Multi-omics and functional analysis reveal novel consequences of monosomy
- Every organism contains a characteristic number of chromosomes that have to be segregated equally into
two daughter cells during mitosis. Any error during chromosome segregation results in daughter cells that
lost or gained a chromosome, a condition known as aneuploidy. Several studies from our laboratory and
across the world have previously shown that aneuploidy per se strongly affects cellular physiology.
However, these studies were limited mainly to the chromosomal gains due to the availability of several
model systems. Strikingly, no systemic study to evaluate the impact of chromosome loss in the human
cells has been performed so far. This is mainly due to the lack of model systems, as chromosome loss is
incompatible with survival and drastically reduces cellular fitness. During my PhD thesis, for the first time,
I used diverse omics and biochemical approaches to investigate the consequences of chromosome losses
in human somatic cells.
Using isogenic monosomic cells derived from the human cell line RPE1 lacking functional p53, we showed
that, similar to the cells with chromosome gains, monosomic cells proliferate slower than the parental
cells and exhibit genomic instability. Transcriptome and proteome analysis revealed that the expression
of genes encoded on the monosomic chromosomes was reduced, as expected, but the abundance was
partially compensated towards diploid levels by both transcriptional and post transcriptional mechanisms.
Furthermore, we showed that monosomy induces global gene expression changes that are distinct to
changes in response to chromosome gains. The most consistently deregulated pathways among the
monosomies were ribosomes and translation, which we validated using polysome profiling and analysis
of translation with puromycin incorporation experiments. We showed that these defects could be
attributed to the haploinsufficiency of ribosomal protein genes (RPGs) encoded on monosomic
chromosomes. Reintroduction of p53 into the monosomic cells uncovered that monosomy is incompatible
with p53 expression and that the monosomic cells expressing p53 are either eliminated or outgrown by
the p53 negative population. Given the RPG haploinsufficiency and ribosome biogenesis defects caused
by monosomy, we show an evidence that the p53 activation in monosomies could be caused by the
defects in ribosomes. These findings were further supported by computational analysis of cancer genomes
revealing those cancers with monosomic karyotype accumulated frequently p53 pathway mutations and
show reduced ribosomal functions.
Together, our findings provide a rationale as to why monosomy is embryonically lethal, but frequently
occurs in p53 deficient cancers.