Researchers from IIT Madras and Sankara Nethralaya have identified biochemical pathways that retinoblastoma (eye cancer) preferentially chooses for growth and survival. They found amino acids are a major source of energy for the tumour tissue, cholesterol synthesis is underutilised and only long and very long chain fatty acids are synthesised. They have identified 13 drug targets.
Based on computational modelling, researchers at the Indian Institute of Technology (IIT) Madras have identified the biochemical pathways that eye cancer (retinoblastoma) preferentially chooses for growth and survival. The pathways chosen are very different from the ones that normal, healthy cells choose.
Retinoblastoma is a childhood tumour, affecting single or both the eyes. Retinoblastoma-related mortality rate is high in Asian and African countries due to its late stage presentation. The current treatment methods — chemotherapy and enucleation — are associated with severe disabilities. Therefore, a systems level understanding of the disease is necessary for suggesting alternative treatment and novel diagnostics.
As a first step, the researchers used tumour samples taken from seven retinoblastoma patients and three normal retina samples. Unlike cell lines, actual patient samples were used and so even fewer samples would suffice for the modelling. The RNA sequence was extracted from the tumour and normal samples as a first step to derive the model.
RNA translates into proteins (enzymes) and the enzymes catalyse the reactions which form part of different pathways. These components are exploited to generate respective data types — RNA sequence data, proteomics data and metabolomics data — each of which can be integrated to derive the model.
For this study, the RNA sequence data and physiological/biochemical information were used to derive patient- and healthy cell-specific models. The subsequent models were then used to analyse the biochemical pathways. “This way we were able to differentiate the biochemical pathways that cancer cells preferentially choose for their survival,” says Dr. Swagatika Sahoo, a DST-INSPIRE faculty at the Department of Chemical Engineering, IIT Madras who co-led the team. The results of the study were published in the journal FEBS Letters.
For instance, unlike health cells which use carbohydrate for energy and survival, the tumour tissue preferentially uses four amino acids instead. “Amino acids are a major source of energy for the tumour tissue, while carbohydrate and fatty acids are used to a lesser extend for energy,” says Dr. Sahoo.
By relying on amino acids for energy, the tumour tissue preserves the fatty acid for other important functions such as signalling and membrane structure.
While amino acids are used at a higher rate, cholesterol synthesis is underutilised by the retinoblastoma tissue. “The reason why the tumour under-utilises cholesterol synthesis is to preserve the redox potential of the cells, thereby mask the diseased condition. Any change in the redox potential is seen as abnormal and can alert the stress pathways,” says Dr. Sahoo.
Unlike normal cells, the tumour tissue specifically synthesised only long and very long chain fatty acids, which play a major role in signalling. The long and very long chain fatty acids synthesised are very different from the ones that normal cells synthesised.
Identifying retinoblastoma subtypes
The researchers were not only able to find significant differences in the biochemical pathways of healthy and retinoblastoma patients but also know the different subtypes of retinoblastoma based on RNA sequence data extracted from the seven patient samples. “The disease subtypes arise because the tumour tissue chooses to synthesise specific fatty acids — long or very long chain fatty acids — for its survival,” Dr. Sahoo says. “The disease subtypes are well known and our model was able to correctly and fully capture this information.”
The researchers compared the metabolism of diseased and health tissue and zeroed in on proteins critical for cancer cells but not the normal cells. “Based on modelling, we identified 13 drug targets that can be used for treating eye cancer. Eight of the 13 targets are already known and drugs that have already been approved for other cancer types are specific to the eight targets. The remaining five are novel drug targets,” says Dr. Karthik Raman from the Department of Biotechnology at IIT Madras and a co-author of the paper.
The approved drugs target mainly the nucleotide metabolism, while the five novel drug targets have been identified for transport proteins. “If you block these transporters [transport proteins] can kill the cancer,” says Dr. Sahoo.