scholarly journals Loss of USP28 and SPINT2 expression promotes cancer cell survival after whole genome doubling

2021 ◽  
Author(s):  
Sara Vanessa Bernhard ◽  
Katarzyna Seget-Trzensiok ◽  
Christian Kuffer ◽  
Dragomir B. Krastev ◽  
Lisa-Marie Stautmeister ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Damage ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Colorectal Cancer Cell Line ◽  
Whole Genome ◽  
Cancer Evolution ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Frequent Event

Abstract Background Whole genome doubling is a frequent event during cancer evolution and shapes the cancer genome due to the occurrence of chromosomal instability. Yet, erroneously arising human tetraploid cells usually do not proliferate due to p53 activation that leads to CDKN1A expression, cell cycle arrest, senescence and/or apoptosis. Methods To uncover the barriers that block the proliferation of tetraploids, we performed a RNAi mediated genome-wide screen in a human colorectal cancer cell line (HCT116). Results We identified 140 genes whose depletion improved the survival of tetraploid cells and characterized in depth two of them: SPINT2 and USP28. We found that SPINT2 is a general regulator of CDKN1A transcription via histone acetylation. Using mass spectrometry and immunoprecipitation, we found that USP28 interacts with NuMA1 and affects centrosome clustering. Tetraploid cells accumulate DNA damage and loss of USP28 reduces checkpoint activation, thus facilitating their proliferation. Conclusions Our results indicate three aspects that contribute to the survival of tetraploid cells: (i) increased mitogenic signaling and reduced expression of cell cycle inhibitors, (ii) the ability to establish functional bipolar spindles and (iii) reduced DNA damage signaling.

scholarly journals USP28 and SPINT2 mediate cell cycle arrest after whole genome doubling

2020 ◽  
Author(s):  
Katarzyna Seget-Trzensiok ◽  
Sara Vanessa Bernhard ◽  
Christian Kuffer ◽  
Dragomir B Krastev ◽  
Mirko Theis ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Damage ◽  
Cell Cycle Arrest ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Whole Genome ◽  
Genome Doubling ◽  
Cycle Arrest ◽  
Whole Genome Doubling ◽  
Mediate Cell

AbstractTetraploidy 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.

scholarly journals Whole Genome Doubling mitigates Muller’s Ratchet in Cancer Evolution

2019 ◽  
Author(s):  
Saioa López ◽  
Emilia Lim ◽  
Ariana Huebner ◽  
Michelle Dietzen ◽  
Thanos Mourikis ◽  
...  
Keyword(s):  
Negative Selection ◽  
Chromosome Complement ◽  
Essential Genes ◽  
Tumour Suppressor Genes ◽  
Whole Genome ◽  
Cancer Genes ◽  
Cancer Evolution ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Strong Negative Selection

AbstractWhole genome doubling (WGD) is a prevalent macro-evolutionary event in cancer, involving a doubling of the entire chromosome complement. However, despite its prevalence and clinical prognostic relevance, the evolutionary selection pressures for WGD have not been investigated. Here, we explored whether WGD may act to mitigate the irreversible, inexorable ratchet-like, accumulation of deleterious mutations in essential genes. Utilizing 1050 tumor regions from 816 non-small cell lung cancers (NSCLC), we temporally dissect mutations to determine their temporal acquisition in relation to WGD. We find evidence for strong negative selection against homozygous loss of essential cancer genes prior to WGD. However, mutations in essential genes occurring after duplication were not subject to significant negative selection, consistent with WGD providing a buffering effect, decreasing the likelihood of homozygous loss. Finally, we demonstrate that loss of heterozygosity and temporal dissection of mutations can be exploited to identify signals of positive selection in lung, breast, colorectal cancer and other cancer types, enabling the elucidation of novel tumour suppressor genes and a deeper characterization of known cancer genes.

scholarly journals Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution

2020 ◽  
Vol 52 (3) ◽  
pp. 283-293 ◽  
Author(s):  
Saioa López ◽  
◽  
Emilia L. Lim ◽  
Stuart Horswell ◽  
Kerstin Haase ◽  
...  
Keyword(s):  
Whole Genome ◽  
Cancer Evolution ◽  
Genome Doubling ◽  
Whole Genome Doubling

scholarly journals Whole-genome doubling-aware copy number phylogenies for cancer evolution with MEDICC2

2021 ◽  
Author(s):  
Marina Petkovic ◽  
Thomas BK Watkins ◽  
Emma C Colliver ◽  
Sofya Laskina ◽  
Charles Swanton ◽  
...  
Keyword(s):  
Copy Number ◽  
Phylogenetic Trees ◽  
Evolutionary Process ◽  
Recent Common Ancestor ◽  
Whole Genome ◽  
Cancer Evolution ◽  
Minimum Evolution ◽  
Genome Doubling ◽  
Most Recent Common Ancestor ◽  
Whole Genome Doubling

Chromosomal instability (CIN) and somatic copy number alterations (SCNA) play a key role in the evolutionary process that shapes cancer genomes. SCNAs comprise many classes of clinically relevant events, such as localised amplifications, gains, losses, loss-of-heterozygosity (LOH) events, and recently discovered parallel evolutionary events revealed by multi-sample phasing. These events frequently appear jointly with whole genome doubling (WGD), a transformative event in tumour evolution, which generates tetraploid or near-tetraploid cells. WGD events are often clonal, occuring before the emergence of the most recent common ancestor, and have been associated with increased CIN, poor patient outcome and are currently being investigated as potential therapeutic targets. While SCNAs can provide a rich source of phylogenetic information, so far no method exists for phylogenetic inference from SCNAs that includes WGD events. Here we present MEDICC2, a new phylogenetic algorithm for allele-specific SCNA data based on a minimum-evolution criterion that explicitly models clonal and subclonal WGD events and that takes parallel evolutionary events into account. MEDICC2 can identify WGD events and quantify SCNA burden in single-sample studies and infer phylogenetic trees and ancestral genomes in multi-sample scenarios. In this scenario, it accurately locates clonal and subclonal WGD events as well as parallel evolutionary events in the evolutionary history of the tumour, timing SCNAs relative to each other. We use MEDICC2 to detect WGD events in 2778 tumours with 98.8% accuracy and show its ability to correctly place subclonal WGD events in simulated and real-world multi-sample tumours, while accurately inferring its phylogeny and parallel SCNA events. MEDICC2 is implemented in Python 3 and freely available under GPLv3 at https://bitbucket.org/schwarzlab/medicc2.

Synthesis, Cytotoxicity and Antioxidant Activity of New Analogs of RC-121 Synthetic Derivatives of Somatostatin

2019 ◽  
Vol 18 (10) ◽  
pp. 1417-1424 ◽  
Author(s):  
Emilia Naydenova ◽  
Diana Wesselinova ◽  
Svetlana Staykova ◽  
Ivan Goshev ◽  
Ljubomir Vezenkov
Keyword(s):  
Antioxidant Activity ◽  
Antioxidant Capacity ◽  
Cell Line ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Colorectal Cancer Cell Line ◽  
Cervical Cancer Cell Line ◽  
Synthetic Derivatives ◽  
Derivatives Of

Background: Based on the structure of RC-121 (D-Phe-c (Cys-Tyr-D-Trp-Lys-Val-Cys)-Thr-NH2, - synthetic derivatives of somatostatin), some analogs were synthesized and tested for in vitro cytotoxic and antioxidant activity. Objectives: The new analogs were modifyed at position 5 with Dap (diaminopropanoic acid), Dab (diaminobutanoic acid) and Orn and at position 6 with the unnatural amino acids Tle (t-leucine). Methods: The in vitro cytotoxic effects of the substances were investigated against a panel of human tumor cell lines HT-29 (Human Colorectal Cancer Cell Line), MDA-MB-23 (Human Breast Cancer Cell Line), Hep G-2 (Human Hepatocellular Carcinoma Cell Line) and HeLa (cervical cancer cell line). The antioxidant capacities were tested by ORAC (Oxygen Radical Antioxidant Capacity) and HORAC (Hydroxyl Radical Averting Capacity) methods. Results: All substances expressed significantly higher antioxidant capacity by comparison with galic acid and Trolox. All substances showed considerable antioxidant capacity as well. Compound 2T (D-Phe-c(Cys-Tyr-DTrp- Dap-Tle-Cys)-Thr-NH2)had the highest antioxidant effect. The compound 4T (D-Phe-c(Cys-Tyr-D-Trp- Orn-Tle-Cys)-Thr-NH2) displayed antiproliferative effect on HeLa cells with IC50 30 µM. The peptide analog 3T (D-Phe-c(Cys-Tyr-D-Trp-Lys-Tle-Cys)-Thr-NH2) exerted the most pronounced inhibition on the cell vitality up to 53%, 56% and 65% resp. against MDA-MB-23, Hep G-2, HeLa in the higher tested concentration. Conclusion: The somatostatin analogs showed moderate influence on the vitality of different tumor cells and could be used in changing their pathology.

scholarly journals Whole-Genome Doubling Affects Pre-miRNA Expression in Plants

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1004
Author(s):  
Salvatore Esposito ◽  
Riccardo Aversano ◽  
Pasquale Tripodi ◽  
Domenico Carputo
Keyword(s):  
Dna Repair ◽  
Mirna Expression ◽  
Building Blocks ◽  
Nucleotide Metabolism ◽  
Integrative Approach ◽  
Whole Genome ◽  
Solanum Commersonii ◽  
Genome Doubling ◽  
Whole Genome Doubling ◽  
Micro Rnas

Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.

Sign in / Sign up

Export Citation Format

Share Document