Distinct genomic profile and specific targeted drug responses in adult cerebellar glioblastoma

MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction

BACKGROUND

Drug response prediction is critical in precision medicine to determine the most effective and safe treatments for individual patients. Traditional prediction methods relying on demographic and genetic data often fall short in accuracy and robustness. Recent graph-based models, while promising, frequently neglect the critical role of atomic interactions and fail to integrate drug fingerprints with SMILES for comprehensive molecular graph construction.

RESULTS

We introduce multimodal multi-channel graph attention network with adaptive fusion (MGATAF), a framework designed to enhance drug response predictions by capturing both local and global interactions among graph nodes. MGATAF improves drug representation by integrating SMILES and fingerprints, resulting in more precise predictions of drug effects. The methodology involves constructing multimodal molecular graphs, employing multi-channel graph attention networks to capture diverse interactions, and using adaptive fusion to integrate these interactions at multiple abstraction levels. Empirical results demonstrate MGATAF's superior performance compared to traditional and other graph-based techniques. For example, on the GDSC dataset, MGATAF achieved a 5.12% improvement in the Pearson correlation coefficient (PCC), reaching 0.9312 with an RMSE of 0.0225. Similarly, in new cell-line tests, MGATAF outperformed baselines with a PCC of 0.8536 and an RMSE of 0.0321 on the GDSC dataset, and a PCC of 0.7364 with an RMSE of 0.0531 on the CCLE dataset.

CONCLUSIONS

MGATAF significantly advances drug response prediction by effectively integrating multiple molecular data types and capturing complex interactions. This framework enhances prediction accuracy and offers a robust tool for personalized medicine, potentially leading to more effective and safer treatments for patients. Future research can expand on this work by exploring additional data modalities and refining the adaptive fusion mechanisms.

Cerebellar glioblastoma in adults: a comparative single-center matched pair analysis and systematic review of the literature

PURPOSE

The rarity of cerebellar glioblastoma presents a significant challenge in clinical practice due to the lack of extensive prognostic data on long-term survival rates, rendering it an underrepresented entity compared to its supratentorial counterpart. This study aims to analyze potential differences in survival outcome between patients with cerebellar and supratentorial glioblastomas.

METHODS

From 2009 to 2020, 8 patients underwent surgical treatment for cerebellar glioblastoma at the authors' institution. These patients were individually matched with a cohort of 205 consecutive patients from our institutional database with supratentorial glioblastoma, taking into account key prognostic parameters. Progression-free survival (PFS) and overall survival (OS) rates were compared. Additionally, we performed a systematic literature review to compile further survival data on cerebellar glioblastoma patients.

RESULTS

The median OS for cerebellar glioblastoma patients was 18 months (95% CI 11-25). The balanced matched-pair analysis showed no significant difference in survival when compared to patients with supratentorial glioblastoma, exhibiting a median OS of 23 months (95% CI 0-62) (p = 0.63). Respective values for PFS were 8 months (95% CI 4-12) for cerebellar and 7 months (95% CI 0-16) for supratentorial glioblastoma (p = 0.2). The systematic review revealed that median OS for cerebellar glioblastoma in current literature ranges from 7 to 21 months.

CONCLUSIONS

The present findings indicate that patients with supra- and infratentorial glioblastoma do not significantly differ in regard to survival outcome parameters. This similarity in prognosis might encourage clinicians to consider surgical interventions for both supra- and infratentorial glioblastoma in a similar manner.

Racial and social-economic inequalities in systemic chemotherapy use among adult glioblastoma patients following surgery and radiotherapy

Not all patients with glioblastoma multiforme (GBM) eligible for systemic chemotherapy after upfront surgery and radiotherapy finally receive it. The information on patients with GBM was retrieved from the surveillance, epidemiology, and end results database. Patients who underwent upfront surgery or biopsy and external beam radiotherapy between 2010 and 2019 were eligible for systemic chemotherapy. The available patient and tumor characteristics were assessed using multivariable logistic regression and chi-squared test. Out of the 16,682 patients eligible, 92.1% underwent systemic chemotherapy. The characteristics linked to the lowest systemic chemotherapy utilization included tumors of the brain stem/cerebellum (P = 0.01), former years of diagnosis (P = 0.001), ≥ 80 years of age (P < 0.001), Hispanic, Non-Hispanic Asian, Pacific Islander, or Black race (P < 0.001), non-partnered status (P < 0.001), and low median household income (P = 0.006). Primary tumor site, year of diagnosis, age, race, partnered status, and median household income correlated with the omission of systemic chemotherapy in GBM in adult patients.

A common tumour in a rare location: a single centre case series of cerebellar glioblastoma

Although glioblastoma is the commonest primary brain tumour in adults, its location in the cerebellum is extremely rare. We present thirteen cases (3 female, 10 male; median age at presentation 56 [age range 21-77]) of surgically managed, histologically confirmed, primary cerebellar glioblastoma (cGB) over a 17 year period (2005-2022). Pre-operative radiological diagnosis was challenging given cGB rarity, although MRI demonstrated ring enhancement in all cases. Surgical management included posterior fossa craniectomy and debulking in 11 cases and burr hole biopsy in two. CSF diversion was necessary in four cases. No evidence of IDH or ATRX gene mutations was found when tested. Survival ranged from 1 to 22 months after diagnosis (mean 10.9 months). We also seek to understand why glioblastoma is rare in this location and discuss potential reasons for this. We hypothesise that increasing anatomical distance from germinal regions and decreased local endogenous neural stem cell activity (which has been associated with glioblastoma) may explain why glioblastoma is rare in the cerebellum. We hereby seek to add to the limited literature on cGB as this is the largest UK cGB series to date.

Understanding the immunosuppressive microenvironment of glioma: mechanistic insights and clinical perspectives

Glioblastoma (GBM), the predominant and primary malignant intracranial tumor, poses a formidable challenge due to its immunosuppressive microenvironment, thereby confounding conventional therapeutic interventions. Despite the established treatment regimen comprising surgical intervention, radiotherapy, temozolomide administration, and the exploration of emerging modalities such as immunotherapy and integration of medicine and engineering technology therapy, the efficacy of these approaches remains constrained, resulting in suboptimal prognostic outcomes. In recent years, intensive scrutiny of the inhibitory and immunosuppressive milieu within GBM has underscored the significance of cellular constituents of the GBM microenvironment and their interactions with malignant cells and neurons. Novel immune and targeted therapy strategies have emerged, offering promising avenues for advancing GBM treatment. One pivotal mechanism orchestrating immunosuppression in GBM involves the aggregation of myeloid-derived suppressor cells (MDSCs), glioma-associated macrophage/microglia (GAM), and regulatory T cells (Tregs). Among these, MDSCs, though constituting a minority (4-8%) of CD45+ cells in GBM, play a central component in fostering immune evasion and propelling tumor progression, angiogenesis, invasion, and metastasis. MDSCs deploy intricate immunosuppressive mechanisms that adapt to the dynamic tumor microenvironment (TME). Understanding the interplay between GBM and MDSCs provides a compelling basis for therapeutic interventions. This review seeks to elucidate the immune regulatory mechanisms inherent in the GBM microenvironment, explore existing therapeutic targets, and consolidate recent insights into MDSC induction and their contribution to GBM immunosuppression. Additionally, the review comprehensively surveys ongoing clinical trials and potential treatment strategies, envisioning a future where targeting MDSCs could reshape the immune landscape of GBM. Through the synergistic integration of immunotherapy with other therapeutic modalities, this approach can establish a multidisciplinary, multi-target paradigm, ultimately improving the prognosis and quality of life in patients with GBM.

KRAS is a molecular determinant of platinum responsiveness in glioblastoma

BACKGROUND

KRAS is the undisputed champion of oncogenes, and despite its prominent role in oncogenesis as mutated gene, KRAS mutation appears infrequent in gliomas. Nevertheless, gliomas are considered KRAS-driven cancers due to its essential role in mouse malignant gliomagenesis. Glioblastoma is the most lethal primary brain tumor, often associated with disturbed RAS signaling. For newly diagnosed GBM, the current standard therapy is alkylating agent chemotherapy combined with radiotherapy. Cisplatin is one of the most effective anticancer drugs and is used as a first-line treatment for a wide spectrum of solid tumors (including medulloblastoma and neuroblastoma) and many studies are currently focused on new delivery modalities of effective cisplatin in glioblastoma. Its mechanism of action is mainly based on DNA damage, inducing the formation of DNA adducts, triggering a series of signal-transduction pathways, leading to cell-cycle arrest, DNA repair and apoptosis.

METHODS

Long-term cultures of human glioblastoma, U87MG and U251MG, were either treated with cis-diamminedichloroplatinum (cisplatin, CDDP) and/or MEK-inhibitor PD98059. Cytotoxic responses were assessed by cell viability (MTT), protein expression (Western Blot), cell cycle (PI staining) and apoptosis (TUNEL) assays. Further, gain-of-function experiments were performed with cells over-expressing mutated hypervariable region (HVR) KRASG12V plasmids.

RESULTS

Here, we studied platinum-based chemosensitivity of long-term cultures of human glioblastoma from the perspective of KRAS expression, by using CDDP and MEK-inhibitor. Endogenous high KRAS expression was assessed at transcriptional (qPCR) and translational levels (WB) in a panel of primary and long-term glioblastoma cultures. Firstly, we measured immediate cellular adjustment through direct regulation of protein concentration of K-Ras4B in response to cisplatin treatment. We found increased endogenous protein abundance and involvement of the effector pathway RAF/MEK/ERK mitogen-activated protein kinase (MAPK) cascade. Moreover, as many MEK inhibitors are currently being clinically evaluated for the treatment of high-grade glioma, so we concomitantly tested the effect of the potent and selective non-ATP-competitive MEK1/2 inhibitor (PD98059) on cisplatin-induced chemosensitivity in these cells. Cell-cycle phase distribution was examined using flow cytometry showing a significant cell-cycle arrest in both cultures at different percentage, which is modulated by MEK inhibition. Cisplatin-induced cytotoxicity increased sub-G1 percentage and modulates G2/M checkpoint regulators cyclins D1 and A. Moreover, ectopic expression of a constitutively active KRASG12V rescued CDDP-induced apoptosis and different HVR point mutations (particularly Ala 185) reverted this phenotype.

CONCLUSION

These findings warrant further studies of clinical applications of MEK1/2 inhibitors and KRAS as 'actionable target' of cisplatin-based chemotherapy for glioblastoma.

Predicting TERT promoter mutation status using 1H-MR spectroscopy and stretched-exponential model of diffusion-weighted imaging in IDH-wildtype diffuse astrocytic glioma without intense enhancement

PURPOSE

Isocitrate dehydrogenase (IDH)-wildtype diffuse astrocytic glioma with telomerase reverse transcriptase (TERT) promoter mutation is defined as glioblastoma by the WHO 2021 criteria, revealing that TERT promotor mutation is highly associated with tumor aggressiveness. The aim of this study was to identify features from MR spectroscopy (MRS) and multi-exponential models of DWI distinguishing wild-type TERT (TERTw) from TERT promoter mutation (TERTm) in IDH-wildtype diffuse astrocytic glioma.

METHODS

Participants comprised 25 adult patients with IDH-wildtype diffuse astrocytic glioma. Participants were classified into TERTw and TERTm groups. Point-resolved spectroscopy sequences were used for MRS data acquisition. DWI was performed with 13 different b-factors. Peak height ratios of NAA/Cr and Cho/Cr were calculated from MRS data. Mean apparent diffusion coefficient (ADC), perfusion fraction (f), diffusion coefficient (D), pseudo-diffusion coefficient (D*), distributed diffusion coefficient (DDC), and heterogeneity index (α) were obtained using multi-exponential models from DWI data. Each parameter was compared between TERTw and TERTm using the Mann-Whitney U test. Correlations between parameters derived from MRS and DWI were also evaluated.

RESULTS

NAA/Cr and Cho/Cr were both higher for TERTw than for TERTm. The α of TERTw was smaller than that of TERTm, while the f of TERTw was higher than that of TERTm. NAA/Cr correlated negatively with α, but not with other DWI parameters. Cho/Cr did not show significant correlations with any DWI parameters.

CONCLUSION

The combination of NAA/Cr and α may have merit in clinical situation to predict the TERT mutation status of IDH-wildtype diffuse astrocytic glioma without intense enhancement.

Molecular Characterization of Adult Tumors Diagnosed as Cerebellar Glioblastomas Identifies Subgroups Associated With Prognosis

Adult tumors diagnosed as cerebellar glioblastoma (cGBM) are rare and their optimal classification remains to be determined. The aim of this study was to identify subgroups of cGBM based on targeted molecular analysis. cGBM diagnosed between 2003 and 2017 were identified from the French Brain Tumor Database and reviewed according to the WHO 2021 classification. The following molecular alterations were studied: IDH1/2 , H3F3A , FGFR1 , BRAF , TERT promoter mutations, EGFR amplification, MGMT promoter methylation, and alternative lengthening of telomere status. DNA methylation profile was assessed in a subset of cases. Eighty-three cGBM were included and could be classified into 6 mutually exclusive subgroups associated with median age at diagnosis (MA) and prognosis: TERT -mutant and/or EGFR -amplified tumors (n=22, 26.5%, MA=62 y, median overall survival [OS]=4 mo), H3K27M-mutant tumors (n=15, 18.1%, MA=48 y, median OS=8 mo), mitogen-activated protein kinases (MAPK) pathway-activated tumors ( FGFR1 , BRAF mutation, or occurring in neurofibromatosis type I patients, n=15, 18.1%, MA=48 y, median OS=57 mo), radiation-associated tumors (n=5, 6%, MA=47 y, median OS=5 mo), IDH-mutant tumors (n=1), and unclassified tumors (n=25, 30.1%, MA=63 y, median OS=17 mo). Most MAPK pathway-activated tumors corresponded to high-grade astrocytomas with piloid features based on DNA methylation profiling. In multivariate analysis, MAPK pathway-activating alterations, ATRX loss of expression, and alternative lengthening of telomere positivity were independently associated with a better outcome and TERT / EGFR alterations with a worse outcome. cGBM display an important intertumoral heterogeneity. Targeted molecular analysis enables to classify the majority of tumors diagnosed as cGBM into mutually exclusive and clinically relevant subgroups. The presence of MAPK pathway alterations is associated with a much better prognosis.

Cerebellar High-Grade Glioma: A Translationally Oriented Review of the Literature

World Health Organization (WHO) grade 4 gliomas of the cerebellum are rare entities whose understanding trails that of their supratentorial counterparts. Like supratentorial high-grade gliomas (sHGG), cerebellar high-grade gliomas (cHGG) preferentially affect males and prognosis is bleak; however, they are more common in a younger population. While current therapy for cerebellar and supratentorial HGG is the same, recent molecular analyses have identified features and subclasses of cerebellar tumors that may merit individualized targeting. One recent series of cHGG included the subclasses of (1) high-grade astrocytoma with piloid features (HGAP, ~31% of tumors); (2) H3K27M diffuse midline glioma (~8%); and (3) isocitrate dehydrogenase (IDH) wildtype glioblastoma (~43%). The latter had an unusually low-frequency of epidermal growth factor receptor (EGFR) and high-frequency of platelet-derived growth factor receptor alpha (PDGFRA) amplification, reflecting a different composition of methylation classes compared to supratentorial IDH-wildtype tumors. These new classifications have begun to reveal insights into the pathogenesis of HGG in the cerebellum and lead toward individualized treatment targeted toward the appropriate subclass of cHGG. Emerging therapeutic strategies include targeting the mitogen-activated protein kinases (MAPK) pathway and PDGFRA, oncolytic virotherapy, and immunotherapy. HGGs of the cerebellum exhibit biological differences compared to sHGG, and improved understanding of their molecular subclasses has the potential to advance treatment.

Establishment of a cell senescence related prognostic model for predicting prognosis in glioblastoma

Background: Glioblastoma (GBM) is highly malignant and has a worse prognosis with age, and next-generation sequencing (NGS) provides us with a huge amount of information about GBM. Materials and Methods: Through the enrichment scores of cell senescence-related pathways, we constructed a consensus matrix and mined molecular subtypes and explored the differences in pathological, immune/pathway and prognostic. Also we identified key genes related to cell senescence characteristics using least absolute shrinkage and selection operator (Lasso) regression and univariate COX regression analysis models. The use of risk factor formats to construct clinical prognostic models also explored the differences in immunotherapy/chemotherapy within the senescence-related signatures score (SRS.score) subgroups. Decision trees built with machine learning to identify the main factors affecting prognosis have further improved the prognosis model and survival prediction. Results: We obtained seven prognostic-related pathways related to cell senescence. We constructed four different molecular subtypes and found patients with subtype C1 had the worst prognosis. C4 had the highest proportion of patients with IDH mutations. 1005 differentially expressed genes (DEGs) were analyzed, and finally 194 Risk genes and 38 Protective genes were obtained. Eight key genes responsible for cell senescence were finally identified. The clinical prognosis model was established based on SRS.score, and the prognosis of patients with high SRS.score was worse. SRS.score and age were the vital risk factors for GBM patients through decision tree model mining. Conclusion: We constructed a clinical prognosis model that could provide high prediction accuracy and survival prediction ability for adjuvant treatment of patients with GBM.

miR-124 regulates early isolation-induced social abnormalities via inhibiting myelinogenesis in the medial prefrontal cortex

Patients with autism spectrum disorder (ASD) typically experience substantial social isolation, which may cause secondary adverse effects on their brain development. miR-124 is the most abundant miRNA in the human brain, acting as a pivotal molecule regulating neuronal fate determination. Alterations of miR-124 maturation or expression are observed in various neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. In the present study, we analyzed a panel of brain-enriched microRNAs in serums from 2 to 6 year old boys diagnosed with ASD. The hsa-miR-124 level was found significantly elevated in ASD boys than in age and sex-matched healthy controls. In an isolation-reared weanling mouse model, we evidenced elevated mmu-miR-124 level in the serum and the medial prefrontal cortex (mPFC). These mice displayed significant sociability deficits, as well as myelin abnormality in the mPFC, which was partially rescued by expressing the miR-124 sponge in the bilateral mPFC, ubiquitously or specifically in oligodendroglia. In cultured mouse oligodendrocyte precursor cells, introducing a synthetic mmu-miR-124 inhibited the differentiation process through suppressing expression of nuclear receptor subfamily 4 group A member 1 (Nr4a1). Overexpressing Nr4a1 in the bilateral mPFC also corrected the social behavioral deficits and myelin impairments in the isolation-reared mice. This study revealed an unanticipated role of the miR-124/Nr4a1 signaling in regulating early social experience-dependent mPFC myelination, which may serve as a potential therapy target for social neglect or social isolation-related neuropsychiatric disorders.

ATRX-dependent SVCT2 mediates macrophage infiltration in the glioblastoma xenograft model

Alpha thalassemia/mental retardation syndrome X-linked (ATRX) mutation impairs DNA damage repair in glioblastoma (GBM), making these cells more susceptible to treatment, which may contribute to the survival advantage in GBM patients containing ATRX mutations. To better understand the role of ATRX in GBM, genes correlated with ATRX expression were screened in the Cancer Genome Atlas (702 cases) and Chinese Glioma Genome Atlas (325 cases) databases. Sodium-vitamin C cotransporter 2 (SVCT2) was the most positively correlated gene with ATRX expression. ATRX (about 1.99-fold) and SVCT2 (about 2.25-fold) were upregulated in GBM tissues from 40 patients compared to normal brain tissues from 23 subjects. ShSVCT2 transfection did not alter the in vitro viability of GL261 cells. At the same time, it could inhibit the proliferation of GL261 cells in the orthotopic transplantation model with diminished infiltrating macrophages (CD45^highCD11b⁺), down-regulated chemokine (C-C motif) ligand 2 (Ccl2), Ccl4, C-X-C motif chemokine ligand 1 (Cxcl1), and Cxcl15 expression, and decreased p-IκBα and p-c-Jun expression. Effect of ShSVCT2 transfection could be reversed by overexpression of SVCT2. siRNA interference of ATRX-dependent SVCT2 signal with shSVCT2 could inhibit tumor cell proliferation in Glu261-LuNeo xenograft tumor model with more survival advantage, probably by the inhibited macrophage chemotaxis. These results indicate that ATRX-dependent SVCT2-mediated chemokine-induced macrophage infiltration is regulated by the NF-κB pathway, which could be considered as treatment targets.

Rapid Brainstem Infiltration of a Cerebellar Glioblastoma

A 79-year-old female complained of a one-month history of imbalance and headache. Brain MRI showed an irregular rim enhancing solid and cystic mass centered in the superomedial left cerebellar hemisphere. Resection of the lesion was recommended; however, the patient opted to undergo the procedure the following month because of the nearby Christmas holidays. When the patient returned 30 days later, a new brain MRI showed an enlargement of the cerebellar mass, extending to the brainstem and infiltrating the left brachium pontis, left posterior aspect of the tegmentum of the pons, and posterolateral medulla oblongata. Subtotal resection was performed without complications, and pathology was compatible with a primary cerebellar glioblastoma negative for IDH1/2 gene mutation. Because of the poor prognosis, the patient and her family members opted for hospice treatment, with the patient dying three weeks later. This case illustrates that cerebellar glioblastoma can rapidly infiltrate the brainstem.

Transcription factors specificity protein and nuclear receptor 4A1 in pancreatic cancer

Specificity protein (Sp) transcription factors (TFs) Sp1, Sp3 and Sp4, and the orphan nuclear receptor 4A1 (NR4A1) are highly expressed in pancreatic tumors and Sp1 is a negative prognostic factor for pancreatic cancer patient survival. Results of knockdown and overexpression of Sp1, Sp3 and Sp4 in pancreatic and other cancer lines show that these TFs are individually pro-oncogenic factors and loss of one Sp TF is not compensated by other members. NR4A1 is also a pro-oncogenic factor and both NR4A1 and Sp TFs exhibit similar functions in pancreatic cancer cells and regulate cell growth, survival, migration and invasion. There is also evidence that Sp TFs and NR4A1 regulate some of the same genes including survivin, epidermal growth factor receptor, PAX3-FOXO1, α5- and α6-integrins, β1-, β3- and β4-integrins; this is due to NR4A1 acting as a cofactor and mediating NR4A1/Sp1/4-regulated gene expression through GC-rich gene promoter sites. Several studies show that drugs targeting Sp downregulation or NR4A1 antagonists are highly effective inhibitors of Sp/NR4A1-regulated pathways and genes in pancreatic and other cancer cells, and the triterpenoid celastrol is a novel dual-acting agent that targets both Sp TFs and NR4A1.

Diffuse Gliomas of the Brainstem and Cerebellum in Adults Show Molecular Heterogeneity

Posterior fossa (PF) diffuse gliomas in pediatric patients frequently harbor the H3 K27M mutation. Among adults, PF diffuse gliomas are rare, with limited data regarding molecular features and clinical outcomes. We identified 28 adult PF diffuse glioma patients (17 males; median: 50 y, range: 19 to 78 y), with surgery performed at our institution (13 brainstem; 15 cerebellum). Histologic subtypes included anaplastic astrocytoma (n=21), glioblastoma (n=6), and diffuse astrocytoma (n=1). Immunohistochemistry was performed for H3 K27M (n=26), IDH1-R132H (n=28), and ATRX (n=28). A 150-gene neuro-oncology-targeted next-generation sequencing panel was attempted in 24/28, with sufficient informative material in 15 (51.7%). Tumors comprised 4 distinct groups: driver mutations in H3F3A (brainstem=4; cerebellum=2), IDH1 (brainstem=4; cerebellum=4), TERT promotor mutation (brainstem=0; cerebellum=3), and none of these (n=5), with the latter harboring mutations of TP53, PDGFRA, ATRX, NF1, and RB1. All TERT promoter-mutant cases were IDH-wild-type and arose within the cerebellum. To date, 20 patients have died of disease, with a median survival of 16.3 months, 1-year survival of 67.5%. Median survival within the subgroups included: H3F3A=16.4 months, IDH mutant=113.4 months, and TERT promoter mutant=12.9 months. These findings suggest that PF diffuse gliomas affecting adults show molecular heterogeneity, which may be associated with patient outcomes and possible response to therapy, and supports the utility of molecular testing in these tumors.

The topology of data: Opportunities for cancer research

Motivation

Topological methods have recently emerged as a reliable and interpretable framework for extracting information from high-dimensional data, leading to the creation of a branch of applied mathematics called Topological Data Analysis (TDA). Since then, TDA has been progressively adopted in biomedical research. Biological data collection can result in enormous datasets, comprising thousands of features and spanning diverse datatypes. This presents a barrier to initial data analysis as the fundamental structure of the dataset becomes hidden, obstructing the discovery of important features and patterns. TDA provides a solution to obtain the underlying shape of datasets over continuous resolutions, corresponding to key topological features independent of noise. TDA has the potential to support future developments in healthcare as biomedical datasets rise in complexity and dimensionality. Previous applications extend across the fields of neuroscience, oncology, immunology and medical image analysis. TDA has been used to reveal hidden subgroups of cancer patients, construct organizational maps of brain activity and classify abnormal patterns in medical images. The utility of TDA is broad and to understand where current achievements lie, we have evaluated the present state of TDA in cancer data analysis.

Results

This article aims to provide an overview of TDA in Cancer Research. A brief introduction to the main concepts of TDA is provided to ensure that the article is accessible to readers who are not familiar with this field. Following this, a focussed literature review on the field is presented, discussing how TDA has been applied across heterogeneous datatypes for cancer research.

Cerebellar anaplastic astrocytoma in adult patients: 15 consecutive cases from a single institution and literature review

Adult cerebellar anaplastic astrocytomas (cAA) are rare entities and their clinical and genetic appearances are still ill defined. Previously, malignant gliomas of the cerebellum were combined and reviewed together (cAA and cerebellar glioblastomas (cGB), that could have possibly affected overall survival (OS) and progression-free survival (PFS). We present characteristics of 15 adult patients with cAA and compared them to a series of 45 patients with a supratentorial AA (sAA) in order to elicit the effect of tumor location on OS and PFS. The mean age at cAA diagnosis was 39.3 years (range 19-72). A history of neurofibromatosis type I was noted in 1 patient (6.7%). An IDH-1 mutation was identified in 6/15 cases and a methylated MGMT promoter in 5/15 cases. Patients in study and control groups were matched in age, sex and IDH-1 mutation status. Patients in a study group tended to present with longer overall survival (50 vs. 36.5 months), but the difference did not reach statistical significance. In both cAA and supratentorial AA groups presence of the IDH-1 mutation remains a positive predictor for the prolonged survival. The present study suggests that adult cAA constitute a group of gliomas with relatively higher rate of IDH-1 mutations and prognosis similar to supratentorial AA. The present study is the first to systematically compare cAA and supratentorial AA with respect to their genetic characteristics and suggests that both groups show a similar survival prognosis.

The inverse paradigm and the ancestral cell of IDH-wildtype glioblastoma

Rethinking IDH-wildtype glioblastoma through its unique features can help researchers find innovative and effective treatments. It is currently emerging that, after decades of therapeutic impasse, some traditional concepts regarding IDH-wildtype glioblastoma need to be supplemented and updated to overcome therapeutic resistance. Indeed, multiple clinical aspects and recent indirect and direct experimental data are providing evidence that the supratentorial brain parenchyma becomes entirely and quiescently micro-infiltrated long before primary tumor bulk growth. Furthermore, they are indicating that the known micro-infiltration that occurs during the IDH-wildtype glioblastoma growth and evolution is not at the origin of distant relapses. It follows that the ubiquitous supratentorial brain parenchyma micro-infiltration as a source for the development of widespread distant recurrences is actually due to the silent stage that precedes tumor growth rather than to the latter. All this implies that, in addition to the heterogeneity of the primary bulk, there is a second crucial cause of therapeutic resistance that has never hitherto been identified and challenged. In this regard, the ancestral founder cancer stem cell (CSC) appears as the key cell that can link the two causes of resistance.

Comprehensive Molecular Characterization of Chinese Patients with Glioma by Extensive Next-Generation Sequencing Panel Analysis

Background

Tremendous efforts have been made to explore biomarkers for classifying and grading glioma. However, the majority of the current understanding is based on public databases that might not accurately reflect the Asian population. Here, we investigated the genetic landscape of Chinese glioma patients using a validated multigene next-generation sequencing (NGS) panel to provide a strong rationale for the future classification and prognosis of glioma in this population.

Methods

We analyzed 83 samples, consisting of 71 initial treatments and 12 recurrent surgical tumors, from 81 Chinese patients with gliomas by performing multigene NGS with an Acornmed panel targeting 808 cancer-related hotspot genes, including genes related to glioma (hotspots, selected exons or complete coding sequences) and full-length SNPs located on chromosomes 1 and 19.

Results

A total of 76 (91.57%) glioma samples had at least one somatic mutation. The most commonly mutated genes were TP53, TERT, IDH1, PTEN, ATRX, and EGFR. Approximately one-third of cases exhibited more than one copy number variation. Of note, this study identified the amplification of genes, such as EGFR and PDGFRA, which were significantly associated with glioblastoma but had not been previously used for clinical classification (P<0.05). Significant differences in genomic profiles between different pathological subtypes and WHO grade were observed. Compared to the MSKCC database primarily comprised of Caucasians, H3F3A mutations and MET amplifications exhibited higher mutation rates, whereas TERT mutations and EGFR and CDKN2A/B copy number variations presented a lower mutation rate in Chinese patients with glioma (P<0.05).

Conclusion

Our multigene NGS in the simultaneous evaluation of multiple relevant markers revealed several novel genetic alterations in Chinese patients with glioma. NGS-based molecular analysis is a reliable and effective method for diagnosing brain tumors, assisting clinicians in evaluating additional potential therapeutic options, such as targeted therapy, for glioma patients in different racial/ethnic groups.

MEK inhibitors - novel targeted therapies of neurofibromatosis associated benign and malignant lesions

MAP/ERK kinase 1 and 2 (MEK 1/2) inhibitors (MEKi) are investigated in several trials to treat lesions that arise from pathogenic variants of the Neurofibromatosis type 1 and type 2 genes (NF1, NF2). These trials showed that MEKi are capable to shrink volume of low grade gliomas and plexiform neurofibromas in NF1. Targeting other lesions being associated with a high morbidity in NF1 seems to be promising. Due to involvement of multiple pathways in NF2 associated lesions as well as in malignant tumors, MEKi are also used in combination therapies. This review outlines the current state of MEKi application in neurofibromatosis and associated benign and malignant lesions.

Real-world validity of randomized controlled phase III trials in newly diagnosed glioblastoma: to whom do the results of the trials apply?

Background

The survival rates in population-based series of glioblastoma (GBM) differ substantially from those reported in clinical trials. This discrepancy may be attributed to that patients recruited to trials tend to be younger with better performance status. However, the proportion and characteristics of the patients in a population considered either eligible or ineligible for trials is unknown. The generalizability of trial results is therefore also uncertain.

Methods

Using the Cancer Registry of Norway and the Brain Tumor Database at Oslo University Hospital, we tracked all patients within a well-defined geographical area with newly diagnosed GBM during the years 2012–2017. Based on data from these registries and the medical records, the patients were evaluated for trial eligibility according to criteria employed in recent phase III trials for GBM.

Results

We identified 512 patients. The median survival was 11.7 months. When we selected a potential trial population at the start of concurrent chemoradiotherapy (radiotherapy [RT]/ temozolomide [TMZ]) by the parameters age (18–70 y), passed surgery for a supratentorial GBM, Eastern Cooperative Oncology Group (ECOG) ≤2, normal hematologic, hepatic and renal function, and lack of severe comorbidity, 57% of the patients were excluded. Further filtering the patients who progressed during RT/TMZ and never completed RT/TMZ resulted in exclusion of 59% and 63% of the patients, respectively. The survival of patients potentially eligible for trials was significantly higher than of the patients not fulfilling trial eligibility criteria (P < .0001).

Conclusions

Patients considered eligible for phase III clinical trials represent a highly selected minority of patients in a real-world GBM population.

Clinical features associated with the efficacy of chemotherapy in patients with glioblastoma (GBM): a surveillance, epidemiology, and end results (SEER) analysis

Background

Glioblastoma (GBM) is a highly malignant brain tumor with poor survival and prognosis. Randomized trials have demonstrated that chemotherapy improves survival in patients with GBM. This study aims to examine the clinical characteristics that are potentially associated with the efficacy of chemotherapy and the risk factors of GBM.

Methods

A total of 25,698 patients diagnosed with GBM were identified between 2004 and 2015 from the Surveillance, Epidemiology, and End Results (SEER). The clinical and demographic variables between groups were examined by Student’s t-test and Pearson’s chi-square test. GBM-specific survival (GBMSS) and overall survival (OS) were evaluated using the Kaplan-Meier method with the log-rank test. Univariable and multivariable analyses were also performed using the Cox proportional hazards model to identify statistically significant prognostic factors.

Results

Patients who received chemotherapy had better overall survival (median OS 13 vs. Three months, HR = 1.9224, 95%CI 1.8571–1.9900, p < 0.0001) and better GBMSS (median GBMSS of 12 vs. Three months, HR = 1.9379, 95%CI 1.8632–2.0156, p < 0.0001), compared to patients who did not. Further subgroup analysis revealed that among patients who underwent chemotherapy, those who were younger, with a supratentorial tumor, received surgery, or radiotherapy had both improved OS and GBMSS. Age, race, tumor location, tumor size, and treatments were identified as independent prognostic factors by multivariable analyses for patients with glioblastoma.

Conclusion

Patients with GBM who were younger (< 65 years), underwent surgery, or radiotherapy can benefit more from chemotherapeutic regimens. Age, race, tumor size, tumor location, surgery, radiotherapy, and chemotherapy were factors associated with the prognosis of patients with GBM.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-07800-0.

Management, functional outcomes and survival in a French multicentric series of 118 adult patients with cerebellar glioblastoma

PURPOSE

To analyze the outcomes and predictors in a large series of cerebellar glioblastomas in order to guide patient management.

METHODS

The French brain tumor database and the Club de Neuro-Oncologie of the Société Française de Neurochirurgie retrospectively identified adult patients with cerebellar glioblastoma diagnosed between 2003 and 2017. Diagnosis was confirmed by a centralized neuropathological review.

RESULTS

Data from 118 cerebellar glioblastoma patients were analyzed (mean age 55.9 years, 55.1% males). The clinical presentation associated raised intracranial pressure (50.8%), static cerebellar syndrome (68.6%), kinetic cerebellar syndrome (49.2%) and/or cranial nerve disorders (17.8%). Glioblastomas were hemispheric (55.9%), vermian (14.4%) or both (29.7%). Hydrocephalus was present in 49 patients (41.5%). Histologically, tumors corresponded either to IDH-wild-type or to K27-mutant glioblastomas. Surgery consisted of total (12.7%), subtotal (35.6%), partial resection (33.9%) or biopsy (17.8%). The postoperative Karnofsky performance status was improved, stable and worsened in 22.4%, 43.9% and 33.7% of patients, respectively. Progression-free and overall survivals reached 5.1 months and 9.1 months, respectively. Compared to other surgical strategies, total or subtotal resection improved the Karnofsky performance status (33.3% vs 12.5%, p < 0.001), prolonged progression-free and overall survivals (6.5 vs 4.3 months, p = 0.015 and 16.7 vs 6.2 months, p < 0.001, respectively) and had a comparable complication rate (40.4% vs 31.1%, p = 0.29). After total or subtotal resection, the functional outcomes were correlated with age (p = 0.004) and cerebellar hemispheric tumor location (p < 0.001) but not brainstem infiltration (p = 0.16).

CONCLUSION

In selected patients, maximal resection of cerebellar glioblastoma is associated with improved onco-functional outcomes, compared with less invasive procedures.

A review of glioblastoma tumors with primitive neuronal component and a case report of a patient with this uncommon tumor at a rare location

Glioblastoma with primitive neuronal component should be considered as a differential diagnosis of infratentorial tumors.

Comparative Analysis of Survival Outcomes and Prognostic Factors of Supratentorial versus Cerebellar Glioblastoma in the Elderly: Does Location Really Matter?

BACKGROUND

Cerebellar glioblastomas (cGBMs) are rare tumors that are uncommon in the elderly. In this study, we compare survival outcomes and identify prognostic factors of cGBM compared with the supratentorial (stGBM) counterpart in the elderly.

METHODS

Data from the SEER 18 registries were used to identify patients with a glioblastoma (GBM) diagnosis between 2000 and 2016. The log-rank method and a multivariable Cox proportional hazards regression model were used for analysis.

RESULTS

Among 110 elderly patients with cGBM, the median age was 74 years (interquartile range [IQR], 69-79 years), 39% were female and 83% were white. Of these patients, 32% underwent gross total resection, 73% radiotherapy, and 39% chemotherapy. Multivariable analysis of the unmatched and matched cohort showed that tumor location was not associated with survival; in the unmatched cohort, insurance status (hazard ratio [HR], 0.11; IQR, 0.02-0.49; P = 0.004), gross total resection (HR, 0.53; IQR, 0.30-0.91; P = 0.022), and radiotherapy (HR, 0.33; IQR, 0.18-0.61; P < 0.0001) were associated with better survival. Patients with cGBM and stGBM undergoing radiotherapy (7 months vs. 2 months; P < 0.001) and chemotherapy (10 months vs. 3 months; P < 0.0001) had improved survival. Long-term mortality was lower for cGBM in the elderly at 24 months compared with the stGBM cohort (P = 0.007).

CONCLUSIONS

In our study, elderly patients with cGBM and stGBM have similar outcomes in overall survival, and those undergoing maximal resection with adjuvant therapies, independent of tumor location, have improved outcomes. Thus, aggressive treatment should be encouraged for cGBM in geriatric patients to confer the same survival benefits seen in stGBM. Single-institutional and multi-institutional studies to identify patient-level prognostic factors are warranted to triage the best surgical candidates.

Treatment patterns and outcomes for cerebellar glioblastoma in the concomitant chemoradiation era: A National Cancer database study

Cerebellar glioblastoma (GB) is much rarer than its supratentorial counterpart, and potentially of different molecular origin. Prior database studies are of limited size and reported on patients who preceded the validation of temozolomide. Thus, we provide an updated population-based analysis of the treatment trends and outcomes since the standardization of GB adjuvant chemoradiation. Patients diagnosed with primary cerebellar and supratentorial GB were identified from the National Cancer Database spanning 2005-2015. Patients were characterized by demographics, extent of resection, and adjuvant chemotherapy or radiation status. Cohorts were primarily and secondarily assessed for overall survival by tumor site and treatment history, respectively. A total of 655 patients with cerebellar GB were identified (0.6%). Cerebellar GB patients, compared to supratentorial GB were more likely to undergo a biopsy or subtotal resection (13.4% vs 9.3% and 16.0% vs 13.4%, p-value < 0.001), and less likely to pursue adjuvant therapy (48.4% vs 52.7%, p-value < 0.001). Overall median survivals were 9.3 and 9.4 months, respectively. On multivariable analysis, gross total resection, radiation, and chemotherapy were found to be predictors of improved overall survival (HR 0.77, p = 0.038; HR 0.67, p < 0.001; and HR = 0.77, p = 0.030, respectively). While many management principles are currently shared between cerebellar and supratentorial GB, aggressive regimens appear less frequently prescribed. Survival continues to match supratentorial outcomes and may benefit from future, systemic guidance by distinguishing molecular features.

A Glioblastoma Genomics Primer for Clinicians

New discoveries in Glioblastoma (GBM) biology have been made using genomics data. Genomic markers are routinely integrated into clinical neurosurgical practice. In this manuscript, we review the fundamentals of genomics such as the differences between first, second, and third generation sequencing technology. We also review the impact of single cell genomics in understanding the complex heterogenous GBM microenvironment. Finally, we will discuss advances in epigenetics that have lent insights into treatment resistance. The integration of genomics into neuro-oncology clinical practice is routine and will continue to expand with the expansion of precision of medicine. We provide a primer for clinicians.

Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities

In this multi-institutional study we compiled a retrospective cohort of 86 posterior fossa tumors having received the diagnosis of cerebellar glioblastoma (cGBM). All tumors were reviewed histologically and subjected to array-based methylation analysis followed by algorithm-based classification into distinct methylation classes (MCs). The single MC containing the largest proportion of 25 tumors diagnosed as cGBM was MC anaplastic astrocytoma with piloid features representing a recently-described molecular tumor entity not yet included in the WHO Classification of Tumours of the Central Nervous System (WHO classification). Twenty-nine tumors molecularly corresponded to either of 6 methylation subclasses subsumed in the MC family GBM IDH wildtype. Further we identified 6 tumors belonging to the MC diffuse midline glioma H3 K27 M mutant and 6 tumors allotted to the MC IDH mutant glioma subclass astrocytoma. Two tumors were classified as MC pilocytic astrocytoma of the posterior fossa, one as MC CNS high grade neuroepithelial tumor with BCOR alteration and one as MC control tissue, inflammatory tumor microenvironment. The methylation profiles of 16 tumors could not clearly be assigned to one distinct MC. In comparison to supratentorial localization, the MC GBM IDH wildtype subclass midline was overrepresented, whereas the MCs GBM IDH wildtype subclass mesenchymal and subclass RTK II were underrepresented in the cerebellum. Based on the integration of molecular and histological findings all tumors received an integrated diagnosis in line with the WHO classification 2016. In conclusion, cGBM does not represent a molecularly uniform tumor entity, but rather comprises different brain tumor entities with diverse prognosis and therapeutic options. Distinction of these molecular tumor classes requires molecular analysis. More than 30% of tumors diagnosed as cGBM belong to the recently described molecular entity of anaplastic astrocytoma with piloid features.

The 2019 mathematical oncology roadmap

Whether the nom de guerre is Mathematical Oncology, Computational or Systems Biology, Theoretical Biology, Evolutionary Oncology, Bioinformatics, or simply Basic Science, there is no denying that mathematics continues to play an increasingly prominent role in cancer research. Mathematical Oncology-defined here simply as the use of mathematics in cancer research-complements and overlaps with a number of other fields that rely on mathematics as a core methodology. As a result, Mathematical Oncology has a broad scope, ranging from theoretical studies to clinical trials designed with mathematical models. This Roadmap differentiates Mathematical Oncology from related fields and demonstrates specific areas of focus within this unique field of research. The dominant theme of this Roadmap is the personalization of medicine through mathematics, modelling, and simulation. This is achieved through the use of patient-specific clinical data to: develop individualized screening strategies to detect cancer earlier; make predictions of response to therapy; design adaptive, patient-specific treatment plans to overcome therapy resistance; and establish domain-specific standards to share model predictions and to make models and simulations reproducible. The cover art for this Roadmap was chosen as an apt metaphor for the beautiful, strange, and evolving relationship between mathematics and cancer.