down the translational science path.

“The grant has led to additional grant funding for my research. It’s allowed me to build my own team within the Cancer and Ageing Research Program (CARP). I wouldn’t have been able to get where I am without it. It was critical at that career stage and my research has really gained momentum from that initial funding.”

Predicting cancer patient response to immunotherapy treatment

The liquid biopsy test being developed by Dr Kulasinghe has the potential to be adapted to inform clinicians how patients with head and neck, and non-small cell lung cancers will respond to immunotherapies.

The new generation of immunotherapy treatments prevent or treat disease by stimulating an immune response. Hailed as a ‘game changer’ for several solid tumours, not all patients respond to the treatments and there are currently no tests to identify which patients are best suited to the therapy.

Supported by Cure Cancer and a Garnett Passe and Rodney Williams Memorial Foundation grant, Dr Kulasinghe aims to develop a prognostic tool by using novel digital spatial-mapping technologies to identify biomarkers present in tumour biopsies.

Spatially mapping tumours is enabling greater insights into understanding the underlying tumour biology by intricately characterising the cell-cell interactions. In this way, Dr Kulasinghe says he aims to gain a better understanding of what is happening inside these tumours, at the tumour-stroma interface and to identify tumour-immune cell interactions that may help researchers predict a patient’s response to immunotherapy.

“My work aims to comprehensively assess the tumour tissue of the patient.

“If we can make individualised assessments of a patient’s tumour and identify biomarkers for targeted therapies, we’re likely to see the greatest benefit.

“Ultimately, knowing more about a patient’s individual tumour and metastatic potential by sampling the liquid biopsy will help guide a personalised approach to treating the patient.”

 Predicting COVID-19 patient susceptibility to lung disease

At the onset of the COVID-19 pandemic, Dr Kulasinghe and fellow TRI researchers, Dr Fernando Guimaraes and Professor Gabrielle Belz, realised they could apply spatial biology approaches to tissue collected from COVID-19 patients.

Working with collaborators in Australia and Brazil, they compared tissue samples from patients with influenza, the Swine Flu and those with COVID-19. They were able to identify gene signatures, which could be potentially useful as triage biomarkers as they stratify disease severity in COVID-19.

“By spatially mapping cell types within the lungs and other respiratory disease states, we’ve identified a number of immune-related genes both exclusive to and shared with those infected by COVID-19,” says Dr Kulasinghe.

“We found one particular type 1 interferon gene was expressed at levels multiple times higher in COVID than in patients with influenza, and the expression levels appear to be higher in patients who go on to develop severe lung problems. This could be very useful to triage patients at the time of diagnosis. In theory, clinicians could order a fast test to see whether or not the patient has COVID and if so, whether or not they need to be hospitalised.

“We believe this is a new finding for the field and are looking to validate the findings with the COVID-Critical and PREDICT-19 consortiums. This study will be important in the future for cancer as well, especially for lung cancer patients who have COVID-19 infections.”

The research was recognised in the 2020 AusBiotech and Johnson & Johnson Innovation Excellence Awards, with the AusBiotech COVID-19 Life Science Sector Collaboration Award and Industry’s Choice Award. The work was also presented at the 3rd Spatial Genomics Summit and AACR COVID-19 and Cancer conferences in early 2021.

The team are now working with a biotech company to commercialise the diagnostic. [Read the media release]

Following this promising study, Dr Kulasinghe is expanding his COVID-19 research program. In late 2020, he was awarded a QUT ECR Team grant to investigate whether the SARS-CoV-2 virus crosses the placenta. He is collaborating on the project with a number of TRI-based researchers including Professor Vicky Clifton from Mater Research.

He is also collaborating with Professor John Fraser and the COVID-Critical network to look at how COVID-19 affects the heart.

Understanding the tumour microenvironment

A third area of research which interest Dr Kulasinghe is using spatially mapping to better understand the tumour microenvironment in melanoma and skin cancers. He is collaborating on the project  with several clinicians thanks to fundng from the PA Research Foundation and Metro South Health Research Support Scheme.

Princess Alexandra Hospital Senior Radiation Oncologist and Director of Radiation Oncology Research, Professor Sandro Porceddu says the technology could change the way clinicians treat skin cancer.

“Working with Arutha to use digital spatial profiling skin cancer has the potential to be a clinical game changer in our understanding of treatment response to immunotherapy in skin cancer,” says Professor Proceddu.

The research team is using the technique to look at disease states with resolutions that have not been possible before.

Dr Kulasinghe says it even makes normal tissue look fascinating.

“The technology is allowing us to understand tumour-immune cell interactions. The ultimate goal is to understand the tumour intrinsically and be able to walk across it in space and time. It also involves a lot of modelling to understand what’s going on at the cellular level, but I describe it as being like a GPS to understand the tumour biology.”

About Dr Kulasinghe

Dr Arutha Kulasinghe completed his Bachelor of Science and Honours majoring in Medical Microbiology at the University of Pretoria (South Africa). In 2014, he undertook his PhD studies in the investigation of circulating tumour cells in head and neck cancers at the Queensland University of Technology (QUT), receiving his doctorate in 2017.

In 2019, Dr Kulasinghe began a Peter Doherty NHMRC Early Career Fellowship to develop biomarkers of immunotherapy response in head and neck squamous cell carcinoma (HNSCC) and lung cancer. His research aims to use spatial analysis of the tumour microenvironment and profiling of liquid biopsy to identify biomarkers of response to immune checkpoint inhibitors. Dr Kulasinghe’s research is supported by several funding agencies, including the NHMRC, Cure Cancer, GPRWMF, PA Research Foundation and the Translational Research Institute.

Recent journal publications on this body of research

• Kulasinghe A, CW Tan, Cooper C, Short K, Davis M, Guimaraes FSF, Belz G, O’Byrne K et al., Spatial Profiling of Lung SARS-CoV-2 and Influenza Virus Infection Dissects Virus-Specific host Responses and Gene Signatures. medRxiv 2020. doi.org/10.1101/2020.11.04.20225557
• Sadeghi Rad H, Monkman J, Warkiani ME, Ladwa R, O'Byrne K, Rezaei N, Kulasinghe A. Understanding the tumor microenvironment for effective immunotherapy. Med Res Rev. 2020 Dec 4. doi: 10.1002/med.21765. Online ahead of print.

• Monkman J, Taheri T, Ebrahimi Warkiani M, O'Leary C, Ladwa R, Richard D, O'Byrne K, Kulasinghe A. High-Plex and High-Throughput Digital Spatial Profiling of Non-Small-Cell Lung Cancer (NSCLC). Cancers (Basel). 2020 Nov 27;12(12):E3551. doi: 10.3390/cancers12123551.

• Sadeghi Rad H, Bazaz SR, Monkman J, Warkiani ME, Rezaei N, O’Byrne K, Kulasinghe A. The evolving landscape of predictive biomarkers in immuno-oncology with a focus on spatial technologies. Clinical and Translational Immunology 2020. doi: 10.1002/cti2.1215. eCollection 2020.

• Herath S, Bazaz SR, Monkman J, Warkiani ME, Richard D, O’Byrne K, Kulasinghe A. Circualting tumor cell clusters: Insights into tumour dissemination and metastasis. Expert Reviews in Molecular Diagnostics 2020. doi: 10.1080/14737159.2020.1846523.