An enormous part of our DNA that scientists once knew relatively little about is emerging as a new hunting ground for cancer research, with a QIMR Berghofer-led team uncovering almost 95,000 previously unannotated molecules to investigate.
The molecules are known as long non-coding RNAs, or lncRNAs. They can be difficult to detect because they may occur in tiny quantities and sometimes only in particular cells or diseases.
Looking across 13 cancer types, including breast, brain, bowel and skin cancers, the researchers identified 219,442 potential lncRNAs. When compared with five existing databases, 94,795 were found to be previously unannotated.
The study, published in Nature Methods, gives researchers a much bigger pool of molecules to investigate as they try to understand what is happening inside different cancers.
A clearer view inside tumour tissue
For decades, genetics concentrated heavily on the one to two per cent of the genome that contains instructions for making proteins. Much of the rest was once loosely dismissed as “junk DNA”, but advances in research have revealed a far more complicated picture.
Long non-coding RNAs don’t make proteins themselves, yet they can be involved in regulating genes and other processes within cells. Their scarcity and tendency to appear in particular cell types have made many of them difficult to study.
The QIMR Berghofer-led research brought together single-cell and spatial analysis, allowing scientists to examine where lncRNAs appeared within tumour tissue rather than simply detecting their presence.
Researchers could then look for patterns, including whether particular molecules appeared in certain cancer cells and how their location related to protein-coding genes and other biological features.
The published study went further by experimentally validating identified lncRNAs across seven cancer types using several spatial technologies.
Now comes the search for the important ones
The enormous dataset has been turned into a freely available online atlas called SPanC-Lnc, where researchers can explore lncRNAs across different cancers, cells and locations within tumour tissue.
Associate Professor Quan Nguyen, director of QIMR Berghofer’s National Centre for Spatial Tissue and AI Research, described this relatively uncharted part of the genome as a potential “goldmine” for new cancer biomarkers and therapeutic approaches.
The scale of the discovery does need perspective. The 94,795 previously unannotated lncRNAs are not 94,795 potential treatments waiting to be developed.
Instead, researchers now have thousands of additional leads that can be narrowed down through laboratory work to establish what individual molecules actually do and whether some could ultimately prove useful in detecting, diagnosing or treating cancer.
First author Dr Prakrithi Pavithra said understanding the biology behind cancer was particularly important because cancers can behave differently between patients and current treatments do not work for everyone.
Researchers involved in the project have already contributed to separate work on an lncRNA associated with the most common form of breast cancer, which is being investigated as the basis for a potential RNA-based therapy.
For the QIMR Berghofer team, the new atlas provides something more immediate: a much clearer map of genetic territory that cancer researchers have only begun to explore.
Published 2-September-2026
