Dataset Information

Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas.

ABSTRACT: Genetic alterations help predict the clinical behavior of diffuse gliomas, but some variability remains uncorrelated. Here, we demonstrate that haploinsufficient deletions of chromatin-bound tumor suppressor NFKB inhibitor alpha (NFKBIA) display distinct patterns of occurrence in relation to other genetic markers and are disproportionately present at recurrence. NFKBIA haploinsufficiency is associated with unfavorable patient outcomes, independent of genetic and clinicopathologic predictors. NFKBIA deletions reshape the DNA and histone methylome antipodal to the IDH mutation and induce a transcriptome landscape partly reminiscent of H3K27M mutant pediatric gliomas. In IDH mutant gliomas, NFKBIA deletions are common in tumors with a clinical course similar to that of IDH wild-type tumors. An externally validated nomogram model for estimating individual patient survival in IDH mutant gliomas confirms that NFKBIA deletions predict comparatively brief survival. Thus, NFKBIA haploinsufficiency aligns with distinct epigenome changes, portends a poor prognosis, and should be incorporated into models predicting the disease fate of diffuse gliomas.

SUBMITTER: Bredel M

PROVIDER: S-EPMC10314122 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas.

Bredel Markus M Espinosa Lluís L Kim Hyunsoo H Scholtens Denise M DM McElroy Joseph P JP Rajbhandari Rajani R Meng Wei W Kollmeyer Thomas M TM Malta Tathiane M TM Quezada Michael A MA Harsh Griffith R GR Lobo-Jarne Teresa T Solé Laura L Merati Aran A Nagaraja Surya S Nair Sindhu S White Jaclyn J JJ Thudi Nanda K NK Fleming Jessica L JL Webb Amy A Natsume Atsushi A Ogawa Seishi S Weber Ruthild G RG Bertran Joan J Haque S Jaharul SJ Hentschel Bettina B Miller C Ryan CR Furnari Frank B FB Chan Timothy A TA Grosu Anca-Ligia AL Weller Michael M Barnholtz-Sloan Jill S JS Monje Michelle M Noushmehr Houtan H Jenkins Robert B RB Rogers C Leland CL MacDonald David R DR Pugh Stephanie L SL Chakravarti Arnab A

Cell reports. Medicine 20230601 6

Genetic alterations help predict the clinical behavior of diffuse gliomas, but some variability remains uncorrelated. Here, we demonstrate that haploinsufficient deletions of chromatin-bound tumor suppressor NFKB inhibitor alpha (NFKBIA) display distinct patterns of occurrence in relation to other genetic markers and are disproportionately present at recurrence. NFKBIA haploinsufficiency is associated with unfavorable patient outcomes, independent of genetic and clinicopathologic predictors. NFK ...[more]

PMID: 37343523

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Project description:BackgroundMutations in telomerase reverse transcriptase promoter (TERTp) and isocitrate dehydrogenase 1 and 2 (IDH) offer objective markers to assist in classifying diffuse gliomas into genetic subgroups. However, traditional mutation detection techniques lack sensitivity or have long turnaround times or high costs. We developed GliomaDx, an allele-specific, locked nucleic acid-based quantitative PCR assay to overcome these limitations and sensitively detect TERTp and IDH mutations.MethodsWe evaluated the performance of GliomaDx on cell line DNA and frozen tissue diffuse glioma samples with variable tumor percentage to mimic use in clinical settings and validated low percentage variants using sensitive techniques including droplet digital PCR (ddPCR) and next-generation sequencing. We also developed GliomaDx Nest, which incorporates a high-fidelity multiplex pre-amplification step prior to allele-specific PCR for low-input formalin-fixed paraffin embedded (FFPE) samples.ResultsGliomaDx detects the TERTp and IDH1 alterations at an analytical sensitivity of 0.1% mutant allele fraction, corresponding to 0.2% tumor cellularity. GliomaDx identified TERTp/IDH1 alterations in a cohort of frozen tissue samples with variable tumor percentage of all major diffuse glioma histologic types. GliomaDx Nest is able to detect these hotspot mutations with similar sensitivity from pre-amplified samples and was successfully tested on a cohort of clinical FFPE samples. Testing of a cohort of previously identified TERTpWT-IDHWT gliomas (by Sanger sequencing) revealed that 26.3% harbored low-percentage mutations. Analysis by ddPCR and whole exome sequencing of these tumors confirmed the low mutant fraction of these alterations and overall mutation-based tumor purity.ConclusionsOur results show that GliomaDx can rapidly detect TERTp/IDH mutations with high sensitivity, identifying cases that might be missed due to the lack of sensitivity of other techniques. This approach may facilitate more objective classification of diffuse glioma samples in clinical settings such as intraoperative diagnosis or in testing cases with low tumor purity.

Project description:BackgroundThe 2016 World Health Organization (WHO) classification of central nervous system tumors stratifies isocitrate dehydrogenase (IDH)-mutant gliomas into 2 major groups depending on the presence or absence of 1p/19q codeletion. However, the grading system remains unchanged and it is now controversial whether it can be still applied to this updated molecular classification.MethodsIn a large cohort of 911 high-grade IDH-mutant gliomas from the French national POLA network (including 428 IDH-mutant gliomas without 1p/19q codeletion and 483 anaplastic oligodendrogliomas, IDH-mutant and 1p/19q codeleted), we investigated the prognostic value of the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene homozygous deletion as well as WHO grading criteria (mitoses, microvascular proliferation, and necrosis). In addition, we searched for other retinoblastoma pathway gene alterations (CDK4 amplification and RB1 homozygous deletion) in a subset of patients. CDKN2A homozygous deletion was also searched in an independent series of 40 grade II IDH-mutant gliomas.ResultsCDKN2A homozygous deletion was associated with dismal outcome among IDH-mutant gliomas lacking 1p/19q codeletion (P < 0.0001 for progression-free survival and P = 0.004 for overall survival) as well as among anaplastic oligodendrogliomas, IDH-mutant + 1p/19q codeleted (P = 0.002 for progression-free survival and P < 0.0001 for overall survival) in univariate and multivariate analysis including age, extent of surgery, adjuvant treatment, microvascular proliferation, and necrosis. In both groups, the presence of microvascular proliferation and/or necrosis remained of prognostic value only in cases lacking CDKN2A homozygous deletion. CDKN2A homozygous deletion was not recorded in grade II gliomas.ConclusionsOur study pointed out the utmost relevance of CDKN2A homozygous deletion as an adverse prognostic factor in the 2 broad categories of IDH-mutant gliomas stratified on 1p/19q codeletion and suggests that the grading of these tumors should be refined.

Project description:ObjectiveTo explain adult-type diffuse gliomas heterogeneity through diffusion kurtosis imaging-based habitat characteristics and develop and validate a comprehensive model for predicting isocitrate dehydrogenase (IDH) status.Materials and methodsIn this prospective secondary analysis, 103 participants (mean age, 52 years; range, 21-77; 54 [52%] male) pathologically diagnosed with adult-type diffuse gliomas were enrolled between June 2018 and February 2022. The Otsu method was used to generate habitat maps with mean diffusivity (MD) and mean kurtosis (MK) for a total of 4 subhabitats containing 16 habitat features. Habitat heatmaps were created based on the Pearson correlation coefficient. The Habitat imAging aNd clinicraD INtegrated prEdiction SyStem (HANDINESS) was created by combining clinical features, conventional MRI morphological features, and habitat image features. ROC, calibration curve, and decision curve analyses were used to select the optimal model after 32 pipelines for model training and validation.ResultsIn the restricted diffusion and high-density subhabitat, MK was highly correlated with MD (R2 = 0.999), volume (0.608) and percentage of volume (0.663), and this region had the highest MK value (P<.001). The unrestricted diffusion and low-density subhabitat had the highest MD value (P<.001). When MK was less than the Otsu threshold, there was still a difference between restricted diffusion and low-density and unrestricted diffusion and low-density subhabitats (P<.01). The HANDINESS enabled more accurate prediction of the IDH status in the training (AUC=0.951 [0.902-0.987]) and internal validation cohorts (0.938 [0.881-0.949]). AUC values for single-modality models and independent factors ranged from 0.593 to 0.916. Calibration and decision curve analyses showed that the HANDINESS demonstrated a high level of clinical applicability and predictive consistency.ConclusionDiffusion kurtosis imaging-based habitat analysis provides additional important information on microscopic tumor spatial heterogeneity. The HANDINESS has higher diagnostic performance and robustness than single-modality models.

Dataset Information

Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas.

Publications

Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas.

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