Alpha Thalassemia/mental Retardation Syndrome X-linked Research Articles

EPCO-25. TRANSPOSABLE ELEMENTS INDUCE ONCO-EXAPTATION EVENTS IN MALIGNANT ATRX-DEFICIENT GLIOMAS

Abstract Deficiency of ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a core member of SWI/SNF family chromatin regulator is altered in diffuse gliomas and coexist with IDH1/2 mutations in adults and histone G34R/V alterations in pediatric populations. Loss of ATRX has been associated with global alterations in chromatin accessibility and epigenomics landscape, however, the detail mechanism behind the oncogenic transformation remains elusive. Integrating transcriptomics and in-depth positional epigenome analysis over repetitive DNA sequences in progenitor and tumors models of murine and human gliomas, we describe ATRX-deficient gliomas is fundamentally a disease of altered Transposable Elements (TE’s) and regulates neuronal differentiation and cell motility in gliomas, as validated pharmacologically and genetically. Epigenome assessment reported de-repression of LINE-1 (Long interspersed nuclear elements-1), specifically at Lamina-Associated Domains (LADs) with gain of enhancer histone marks, with association in chromatin loops/topology in ATRX-deficient glioma cells. Moreover, our single cell-RNA seq analysis focusing on TE’s and molecular docking studies in human glioma stem cells demonstrated LINE-1 regulates oncogenic alternative splicing events and neuro-developmental signatures. Expanding the analysis, we identified a subset of evolutionary young regulatory TE’s to play critical role in ATRX-deficient gliomas involved in neuronal differentiation phenotype. To summarize, our cross-species analysis establishes tangible links between ATRX deficiency and multiscale dysregulated 3D-epigenomic architecture that hijack regulates onco-exaptation programs in gliomas. We further discover that enhancer-like TE’s fine-tune the transcriptional program with important clinical implications, that could help in developing treatment options in malignant gliomas.

Study of Molecular Markers in Glioma and Their Association with Clinicopathological Features.

Central nervous system tumors are a major cause of morbidity and mortality worldwide. The most prevalent type of primary brain tumor is glioma. The exploration of significant genetic, epigenetic, and transcriptional abnormalities has not only improved our understanding of glioma pathogenesis but has also revealed that these molecular alterations can serve as useful diagnostic markers for more precise classification and are linked to better treatment response and prognosis. Hence, incorporating molecular markers into routine tumor classification is a major priority in modern glioma diagnostics. The aim is to assess the mutation status of isocitrate dehydrogenase (IDH)-1, alpha-thalassemia/mental retardation syndrome X-linked (ATRX), and tumor protein 53 in glioma, and look for their association with various clinicopathological features. A single-center prospective cohort study, where all biopsies of glioma (January 2019 to July 2020) were evaluated, and immunohistochemistry was performed to assess the expression of IDH-1, ATRX, p53, and Ki-67 index. The data were analyzed using IBM SPSS-24 software. Immunohistochemistry was performed in 123 consecutive cases of glioma. IDH-1 mutation was noted in 54 (43.9%) cases and these patients frequently presented with "seizures" (P = 0.006). The expression was maximum in World Health Organization (WHO) grade 2 tumors (65.4%) (P < 0.001), with the highest frequency in oligodendrogliomas (100% in WHO grade 2 and 3). Furthermore, these tumors showed lower proliferative indices (P = 0.001). ATRX mutation was noted in 59 (48%) and p53 overexpression was noted in 76 (61.8%) cases. These mutations were significantly associated with astrocytic phenotype (P = 0.03). Molecular characterization of glioma is an important step in modern glioma diagnostics and immunohistochemistry can play an important role. IDH-1 mutation is commonly observed in adults, frontal lobe location, patients presenting with seizures, and WHO grade 2 tumors with the highest frequencies in oligodendrogliomas. ATRX and p53 can be used as surrogate markers for tumors of astrocytic lineage.

Multi-pool chemical exchange saturation transfer MRI in glioma grading, molecular subtyping and evaluating tumor proliferation.

To evaluate the performance of multi-pool Chemical exchange saturation transfer (CEST) MRI in prediction of glioma grade, isocitrate dehydrogenase (IDH) mutation, alpha-thalassemia/mental retardation syndrome X-linked (ATRX) loss and Ki-67 labeling index (LI), based on the fifth edition of the World Health Organization classification of central nervous system tumors (WHO CNS5). 95 patients with adult-type diffuse gliomas were analyzed. The amide, direct water saturation (DS), nuclear Overhauser enhancement (NOE), semi-solid magnetization transfer (MT) and amine signals were derived using Lorentzian fitting, and asymmetry-based amide proton transfer-weighted (APTwasym) signal was calculated. The mean value of tumor region was measured and intergroup differences were estimated using student-t test. The receiver operating curve (ROC) and area under the curve (AUC) analysis were used to evaluate the diagnostic performance of signals and their combinations. Spearman correlation analysis was performed to evaluate tumor proliferation. The amide and DS signals were significantly higher in high-grade gliomas compared to low-grade gliomas, as well as in IDH-wildtype gliomas compared to IDH-mutant gliomas (all p < 0.001). The DS, MT and amine signals showed significantly differences between ATRX loss and retention in grade 2/3 IDH-mutant gliomas (all p < 0.05). The combination of signals showed the highest AUC in prediction of grade (0.857), IDH mutation (0.814) and ATRX loss (0.769). Additionally, the amide and DS signals were positively correlated with Ki-67 LI (both p < 0.001). Multi-pool CEST MRI demonstrated good potential to predict glioma grade, IDH mutation, ATRX loss and Ki-67 LI.

Pathological Evaluation of Diffuse Gliomas Using IDH1 and ATRX in a Resource-Limited Setting.

Classification of gliomas based on tumor histology remains the gold standard in the diagnosis and prognosis of gliomas. However, the recent World Health Organization (WHO) classificationhas included molecular studies for diagnosis and prognostication. Immunohistochemical markers such as isocitrate dehydrogenase 1 (IDH1) and alpha thalassemia/mental retardation syndrome X-linked (ATRX)can be used for the diagnosis andprognosis of the majority of gliomas. We aim to study the frequencies of IDH1 and ATRX mutations in diffuse gliomas using surrogate immunohistochemical markers and correlate histopathological findings of gliomas with immunohistochemical findings. This was a retrospective study of one-year duration from January 2022 to December 2022, conducted in the department of pathology. Relevant data was retrieved from medical records. Histopathology blocks were collected and sent for immunohistochemical studies using tissue microarray for IDH1 and ATRX. Qualitative data were expressed in percentages and proportions. The difference in proportion was calculated using the chi-square test, and a p-value of <0.005 was taken as significant. A total of 51 cases of diffuse gliomas were included in the study. The frequency of IDH1-positive diffuse astrocytomas was 33 (64.7%), and loss of ATRX was seen in 12 (23.5%) cases. Immunohistochemistry serves as a surrogate marker to detect molecular alterations in diffuse gliomas.

Remodeling of perturbed chromatin can initiate de novo transcriptional and post-transcriptional silencing

In eukaryotes, repetitive DNA can become silenced de novo, either transcriptionally or post-transcriptionally, by processes independent of strong sequence-specific cues. The mechanistic nature of such processes remains poorly understood. We found that in the fungus Neurospora crassa, de novo initiation of both transcriptional and post-transcriptional silencing was linked to perturbed chromatin, which was produced experimentally by the aberrant activity of transcription factors at the tetO operator array. Transcriptional silencing was mediated by canonical constitutive heterochromatin. On the other hand, post-transcriptional silencing resembled repeat-induced quelling but occurred normally when homologous recombination was inactivated. All silencing of the tetO array was dependent on SAD-6, fungal ortholog of the SWI/SNF chromatin remodeler ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-Linked), which was required to maintain nucleosome occupancy at the perturbed locus. In addition, we found that two other types of sequences (the lacO array and native AT-rich DNA) could also undergo recombination-independent quelling associated with perturbed chromatin. These results suggested a model in which the de novo initiation of transcriptional and post-transcriptional silencing is coupled to the remodeling of perturbed chromatin.

Latest Developments in Magnetic Resonance Imaging for Evaluating the Molecular Microenvironment of Gliomas.

The 2021 World Health Organization (WHO) Classification of Tumors of the Central Nervous System has brought a transformative shift in the categorization of adult gliomas. Departing from traditional histological subtypes, the new classification system is guided by molecular genotypes, particularly the Isocitrate Dehydrogenase (IDH) mutation. This alteration reflects a pivotal change in understanding tumor behavior, emphasizing the importance of molecular profiles over morphological characteristics. Gliomas are now categorized into IDH-mutant and IDH wildtype, with significant prognostic implications. For IDH-mutant gliomas, the concurrent presence of Alpha-Thalassemia/mental retardation syndrome X-linked (ATRX) gene expression and co-deletion of 1p19q genes further refine classification. In the absence of 1p19q co-deletion, further categorization depends on the phenotypic expression of CDKN2A/B. Notably, IDH wildtype gliomas exhibit a poorer prognosis, particularly when associated with TERT promoter mutations, EGFR amplification, and +7/-10 co-deletion. Although not part of the new guidelines, the methylation status of the MGMT gene is crucial for guiding alkylating agent treatment. The integration of structural and functional Magnetic Resonance Imaging (MRI) techniques may play a vital role in evaluating these genetic phenotypes, offering insights into tumor microenvironment changes. This multimodal approach may enhance diagnostic precision, aid in treatment planning, and facilitate effective prognosis evaluation of glioma patients.

Image Omics Nomogram Based on Incoherent Motion Diffusion-Weighted Imaging in Voxels Predicts ATRX Gene Mutation Status of Brain Glioma Patients.

This study aimed to construct an imaging genomics nomogram based on intravoxel incoherent motion diffusion-weighted imaging (IVIM-DWI) to predict the status of the alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene in patients with brain gliomas. We retrospectively analyzed routine MR and IVIM-DWI data from 85 patients with pathologically confirmed brain gliomas from January 2017 to May 2023. The data were divided into a training set (N=61) and a test set (N=24) in a 7:3 ratio. Regions of interest (ROIs) of brain gliomas, including the solid tumor region (rCET), edema region (rE), and necrotic region (rNec), were delineated using 3D-Slicer software and projected onto the D, D*, and f sequences. A total of 1037 features were extracted from each ROI, resulting in 3111 features per patient. Age was incorporated in the calculation of the Radscore, and a clinical-imaging genomics combined model was constructed, from which a nomogram graph was generated. Separate models were built for the D, D*, and f parameters. The AUC value of the D parameter model was 0.97 (95% CI: 0.93-1.00) in the training set and 0.91 (95% CI: 0.79-1.00) in the validation set, which was significantly higher than that of the D* parameter model (0.90, 0.82) and the f parameter model (0.89, 0.91). The imaging genomics nomogram based on IVIM-DWI can effectively predict the ATRX gene status of patients with brain gliomas, with the D parameter showing the highest efficacy.

Glioblastomas with and without peritumoral fluid-attenuated inversion recovery (FLAIR) hyperintensity present morphological and microstructural differences on conventional MR images.

Glioblastoma (GB) without peritumoral fluid-attenuated inversion recovery (FLAIR) hyperintensity is atypical and its characteristics are barely known. The aim of this study was to explore the differences in pathological and MRI-based intrinsic features (including morphologic and first-order features) between GBs with peritumoral FLAIR hyperintensity (PFH-bearing GBs) and GBs without peritumoral FLAIR hyperintensity (PFH-free GBs). In total, 155 patients with pathologically diagnosed GBs were retrospectively collected, which included 110 PFH-bearing GBs and 45 PFH-free GBs. The pathological and imaging data were collected. The Visually AcceSAble Rembrandt Images (VASARI) features were carefully evaluated. The first-order radiomics features from the tumor region were extracted from FLAIR, apparent diffusion coefficient (ADC), and T1CE (T1-contrast enhanced) images. All parameters were compared between the two groups of GBs. The pathological data showed more alpha thalassemia/mental retardation syndrome X-linked (ATRX)-loss in PFH-free GBs compared to PFH-bearing ones (p < 0.001). Based on VASARI evaluation, PFH-free GBs had larger intra-tumoral enhancing proportion and smaller necrotic proportion (both, p < 0.001), more common non-enhancing tumor (p < 0.001), mild/minimal enhancement (p = 0.003), expansive T1/FLAIR ratio (p < 0.001) and solid enhancement (p = 0.009), and less pial invasion (p = 0.010). Moreover, multiple ADC- and T1CE-based first-order radiomics features demonstrated differences, especially the lower intensity heterogeneity in PFH-free GBs (for all, adjusted p < 0.05). Compared to PFH-bearing GBs, PFH-free ones demonstrated less immature neovascularization and lower intra-tumoral heterogeneity, which would be helpful in clinical treatment stratification. Glioblastomas without peritumoral FLAIR hyperintensity show less immature neovascularization and lower heterogeneity leading to potential higher treatment benefits due to less drug resistance and treatment failure. • The study explored the differences between glioblastomas with and without peritumoral FLAIR hyperintensity. • Glioblastomas without peritumoral FLAIR hyperintensity showed less necrosis and contrast enhancement and lower intensity heterogeneity. • Glioblastomas without peritumoral FLAIR hyperintensity had less immature neovascularization and lower tumor heterogeneity.

Multimodal-based machine learning strategy for accurate and non-invasive prediction of intramedullary glioma grade and mutation status of molecular markers: a retrospective study

BackgroundDetermining the grade and molecular marker status of intramedullary gliomas is important for assessing treatment outcomes and prognosis. Invasive biopsy for pathology usually carries a high risk of tissue damage, especially to the spinal cord, and there are currently no non-invasive strategies to identify the pathological type of intramedullary gliomas. Therefore, this study aimed to develop a non-invasive machine learning model to assist doctors in identifying the intramedullary glioma grade and mutation status of molecular markers. MethodsA total of 461 patients from two institutions were included, and their sagittal (SAG) and transverse (TRA) T2-weighted magnetic resonance imaging scans and clinical data were acquired preoperatively. We employed a transformer-based deep learning model to automatically segment lesions in the SAG and TRA phases and extract their radiomics features. Different feature representations were fed into the proposed neural networks and compared with those of other mainstream models. ResultsThe dice similarity coefficients of the Swin transformer in the SAG and TRA phases were 0.8697 and 0.8738, respectively. The results demonstrated that the best performance was obtained in our proposed neural networks based on multimodal fusion (SAG-TRA-clinical) features. In the external validation cohort, the areas under the receiver operating characteristic curve for graded (WHO I–II or WHO III–IV), alpha thalassemia/mental retardation syndrome X-linked (ATRX) status, and tumor protein p53 (P53) status prediction tasks were 0.8431, 0.7622, and 0.7954, respectively.ConclusionsThis study reports a novel machine learning strategy that, for the first time, is based on multimodal features to predict the ATRX and P53 mutation status and grades of intramedullary gliomas. The generalized application of these models could non-invasively provide more tumor-specific pathological information for determining the treatment and prognosis of intramedullary gliomas.

Novel genetically engineered H3.3G34R model reveals cooperation with ATRX loss in upregulation of Hoxa cluster genes and promotion of neuronal lineage.

Pediatric high-grade gliomas (pHGGs) are aggressive pediatric CNS tumors and an important subset are characterized by mutations in H3F3A, the gene that encodes Histone H3.3 (H3.3). Substitution of Glycine at position 34 of H3.3 with either Arginine or Valine (H3.3G34R/V), was recently described and characterized in a large cohort of pHGG samples as occurring in 5-20% of pHGGs. Attempts to study the mechanism of H3.3G34R have proven difficult due to the lack of knowledge regarding the cell-of-origin and the requirement for co-occurring mutations for model development. We sought to develop a biologically relevant animal model of pHGG to probe the downstream effects of the H3.3G34R mutation in the context of vital co-occurring mutations. We developed a genetically engineered mouse model (GEMM) that incorporates PDGF-A activation, TP53 loss and the H3.3G34R mutation both in the presence and loss of Alpha thalassemia/mental retardation syndrome X-linked (ATRX), which is commonly mutated in H3.3G34 mutant pHGGs. We demonstrated that ATRX loss significantly increases tumor latency in the absence of H3.3G34R and inhibits ependymal differentiation in the presence of H3.3G34R. Transcriptomic analysis revealed that ATRX loss in the context of H3.3G34R upregulates Hoxa cluster genes. We also found that the H3.3G34R overexpression leads to enrichment of neuronal markers but only in the context of ATRX loss. This study proposes a mechanism in which ATRX loss is the major contributor to many key transcriptomic changes in H3.3G34R pHGGs. GSE197988.

EPCO-23. DYSFUNCTION OF LARGE H3K9ME3 DOMAINS IN ATRX DEFICIENT GLIOMAS INDUCES GENETIC REARRANGEMENTS AND LATENT DEVELOPMENTAL SIGNALING NETWORKS THROUGH SUPER-ENHANCER LANDSCAPES

Abstract Somatic alterations in ATRX (Alpha Thalassemia/Mental Retardation Syndrome X-linked), a member of SWI/SNF family chromatin regulator has been found to be frequently mutated in diffuse gliomas and defines molecular subtypes with aggressive behavior. Mechanistically, ATRX regulates incorporation of histone H3.3 into chromatin sites across the genome, maintains alternative lengthening of telomeres and establishes genomic distribution of polycomb responsive genes. To understand in depth role of ATRX in gliomas, we performed ChIP-seq and/or Cut-and-tag for histone marks that define active transcription, enhancers, repressors, gene bodies and CTCF on Atrx intact and deficient mNPCs (mouse Neural Progenitor Cells). Our integrated analysis reports depletion of H3K9me3 loci’s that coincidently enriched with Atrx binding sites and Lamina-Associated Domains with genes enriched for cell cycle, motility and chromosome organization. This chromatin perturbations at heterochromatin domains was further confirmed in our Hi-C analysis with switching of A-B and B-A compartments, reorganization of TADs with occasional CTCF marks and gain of novel interacting loops that showed gene expression leakage required for gliomagenesis using Capture Hi-C. Notably, we observed aberrant levels of endogenous retroviral elements (ERVs) family members, including upregulation of Line-1 elements in mNPCs and patient derived glioma stem cells (GSCs) and our analysis shows increased copy number variations in ATRX deficient gliomas as a consequence of Line-1 activation in these subsets of tumors. Finally, our integrated omics- analysis demonstrates enrichment of super-enhancers in Atrx deficient background with several putative druggable candidates for clinical benefits. As an example, we show presence of H3K27ac super-enhancer over HOXA locus and targeting pan-HOXA genes using small inhibitor peptides diminished proliferation and migration of mNPCs and GSCs with increased in cell apoptosis with alterations in downstream developmental signaling pathways. To summarize,our data establishes tangible links between Atrx deficiency and multiscale dysregulated cellular phenotype in gliomas with identifying novel targets for therapy.

ATRX modulates the escape from a telomere crisis.

Telomerase activity is the principal telomere maintenance mechanism in human cancers, however 15% of cancers utilise a recombination-based mechanism referred to as alternative lengthening of telomeres (ALT) that leads to long and heterogenous telomere length distributions. Loss-of-function mutations in the Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) gene are frequently found in ALT cancers. Here, we demonstrate that the loss of ATRX, coupled with telomere dysfunction during crisis, is sufficient to initiate activation of the ALT pathway and that it confers replicative immortality in human fibroblasts. Additionally, loss of ATRX combined with a telomere-driven crisis in HCT116 epithelial cancer cells led to the initiation of an ALT-like pathway. In these cells, a rapid and precise telomeric elongation and the induction of C-circles was observed; however, this process was transient and the telomeres ultimately continued to erode such that the cells either died or the escape from crisis was associated with telomerase activation. In both of these instances, telomere sequencing revealed that all alleles, irrespective of whether they were elongated, were enriched in variant repeat types, that appeared to be cell-line specific. Thus, our data show that the loss of ATRX combined with telomere dysfunction during crisis induces the ALT pathway in fibroblasts and enables a transient activation of ALT in epithelial cells.

The chromatin remodeling protein ATRX positively regulates IRF3-dependent type I interferon production and interferon-induced gene expression.

The chromatin remodeling protein alpha thalassemia/mental retardation syndrome X-linked (ATRX) is a component of promyelocytic leukemia nuclear bodies (PML-NBs) and thereby mediates intrinsic immunity against several viruses including human cytomegalovirus (HCMV). As a consequence, viruses have evolved different mechanisms to antagonize ATRX, such as displacement from PML-NBs or degradation. Here, we show that depletion of ATRX results in an overall impaired antiviral state by decreasing transcription and subsequent secretion of type I IFNs, which is followed by reduced expression of interferon-stimulated genes (ISGs). ATRX interacts with the transcription factor interferon regulatory factor 3 (IRF3) and associates with the IFN-β promoter to facilitate transcription. Furthermore, whole transcriptome sequencing revealed that ATRX is required for efficient IFN-induced expression of a distinct set of ISGs. Mechanistically, we found that ATRX positively modulates chromatin accessibility specifically upon IFN signaling, thereby affecting promoter regions with recognition motifs for AP-1 family transcription factors. In summary, our study uncovers a novel co-activating function of the chromatin remodeling factor ATRX in innate immunity that regulates chromatin accessibility and subsequent transcription of interferons and ISGs. Consequently, ATRX antagonization by viral proteins and ATRX mutations in tumors represent important strategies to broadly compromise both intrinsic and innate immune responses.

Diagnostic algorithm for pathological evaluation of gliomas in a resource-constrained setting.

Gliomas are the most common primary intracranial tumors. The current World Health Organization (WHO) classification of central nervous system tumors recommends integrated histo-molecular diagnosis of gliomas. However, molecular testing is not available in even most of the advanced centers of our country, and histopathology aided with immunohistochemistry (IHC) is still widely used for diagnosis. Immunohistochemical markers such as iso-citrate dehydrogenase1 (IDH1) and Alpha Thalassemia/Mental Retardation Syndrome X-linked (ATRX) can be reliably used for the correct diagnosis, prognosis, and treatment of gliomas. We aimed to develop a diagnostic algorithm by integrating morphology, IDH1, and ATRX status of gliomas seen in our institute for 1 year. Analytical cross-sectional study. This study included 60 histopathologically confirmed cases of astrocytic (n = 51) and oligodendroglial tumors (n = 9). Clinical, radiological, and histopathological features were noted and tumor grades assigned according to the WHO recommendations. IDH1 and ATRX mutation status was evaluated using IHC. The tumors were divided into three molecular groups on the basis of their IDH1 and ATRX mutation status: (1) Group 1: IDH1 negative and ATRX positive, (2) Group 2: IDH1 positive and ATRX positive, (3) Group 3: IDH1 positive and ATRX negative. The mean age of presentation was 45.0 ± 15.8 years with a male-to-female ratio of 2:1. Seizures, headache, and hemiparesis were the most common modes of presentation. The tumor subtypes studied were glioblastoma (n = 32), anaplastic astrocytoma (n = 7), diffuse astrocytoma (n = 6), oligodendroglioma (n = 6), pilocytic astrocytoma (n = 6), and anaplastic oligodendroglioma (n = 3). IDH1 mutation was present in 26 cases including anaplastic astrocytoma (n = 7), diffuse astrocytoma (n = 6), oligodendroglioma (n = 5), secondary glioblastoma (n = 5), and anaplastic oligodendroglioma (n = 3). ATRX mutation, i. e., loss of ATRX was observed in 17 cases including diffuse astrocytoma (n = 5), anaplastic astocytoma (n = 5), anaplastic oligodendroglioma (n = 3), oligodendroglioma (n = 3), and secondary glioblastoma (n = 1). All six cases of pilocytic astrocytoma were negative for IDH1 and ATRX mutation. There were 34 patients in Group 1 (IDH1- and ATRX +), nine cases in Group 2 (IDH1 + and ATRX +), and 17 patients in Group 3 (IDH1 + and ATRX-). Diagnosis of gliomas should be based on a detailed clinicoradiological and histopathological assessment, followed by genotypic characterization. Evaluation for IDH1and ATRX status has both diagnostic and prognostic value as it helps in differentiating gliomas from reactive gliosis, primary glioblastoma from secondary glioblastoma, and pilocytic astrocytoma (WHO grade I) from diffuse astrocytoma (WHO grade II). Tumors with IDH1 mutations have a better outcome than those with wild-type IDH. IHC can serve as a useful surrogate to conventional molecular tests in resource-constrained settings. By devising an algorithm based on morphological and IHC features, we were able to stratify gliomas into three prognostic subgroups.

5-Aminolevulinic Acid (5-ALA)-Induced Protoporphyrin IX Fluorescence by Glioma Cells-A Fluorescence Microscopy Clinical Study.

Simple Summary5-aminolevulinic acid (5-ALA)-induced PpIX fluorescence is used in neurosurgery for intraoperative identification of high-grade glioma tissue. In this paper, using a fluorescence microscopy analysis on human tumor specimens, we assessed the actual number of fluorescence-positive tumor cells both in low-grade and high-grade glioma, and the ability of 5-ALA to cross the blood–brain barrier (BBB). We found that in high-grade gliomas, 32.7–75.5 percent of cells display 5-ALA induced PpIX fluorescence, whereas in low-grade gliomas the tumor cells did not fluoresce following 5-ALA. Immunofluorescence for BBB components suggested that 5-ALA does not cross the un-breached BBB. These findings are of crucial importance in planning neurosurgical resection of gliomas.5-aminolevulinic acid (5-ALA)-induced PpIX fluorescence is used by neurosurgeons to identify the tumor cells of high-grade gliomas during operation. However, the issue of whether 5-ALA-induced PpIX fluorescence consistently stains all the tumor cells is still debated. Here, we assessed the cytoplasmatic signal of 5-ALA by fluorescence microscopy in a series of human gliomas. As tumor markers, we used antibodies against collapsin response-mediated protein 5 (CRMP5), alpha thalassemia/mental retardation syndrome X-linked (ATRX), and anti-isocitrate dehydrogenase 1 (IDH1). In grade III–IV gliomas, the signal induced by 5-ALA was detected in 32.7–75.5 percent of CRMP5-expressing tumor cells. In low-grade gliomas (WHO grade II), the CRMP5-expressing tumor cells did not fluoresce following 5-ALA. Immunofluorescence with antibodies that stain various components of the blood–brain barrier (BBB) suggested that 5-ALA does not cross the un-breached BBB, in spite of its small dimension. To conclude, 5-ALA-induced PpIX fluorescence has an established role in high-grade glioma surgery, but it has limited usefulness in surgery for low-grade glioma, especially when the BBB is preserved.

Monocentric evaluation of Ki-67 labeling index in combination with a modified RPA score as a prognostic factor for survival in IDH-wildtype glioblastoma patients treated with radiochemotherapy

PurposeThe prognosis for glioblastoma patients remains dismal despite intensive research on better treatment options. Molecular and immunohistochemical markers are increasingly being investigated as understanding of their role in disease progression grows. O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation has been shown to have prognostic and therapeutic relevance for glioblastoma patients. Other markers implicated in tumor formation and/or malignancy are p53, Alpha thalassemia/mental retardation syndrome X-linked (ATRX), Epidermal Growth Factor Receptor splice variant III (EGFRvIII), and Ki-67, with loss of nuclear ATRX expression and lower Ki-67 index being associated with prolonged survival. For p53 and EGFRvIII the data are contradictory. Our aim was to investigate the markers mentioned above regarding progression-free (PFS) and overall survival (OS) to evaluate their viability as independent prognostic markers for our patient collective.MethodsIn this retrospective study, we collected data on patients undergoing radiotherapy due to isocitrate dehydrogenase (IDH) wildtype glioblastoma at a single university hospital between 2014 and 2020.ResultsOur findings confirm Ki-67 labeling index ≤ 20% as an independent prognostic factor for prolonged PFS as well as MGMT promoter methylation for both prolonged PFS and OS, in consideration of age and Eastern Cooperative Oncology Group (ECOG) status, chemotherapy treatment, and total radiation dose for PFS as well as additionally sex, resection status, and receipt of treatment for progression or recurrence for OS. Additionally, Ki-67 labeling index ≤ 20% showed a significant correlation with prolonged OS in univariate analysis. Modification of the recursive partitioning analysis (RPA) score to include Ki-67 labeling index resulted in a classification with the possible ability to distinguish long-term-survivors from patients with unfavorable prognosis.ConclusionMGMT promoter methylation and Ki-67 labeling index were independent predictors of survival in our collective. We see further studies pooling patient collectives to reach larger patient numbers concerning Ki-67 labeling index as being warranted.

The effect of preoperative prognostic nutritional index on outcome in glioblastoma multiforme patients

Background/Aim: Glioblastoma multiforme (GBM) is the most common primary malignant brain tumor subtype with a poor prognosis despite various treatments. Some prognostic markers on survival (such as age, Eastern Cooperative Oncology Group Performance Score (ECOG-PS), isocitrated hydrogenase (IDH) status, alpha thalassemia/mental retardation syndrome X-linked (ATRX) mutation status, possibility of extensive surgery) have been defined. Prognostic Nutritional Index (PNI) has been evaluated in various cancers (such as lung, esophagus, and pancreas), and patients with a low PNI score have been associated with a poor prognosis for overall survival (OS). Our study aimed to examine the effectiveness of molecular and demographic characteristics and preoperative PNI score that may affect OS in GBM patients. Methods: In this retrospective cohort study, GBM diagnosed patients who were 18 years old or older, were included in the study. We measured their pretreatment PNI score and performed multivariate Cox regression analyses of OS in GBM patients. Results: A total of 107 patients were included in the study. Median age was 58 (range, 32-83) years. 72 patients (67.3%) were male and 35 patients (32.7%) were female. The mean preoperative PNI level was calculated as 50.5. The median overall-survival (mOS) was 19.7 months and the median time to progression (mTTP) was 8.1 months. There was no statistically significant result on overall survival in the univariate analysis of patients with PNI>50.5 (P=0.121). In multivariate analysis, being 70 years or older (P=0.012), IDH-1 wild and ATRX mutant patients (P=0.016), IDH-1 mutant and ATRX wild patients (P=0.037), and TTP 12 months and older (P<0.001) were considered as independent risk factors on overall survival. Conclusions: In our study, the effect of preoperative PNI score on survival could not be demonstrated. Further studies are needed to elucidate the potential impact of PNI on outcomes in patients with GBM.

Radiomics-based prediction of multiple gene alteration incorporating mutual genetic information in glioblastoma and grade 4 astrocytoma, IDH-mutant

PurposeIn glioma, molecular alterations are closely associated with disease prognosis. This study aimed to develop a radiomics-based multiple gene prediction model incorporating mutual information of each genetic alteration in glioblastoma and grade 4 astrocytoma, IDH-mutant.MethodsFrom December 2014 through January 2020, we enrolled 418 patients with pathologically confirmed glioblastoma (based on the 2016 WHO classification). All selected patients had preoperative MRI and isocitrate dehydrogenase (IDH) mutation, O-6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, epidermal growth factor receptor amplification, and alpha-thalassemia/mental retardation syndrome X-linked (ATRX) loss status. Patients were randomly split into training and test sets (7:3 ratio). Enhancing tumor and peritumoral T2-hyperintensity were auto-segmented, and 660 radiomics features were extracted. We built binary relevance (BR) and ensemble classifier chain (ECC) models for multi-label classification and compared their performance. In the classifier chain, we calculated the mean absolute Shapley value of input features.ResultsThe micro-averaged area under the curves (AUCs) for the test set were 0.804 and 0.842 in BR and ECC models, respectively. IDH mutation status was predicted with the highest AUCs of 0.964 (BR) and 0.967 (ECC). The ECC model showed higher AUCs than the BR model for ATRX (0.822 vs. 0.775) and MGMT promoter methylation (0.761 vs. 0.653) predictions. The mean absolute Shapley values suggested that predicted outcomes from the prior classifiers were important for better subsequent predictions along the classifier chains.ConclusionWe built a radiomics-based multiple gene prediction chained model that incorporates mutual information of each genetic alteration in glioblastoma and grade 4 astrocytoma, IDH-mutant and performs better than a simple bundle of binary classifiers using prior classifiers’ prediction probability.

Abstract 458: Characterization of ATRX polyclonal, application of immunohistochemical analysis on astrocytoma and glioblastoma

Abstract Introduction: Alpha thalassemia/mental retardation syndrome X-linked (ATRX) plays a role in chromatin regulation and maintenance of telomeres. It regulates incorporation of histone H3.3 into telomeric chromatin. ATRX is also a major component of various essential cellular pathways such as DNA replication and repair, chromatin higher-order structure regulation, and gene transcriptional regulation. ATRX loss was observed in grades II/III astrocytomas, oligoastrocytomas, oligodendrogliomas, and glioblastomas. In grades II/III gliomas, most ATRX-loss cases had IDH1/2 mutations. Assessment of ATRX loss by IHC staining captures the majority of mutations, giving a reasonable sensitivity in neuropathology diagnostics. In this study, the specificity and sensitivity of ATRX were analyzed on multiple tissues focusing on Astrocytoma and Glioblastoma tissues. Materials and Methods: IHC staining has been performed by using formalin-fixed paraffin-embedded tissue with standard deparaffinization steps and a heat-induced retrieval method using a citrate buffer solution in a pressure cooker (Decloaking chamber). Antibody was incubated for 30 minutes, followed by HRP detection and DAB solution for visualization. Slides were stained using semi-automated staining system (intelliPATH). ATRX polyclonal antibody [Biocare Medical, California, USA] diluted in a carrier at an optimal concentration with standard protocol. Results: ATRX stained 44% of diffuse and anaplastic astrocytoma and 57% of glioblastoma. Also, cross-reactivity testing determined ATRX polyclonal may stain normal brain in some cases. A more comprehensive data evaluation shown below: Conclusions: ATRX polyclonal shows a potential advantage when diagnosing brain tumors (especially astrocytoma and glioblastomas) even if some cross reactivity can be observed. ATRX in conjunction with other brain marker antibodies can offer a better tool in diagnosing brain tumors. Diseased Tissue Specificity and SensitivityTissuePositive CasesTotal Cases% +Astrocytoma163644Glioblastoma4757Breast Cancer132748Colon Cancer84020Lung Cancer245246Prostate Cancer164238Normal Tissue Cross-ReactivityCerebrum51145Cerebellum2367 Citation Format: Jose Jonathan Diaz, Tatiana Scoggin, Jason Ramos. Characterization of ATRX polyclonal, application of immunohistochemical analysis on astrocytoma and glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 458.

Loss of ATRX confers DNA repair defects and PARP inhibitor sensitivity

Alpha Thalassemia/Mental Retardation Syndrome X-Linked (ATRX) is mutated frequently in gliomas and represents a potential target for cancer therapies. ATRX is known to function as a histone chaperone that helps incorporate histone variant, H3.3, into the genome. Studies have implicated ATRX in key DNA damage response (DDR) pathways but a distinct role in DNA repair has yet to be fully elucidated. To further investigate the function of ATRX in the DDR, we created isogenic wild-type (WT) and ATRX knockout (KO) model cell lines using CRISPR-based gene targeting. These studies revealed that loss of ATRX confers sensitivity to poly(ADP)-ribose polymerase (PARP) inhibitors, which was linked to an increase in replication stress, as detected by increased activation of the ataxia telangiectasia and Rad3-related (ATR) signaling axis. ATRX mutations frequently co-occur with mutations in isocitrate dehydrogenase-1 and -2 (IDH1/2), and the latter mutations also induce HR defects and PARP inhibitor sensitivity. We found that the magnitude of PARP inhibitor sensitivity was equal in the context of each mutation alone, although no further sensitization was observed in combination, suggesting an epistatic interaction. Finally, we observed enhanced synergistic tumor cell killing in ATRX KO cells with ATR and PARP inhibition, which is commonly seen in HR-defective cells. Taken together, these data reveal that ATRX may be used as a molecular marker for DDR defects and PARP inhibitor sensitivity, independent of IDH1/2 mutations. These data highlight the important role of common glioma-associated mutations in the regulation of DDR, and novel avenues for molecularly guided therapeutic intervention.