Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems‐level property in cancer

Abstract

The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage‐sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post‐translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post‐translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems‐level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed “gene dosage sensor loops.” These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.

Next generation sequencing technologies to address aberrant mRNA translation in cancer

“…Consequently, the direct use of RNA-seq is not an appropriate tool for measuring protein abundance. This is even exacerbated in the case of cancer studies, due to the existence of multiple DNA copy number variations affecting gene expression that are then compensated at the protein level, reducing the correlation between mRNAs and proteins (reviewed in 9 ).…”