Abstract
Background
High-grade gliomas, the most common primary brain tumors, are highly lethal and treatment options remain limited. Despite advances in genomic technologies, there are few molecular ...biomarkers to guide precision medicine for high-grade glioma. Here, we aimed to identify the clinicogenomic features associated with its prognosis and recurrence patterns.
MATERIALS/METHODS
Our single-institution retrospective analysis included 182 patients diagnosed with high-grade gliomas who underwent next-generation sequencing targeting 82 brain tumor-relevant genes. Clinicopathological status, treatment characteristics, survival, and genomic profiles were analyzed.
RESULTS
At a median follow-up of 23 months (range, 2-229 months), 151 patients (83%) had progression or recurrences. Local and distant recurrences were observed in 132 (72.5%) and 101 (54.9%) patients, respectively. The most common genomic variants in high-grade gliomas were TP53 (42.9%), IDH1/2 (23.1%), TERT promoter (38.5%), ATRX (13.2%), H3F3A (7.1%), and SETD2 (6.0%) mutation. Regarding copy number variants, amplification of EGFR (20.9%), PDGFRA (9.9%), MYCN (2.2%) and loss of CDKN2A/2B (49.5%), PTEN (37.9%), RB1 (17.6%), and 1p19q codeletion(9.3%) were the most common copy number aberrations. On multivariate cox regression anlalysis, MYCN amplification (HR 6.08 95% CI 1.91-19.35, p = 0.002), and SETD2 mutation (HR 0.19 95% CI 0.06-0.62, p =0.06) were independent predictors of overall survival, in relation to previously established prognostic factors including age, Eastern Cooperative Oncology Group Performance Status (ECOG PS) scale, extent of resection, MGMT promoter methylation, and IDH1/2 mutation. Interestingly, MYCN amplification (HR 5.24 95% CI 1.69-16.27, p = 0.004), SETD2 mutation (HR 0.35 95% CI 0.12-0.99, p =0.048) were independent predictors of failure from distant recurrences.
CONCLUSION
The assessment of genomic characteristics in conjunction with pattern of failure for high-grade glioma aids to identify patients who are likely to benefit from personalized medicine. We identified SETD2 mutation, and MYCN as a prognostic biomarkers with potential therapeutic implications in patients with high-grade glioma.
Abstract
While tumors of the nervous system (NS) are rare, they contribute to significant morbidity and mortality. Despite advances in imaging technology, initial diagnosis and characterization of ...treatment response remains problematic for devastating tumors such as glioblastoma (GBM). A liquid biopsy can provide a minimally-invasive and serial source of biomarkers to supplement current diagnostic methods. Here, we utilize a unique characteristic of NS tumors including GBM and schwannoma/neurofibroma – the overexpression of the a2 variant of the IL-13 receptor which is not detectable in normal tissue. Previously, we have shown that IL13Ra2 is elevated in the plasma of some GBM patients above baseline levels. We hypothesize that the presence of circulating IL13Ra2 not only predicts the level of this receptor in the tumor tissue, but also has clinical prognostic value. Here, we used ELISA to measure the plasma levels of IL13Ra2 in the GBM (n=77) and schwannoma/neurofibroma (n=15) patients and correlated these levels to tumor levels, diagnosis, and clinical characteristics. We have demonstrated that elevated levels of plasma IL13Ra2 correlated with tumor presence compared to non-tumor controls for both GBM and schwannoma/neurofibroma patients, indicating this biomarker’s diagnostic utility. Further, for both GBM and schwannoma/neurofibroma patients the plasma concentration of IL13Ra2 is correlated to its tumor concentration, indicating that sampling patient plasma could provide insight into the tumor’s composition. Finally, elevated levels of IL13Ra2 protein in the tumor and plasma of GBM patients predicted longer patient survival. These exciting findings lay the groundwork for a plasma-based NS tumor liquid biopsy.
Abstract
Glioblastoma remains a highly malignant and intrinsically resistant brain tumor. Despite intensive research through which numerous potential druggable targets were identified, virtually all ...clinical trials of the past 20 years failed to improve the outcome for the vast majority of GBM patients. However, the identification of small subgroups of patients that showed an exceptional response across several trials, implies that, when selected more carefully, some GBM patients could probably still benefit from these therapies. Identifying these patients requires that suitable biomarkers are identified. In this project, we reassessed the molecular mechanisms of ten actionable compounds (selected from previously failed trials but for which exceptional responders had been observed) in a set of carefully selected patient-derived cell lines that were sensitive/resistant to the selected therapies. Moreover, to deal with tumor heterogeneity, we used a multi-omic functional precision oncology approach, combining scRNA-seq and CyTOF, to identify drug-specific biomarkers by comparing control and treated samples at single-cell resolution. By subsequently correlating the molecular signatures to eventual cytotoxicity profiles, we could identify intrinsically responsive tumor cells at the single-cell level within hours following drug exposure. Overall, this work lays the foundation for an actionable functional diagnostic assay that could help to identify eligible GBM patients in future clinical trials.
Abstract
BACKGROUND
In the updated 2021 WHO classification, diffuse gliomas were strictly reclassified by molecular statuses. In glioblastoma (GBM), the prognostic significance of the resection has ...been shown, but the excision rate to be achieved in the new classification has not been defined. Moreover, the correlation between the extent of resection (EOR) and the prognosis is still controversial for other gliomas.
METHODS
IDH 1/2 mutations and TERT promoter mutations were analyzed by Sanger sequencing, 1p/19q co-deletion by microsatellite or MLPA, and EGFR amplification and CDKN2A deletions by MLPA. The correlation between the resection rate and prognosis of each tumor type in the 2021/2016 WHO classification was analyzed retrospectively.
RESULTS
According to the 2021 classification, 293 patients with GBM, IDH-wild type, 68 with astrocytoma, IDH-mutant (2/3/4 22/26/20), and 58 with oligodendroglioma, IDH-mutant and 1p/19q co-deleted were identified. Based on the 2016 classification, they were diagnosed as 314 GBM, 106 astrocytoma (Gd II/III 37/69), and 59 oligodendroglioma. For GBM, IDH-wild type (2021 classification), a prolonged OS benefit was observed with >25% removal (p=0.042), whereas, more than 20% of tumor removal for patients with GBM (2016 classification) resulted in OS prolongation. EOR was a significant favorable prognostic factor for grade II/III astrocytoma by the 2016 classification, but not for astrocytoma, IDH-mutant (grade 2/3) in the 2021 classification. When analyzed only in patients with astrocytoma, IDH-mutant by the 2021 classification, EOR was not significantly prognostic, suggesting that poorer prognosis of patients with unresectable IDH-wild type astrocytomas (2016 classification) might have a negative impact on the outcome.
CONCLUSION
There was a strong correlation between EOR and prognosis in patients with GBM, and >25% removal was considered significant according to the 2021 classification. For astrocytoma in the 2021 classification, EOR did not show a prognostic significance, but further validation including grading effect is warranted.
Abstract
Diagnosis of Glioblastoma (GBM) remains a clinical challenge, currently relying on symptomatic presentation of the tumour, brain imaging and invasive biopsy. Description of effective ...biomarkers in biofluids could prove invaluable in GBM diagnosis. Extracellular vesicles (EVs) are essential to intercellular crosstalk in the tumour bulk and circulating EVs have been described as a potential reservoir of GBM biomarkers. Our work focuses on the: (i) isolation of EVs from blood liquid biopsies of GBM patients. (ii) Characterisation of their transcriptomic and proteomic cargoes to identify/validate novel candidate GBM biomarkers that could improve GBM diagnosis/prognosis. (iii) For cases where the original GBM tumour tissues are available, we will examine the expression of the identified biomarker signatures (derived from blood-EVs) to see if the content of EVs mirrors the transcriptomic/proteomic profile of the original tissue. Similar comparisons will be performed in GBM cohorts available in TCGA. Ultimately, in future studies, transcriptomic/proteomic analyses will be assessed during patients’ follow-ups to correlate the observed biomarker profiles with MRI data,treatment,recurrence, including molecular and clinical features.Our preliminary data comparing the proteomic cargoes of EVs derived from GBM patients (n=15) and those from healthy volunteers (n=10) indicated the presence of a GBM inflammatory biomarker signature comprising members of the complement and regulators of inflammation and coagulation. Bioinformatic analysis highlighted that all potential markers exclusively identified in patient samples have been linked with either GBM diagnosis,prognosis or associated signalling, suggesting that sEVs protein cargo could mirror the landscape of the original tumour and that selective circulating sEV-derived proteins might be used as hallmarks for GBM patients.Overall, this study is a step forward in the development of a non-invasive liquid biopsy approach for the identification of valuable biomarkers that could significantly improve GBM diagnosis and, consequently, patients’ prognosis and quality of life.
Abstract
BACKGROUND
The molecular landscape of adult diffuse glioma has been extensively characterized by gene expression and DNA methylation profiling, but less attention has been paid to somatic ...copy number alteration (SCNA) data. This study aimed to give a rigorous, survival-focused analysis of glioma genome-wide SCNA data that builds on our previous work.
METHODS
Detailed survival analyses were conducted on the substructure of UMAP projections of all TCGA glioma (Nf1092), exclusively astrocytic glioma (Nf914), and exclusively IDH-wildtype glioma (Nf528). Results were validated with data from the Glioma Longitudinal Analysis Consortium (GLASS) (Nf224). Clinical factors such as age and MGMT methylation were tested in multivariate survival analyses.
RESULTS
A UMAP projection of TCGA glioma SCNA data generated three distinct clusters composed of entirely oligodendroglioma, predominantly IDH-mutant astrocytoma (C-IDHmut-astro), and predominantly IDH-wildtype glioma (C-IDHwt), respectively. For astrocytic tumors, cluster assignment was independently prognostic of IDH status (p< 0.001): TCGA IDH-mutant astrocytomas that clustered in C-IDHwt had poorer outcomes than their counterparts (p< 0.04) and IDH-wildtype tumors that clustered in C-IDHmut-astro fared better than those that did not (p< 0.01). The distribution of GLASS astrocytic tumors, which is skewed for better survival, supported our results in IDH-wildtype glioblastoma (p< 0.001, Fisher’s). Among four distinct subclusters of TCGA IDH-wildtype glioblastomas, the largest was significantly or marginally significantly negatively prognostic compared to each other cluster (p=0.048, p=0.059, p=0.027) and their combination (p=0.002). In the GLASS dataset, inclusion in the largest subcluster was also prognostic (p=0.013) and similar trends were observed between individual clusters (p=0.21, p=0.036, p=0.083). Furthermore, membership to the largest cluster was independently prognostic of MGMT methylation status and several published IDH-wildtype glioblastoma subtypes in the TCGA.
CONCLUSIONS
Unsupervised learning of genome-wide SCNA has prognostic implications for astrocytic glioma. SCNA cluster membership is independently prognostic of MGMT methylation status.
Abstract
BACKGROUND
GBM genomic profiling relies on sequencing a limited tumor tissue sample, which is invasive and may underrepresent molecular heterogeneity. CSF, which can be obtained less ...invasively, is in intimate contact with tumor lesions and may better capture the full genomic profile of the tumor. However, datasets with contemporaneously collected CSF and tissue to support this claim have been lacking. To evaluate the performance of CSF NGS, we conducted a pilot study in patients with GBM undergoing a resection for suspected recurrence following first-line chemoradiotherapy.
METHODS
Paired CSF and tissue samples were sequenced using a hybrid capture-based NGS assay. Clinically meaningful variants were defined as those that are potentially targetable using off-label or clinical trial options, exhibit prognostic value, or may predict response or resistance to specific treatments.
RESULTS
Eighteen patients were enrolled, and 13 of 18 CSF samples (72.2%) were sequenced successfully. At least one variant was detected in all CSF samples analyzed. A median of 7 variants (range 1—67) was detected per sample across 54 genes. The median variant allele fraction was 0.6% (range 0.2—72.4%). Among 38 clinically meaningful genes, 102 variants were detected; 25 (24.5%) were detected in both tissue and CSF, while 60 (58.8%) were detectable solely in CSF. Hypermutation was detected by CSF in one patient. Of the 82 variants detected in this patient’s tumor, 15 (18.3%) were identified in both tissue and CSF, 15 (18.3%) were identified only in the tissue, and 52 (63.2%) were identified only in the CSF.
CONCLUSIONS
CSF NGS detects clinically meaningful variants at a substantial rate and frequently identifies mutations not detected by matched tissue NGS. These results suggest that CSF may be a suitable source material for tumor profiling, overcoming the limitations of tissue, and may also provide a more comprehensive tumor profile.
Abstract
Glioblastoma responses to immune checkpoint inhibition (ICI) are rare, and the molecular mechanisms underlying ICI responses are incompletely understood. Thus, serial glioblastoma samples ...are valuable resources for identifying biomarkers or therapeutic targets to increase the efficacy of ICI in patients with glioblastoma. We obtained paired glioblastoma samples from 7 patients who underwent sequential surgery, ICI, and eventual salvage surgery for recurrence. Patients were distinguished as ICI responders (n=3) or non-responders (n=4) based on (1) MRI evidence of tumor stability/reduction over 6+ months after ICI, or (2) pathologic evidence of predominant treatment effect at the time of salvage surgery after ICI. FFPE sections from each tumor (n=14) were stained using H&E or IHC/IF for macrophages/microglia (CD68) or T cells (CD3) and analyzed using light or fluorescence microscopy. Six regions-of-interest (ROIs) comprising viable tumor were selected neuropathologist from each sample (n=84 ROIs). ROIs were analyzed using quantitative spatial profiling of 72 proteins on the Nanostring Digital Profiler platform. Glioblastomas responding to ICI were enriched in T-cell proteins (CD3, CD4, CD8) and T-cell activation markers (CD25) at the time of salvage compared to initial surgery. Markers of MAPK signaling were suppressed in pre-ICI samples compared to post-ICI samples in responders. p-ERK was suppressed in post-ICI samples compared to pre-ICI samples in non-responders. Myeloid proteins (CD68, CD163, CD11c) were enriched in post-ICI samples compared to pre-ICI samples in non-responders. Principle components analysis revealed p-ERK and immune proteins (CD3, CD4, CD8, CD20, CD11c, CTLA4, CD68, CD45, CD56, and CD127) accounted for 62% of the variance among pre-ICI and post-ICI samples in responders. In conclusion, temporospatial protein profiling of human glioblastomas reveals molecular mechanisms and biomarkers underlying responses to immune checkpoint inhibition. These data establish a foundation for functional studies to reprogram the immunosuppressive glioblastoma microenvironment and sensitize tumors to immune checkpoint inhibition.
Abstract
Tetraspanin 12 (TSPAN12), a member of the tetraspanin family that are increasingly known to be involved in various mechanisms of tumor progression, mediates various cellular signaling ...processes in cancer cells. With respect to the brain, previous studies have shown that TSPAN12 is related with the maturation of a membrane-associated metalloproteinase 10 and the production of amyloid β plaque, but there are no studies related to brain tumors to date. Therefore, we designed this study to investigate the role of TSPAN 12 on malignant glioma (MG) cells and patients. TSPAN12 silencing in MG cells significantly progressed cell proliferation, migration and invasion capacities, and extracellular matrix adhesion ability as well as stem cell properties, in vitro. Mechanistically, we identified that FAK and ERK signaling were involved in MG cells with TSPAN12 expression. Moreover, clinical analysis of MG patient tissues microarray showed that the expression level of TSPAN12 was negatively correlated with the prognosis in MG patients. Collectively, more studies are needed, but we suggest that TSPAN12 can be used as an alternative biomarker to predict the prognosis of MG patient and help develop MG treatment strategies.
Abstract
Although high-dose methotrexate (HD-MTX)-based chemotherapy, such as rituximab, HD-MTX, procarbazine and vincristine (R-MPV) regimen, has significantly prolonged the survival of patients ...with primary central nervous system lymphoma (PCNSL), predictive factors for response to R-MPV have not yet been investigated. Then, we investigated the correlation of MYD88 L265P and CD79B Y196 mutations, which are the most frequently found molecular alterations in PCNSL, with prognosis of patients with PCNSL treated with R-MPV. 47 and 21 patients with PCNSL treated with R-MPV and HD-MTX respectively were included, and correlation of their MYD88 and CD79B status with prognosis was analyzed. R-MPV achieved an excellent tumor control rate (61.6% and 69.9% of 5-year progression-free and overall survival rates, respectively). Among the 47 patients, 36 harbored MYD88 L265P or CD79B Y196 mutations. While the MYD88 L265P mutation had no significant effect on survival, patients with CD79B Y196 mutations exhibited prolonged survival (P < 0.05). However, the association of the CD79B Y196 mutation with a better prognosis was not observed in the HD-MTX cohort, which indicated that the CD79B Y196 mutation was a predictive marker for a favorable response to R-MPV. Furthermore, we established an all-in-one rapid genotyping system for these genetic mutations. This system enabled the detection of these genetic mutations in a small amount of biopsy samples within 90 min. In conclusion, we revealed that the CD79B Y196 mutation is associated with a good response to R-MPV, and the rapid and accurate genotyping system for MYD88 L265P and CD79B Y196 mutations that we developed in this study will enable reliable rapid molecular diagnosis and early prediction of response to R-MPV, which might help to determine the best treatment strategy for PCNSL.
