Discovering Cancer Mechanisms Using Tumor Metabolism Atlas
A new way of identifying the deep mechanisms of cancer is provided by an atlas that categorizes gene activity and the levels of small molecules called metabolites in tumor samples, according to researchers at Weill Cornell Medicine and Memorial Sloan Kettering Cancer Center.
The researchers, who published their work in Nature Metabolism, created the Cancer Atlas of Metabolic Profiles (CAMP) by combining new and existing datasets on metabolites and gene activity.
‘Analyzing the metabolic profiles of various cancers reveals two varying classes of interaction between genetic and metabolic changes.#cancer #metabolites #cancer mutations’
The Atlas contains data from 988 tumor and normal-tissue control samples across 11 different cancer types. The scientists' analysis of the data revealed two broad classes of gene-metabolite connections that point to mechanisms at work across cancer types ().
This work addresses the basic question of how changes to metabolite levels and gene expression levels are coordinated. The answer they deliver is beautiful and nuanced: this coordination emerges in tandem from the molecular action of genetically-encoded enzymes and their metabolite substrates, as well as from the presence of metabolically unique immune cells in the tumor microenvironment.
New Atlas Will Help Us Build a Core Understanding of How Cancer Functions
Metabolites are small organic molecules used in or produced by metabolic processes in tissues and the bloodstream. They often work in biochemical reactions that provide energy to cells or serve as building blocks for proteins, sugars, lipids, DNA, and RNA.The pattern of metabolite levels in tissues is one of the important layers of information in biology, and researchers already know that key events in cancer, such as tumor development and the acquisition of drug resistance, are accompanied by significant changes in metabolites ().
Relating these cancer-associated metabolite changes to changes in gene activity helps scientists understand why these metabolite changes occur-for example, which enzymes or other proteins are driving the changes. In some cases, disrupting those mechanisms could help fight the cancer.
The CAMP database the scientists created is meant to facilitate such analyses, for it is the largest-ever harmonized collection of data on metabolite and gene activity levels in primary tumor samples. Putting it together was a serious challenge, though.
Having painstakingly aligned the disparate features of the individual datasets, the scientists sought clues to broad cancer mechanisms by looking for gene-metabolite relationships that were prominent across all cancer types covered in the database.
One pattern they found was expected: Some metabolites were strongly correlated with genes encoding enzymes and other proteins with roles in producing metabolites or otherwise regulating their levels. Identifying genes that control cancer-associated metabolite levels can help in further investigations of these metabolites' possible roles in driving cancer ().
In the other prominent pattern, the team discovered, some metabolites were strongly linked to the activities of broad sets of genes-genes not related to metabolite production and processing. Looking closely at the genes involved, it appears that immune cells are massively impacting the metabolite profiles of these tumor samples.
The results underscore the importance of understanding the contributions of different cell types in tumor samples. To that end, researchers now plan to move to more advanced techniques that can "map" gene activity and metabolite levels at precise locations across tumor samples.
References:
- A multimodal atlas of tumour metabolism reveals the architecture of gene-metabolite covariation - (https:www.nature.com/articles/s42255-023-00817-8)
- Metabolic interventions in the immune response to cancer - (https:www.nature.com/articles/s41577-019-0140-9)
- An atlas of human metabolism - (https:www.science.org/doi/full/10.1126/scisignal.aaz1482)
Source: Eurekalert