Generation of genetic and epigenetic variation during cellular senescence and early tumorigenesis in a human and nonhuman primate lung fibroblast model
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Abstract
Cellular senescence has garnered greater attention as a fundamental contributor to chronic
illness and functional decline in aging. Once they exceed a finite number of cell divisions,
senescent cells undergo permanent growth arrest while still being metabolically active.
By accumulation they pose significant challenges to the organism. The present work
provides two approaches to investigate senescence in a human lung fibroblast model both
genetically and epigenetically while incorporating induced tetraploidy as an early
tumorigenesis model. First, I compared small non-coding RNA and transcriptomic
changes in proliferating, senescent, and tetraploid IMR-90 cells by conducting sncRNA
sequencing, transcriptomic NGS and a subsequent bioinformatical analysis. Overall, both
senescent and tetraploid IMR-90 cells exhibit amplified miRNA profiles that are pertinent
to cancer progression and inflammation, as demonstrated through miRNA ontology
analysis. This provides a unique opportunity to investigate the relationship between cell
proliferation arrest, excessive cell proliferation, and aberrant replication. Of particular
interest is hsa-miR-29a-3p, which displays significant upregulation in senescent IMR-90
cells, suggesting its yet to be described potential as a reliable senescence marker in human
fibroblasts. The hypothesis that decreasing miR-29a-3p levels may increase longevity has
some merit. However, inhibiting miR-29a-3p in proliferating cells led to the accumulation
of stress responses and the appearance of senescence-related patterns, as evidenced by
the observed biomarkers. Consequently, the inhibition had adverse outcomes, indicating
an association with the antagonistic pleiotropy model of aging. Epigenetic alterations,
including loss of repressive constitutive heterochromatin, may result in LINE-1
derepression, a phenomenon often connected with senescence. In addition to epigenetic
changes, structural variations in aging genomes can be caused by de novo
retrotranspositions of transposable elements like SVAs, as well as de novo insertions of
accumulated mitochondrial DNA into nuclear DNA. A kinetic enrichment approach was
utilized to detect the nuclear flanks of de novo SVA insertions in senescent genomes. The
technique was coupled with deep sequencing. Furthermore, the genomes of proliferating
and senescent IMR-90 cells were compared through deep sequencing or by enriching
nuclear DNA with AluScan technology. Evidence was uncovered for de novo SVA and
numts integrations in senescent IMR-90 cells using both methods. I hypothesize that the
structural disparities have an impact on the mechanisms associated with cellular
senescence in human lung fibroblasts.