Biology subjects

Kyriakidou, M.

Publications and source records attributed to Kyriakidou, M..

3 recordsLinked to original sources

bioRxiv2026

Telomere Dysfunction in Human Astrocytes Drives Acrocentric Chromosome Instability and Nucleolar Reorganization

Loss of p53 and Rb enables continued cell division despite progressive telomere erosion, ultimately triggering telomere crisis. While recent work has clarified mechanisms of chromatin bridge resolution, the longitudinal dynamics of structural damage through crisis remain incompletely understood. We transduced normal human astrocyte (NHA) cells with HPV18 E6/E7 and tracked them across extended population doublings. NHA E6/E7 cells showed progressive telomere shortening, anaphase bridges, and a growth plateau consistent with crisis. Multicolor FISH revealed subclonal chromosomal abnormalities largely invisible to short-read sequencing, with acrocentric chromosomes disproportionately affected: chromosome 13 was abnormal in over 92% of metaphases, and chromosomes 21 and 22 were similarly enriched. Translocations involving chromosome 13 were transient, replaced at later passages, while numerical aberrations persisted. Immunofluorescence revealed compact spherical nucleoli replaced by dispersed necklace-like structures, indicating a large-scale reorganization of nucleolar structure in response to telomere dysfunction. To determine whether these changes reflected altered chromosomal organization in the nucleus, we performed Hi-C and deployed KaryoScope, our alignment-free k-mer-based approach that recovers trans-chromosomal signal from repetitive acrocentric short arms. Inter-chromosomal contacts among nucleolar organizing region-bearing acrocentric chromosomes were markedly and persistently depleted in E6/E7 cells. Together, cytogenetic, imaging, and chromatin-contact data identify the nucleolus as a structural nexus linking telomere dysfunction to large-scale genomic rearrangement.

cancer biology↗

bioRxiv2025

Cell-Free DNA Reveals the Longitudinal Effects of Temozolomide Treatment and Host Co-Culture in Glioblastoma Models

Glioblastoma (GBM) is a highly aggressive brain tumor with limited options for longitudinal monitoring. We evaluated the potential of cell-free DNA (cfDNA) as a real-time biomarker of tumor burden under tightly controlled conditions. We measured the cfDNA release dynamics, fragmentation sizes, and variant allele frequencies (VAF) in patient-derived GBM cell cultures. Time series of cfDNA were collected and analyzed in treatment-naive monocultures, during temozolomide (TMZ) treatment, and in co-culture with normal human astrocyte (NHA) cells. Longitudinal collection of media from individual cultures demonstrated that cfDNA yield increased, indicating the ability to use cfDNA to track tumor burden over time. Using a co-culture system, we deconvoluted cfDNA admixtures by analyzing yield, fragment size patterns, and cell line-specific variants. The exclusive detection of NHA- and GBM-specific mutations confirmed the distinct contributions of each cell type. Finally, TMZ treatment of GBM cells prompted an increase in cfDNA yield and VAF, suggesting that the effects of therapy could be measured using cfDNA. These findings support cfDNA as a non-invasive biomarker for real-time monitoring of GBM progression and treatment response, with clinical potential as a liquid biopsy tool in glioblastoma management. KEY POINTSO_LIcfDNA yield and variant allele frequencies (VAFs) correlate with GBM tumor burden. C_LIO_LIcfDNA properties can be used to differentiate between cell types in a mixed population. C_LIO_LITMZ treatment increases cfDNA yield and VAFs, reflecting treatment response. C_LI IMPORTANCE OF THE STUDYThis study highlights the potential of cell-free DNA (cfDNA) as a non-invasive biomarker for monitoring glioblastoma (GBM) progression and treatment response. By utilizing in-vitro models, we demonstrate that cfDNA yield, fragmentation patterns, and variant allele frequencies (VAFs) can effectively identify treatment-induced changes, such as those induced by temozolomide (TMZ) treatment, providing insights into therapeutic response. These results have significant translational implications, as cfDNA could serve as a real-time liquid biopsy tool for monitoring GBM progression, assessing treatment efficacy, and identifying early signs of treatment resistance in clinical settings. The ability to track tumor dynamics non-invasively holds great promise for improving GBM patient management and guiding personalized therapeutic approaches.

cancer biology↗

bioRxiv2023

Cancer cell sedimentation in 3D cultures reveals active migration regulated by self-generated gradients and adhesion sites

Cell sedimentation in 3D hydrogel cultures refers to the vertical migration of cells towards the bottom of the space. To explain this poorly understood phenomenon, we conducted a multiscale experimental and mathematical examination of 3D cancer growth in triple negative breast cancer cells. Migration was examined in the presence and absence of Paclitaxel, in high and low adhesion environments and in the presence of fibroblasts. The observed behaviour was modeled by hypothesizing active migration due to self-generated chemotactic gradients. Our results confirmed this hypothesis, whereby migration was regulated by the MAPK and TGF-{beta} pathways. The mathematical model enabled us to describe the experimental data in absence (normalized error< 40%) and presence of Paclitaxel (normalized error< 10%), suggesting inhibition of random motion and advection in the latter case. Inhibition of sedimentation in low adhesion and co-culture experiments further supported the conclusion that cells actively migrated downwards due to the presence of signals produced by cells already attached to the adhesive glass surface.

bioengineering↗