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.

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Author:Narendra Chunduri
Advisor:Zuzana Storchova
Document Type:Doctoral Thesis
Language of publication:English
Publication Date:2022/06/09
Year of Publication:2021
Publishing Institute:Technische Universität Kaiserslautern
Granting Institute:Technische Universität Kaiserslautern
Acceptance Date of the Thesis:2021/07/14
Date of the Publication (Server):2022/06/10
Number of page:130
Faculties / Organisational entities:Kaiserslautern - Fachbereich Biologie
DDC-Cassification:5 Naturwissenschaften und Mathematik / 500 Naturwissenschaften
Licence (German):Creative Commons 4.0 - Namensnennung, nicht kommerziell, keine Bearbeitung (CC BY-NC-ND 4.0)