Biology subjects

Stamatiou, K.

Publications and source records attributed to Stamatiou, K..

6 recordsLinked to original sources

bioRxiv2025

A CDCA2 - MYC positive feedback loop controls cancer cells survival

MYC transcription factors are encoded by a small family of genes which include, in addition to the prototype member MYC, MYCN and MYCL. The majority of human cancers display expression alterations of MYC genes and their products, making this group of oncoproteins among the most relevant therapeutic targets in oncology. MYC is regulated at multiple levels, and protein phosphorylation is a critical mechanism used by the cell to modulate MYC stability and activity. Although there is a reasonable knowledge of the kinases required for MYC modifications, the counteracting phosphatases have been relatively understudied. Here we have investigated the role of the chromatin remodelling factor and protein phosphatase 1 (PP1) regulatory subunit CDCA2, also known as RepoMan, in the regulation of MYC proteins in cancer cells. Using RNA interference and regulatable degron-mediated degradation of CDCA2, we demonstrate that the PP1 subunit is required for MYC and MYCN stabilisation and viability of triple negative breast cancer, neuroblastoma and colon cancer cells. Proximity ligation assays indicate that both MYC and MYCN are in close proximity of CDCA2 in vivo. Furthermore, chromatin immunoprecipitation data and promoter mutation studies establish that CDC2A is a bone-fide MYC target gene in cancer cells, revealing a reciprocal regulatory loop that could be exploited for therapeutic purposes.

cell biology↗

bioRxiv2025

Illuminating oncogenic KRAS signaling by multi-dimensional chemical proteomics

Mutated KRAS is among the most frequent activating genetic alterations in cancer and drug discovery efforts have led to inhibitors that block its activity. To better understand oncogenic KRAS signaling and the cytostatic effects of drugs, we performed comprehensive dose-dependent proteome-wide target deconvolution, pathway engagement and protein expression characterization of KRAS, MEK, ERK, SHP2 and SOS1 inhibitors in pancreatic (KRAS G12C, G12D) and lung cancer (KRAS G12C) cells. Analysis of the resulting 687,954 dose-response curves available online revealed both common and cell line-specific signaling networks dominated by oncogenic KRAS activity. Time-dose experiments separated early KRAS-MEK-ERK from CDK-mediated signaling that cause cells to exit from the cell cycle. This transition to a quiescent state occurred without substantial proteome re-modelling but extensive changes of protein phosphorylation and ubiquitylation. The collective data highlights the complexity of KRAS signaling in cancer and places a large number of new proteins into this functional context.

cell biology↗

bioRxiv2024

Multi-omic analyses reveal a differential contribution of chromatin-associated PP1 holoenzymes to mitotic exit and G1 re-establishment.

Mitotic exit is an important part of the cell cycle that requires coordination of many chromatin and cytoskeleton remodelling events to successfully complete cell division and maintain cell identity. Protein de-phosphorylation is a key step in directing mitotic exit and Protein phosphatase (PP1) is essential to this process, however the specific contribution of its numerous targeting subunits is still unknown. Here we have investigated the function of three chromatin-associated PP1 targeting subunits in exiting mitosis Repo-Man, Ki-67 and PNUTS. We have generated endogenously tagged, auxin-degradable alleles for each subunit and used a multi-omic approach to address their specific contribution towards transcription resumption, chromatin accessibility and protein phosphorylation at the transition from mitosis to G1. This approach has identified their distinct role in mitotic exit, provided unique datasets for the cell cycle community, and highlighted novel functions for Ki-67 and Repo-Man in genome stability and organisation.

cell biology↗

bioRxiv2023

Ki-67 is necessary during DNA replication for forks protection and genome stability

BackgroundThe proliferation antigen Ki-67 has been widely used in clinical settings for cancer staging for many years but investigations on its biological functions have lagged. Recently, Ki-67 was shown to regulate both the composition of the chromosome periphery and chromosome behaviour in mitosis as well as to play a role in heterochromatin organisation and gene transcription. However, a role for Ki-67 in regulating cell cycle progression has never been reported. The progress towards understanding Ki-67 function have been limited by the tools available to deplete the protein coupled to its abundance and fluctuation during the cell cycle. ResultsHere we have used an auxin-inducible degron tag (AID) to achieve a rapid and homogeneous degradation of Ki-67 in HCT116 cells. This system, coupled with APEX2 proteomics and phospho-proteomics approaches, allowed us to show for the first time that Ki-67 plays a role during DNA replication. In its absence, DNA replication is severely delayed, the replication machinery is unloaded, causing DNA damage that is not sensed by the canonical pathways and dependant on HUWE1 ligase. This leads to replication and sister chromatids cohesion defects, but it also triggers an interferon response mediated by the cGAS/STING pathway in all the cell lines tested. ConclusionsWe have unveiled a new function of Ki-67 in DNA replication and genome maintenance that is independent of its previously known role in mitosis and gene regulation.

cell biology↗

bioRxiv2022

CCDC86/Cyclon is a novel Ki-67 interacting protein important for cell division

The chromosome periphery is a network of proteins and RNAs that coats the outer surface of mitotic chromosomes. Despite the identification of new components, the functions of this complex compartment are poorly characterised. In this study we identified a novel chromosome periphery-associated protein CCDC86/cyclon. Using a combination of RNAi (RNA interference), microscopy and biochemistry, we studied the functions of CCDC86/cyclon in mitosis. CCDC86/cyclon depletion resulted in partial disorganisation of the chromosome periphery with partial alterations in the localization of Ki-67 and Nucleolin and the formation of abnormal cytoplasmic aggregates. Furthermore, CCDC86/cyclon-depleted cells displayed errors in chromosome alignment, altered spindle length and increased apoptosis. These results suggest that, within the chromosome periphery, different subcomplexes that include CCDC86/cyclon, Nucleolin and B23 are required for mitotic spindle regulation and correct kinetochore-microtubule attachments, thus contributing to chromosome segregation in mitosis. Moreover, we have identified CCDC86/cyclon as a MYC-N regulated gene whose expression levels represent a powerful marker for prognostic outcomes in neuroblastoma. Summary statementHere we report the identification of CCDC86/cyclon as novel component of the perichromosomal layer. CCDC86 is important for chromosome segregation and represents a strong prognostic marker for neuroblastoma patients.

cell biology↗

bioRxiv2020

Reducing error and increasing reliability of wildlife counts from citizen science surveys: counting Weddell Seals in the Ross Sea from satellite images

Citizen science programs can be effective at collecting information at large temporal and spatial scales. However, sampling bias is a concern in citizen science datasets and can lead to unreliable estimates. We address this issue with a novel approach in a first-of-its-kind citizen science survey of Weddell seals for the entire coast of Antarctica. Our citizen scientists inspected very high-resolution satellite images to tag any presumptive seals hauled out on the fast ice during the pupping period. To assess and reduce the error in counts in term of bias and other factors, we ranked surveyors on how well they agreed with each other in tagging a particular feature (presumptive seal), and then ranked these features based on the ranking of surveyors placing tags on them. We assumed that features with higher rankings, as determined by "the crowd wisdom," were likely to be seals. By comparing citizen science feature ranks with an experts determination, we found that non-seal features were often highly ranked. Conversely, some seals were ranked low or not tagged at all. Ranking surveyors relative to their peers was not a reliable means to filter out erroneous or missed tags; therefore, we developed an effective correction factor for both sources of error by comparing surveyors tags to those by the expert. Furthermore, counts may underestimate true abundance due to seals not being present on the ice when the image was taken. Based on available on-the-ground haul-out location counts in Erebus Bay, the Ross Sea, we were able to correct for the proportion of seals not detected through satellite images after accounting for year, time-of-day, location (islet vs. mainland locations), and satellite sensor effects. We show that a prospective model performed well at estimating seal abundances at appropriate spatial scales, providing a suitable methodology for continent-wide Weddell Seal population estimates.

ecology↗