Divergent proteome tolerance against gain and loss of chromosome arms

Aneuploidy, defined as the abnormal gain or loss of chromosomes or chromosome arms, causes human genetic syndromes and many cancers. For example, in lung squamous cell carcinoma, chromosome 3q is gained in over 60% of tumors, while chromosome 3p loss occurs in 78% of tumors. However, how the cellular proteome tolerates the gain or loss of chromosomes—a fundamental question in aneuploidy research—remains controversial. We and others have previously reported that aneuploid eukaryotic cells enhance the dynamic degradation of unbound protein complex subunits encoded by excessive chromosomes, maintaining protein complex stoichiometry for cellular biochemical reactions. This mechanism was recently speculated to occur in both gain and loss-type aneuploidies. However, this means that loss-type aneuploid cells would have to degrade all proteins not encoded by the aneuploid (deficient) chromosome but participating in the same protein complexes to a much lower level, which is not economic for the proteomic organization.

In the present work, using a CRISPR engineering strategy, we generated an isogenic chromosome 3 isogenic aneuploidy model exhibiting either 3p loss or 3q gain in lung epithelial cells, along with euploid controls. We then performed a systems analysis of protein abundance, turnover, and thermal stability using mass spectrometry (MS) technologies, including data-independent acquisition (DIA)-MS quantification, dynamic SILAC or pulse SILAC (pSILAC) labeling with plex-DIA, and cellular thermal shift assays (CETSA), on a series of isogenic cells. Our plex-DIA data, based on nearly 9,000 proteins, remarkably found no changes in protein degradation rate for complex-in or complex-out 3p proteins in 3p loss cells, demonstrating that deficient gene copies due to chromosomal loss do not entail slower protein degradation. Instead, we discovered that protein dosage compensation is tightly associated with a relatively enhanced synthesis rate of 3p-encoded proteins participating in protein complexes. Additionally, the interaction partners of proteins encoded by duplicated 3q or deleted 3p are both pervasively regulated post-transcriptionally (mRNA-protein correlations are barely 0.047~0.13). CETSA results further show that proteins encoded on deleted 3p exhibit higher thermal stability, implying the presence of stronger protein-protein interactions. In stark contrast, thermal stability is not regulated for 3q proteins in 3q gain cells. Finally, to corroborate the tolerance mechanism of selective protein translation in lost-type aneuploidy, we found that cytosolic ribosomal proteins, although downregulated, are dramatically stabilized at the post-translational level through longer protein lifetimes and higher thermal stability in 3p loss cells, suggesting a fine-tuning of the protein synthesis process.

In summary, our results demonstrate that cells utilize distinct proteome response mechanisms to tolerate the gain and loss types of aneuploidies.