Evolution of GBM through therapy
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ABSTRACT:
PROVIDER: EGAS00001003546 | EGA |
REPOSITORIES: EGA
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Project description:Primary glioblastoma (GBM) tumours recur following therapy, owing to treatment resistance mechanisms in unresectable cells. We have sequenced RNA from paired primary and locally recurrent GBM tumours to begin characterising therapy resistant cells and thereby infer the mechanisms by which they evaded treatment. Exome sequencing data from these samples were included in the first data release from the Glioma Longitudinal AnalySiS (GLASS) consortium
| EGAS00001003790 | EGA
Project description:Resistant tumours are thought to arise from the action of Darwinian selection on intratumoral genetic heterogeneity. However, clonal selection is incompatible with the late recurrence often characterising luminal breast cancers treated with endocrine therapy (ET), suggesting a more complex interplay between genetic and non-genetic factors. In the present study, we dissect the contributions of clonal genetic diversity and transcriptional plasticity during the early and late phases of ET at single-cell resolution. Using single-cell RNA-sequencing and imaging we disentangle the transcriptional variability of plastic cells and define a rare sub-population of pre-adapted (PA) cells which undergoes further transcriptomic reprogramming and copy number changes to acquire full resistance. PA cells show reduced oestrogen receptor α activity but increased features of quiescence and migration. We find evidence for sub-clonal expression of this PA signature in primary tumours and for dominant expression in clustered circulating tumour cells. We propose a multi-step model for ET resistance development and advocate the use of stage-specific biomarkers.
2019-07-17 | GSE122743 | GEO
Project description:Glioblastomas (GBM) are the most common primary CNS tumor. GBMs often recur as highly aggressive, intractable, therapy resistant tumors. Key molecular regulators of acquired radiation resistance in recurrent GBM are largely unknown with a dearth of accurate pre-clinical models. To address this, we generated eight GBM patient-derived xenograft (PDX) models of acquired radiation-therapy selected (RTS) resistance compared with same-patient, treatment naïve (RTU) PDX. A novel bioinformatics pipeline analyzed phenotypic, transcriptomic and kinomic alterations, identifying long non-coding RNAs (lncRNAs) and targetable, PDX-specific kinases. We observed differential transcriptional enrichment of DNA damage repair (DDR) pathways in our RTS models. Multiple molecular routes to acquired radiation-resistance were revealed in our models including PDX-specific kinases that we validated with targeted small molecule inhibitors (SMIs). We identified 184, mostly novel, lncRNAs differentially regulated between RTU and RTS PDX. Several of these lncRNAs were associated with transcriptional changes in DDR, cell cycle progression, stemness, and chromatin remodeling pathways. This study identifies lncRNAs as potential key regulators in recurrent GBM and therapy resistance. We also demonstrate that SMIs aimed at lncRNA-related signaling pathways may represent a novel therapeutic approach for recurrent GBM tumors.
2022-07-01 | GSE206225 | GEO
Project description:The scarcity of effective treatment options for high grade brain tumours has led to a wide ranging search for alternative means of therapy for these difficult to treat tumours. Electrical field therapy is one such area that has been considered. The OptuneTM system is an FDA approved novel anti-mitotic device that delivers continuous alternating electric fields to the patient for the treatment of primary and recurrent Glioblastoma multiforme (GBM) (tumor treating fields - TTFields). Alternative electric fields delivery systems are also being investigated for the treatment of various cancers.To further explore alternative potential mechanisms of electric fields as a whole, we ran Optune, DBS electric fields treated and control untreated KNS42, U87 and GIN-31 (primary) cell lines on Clariom S Human Assays to produce genome-wide expression data.
2020-10-01 | E-MTAB-9043 | biostudies-arrayexpress
Project description:<h4><strong>BACKGROUND:</strong> Elevated choline kinase alpha (ChoK) is observed in most solid tumours including glioblastomas (GBM), yet until recently, inhibitors of ChoK have demonstrated limited efficacy in GBM models. Given that hypoxia is associated with GBM therapy resistance, we hypothesised that tumour hypoxia could be responsible for such limitations. We therefore evaluated in GBM cells, the effect of hypoxia on the function of JAS239, a potent ChoK inhibitor.</h4><h4><strong>METHODS:</strong> Rodent (F98 and 9L) and human (U-87 MG and U-251 MG) GBM cell lines were subjected to 72 hours of hypoxia conditioning and treated with JAS239 for 24 hours. NMR metabolomic measurements and analyses were performed to evaluate the signalling pathways involved. In addition, cell proliferation, cell cycle progression and cell invasion were measured in cell monolayers and 3D spheroids, with or without JAS239 treatment in normoxic or hypoxic cells to assess how hypoxia affects JAS239 function.</h4><h4><strong>RESULTS:</strong> Hypoxia and JAS239 treatment led to significant changes in the cellular metabolic pathways, specifically the phospholipid and glycolytic pathways associated with a reduction in cell proliferation via induced cell cycle arrest. Interestingly, JAS239 also impaired GBM invasion. However, JAS239 effects were variable depending on the cell line, reflecting the inherent heterogeneity observed in GBMs.</h4><h4><strong>CONCLUSION:</strong> Our findings indicate that JAS239 and hypoxia can deregulate cellular metabolism, inhibit proliferation and alter cell invasion. These results may be useful for the design of new therapeutic strategies based on ChoK inhibition that can act on multiple pro-tumorigenic features.</h4>
2024-06-18 | MTBLS6212 | MetaboLights
Project description:Glioblastoma (GBM) is the most lethal brain tumour that occurs in adults and treatment for GBM has been largely unsuccessful. Ionizing radiation (IR) and chemotherapeutic agents are employed as standard of care treatment for GBM patients and both result in DNA damage. Previous data identified phosphorylation of PTEN at tyrosine 240 (pY240) in samples from patients with recurrent GBM receiving standard of care treatment and was associated with decreased overall survival. Here we demonstrate that pY240 PTEN that was triggered by FGFR2 signaling, enhanced DNA repair by facilitating the loading of PTEN onto chromatin through its interaction with KI-67 and subsequent recruitment of the DNA repair protein, RAD51, to sites of DNA damage. Thus, tumour cells with pY240 PTEN are efficient at repairing DNA damage which would be predicted to result in resistance to therapy. These findings suggest the FGFR-pY240 PTEN-DNA repair mechanism as a therapeutic target for enhancing GBM therapy.
2017-08-07 | MSV000081423 | MassIVE
Project description:Glioblastomas (GBM) are routinely treated with high doses of ionizing radiation (IR), yet these tumors recur quickly, and the recurrent tumors are highly therapy resistant. Here, we report that IR-induced senescence of tumor cells counterintuitively spurs GBM recurrence, driven by the senescence-associated secretory phenotype (SASP). We find that irradiated GBM cell lines and patient derived xenograft (PDX) cultures senesce rapidly in a p21-dependent manner. Senescent glioma cells upregulate SASP genes and secrete a panoply of SASP factors, prominently interleukin IL-6, an activator of the JAK-STAT3 pathway. These SASP factors collectively activate the JAK-STAT3 and NF-kB pathways in non-senescent GBM cells, thereby promoting tumor cell proliferation and SASP spreading. Transcriptomic analyses of irradiated GBM cells and the TCGA database reveal that the cellular inhibitor of apoptosis protein 2 (cIAP2), encoded by the BIRC3 gene, is a critical survival factor for senescent glioma cells. Senescent GBM cells not only upregulate BIRC3 but also induce BIRC3 expression and promote radioresistance in non-senescent tumor cells. We find that SMAC mimetics targeting cIAP2 act as novel senolytics that trigger apoptosis of senescent GBM cells with minimal toxicity towards normal brain cells. Finally, using both PDX and syngeneic mouse models of GBM, we show that the SMAC mimetic birinapant, administered as an adjuvant therapy after radiotherapy, can eliminate senescent GBM cells and prevent the emergence of recurrent tumors. Taken together, our results clearly indicate that significant improvement in GBM patient survival may become possible in the clinic by eliminating senescent cells arising after radiotherapy
2025-01-17 | GSE271928 | GEO
Project description:Glioblastoma multiforme (GBM), a WHO grade IV glioma is the most common and malignant primary cancer of the central nervous system with a grim median survival of 16 to 17 months upon diagnosis. Radiotherapy is the standard first line treatment for newly diagnosed patients with gliomas, but its effectiveness is limited given their intrinsic resistance and propensity for recurrence. Although possible mechanisms have been attributed to GBM resistance to radiation treatments, the molecular mechanisms regulating radiation resistance of GBM are still unclear.
2019-07-23 | GSE86213 | GEO
Project description:Macrophages accumulate with glioblastoma multiforme (GBM) progression, and can be acutely targeted via inhibition of colony stimulating factor-1 receptor (CSF-1R) to regress high-grade tumors in animal models. However, whether and how resistance emerges in response to sustained CSF-1R blockade is unknown. Here, we investigate whether long-term CSF-1R inhibition can stably regress GBM in preclinical trials. We show that while overall survival is significantly prolonged, tumors recur eventually in >50% of mice. Upon isolation and transplantation of recurrent tumor cells into naïve animals, gliomas re-establish sensitivity to CSF-1R inhibition, indicating that resistance is microenvironment-driven. PI3K pathway activity was elevated in recurrent GBM, driven by macrophage-derived IGF-1 and tumor cell IGF-1R. Consequently, combining IGF-1R or PI3K blockade with continuous CSF-1R inhibition in recurrent tumors significantly prolonged overall survival. By contrast, monotherapy with IGF-1R or PI3K inhibitors in rebound or treatment-naïve tumors was less effective, indicating the necessity of combination therapy to expose PI3K signaling-dependency in recurrent disease. Our findings thus reveal a potential therapeutic approach for treating resistance to CSF-1R inhibitors in the clinical setting.
2016-05-20 | GSE80399 | GEO
Project description:Background: Hypoxia gene signatures measured in a biopsy are promising biomarkers in prostate cancer. We determined the ability of a previously developed signature to correctly classify tumours as more or less hypoxic and investigated how intratumour heterogeneity affected its biomarker performance. Methods: The 32-gene signature was determined from gene expression data of 141 biopsies from the dominant (index) lesion of 94 patients treated with prostatectomy. Hypoxic fraction was measured by pimonidazole immunostaining of whole-mount and biopsy sections and used as reference standard for hypoxia. Results: The signature was correlated with hypoxic fraction in whole-mount sections, and the parameters showed almost the same association with tumour aggressiveness. Gene- and pimonidazole-based classification of patients differed considerably. However, the signature had low intratumour heterogeneity compared to hypoxic fraction in biopsies and showed prognostic significance in three independent cohorts. Conclusion: The biopsy-based 32-gene signature from the index lesion reflects hypoxia-related aggressiveness in prostate cancer.
2022-04-01 | GSE178631 | GEO