Researchers at The University of Texas MD Anderson Cancer Centre have developed a new computational approach designed to better account for changes in gene expression within tumours relative to their unique microenvironments.

This approach outperformed current methods for predicting chemotherapy response in patients with triple-negative breast cancer (TNBC).

The new tool, developed by Wenyi Wang, Ph.D., professor of Bioinformatics and Computational Biology, and colleagues, was published in Cell Reports Medicine.

It aims to improve upon similar methods to predict treatment responses using an approach known as deconvolution, which involves breaking down, calculating and interpreting cellular differences.

This approach also revealed novel insights into population-level characteristics of TNBC.

“Deconvolution strategies are not one size fits all,” Wang said.

“We’re focused on making these methods more accessible to researchers without extensive computational backgrounds, with the goal of translating these powerful analytical approaches into practical tools that the broader cancer research community can readily apply to advance precision medicine.”

What tools do researchers currently have to predict treatment outcomes?

Knowing that there are many computational tools available, Wang and colleagues recently published a comprehensive guide that details 43 of these deconvolution methods.

Their goal was to help researchers without extensive computational backgrounds to understand which method might work best for their study-specific goals.

However, while existing classification strategies measure cell composition, they do not take into consideration the changes that occur in gene expression within tumours in relation to their unique microenvironments.

To address this, the researchers collaborated with MD Anderson’s Institute for Data Science in Oncology (IDSO) and Department of Breast Medical Oncology to develop an integrative bulk analysis that also considers tumour-specific total mRNA expression (TmS).

This approach accounts for the ratio of tumour cells relative to non-tumour cells as a way of identifying cancer-specific mechanisms.

While normal cells have mRNA expression directly proportional to chromosome numbers, cancer cells have an abnormal number of chromosomes.

The TmS biomarker factors this in, accounting for gene expression changes relative to chromosome numbers in cancer cells.

This biomarker further factors in changes in RNA activities in tumour microenvironment cells as compared to tumour cells.

What did the researchers find from using the TmS biomarker?

In a dataset of 575 patients with TNBC across ethnically diverse cohorts, the TmS biomarker was able to accurately sort patients into those with high-TmS, or favourable prognosis, and low-TmS, or poor prognosis.

The biomarker outperformed current methods to predict chemotherapy response, highlighting its potential as an effective starting point for patient stratification to optimise treatment selection.

Importantly, this prognostic biomarker applies across populations, while also highlighting that there are key differences in the tumour microenvironments of high-TmS Western and Asian ethnic groups that could allow clinicians to also match additional treatments likely to work more effectively for each population.

While further validation is needed to advance this tool in the clinic, these results suggest that the TmS biomarker is a promising approach to optimise treatment selection across diverse populations.

Source: University of Texas M. D. Anderson Cancer Center