Biology subjects

Boekenkamp, J.-E.

Publications and source records attributed to Boekenkamp, J.-E..

3 recordsLinked to original sources

bioRxiv2024

Aneuploidy-induced proteostasis disruption impairsmitochondrial functions and mediates aggregation ofmitochondrial precursor proteins through SQSTM1/p62

Aberrant chromosomal content, or aneuploidy, profoundly affects cellular physiology. Even a gain of a single chromosome disrupts proteostasis due to overexpression of numerous proteins. Consequently, cells accumulate SQSTM1/p62-positive cytosolic bodies and show altered proteasomal and lysosomal activity. To elucidate the p62 interaction network in aneuploid cells, we conducted p62 immunoprecipitation and proximity labeling assays followed by mass spectrometry analysis. Our investigation revealed the enrichment of mitochondrial proteins within the cytosolic p62 interactome and proxitome in aneuploid cells, but not in the proxitome spatially confined to autophagosomes. Immunofluorescence microscopy confirmed increased colocalization of p62 with novel interactors and with mitochondrial proteins in polysomic cells. Moreover, we observed mitochondrial defects characterized by increased perinuclear clustering, reduced oxygen consumption, and reduced mitochondrial DNA abundance in polysomic cells. Furthermore, we demonstrate that polysomic cells exhibit reduced import of mitochondrial proteins and accumulation of mitochondrial precursor proteins in the cytosol. Our data suggest that proteotoxic stress induced by chromosome gains leads to the sequestration of mitochondrial precursor proteins into cytosolic p62-bodies and compromises mitochondrial function.

cell biology↗

bioRxiv2024

Proteogenomic analysis reveals adaptive strategies to alleviate the consequences of aneuploidy in cancer

Aneuploidy is prevalent in cancer and associates with fitness advantage and poor patient prognosis. Yet, experimentally induced aneuploidy initially leads to adverse effects and impaired proliferation, suggesting that cancer cells must adapt to aneuploidy. We performed in vitro evolution of cells with extra chromosomes and obtained cell lines with improved proliferation and gene expression changes congruent with changes in aneuploid cancers. Integrated analysis of cancer multi-omics data and model cells revealed increased expression of DNA replicative and repair factors, reduced genomic instability, and reduced lysosomal degradation. We identified E2F4 and FOXM1 as transcription factors required for adaptation to aneuploidy in vitro and in cancers and validated this finding. The adaptation to aneuploidy also coincided with specific copy number aberrations that correlate with poor patient prognosis. Chromosomal engineering mimicking these aberrations improved aneuploid cell proliferation, while loss of previously present extra chromosome impaired it. The identified common adaptation strategies suggest replication stress, genomic instability, and lysosomal stress as common liabilities of aneuploid cancers.

genetics↗

bioRxiv2020

USP28 and SPINT2 mediate cell cycle arrest after whole genome doubling

Tetraploidy is frequent in cancer and whole genome doubling shapes the evolution of cancer genomes, thereby driving the transformation, metastasis and drug resistance. Yet, human cells usually arrest when they become tetraploid due to p53 activation that leads to CDKN1A expression, cell cycle arrest, senescence or apoptosis. To uncover the barriers that block proliferation of tetraploids, we performed an RNAi mediated genome-wide screen in a human cancer cell line. We identified 140 genes whose depletion improved survival of tetraploids and characterized in depth two of them: SPINT2 and USP28. We show that SPINT2 is a general regulator of CDKN1A, regulating its transcription via histone acetylation. By mass spectrometry and immunoprecipitation, we show that USP28 interacts with NuMA1 and affects centrosome clustering. Moreover, tetraploid cells accumulate DNA damage and loss of USP28 reduces checkpoint activation. Our results indicate three aspects that contribute to survival of tetraploid cells: i) increased mitogenic signaling and reduced expression of cell cycle inhibitors, ii) the ability to establish functional bipolar spindle, and iii) reduced DNA damage signaling.

cell biology↗