Decoding the cancer cell proteome: A delicate equilibrium with the genome and epigenome

With an estimated 10 000–1 000 000 distinct proteoforms present across human cells, tissues, and fluids—each shaped by more than 200 types of post-translational modifications (PTMs)—the proteome holds a vast reservoir of biological information that cannot be fully revealed through genomic or transcriptomic analyses alone.¹ Indeed, mapping cancer proteome has historically lagged behind genomic and transcriptome studies. Factors contributing to this lag include the relatively larger tissue size required for proteomics as compared to nucleic acid profiling, and historically lower sensitivity of protein profiling platforms for detection of low-abundant (biomarker) proteins. First, DMG tumor cells are hypomethylated at several molecular levels. These include reduced levels of histone methylation. First, DMG tumor cells exhibit loss of histone 3 trimethyl mark (H3me3), an epigenetic regulating residue. This loss of a repressive mark leads to transcriptional activation of oncogenes and growth-promoting pathways. Additionally, DMGs exhibit a global loss of DNA methylation. Collectively, these epigenetic aberrations contribute to tumor stemness, the aggressive phenotype, and thus facilitate tumor growth and resistance to treatments.

In this issue, Anguraj Vadivel et al.² characterize the proteomic landscape of pediatric DMG, with a particular focus on the methyl- and phospho-proteome. The authors use an array of molecular profiling platforms to investigate the dependency of DMG tumors on methylation signaling pathways, including methyl transferases and their potential as a therapeutic opportunity. Among these, METTL13, METTL21B, PAK2, PRKACA, and AKT1 are identified as main pro-tumorigenic proteins. A major finding of their manuscript is the discovery that non-histone proteins, including transcription factors and signaling proteins, are often hypomethylated in DMG, leading to changes in oncogenic signaling, influencing cell metabolism, apoptosis, and differentiation. Their findings emphasize the delicate balance between genome and proteome that needs further investigation.

Our group was the first to generate a proteome profile of tumors from DMG patients.³ Subsequently, recent technological advancements and higher availability of surgical and postmortem tissue have resulted in a surge in proteomic profiling of pediatric brain malignancies. A review of the literature shows a number of DMG protein profiling reports that have expanded our understanding of tumor biology.

Recent proteomic profiling advancements have also enabled researchers to create a draft map of the human proteome.¹ Proteogenomics and phosphoproteogenomics, capturing the functional readout of cellular activity at a given time point, are also increasingly incorporated into clinical settings.⁴ The result is the establishment of a foundation for developing therapeutic strategies that target the biological mechanisms driving cancer progression and understanding interactions between oncogenes and oncogenic signaling in a number of malignancies.⁵

However, employing next-generation proteomics techniques in DMG research presents significant challenges.⁶ The rarity of the disease, the sensitive anatomical location that limits tissue accessibility, and the small sample sizes obtained through stereotactic biopsies create obstacles for applying these technologies. Nonetheless, high-resolution proteomics, a technique that provides precise measurements of mass-to-charge ratio, represents a crucial advancement in DMG research, as implementing these strategies could greatly aid in mapping the DMG proteome and its PTMs. Potential direct benefits from these insights include identifying antigens for novel immuno-oncology treatments and novel disease signaling pathways.

The development of epigenetic regulating pharmacological agents that modulate or target PTMs is widely regarded as a viable strategy for cancer treatment. Within this framework, inhibitors of histone methyltransferases (HMTs) have received notable attention. This growing interest is primarily due to the limited success achieved with targeting histone acetylation and the expectation of greater specificity from modulating histone methylation. Currently, a number of preclinically promising HMT inhibitors have been advanced to phase I or phase II⁷; however, their clinical efficacy remains to be determined.

The report by Anguraj Vadivel et al. shows that METTL13 knockdown improves survival of DMG in vivo models. METTL13 knockdown resulted in a reduction of EEF1A protein. These results suggest that targeting methyltransferases involved in EEF1A1 methylation may be an effective strategy to disrupt protein synthesis, thereby hindering the proliferation of DMG cells as part of a combination therapeutic approach. In this regard, cancers that are driven by PI3K-AKT activation show increased sensitivity to EEF1A inhibitors.⁸ Thus, it is plausible to consider combining EEF1A inhibitors with PI3K-Akt inhibitors, such as paxalisib,⁹ currently under clinical investigation for the treatment of DMG (NCT05009992) with DMG.¹⁰

The interplay between methylation of histone and non-histone proteins warrants further studies to fully elucidate tumor epigenetic landscape. Understanding the role of non-histone methylation in DMG may provide novel options for targeted therapies. Methylation modification of non-histone proteins is emerging as a critical factor in cancer biology, influencing various cellular mechanisms that contribute to the tumor’s aggressiveness. Further research is warranted to improve understanding of DMG biology and provide novel therapeutic for effective treatment of children diagnosed with this incurable brain cancer.

Conflict of interest

The authors declare no conflict of interest.

Funding

The authors would like to thank the following for financial support: Isabella Kerr Foundation, Swiss to Cure DIPG Foundation, ChadTough Defeat DIPG fellowship, Rising Tide Foundation (CCR-20-500), Swiss National Science Foundation - Sinergia (CRSII5_198739), National Institutes of Health (CA266596), and Borne Hjernecancer Fonden