Biology subjects

Tapinos, N.

Publications and source records attributed to Tapinos, N..

10 recordsLinked to original sources

bioRxiv2026

A long-read RNA sequencing and polysome profiling framework reveals transposable element-driven transcript diversity and translational rewiring in glioblastoma

BackgroundTransposable elements (TEs) account for over half of the human genome and are often derepressed in cancer. TEs can add cryptic splice sites, undergo exonization, and generate gene-TE fusion transcripts, but the combined effects of TEs on RNA processing and translation in glioblastoma stem cells (GSCs) remains incompletely elucidated. ResultsWe combined long-read RNA sequencing with polysome profiling in four patient-derived GSCs and two neural stem cell (NSC) controls to resolve TE-associated transcript diversity and its relationship to ribosomal engagement. Across GSCs, we identified 13,421 alternative splicing (AS) events, 3,077 of which contained TEs within 150 bp of splice junctions. AS sites proximal to TEs were associated with increased isoform switching compared to non-TE-associated AS sites (odds ratio 2.9 - 4.3). Moreover, AS isoforms generated from TE-proximal sites were more likely to exhibit altered ribosomal association (odds ratio 2.54). Directional shifts were observed, with shorter isoforms associating with monosome fractions and longer isoforms with polysome fractions. To enable systematic detection of gene - TE chimeric transcripts, we developed FuTER (Fusion TE Reporter), a long-read-based framework for identifying TE-associated fusions. Application to GSC datasets identified 78 GSC enriched fusion transcripts, several supported by breakpoint-spanning reads in polysome fractions, consistent with ribosome association. ConclusionsOur data suggest that TEs correlate with abnormal splicing activity and altered ribosome engagement in glioblastoma stem cells. By integrating long-read sequencing with polysome profiling and fusion detection, we establish a framework for analysis of TE-induced transcript diversity and its effects on cancer evolution and plasticity.

cancer biology↗

bioRxiv2025

Multiomic profiling of hypoxic glioblastoma stem cells reveals expansion of subpopulations with distinct epigenetic and CNV profiles

Glioblastoma is characterized by extensive intratumoral heterogeneity driven by dynamic mi-croenvironmental cues such as hypoxia. While transcriptional and epigenetic variability have been separately linked to hypoxia responses, the integrated impact of hypoxia on gene regulation and clonal architecture in glioblastoma stem cells (GSCs) remains poorly defined. We applied singlenucleus multi-omics--integrating RNA-seq and ATAC-seq--to patient-derived GSCs cultured under normoxic or hypoxic conditions. This enabled simultaneous profiling of gene expression and chromatin accessibility within the same cells. Transcription factor (TF) regulatory networks were inferred using Dictys, while RNA-chromatin dynamics were modeled with MultiVelo. Clonal structure and copy number variations (CNVs) were resolved at single-cell resolution using RIDDLER on snATAC-seq data. Hypoxia induced the emergence of four distinct GSC subpopulations with unique transcriptomic and epigenetic profiles enriched for mesenchymal, angiogenic, and proliferative signatures. Regulatory network modeling revealed novel hypoxia-associated TFs--SP2, CREM, and ETV3--that modulate downstream oncogenic pathways. Trajectory analysis uncovered hypoxia-driven reversals in RNA-chromatin coupling, revealing dysregulated future transcriptional states of key genes such as MMP16 and SVIL. CNV profiling identified 13 clonal substructures, with specific clones (e.g., 5, 6, 9) selectively enriched under hypoxia and harboring distinct chromosomal alterations. These results demonstrate coordinated remodeling of GSC gene regulation and clonal fitness in response to hypoxic stress. Our findings reveal that hypoxia drives concurrent epigenetic, transcriptomic, and clonal selection in glioblastoma stem cells. This integrated model of hypoxia-induced plasticity provides mechanistic insights into tumor adaptation and identifies novel regulators that may serve as targets for therapeutic intervention in the hypoxic niche of glioblastoma.

cancer biology↗

bioRxiv2024

Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma.

Cancer cells show remarkable plasticity and can switch lineages in response to the tumor microenvironment. Cellular plasticity drives invasiveness and metastasis and helps cancer cells to evade therapy by developing resistance to radiation and cytotoxic chemotherapy. Increased understanding of cell fate determination through epigenetic reprogramming is critical to discover how cancer cells achieve transcriptomic and phenotypic plasticity. Glioblastoma is a perfect example of cancer evolution where cells retain an inherent level of plasticity through activation or maintenance of progenitor developmental programs. However, the principles governing epigenetic drivers of cellular plasticity in glioblastoma remain poorly understood. Here, using machine learning (ML) we employ cross-patient prediction of transcript expression using a combination of epigenetic features (ATAC-seq, CTCF ChIP-seq, RNAPII ChIP-seq, H3K27Ac ChIP-seq, and RNA-seq) of glioblastoma stem cells (GSCs). We investigate different ML and deep learning (DL) models for this task and build our final pipeline using XGBoost. The model trained on one patient generalizes to another one suggesting that the epigenetic signals governing gene transcription are consistent across patients even if GSCs can be very different. We demonstrate that H3K27Ac is the epigenetic feature providing the most significant contribution to cross-patient prediction of gene expression. In addition, using H3K27Ac signals from patients-derived GSCs, we can predict gene expression of human neural crest stem cells suggesting a shared developmental epigenetic trajectory between subpopulations of these malignant and benign stem cells. Our cross-patient ML/DL models determine weighted patterns of influence of epigenetic marks on gene expression across patients with glioblastoma and between GSCs and neural crest stem cells. We propose that broader application of this analysis could reshape our view of glioblastoma tumor evolution and inform the design of new epigenetic targeting therapies.

cancer biology↗

bioRxiv2024

Heterochromatin spreading in cancer cells through HDAC7 mediated histone H3.3 landscape reprogramming.

Class IIa histone deacetylases (HDACs) are a family of enzymes with minimal histone deacetylase activity but can function as multi-protein interaction hubs. Here we demonstrate the expression of HDAC7, a Class IIa HDAC family member, in glioblastoma tumor tissue from 84 patients, patient-derived glioma stem cells (GSCs) from six patients, and pediatric diffuse pontine glioma (DIPG) cells from three patients. HDAC7 binds to Histone H3.3 and interacts with H3.3 and HIRA on chromatin. Targeted downregulation of HDAC7 expression with a subtype-specific siRNA inhibits the interaction of H3.3 with HIRA while increasing the association of H3.3 with DAXX and H3K9me3. This results in H3.3 being deposited on H3K9me3+/DAPI+ heterochromatin nuclear foci. Inhibition of HDAC7 triggers H3K9me3+ heterochromatin spreading, increased H3K9me3 binding in the cancer genome, and significant alterations in gene expression. Using single molecule DNA fiber approach, we show that HDAC7 inhibition results in a significant increase in replication fork speed without affecting fork symmetry. This altered replication fork speed leads to replication stress, evidenced by phosphorylation of RPA2 and impact on global DNA synthesis, resulting in reduced EdU incorporation. Finally, HDAC7 depletion leads to reduced BRCA2 expression and increased sensitivity of cancer cells to DNA damaging agents. Taken together, these studies uncover the involvement of HDAC7 in the euchromatic H3.3 chaperone network and the effect of HDAC7 depletion on chromatin dynamics, inducing epigenetic restriction and DNA damage in cancer cells.

cancer biology↗

bioRxiv2023

Engineering GliaTrap: a biodegradable non-swelling hydrogel with tuned release of CXCL12 to attract migrating glioblastoma cells

Glioblastoma is the most aggressive type of brain cancer with an average overall survival of 15-21 months after first diagnosis. The relapse is mainly caused by migrating glioblastoma cells that diffuse away from the tumor mass into the brain parenchyma and retain cancer stem cell (GSC) properties. Current therapeutic options are ineffective and inevitably result in relapse, indicating a high unmet medical need for innovative therapies in the treatment of invasive glioblastoma. To address this challenge, we propose a new therapeutic modality: GliaTrap, a biodegradable non-swelling, injectable hydrogel with sustained release of a chemoattractant for GSCs that lures and traps the migrating cells back to the tumor resection cavity. We developed a biodegradable and injectable hyaluronan/collagen II-based (HA/Col) hydrogel that does not swell in vivo. The hydrogel is embedded with CXCL12 loaded liposomes and is tuned for sustained release of CXCL12. The safety profile of liposome-embedded HA/Col hydrogel was determined in-vivo after stereotactic implantation in the mouse brain. The efficacy of GliaTrap to attract GSCs was determined ex vivo using a 3D tumor spheroid model and in-vivo using 3D light-sheet microscopy in orthotopic human glioblastoma xenografts. Our findings suggest that GliaTrap could represent a safe and efficacious new therapeutic approach for glioblastoma and potentially serve as a drug delivery platform to locally deliver tumor-killing agents. One Sentence SummaryGliaTrap is a biodegradable non-swelling hydrogel with tuned release of a chemoattractant to attract invading glioma cells and serve as delivery platform for local therapeutics.

cancer biology↗

bioRxiv2022

EGR2 promoter antisense RNA coordinates chromatin remodeling and spatial genome organization in Schwann cells.

The EGR2 promoter antisense RNA (AS-RNA) recruits chromatin remodeling complexes to inhibit EGR2 transcription following peripheral nerve injury. Here we show that the EGR2-AS-RNA modulates chromatin accessibility and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters of EGR2and C-JUN respectively. Expression of the AS-RNA results in reorganization of the global chromatin landscape and quantitative changes in loop formation and in contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, the EGR2-AS-RNA induces changes in hierarchical TADs and increases transcription factor occupancy on an inter-TAD loop between a super-enhancer regulatory hub and the promoter of mTOR. Our results show that the EGR2-AS-RNA may serve as regulator of chromatin remodeling and spatial genome organization in Schwann cells.

neuroscience↗

bioRxiv2022

The germline factor DDX4 contributes to the chemoresistance of small cell lung cancer cells

Human cancers often re-express germline factors, yet their mechanistic role in oncogenesis and cancer progression remains unknown. Here we demonstrate that DDX4, a germline factor and RNA helicase conserved in all multicellular organisms, contributes to epithelial mesenchyme transition (EMT)-like features and cisplatin resistance in small cell lung cancer (SCLC) cells. DDX4 depletion in H69AR and SHP77 cell lines decreased motility and resistance to cisplatin, whereas its overexpression increased these features. Proteomic analysis suggests that DDX4 upregulates metabolic protein expression related to DNA repair and immune/inflammatory response, suggesting its fundamental function may be in regulating cellular metabolism. Consistent with these trends in cell lines, DDX4 depletion compromised in vivo tumor development while its overexpression enhanced tumor growth even after cisplatin treatment in nude mice. Although the DDX4 expression level in somatic tumors is generally low compared to that in the germline, the relatively higher DDX4 expression in SCLC patients correlates with decreased survival and shows increased expression of EMT and cisplatin resistance markers. Taken together, we conclude that DDX4 influences the survival of SCLC patients by altering cellular metabolism in response to environmental cues such as drug treatments. This fundamental function of DDX4 as a germline factor might be applicable in other cancer types that express DDX4 and may serve as a key to combat specific tumors that are highly resistant to treatments. HighlightsO_LIDDX4 contributes to cellular motility and drug resistance in SCLC cells. C_LIO_LIDDX4-overexpression globally alters the proteome and suppresses cytokine production. C_LIO_LIDDX4 promotes tumorigenesis and drug resistance in vitro and in vivo. C_LIO_LIDDX4 expression correlates with survival in SCLC patients and with immune/inflammatory response both in cell lines and patient samples. C_LI

cancer biology↗

bioRxiv2021

Chi3l1 is a modulator of glioma stem cell states and a therapeutic vulnerability for glioblastoma

Chi3l1 (Chitinase 3-like 1) is a secreted protein highly expressed in glioblastoma. Here, we show that exposure of glioma stem cells (GSCs) to Chi3l1 reduces the CD133+/SOX2+ cells and increases the CD44+/Chi3l1+ cells. Chi3l1 binds to CD44 and induces phosphorylation and nuclear translocation of beta-catenin, Akt and STAT3. Single cell RNA-seq and RNA velocity following incubation of GSCs with Chi3l1 show significant changes in GSC state dynamics driving GSCs towards a mesenchymal expression profile and reducing transition probabilities towards terminal cellular states. ATAC-seq reveals that Chi3l1 increases accessibility of promoters containing MAZ transcription factor footprint. Inhibition of MAZ directly regulates genes with highest expression in cellular clusters exhibiting significant cell state transitions. Finally, targeting Chi3l1 in vivo with a blocking antibody, resets the transcriptomic profile of glioblastoma and inhibits tumor growth. Our work implicates Chi3l1 as modulator of GSC cellular states and demonstrates pre-clinical efficacy of anti-Chi3l1 antibody treatment.

cancer biology↗

bioRxiv2020

miRNA-mediated loss of m6A increases nascent translation in glioblastoma

Within the glioblastoma cellular niche, glioma stem cells (GSCs) can give rise to differentiated glioma cells (DGCs) and, when necessary, DGCs can reciprocally give rise to GSCs to maintain the cellular equilibrium necessary for optimal tumor growth. Here, using ribosome profiling, transcriptome and m6A RNA sequencing, we show that GSCs from patients with different subtypes of glioblastoma share a set of transcripts, which exhibit a pattern of m6A loss and increased protein translation during differentiation. The target sequences of a group of miRNAs overlap the canonical RRACH m6A motifs of these transcripts, many of which confer a survival advantage in glioblastoma. Ectopic expression of the RRACH-binding miR-145 induces loss of m6A, formation of FTO/AGO1/ILF3/miR-145 complexes on a clinically relevant tumor suppressor gene (CLIP3) and significant increase in its nascent translation. Inhibition of miR-145 maintains RRACH m6A levels of CLIP3 and inhibits its nascent translation. This study highlights a critical role of miRNAs in assembling complexes for m6A demethylation and induction of protein translation during GSC state transition. Author SummaryCellular plasticity and epigenetic adaptation of human glioblastoma stem cells to the tumor microenvironment is a hallmark of this devastating disease. With our present work, we discover the relationship between miRNAs and the RNA methylation machinery in human glioblastoma and show how miRNA-induced loss of m6A results in increase in protein translation of clinically important transcripts during glioblastoma stem cell differentiation. Leveraging the dynamic functions of these miRNAs can be important in the design of optimal therapeutics targeted at cancer cell plasticity.

cancer biology↗

bioRxiv2020

Subventricular zone adult mouse neural stem cells and human glioblastoma stem cells require insulin receptor for self-renewal

The insulin receptor (IR) is an evolutionarily conserved signaling protein that regulates development and cellular metabolism. IR signaling regulates neurogenesis in Drosophila; however, a specific role for the IR in maintaining adult neural stem cells (NSCs) in mammals has not been investigated. We show that conditionally deleting the IR reduces adult NSCs of the subventricular zone by [~]70% accompanied by a corresponding increase in progenitors. IR deletion produced hyposmia due to aberrant olfactory bulb neurogenesis. Interestingly, hippocampal neurogenesis was not perturbed nor were hippocampal dependent behaviors. Highly aggressive proneural and mesenchymal glioblastomas (GBMs) had high IR/insulin-like growth factor (IGF) pathway gene expression, and isolated glioma stem cells had an aberrantly high ratio of IR:IGF1R receptors. Moreover, IR knockdown inhibited proneural and mesenchymal GBM tumorsphere growth. Altogether, these data demonstrate that the IR is essential for a subset of normal NSCs as well as for brain tumor cancer stem cell self-renewal.

neuroscience↗