Biology subjects

Comba, A.

Publications and source records attributed to Comba, A..

8 recordsLinked to original sources

bioRxiv2024

Epigenetic Reprogramming of Autophagy Drives Mutant IDH1 Glioma Progression and Response to Radiation

Mutant isocitrate dehydrogenase 1 (mIDH1) exhibits a gain of function mutation enabling 2-hydroxyglutarate (2HG) production and epigenetic reprogramming. This leads to enhanced DNA-damage response and radioresistance in mIDH1 gliomas. RNA-seq and ChIP-seq data revealed that human and mouse mIDH1 glioma neurospheres have downregulated gene ontologies (GOs) related to mitochondrial metabolism and upregulated GOs related to autophagy. Decreased mitochondrial metabolism was accompanied by decreased glycolysis, rendering autophagy a source of energy in mIDH1 gliomas. Human and mouse mutant IDH1 glioma cells exhibited increased expression of pULK1-S555 and enhanced LC3 I/II conversion, indicating augmented autophagy. Additionally, scRNA-seq data from human mIDH1 astrocytoma patients samples showed decreased mitochondrial metabolism and increased autophagy. We further demonstrate that inhibiting autophagy in vivo by systemic administration of synthetic protein nanoparticles encapsulating siRNA targeting Atg7 sensitized mIDH1 glioma cells to radiation-induced cell death, resulting in tumor regression, long-term survival, and immunological memory. In summary, our work uncovered that autophagy is a critical pathway for survival in mIDH1 gliomas and by blocking this pathway we can elicit radiosensitivity in vitro in human and mouse mIDH1 glioma cells, and in vivo in genetically engineered mouse models. Our data also highlights that blocking autophagy has significant potential for clinical translation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/584091v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@111f4a9org.highwire.dtl.DTLVardef@1d5bb30org.highwire.dtl.DTLVardef@f467ecorg.highwire.dtl.DTLVardef@1d2e9b5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Our genetically engineered mIDH1 mouse glioma model harbors IDH1R132H in the context of ATRX and TP53 knockdown. The production of 2-HG elicited an epigenetic reprogramming associated with a disruption in mitochondrial activity and an enhancement of autophagy in mIDH1 glioma cells. Autophagy is a mechanism involved in cell homeostasis related with cell survival under energetic stress and DNA damage protection. Autophagy has been associated with radio resistance. The inhibition of autophagy thus radio sensitizes mIDH1 glioma cells and enhances survival of mIDH1 glioma-bearing mice, representing a novel therapeutic target for this glioma subtype with potential applicability in combined clinical strategies. C_FIG

cancer biology↗

bioRxiv2023

Modeling Glioma Oncostreams In Vitro: Spatiotemporal Dynamics of their Formation, Stability, and Disassembly

Glioblastoma (GBM), known for its invasive nature, remains a challenge in clinical oncology due to its poor prognosis. Only 5% of patients live past 2 years. The extensive intra-tumoral heterogeneity, combined with aggressive infiltration into surrounding healthy brain tissue limits complete resection and reduces the efficiency of therapeutic interventions. In previous studies using ex-vivo 3D explants and in-vivo intravital imaging, we discovered the existence of oncostreams. Oncostreams are accumulations of nematically aligned elongated spindle-like cells constituted by both tumor and non-tumor cells. We observed a direct correlation between the density of oncostreams and glioma aggressiveness, in genetically engineered mouse glioma models, in high-grade human gliomas, and especially in gliosarcomas. Oncostreams play a pivotal role in the intra-tumoral distribution of both tumoral and non-tumoral cells, potentially facilitating collective invasion of neighboring healthy brain tissue. We further identified a unique molecular signature intrinsic to oncostreams, with a prominent overexpression of COL1A1, MMP9, ADAMts2, and ACTA2 - pivotal genes influencing gliomas mesenchymal transformation and potential determinants of tumor malignancy. COL1A1 inhibition in genetic mouse gliomas resulted in the elimination of oncostreams and induced significant changes in the tumor microenvironment, a reduction in mesenchymal-associated gene expression, and prolonged animal survival. Based on this foundation, we endeavored to model glioma oncostreams in vitro, evaluating the potential of various pharmacologic agents on the formation and organization of oncostreams. Using an optimized workflow, oncostreams were established using GFP+ NPA cells (NRAs\shP53\shATRX) derived from a genetically engineered mouse model utilizing the Sleeping Beauty transposon system. In-depth global and localized statistical analysis employing Julia programming and R Studio based in-house scripts provided insights into the behavior and organization of glioma cells. Our in vitro model led us to probe the impact of factors like cell density, cell morphology, collagen coating, exposure to neurotransmitter agonists, and changes in calcium levels. We also explored interventions targeting specific cytoskeleton structures like non-muscle myosin II B and C, myosin, actomyosin, and microtubules on oncostream formation and organization. In conclusion, our data provide novel information on patterns of glioma migration, which will inform mechanisms of glioma collective invasion in vivo. Through quantitative analysis of these pathologically aggressive and invasive structures, we highlight the importance of potential anti-invasion targets in improving outcomes for GBM patients. Integrating anti-invasive molecules with conventional treatments could significantly enhance clinical benefits. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=195 HEIGHT=200 SRC="FIGDIR/small/571722v1_ufig1.gif" ALT="Figure 1"> View larger version (95K): org.highwire.dtl.DTLVardef@31a40corg.highwire.dtl.DTLVardef@1093c09org.highwire.dtl.DTLVardef@1449e7corg.highwire.dtl.DTLVardef@10892_HPS_FORMAT_FIGEXP M_FIG Dynamics of oncostream structure and cellular motility modulation. This graphical abstract represents the intricacies of the oncostream structure, a proposed model for the collective migration of cancer cells. The central diagram illustrates the oncostream structure, delineated by various treatment conditions radiating outward. Each segment displays a fluorescent micrograph showing the effect of specific inhibitors and compounds on cellular oncostream structure. The array of compounds, including TC-I-15 (21 integrin inhibitor), Collagenase, p-nitro Blebbistatin, Cytochalasin-D, BAPTA-AM, Histamine, Glutamate, 4-Hydroxy acetophenone (4-HAP), Rho-Inhibitor, and Rho-Activator I, are marked on each corresponding segment. Quantitative measures of cellular migration speed, expressed in micrometers per hour (m/h) are noted for each treatment. Notably, the top half of the diagram reveals the oncostreams sensitivity to pharmacological drug treatments, whereas the bottom half shows resistance to these treated conditions. This representation emphasizes the selective effects of pharmacological agents on cancer cell motility within the oncostream framework. C_FIG

cancer biology↗

bioRxiv2023

H3.3-G34R Mutation-Mediated Epigenetic Reprogramming Leads to Enhanced Efficacy of Immune Stimulatory Gene Therapy in Pediatric High-Grade Gliomas

Diffuse hemispheric glioma (DHG), H3 G34-mutant, representing 9-15% of cases, are aggressive Central Nervous System (CNS) tumors with poor prognosis. This study examines the role of epigenetic reprogramming of the immune microenvironment and the response to immune-mediated therapies in G34-mutant DHG. To this end, we utilized human G34-mutant DHG biopsies, primary G34-mutant DHG cultures, and genetically engineered G34-mutant mouse models (GEMMs). Our findings show that the G34 mutation alters histone marks deposition at promoter and enhancer regions, leading to the activation of the JAK/STAT pathway, which in turn results in an immune-permissive tumor microenvironment. The implementation of Ad-TK/Ad-Flt3L immunostimulatory gene therapy significantly improved median survival, and lead to over 50% long term survivors. Upon tumor rechallenge in the contralateral hemisphere without any additional treatment, the long-term survivors exhibited robust anti-tumor immunity and immunological memory. These results indicate that immune-mediated therapies hold significant potential for clinical translation in treating patients harboring H3.3-G34 mutant DHGs, offering a promising strategy for improving outcomes in this challenging cancer subtype affecting adolescents and young adults (AYA). STATEMENT OF SIGNIFICANCEThis study uncovers the role of the H3.3-G34 mutation in reprogramming the tumor immune microenvironment in diffuse hemispheric gliomas. Our findings support the implementation of precision medicine informed immunotherapies, aiming at improving enhanced therapeutic outcomes in adolescents and young adults harboring H3.3-G34 mutant DHGs.

cancer biology↗

bioRxiv2022

Scale-free correlations and criticality in explants derived from an orthotopic model of brain cancer

Collective behavior spans several orders of magnitudes of biological organization, ranging from cell colonies, to flocks of birds, to herds of wildebeests. In this work, we investigate collective motion of glioblastoma cells in an ex-vivo experimental model of malignant brain tumors. Using time-resolved tracking of individual glioma cells, we observed collective motion characterized by weak polarization in the (directional) velocities of single cells, with fluctuations correlated over many cell lengths. The correlation length of these fluctuations scales approximately linearly with the total population size, and these scale-free correlations suggest that the system is poised near a critical point. To further investigate the source of this scale-free behavior, we used a data-driven maximum entropy model to estimate the effective length scale (nc) and strength (J) of local interactions between tumor cells. The model captures statistical features of the experimental data, including the shape of the velocity distributions and the existence of long range correlations, and suggests that nc and J vary substantially across different populations. However, the scale and strength of the interactions do not vary randomly, but instead occur on the boundary separating ordered and disordered motion, where the model exhibits classical signs of criticality, including divergences in generalized susceptibility and heat capacity. Our results suggest that brain tumor assemblies are poised near a critical point characterized by scale-free correlations in the absence of strong polarization.

biophysics↗

bioRxiv2021

Systemic delivery of a CXCR4-CXCL12 signaling inhibitor encapsulated in synthetic protein nanoparticles for glioma immunotherapy

Glioblastoma multiforme (GBM) is an aggressive primary brain tumor, with poor prognosis. Major obstacles hampering effective therapeutic response in GBM are tumor heterogeneity, high infiltration of immunosuppressive myeloid cells, and the presence of the blood-brain barrier. The C-X-C Motif Chemokine Ligand 12/ C-X-C Motif Chemokine Receptor 4 (CXCL12/ CXCR4) signaling pathway is implicated in GBM invasion and cell cycle progression. While the CXCR4 antagonists (AMD3100) has a potential anti-GBM effects, its poor pharmacokinetic and systemic toxicity had precluded its clinical application. Moreover, the role of CXCL12/ CXCR4 signaling pathway in anti-GBM immunity, particularly in GBM-mediated immunosuppression has not been elucidated. Here, we developed a synthetic protein nanoparticle (SPNPs) coated with the cell-penetrating peptide iRGD (AMD3100 SPNPs) to target the CXCR4/CXCL12 signaling axis in GBM. We showed that AMD3100 SPNPs effectively blocked CXCR4 signaling in mouse and human GBM cells in vitro as well as in GBM model in vivo. This results in inhibition of GBM proliferation and induction of immunogenic tumor cell death (ICD) leading to inhibition of GBM progression. Our data also demonstrate that blocking CXCR4 sensitizes GBM cells to radiation, eliciting enhanced release of ICD ligands. Combining AMD3100 SPNPs with radiotherapy inhibited GBM progression and led to long-term survival; with 60% of mice remaining tumor-free. This was accompanied by an anti-GBM immune response and sustained immunological memory that prevented tumor recurrence without further treatment. Finally, we showed that systemic delivery of AMD3100 SPNPs decreased the infiltration of CXCR4+ monocytic myeloid-derived suppressor cells to the tumor microenvironment. With the potent ICD induction and reprogrammed immune microenvironment, this strategy has significant potential for future clinical translation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/457953v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@17c9377org.highwire.dtl.DTLVardef@1b5a4dcorg.highwire.dtl.DTLVardef@5aa4eaorg.highwire.dtl.DTLVardef@1011a86_HPS_FORMAT_FIGEXP M_FIG Immunological mechanism targeting Glioblastoma (GBM) upon blocking CXCR4 signaling pathway with AMD3100-conjugated nanoparticles (SPNPs). (1) Radiotherapy induces glioma cell death, followed by Damage-associated molecular patterns (DAMPs) release. Dendritic cells (DC) are activated by DAMPs and migrate to the regional lymph node where they prime cytotoxic T lymphocyte immune response. Tumor-specific cytotoxic T cells infiltrate the tumor and attack glioma cells. (2) Glioma cells express CXCR4, as well its ligand CXCL12. CXCL12 induces glioma cell proliferation and, (3) as well as mobilization in the bone marrow of CXCR4 expressing myeloid MDSC, which will infiltrate the tumor, and inhibit tumor-specific cytotoxic T cells activity. GEMM of glioma when treated systemically with SPNPs AMD3100 SPNPs plus radiation, nanoparticles block the interaction between CXCR4 and CXCL12, thus (4) inhibiting glioma cell proliferation and (5) reducing mobilization in the bone marrow of CXCR4 expressing myeloid MDSC, (6) generating a reduced MDSC tumor infiltration, as well as releasing MDSC inhibition over tumor specific cytotoxic T cell response. C_FIG

cell biology↗

bioRxiv2020

Oncostreams: Self-organization and dynamics determine spatial heterogeneity and malignant behavior in gliomas

Intra-tumoral heterogeneity and diffuse infiltration are hallmarks of glioblastoma that challenge treatment efficacy. However, the mechanisms that set up both tumor heterogeneity and invasion remain poorly understood. Herein, we present a comprehensive spatiotemporal study that aligns distinctive intra-tumoral histopathological structures, oncostreams, with dynamic properties and a unique, actionable, spatial transcriptomic signature. Oncostreams are dynamic multicellular fascicles of spindle-like and aligned cells with mesenchymal properties, detected using ex vivo explants and in vivo intravital imaging. Their density correlates with tumor aggressiveness in genetically engineered mouse glioma models, and high-grade human gliomas. Oncostreams facilitate the intra-tumoral distribution of tumoral and non-tumoral cells, and the invasion of the normal brain. These fascicles are defined by a specific molecular signature that regulates their organization and function. Oncostreams structure and function depend on overexpression of COL1A1. COL1A1 is a central gene in the dynamic organization of glioma mesenchymal transformation, and a powerful regulator of glioma malignant behavior. Inhibition of COL1A1 eliminated oncostreams, reprogramed the malignant histopathological phenotype, reduced expression of the mesenchymal associated genes, induced changes in the tumor microenvironment and prolonged animal survival. Oncostreams represent a novel pathological marker of potential value for diagnosis, prognosis, and treatment.

cancer biology↗

bioRxiv2019

Self-organization in brain tumors: how cell morphology and cell density influence glioma pattern formation

Modeling cancer cells is essential to better understand the dynamic nature of brain tumors and glioma cells, including their invasion of normal brain. Our goal is to study how the morphology of the glioma cell influences the formation of patterns of collective behavior such as flocks (cells moving in the same direction) or streams (cells moving in opposite direction) referred to as oncostream. We have observed experimentally that the presence of oncostreams correlates with tumor progression. We propose an original agent-based model that considers each cell as an ellipsoid. We show that stretching cells from round to ellipsoid increases stream formation. A systematic numerical investigation of the model was implemented in [R]2. We deduce a phase diagram identifying key regimes for the dynamics (e.g. formation of flocks, streams, scattering). Moreover, we study the effect of cellular density and show that, in contrast to classical models of flocking, increasing cellular density reduces the formation of flocks. We observe similar patterns in [R]3 with the noticeable difference that stream formation is more ubiquitous compared to flock formation. Author summarySelf-organization is the formation of large-scale multicellular patterns that result exclusively from the interactions amongst constituent single cells. To establish the existence of self-organization in brain tumors we used agent-based modeling based on data extracted from static and dynamic genetically engineered mouse glioma models. Implementation of our model in [R]2 identifies the dynamics that lead to formation of flocks (cells moving in a single direction), streams (cells moving in two directions), and cells moving as swarms or scattering. Increasing cellular density reduced formation of flocks and increased the formation of streams both in [R]2 and in [R]3. These results demonstrate the detailed mechanism leading to self-organization in brain tumors. As increasing density of oncostreams correlates with tumor malignancy, we establish a pathophysiological link between self-organization of glioma tumors and glioma malignancy. We propose the dismantling of oncostreams as a new therapeutic approach to the treatment of brain tumors.

systems biology↗

bioRxiv2019

THE PROTO-ONCOGENE FYN INHIBITS THE ANTI-GLIOBLASTOMA IMMUNE RESPONSE

BackgroundHigh grade gliomas are aggressive and immunosuppressive brain tumors. Molecular mechanisms that regulate the inhibitory immune tumor microenvironment (TME) and glioma progression remain poorly understood. FYN tyrosine kinase is a downstream target of the oncogenic receptor tyrosine kinases pathway and is overexpressed in human gliomas. FYNs role in vivo in glioma growth remains unknown. We investigated whether FYN regulates glioma initiation, growth and invasion. MethodsWe evaluated the role of FYN using genetically engineered mouse glioma models (GEMM). We also generated FYN knockdown stem cells to induce gliomas in immune-competent and immune-deficient mice (NSG, CD8-/-, CD4-/-). We analyzed molecular mechanism by RNA-Seq and bioinformatics analysis. Flow cytometry was used to characterize immune cellular infiltrates in the FYN knockdown glioma TME. ResultsWe demonstrate that FYN knockdown in diverse immune-competent GEMMs of glioma reduced tumor progression and significantly increased survival. Gene ontologies (GOs) analysis of differentially expressed genes in wild type vs. FYN knockdown gliomas showed enrichment of GOs related to immune reactivity. However, in NSG, CD8-/- and CD4-/- immune-deficient mice, FYN knockdown gliomas failed to show differences in survival. These data suggest that the expression of FYN in glioma cells reduces anti-glioma immune activation. Examination of glioma immune infiltrates by flow-cytometry displayed reduction in the amount and activity of immune suppressive myeloid derived cells (MDSCs) in the FYN glioma TME. ConclusionsGliomas employ FYN mediated mechanisms to enhance immune-suppression and promote tumor progression. We propose that FYN inhibition within glioma cells could improve the efficacy of anti-glioma immunotherapies. Key pointsInhibition of FYN tyrosine kinase in genetically engineered mouse glioma models delays tumor initiation and progression. The oncogenic effects of FYN in vivo are mediated by downregulation of anti-glioma immunity. Importance of the StudyFYN is an effector of receptor tyrosine kinases (RTK) signaling in glioma. However, its role in vivo remains unknown. Our study demonstrates that FYN tyrosine kinase is a novel regulator of the anti-glioma immune response. We show that FYN inactivation suppresses glioma growth, increases survival, and enhances anti-tumor immune reactivity. Our findings suggest that suppressing the expression of FYN in glioma cells could provide a novel therapeutic target.

cancer biology↗