bluuebunny/crossref_metadata_2025_split huggingface dataset:
PATH-24. NOVEL MOLECULAR SUBTYPES IDENTIFIED IN INTRACRANIAL GERM CELL TUMORS SHOWED UNIQUE WHOLE-GENOME METHYLATION PROFILE
Authors: Li Bo , Qiu Xiaoguang 
Published: November 2024

Abstract

BACKGROUND
By integrating whole-genome sequencing (WGS) and RNA-seq data, we found that intracranial germ cell tumors (IGCTs) can be divided into three distinct molecular subtypes: immune-hot, MYC/E2F, and SHH, each characterized by a unique profile of genomic abnormalities. To further define these subtypes, we subsequently performed whole-genome bisulfate sequencing (WGBS) on IGCT tumors

METHODS
Within our prior discovery cohort (n=110), DNA from 84 samples was available for profiling methylation levels using Whole Genome Bisulfite Sequencing (WGBS). Fastq data was aligned to the human reference genome (hg19), with duplicates removed, and DNA methylation was extracted using bismark pipeline (ver0.24.0). After quality control, weight methylation level was calculated for each CpG island as the sum of methylated reads divided by coverage. To identify IGCTs molecular groups, we applied hierarchical consensus k-means clustering to the most variant methylated CpG island (n=1000) across 84 IGCTs tumor tissues. The methylation level of RNA-seq subtypes was visualized to further clarify the molecular subtypes of IGCTs

RESULTS
Unsupervised clustering revealed that IGCTs can be divided into three groups based on the CpG island methylation levels: hypomethylation group (n=32), moderate methylation group (n=27), and hyper methylation group (n=25). The hypomethylation and moderate methylation group are predominantly observed in germinoma (&gt;90%). In contrast, hypermethylation group comprises the majority of non-germinomatous germ cell tumors. Furthermore, these subgroups derived from methylation analysis are highly consistent with the molecular subtypes previously defined through gene transcription profile analysis. We observed that the majority of MYC/E2F subtype (24/33) belonged to the hypomethylation group, whereas the majority of immune-hot subtype (14/23) fell into the moderate methylation group. The SHH subtype was the most common within the hypermethylation group (18/26)

CONCLUSIONS
The three molecular IGCT subtypes showed unique methylation profile. These results indicate different mechanisms of tumorigenesis among the subtypes and pave the way for the clinical application of methylation-based subtyping.
PATH-31. COMPLETE TUMOR DISAPPEARANCE ON BRAIN MRI AFTER STANDARD CHEMORADIATION THERAPY FOR A MOLECULAR GLIOBLASTOMA
Authors: Ahn Jeffrey , Bow Hansen , Eapen Ann , Kong Xiao-Tang 
Published: November 2024

Abstract

INTRODUCTION
Glioblastoma (GBM) is the most aggressive brain tumor. The WHO CNS5 classification has newly incorporated three molecular criteria in diagnosing molecular GBM, including a concurrent gain of chromosome 7 and loss of chromosome 10 (+7/-10), TERT promoter mutation, or EGFR amplification. Despite new classification, the Stupp protocol remains the standard of care for all GBMs. However, it is unclear if the treatment response of the molecular GBM with low grade features is the same as the limited response of the traditional histopathological GBM.

CASE REPORT
A 74-year-old male presented in August of 2023 with new onset left-sided facial numbness. The numbness resolved spontaneously that day. Brain MRI was notable for a diffuse left frontal T2/Flair hyperintense lesion extending across the corpus callosum into the right frontal lobe without definite enhancement. Brain biopsy from 8 sites of the tumor demonstrated a subset of areas with mild hyper-cellularity, suggesting a low-density infiltrating glioma. However, TERT promoter mutation (-124C&gt;T), was detected along with wild-type IDH1, supporting molecular GBM. Studies also found unmethylated MGMT gene promotor. Brain MRIs after 3 and 6 months showed no tumor progression. The patient has remained asymptomatic apart from baseline mild forgetfulness. He was started on the 6-week standard concomitant temozolomide and radiation therapy. Follow-up brain MRI after the above treatment showed complete imaging resolution of the tumor.

DISCUSSION
It is very rare for complete imaging resolution of GBM on brain MRI after standard 6-week chemoradiation therapy. Our case suggests that molecular GBM with low-grade features on imagine and pathology might have a better response to the standard treatment than traditional histopathological GBM even though the molecular GBM patient has unfavorable prognostic factors such as unmethylated MGMT and older age (&gt;70 years old). Our experience emphasizes the heterogenous response of molecular GBM to the current standard treatment.
PATH-37. A NEW SUBTYPE OF DIFFUSE MIDLINE GLIOMA, H3 K27 AND BRAF/FGFR1 CO-ALTERED, EXHIBITS SPECIFIC BIOLOGICAL CHARACTERISTICS AND NEW THERAPEUTIC VULNERABILITIES
Authors: Auffret Lucie , Barry Clémentine , Ajlil Yassine , Tauziède-Espariat Arnault , Mayr Lisa , Simbozel Marie , Kergrohen Thomas , Puiseux Chloé , Riffaud Laurent , Blouin Pascale , Bertozzi Anne-Isabelle , Leblond Pierre , Blomgren Klas , Froelich Sébastien , Picca Alberto , Touat Mehdi , Sanson Marc , Beccaria Kevin , Blauwblomme Thomas , Dangouloff-Ros Volodia , Boddaert Nathalie , Gojo Johannes , Filbin Mariella , Varlet Pascale , Debily Marie-Anne , Grill Jacques , Castel David 
Published: November 2024

Abstract
Diffuse midline gliomas (DMG) H3 K27-altered are incurable grade 4 gliomas and represent a major challenge in neuro-oncology. This tumor type is classified in four subtypes by the 2021 edition of the WHO Classification of the Central Nervous System tumors. However, we recently identified a new subtype of DMG by assembling a retrospective cohort of 60 adult and pediatric DMG cases harboring BRAF or FGFR1 mutations in addition to the H3K27M mutation or EZHIP overexpression. Comprehensive clinical, histological, radiological, and genomic, analyses allowed to identify distinct genotype-phenotype characteristics. Contrary to other DMG, these tumors occur more frequently in the thalamus (27% vs. 70% for BRAFV600E or 58% for FGFR1MUT), and in adults in the case of FGFRMUT tumors. Importantly, these patients display a longer overall survival with a median above three years. Unsupervised analysis of DNA methylation profiles regrouped these MAPK-altered DMG in a methylation cluster distinct from other DMG H3K27, but also lower-grade midline tumors driven by FGFR1 or BRAF mutations Additionally, this new DMG subtype harbors atypical radiological and histopathological profiles with calcification and/or a solid tumor component both for BRAFV600E and FGFR1MUT cases that can suggest this differential diagnosis. Further analyses of the transcriptome of these tumors compared to canonical DMG H3K27-altered showed an expression signature of senescence with activation of a TP53/CDKN1A axis, together with a strong upregulation of the PI3K/AKT/MTOR pathway. Our current modelling of the drug response using patient-derived models of these specific DMG will permit to rapidly prioritize treatment strategies. Additionally, our clinical experience in treating these patients suggests a higher response to everolimus and imipridone ONC201 in this specific subtype. In conclusion, DMG H3 K27 and BRAF/FGFR1 co-altered, represent a new subtype of DMG with distinct specific characteristics compared to canonical DMG H3K27 and data accumulated strongly support their separate stratification in clinical trials and specific therapeutic managements.
PATH-39. AI-BASED IDENTIFICATION OF GLIOMA IDH MUTATIONAL STATUS FROM H&E-STAINED WHOLE SLIDE IMAGES
Authors: Innani Shubham , Baheti Bhakti , Nasrallah MacLean P , Bell W Robert , Bakas Spyridon 
Published: November 2024

Abstract

INTRODUCTION
Isocitrate-dehydrogenase (IDH) mutational status is diagnostically critical in adult gliomas, with prognostic and therapeutic implications. IDH status cannot be determined by sole histologic assessment and requires molecular testing. We hypothesize that AI-based analysis can accurately predict IDH mutational status in glioma, by retrieving sub-visual cues in H&E-stained digitized tissue sections.

MATERIALS AND METHODS
A retrospective discovery cohort of 1,534 cases (756/778 IDH-wildtype/IDH-mutant, including all available grades) from the TCGA-LGG/TCGA-GBM collections was used for model development with 10-fold cross-validation (CV). A replication cohort of 114 cases (82/32 IDH-wildtype/IDH-mutant) from the University of Pennsylvania Health System (UPHS) was used for independent hold-out evaluation. Each 20X magnification whole slide image (WSI) underwent comprehensive curation for elimination of artifactual content, followed by partitioning into 256x256 patches, and feature extraction using pre-trained i) ImageNet weights (baseline), and ii) self-supervised vision transformer (ViT). A weakly-supervised attention-based multiple-instance-learning framework distinguished cases as IDH-wildtype or IDH-mutant, while generating visually interpretable attention heatmaps.

RESULTS
Evaluation on discovery and replication cohorts with the ViT yield accuracy of 90.84% (AUCDiscovery=97.16%) and 93.94% (AUCReplication=97.36%), respectively, with high sensitivity (i.e., high confidence in correctly predicting IDH-wildtype glioma). Comparison of the ViT with the baseline model on the replication cohort indicates the ViT superiority by improvements of 8% and 9.5% in accuracy and AUC, respectively. Histologic assessment of heatmaps indicates IDH-wildtype tumors exhibiting distinct regions of significant pleomorphism and microvascular proliferation, while IDH-mutant tumors exhibit dense nodular cell concentrations, microcystic architecture, and gemistocytic cells.

CONCLUSION
Our accurate H&E-based computational determination of glioma IDH status, with interpretations aligned with human-identifiable features, can contribute to obviating the need for molecular analyses and enable expedited diagnosis even in community healthcare settings. This study robustly identifies morpho-IDH correlates and could enable expedited patient prognostic stratification.
PATH-42. METASTATIC ADENOID CYSTIC CARCINOMA OF BREAST WITH BRAIN METASTASES AND LEPTOMENINGEAL DISEASE
Authors: Farooq Shama , Correia Carlos Eduardo Silva 
Published: November 2024

Abstract

INTRODUCTION
Adenoid cystic carcinoma (ACC) of the breast rarely metastasizes to the brain and leptomeninges. ACC is a rare type of breast cancer, accounting for less than 0.1% of cases. It is usually triple negative, but has a good prognosis when it is confined to the breast. Lymph node involvement is uncommon, occurring in less than 2% of cases, and distant metastases to the brain are extremely rare. Leptomeningeal disease has not been reported yet. Case: In this case, we describe a 57-year-old woman diagnosed with triple-negative ACC of the right breast, which had spread to the axillary lymph nodes and distant metastases to the lung. The diagnosis was confirmed by biopsies of both metastatic sites. The patient received vinorelbine and cisplatin treatment for 11 cycles followed by right needle localized lumpectomy. While awaiting for the next steps in treatment she was admitted to the hospital for altered mental status, saddle anesthesia, and urinary incontinence. Neuraxis MRI revealed numerous hemorrhagic and non-hemorrhagic brain metastasis with diffuse leptomeningeal disease. Cerebrospinal fluid analysis confirmed leptomeningeal disease with positive cytology for atypical epithelioid malignant cells. The patient underwent whole brain radiation and focal radiation treatment to specific areas of leptomeningeal disease. Although she initially improved after the first month of radiation, her condition deteriorated rapidly, preventing the initiation of the next line of treatment with high-dose methotrexate or capecitabine.

DISCUSSION
Adenoid cystic carcinoma of the breast is exceedingly rare however with a very good overall prognosis. It is uncommon for ACC to spread to regional lymph nodes, and even rarer for distant metastasis. Brain metastasis is also infrequently reported. There are no documented cases of metastatic ACC with leptomeningeal disease, so there is no consensus on the best course of treatment.
PATH-46. DETECTION OF CDKN2A/B HOMOZYGOUS DELETION BY DNA METHYLATION AND DNA NEXT GENERATION SEQUENCING: A COMPARISON
Authors: Galbraith Kristyn , Dhasmana Neha , Schroff Chanel , McLennan Sam , Yang Yiying , Shen Guomiao , Snuderl Matija 
Published: November 2024

Abstract
CDKN2A/B homozygous deletion status is critical for grading of several central nervous system (CNS) tumors, including IDH mutant astrocytoma, pleomorphic xanthoastrocytoma, and meningioma. CDKN2A/B status can be assed using variety of methods, but the accuracy varies due to technical and analytical variables. Here we sought to compare sensitivity of CDKN2A/B homozygous deletion detection by NGS and DNA methylation array derived copy number analysis. We retrospectively analyzed 100 CNS tumors diagnosed at NYU Langone Health between 2020 and 2023. All tumors were profiled by whole genome DNA methylation profiling using the Illumina EPIC array. Copy numbers were analyzed using the ‘conumee’ R package and visual inspection. Next-generation sequencing (NGS) analysis was performed by NYU Langone Genome PACT, a 510(k) FDA cleared (K202304) matched tumor-normal 607 gene panel. Variant allele frequency of canonical driver mutations was used to molecularly estimate tumor cell content. Discrepant cases were assed using targeted qPCR. Our cohort of 100 CNS tumors included glioblastoma (N=75), IDH mutant astrocytoma (N=14), oligodendroglioma (N=4), pleomorphic xanthoastrocytoma (N=2), meningioma (N=1), infantile hemispheric glioma (N=1), central neurocytoma (N=1), diffuse midline glioma K27-altered (N=1), and anaplastic pilocytic astrocytoma (N=1). By DNA methylation, CDKN2A/B homozygous deletion was detected in 54 cases, hemizygous deletion was detected in 13 cases, and no deletion was detected in 33 cases. By NGS, CDKN2A/B homozygous deletion was detected in 31 cases, hemizygous deletion was detected in 28, and no deletion was detected in 41 cases. DNA methylation detected a homozygous deletion in 23 cases that were not detected by NGS. All cases of homozygous deletion detected by NGS were also detected by DNA methylation. DNA methylation derived copy number assessment is more sensitive for CDKN2A/B homozygous deletion than next generation sequencing.
PATH-47. AGE-, SEX-, AND GRADE-ASSOCIATED MOLECULAR DIFFERENCES IN A MULTI-INSTITUTIONAL COHORT OF CHOROID PLEXUS TUMORS
Authors: Williams Erik , Hickman Richard , Gultekin Sakir , Juratli Tareq 
Published: November 2024

Abstract

BACKGROUND
Choroid plexus tumors (CPT) are central nervous system tumors where prognosis has been correlated to histologic grade, with aggressive clinical behavior and reduced survival rate in higher grade cases. Here, we present a genomic survey of a large multi-institutional cohort of CPTs across all grades.

MATERIAL AND METHODS
Fifty-eight CPT samples were analyzed by comprehensive genomic profiling (CGP) by a hybrid capture-based DNA sequencing platform (FoundationOne®CDx). Pathology reports, histopathology reviews, and patient clinical data were assessed.

RESULTS
Our cohort included 11 choroid plexus papillomas (CPP; grade 1), 16 atypical CPP (grade 2), and 31 choroid plexus carcinomas (CPC; grade 3). Males were slightly more affected than females (31 vs. 27 cases). Median patient age at tissue sampling was 11 years (range: 1–72 years). Median age of patients with CPC was younger at 3 years compared CPP at 34 years (p &lt; 0.01). Genomic analyses identified three frequent, mutually exclusive mutations in TP53, TERTp, and DAXX. TP53 mutations (n = 15, 26%) were significantly more prevalent in CPC (n=14 CPC, p=0.0003), and were identified predominantly in children (n=12 CPC at &lt;20 years). By contrast, TERT promoter mutations (TERTp; n = 5, 8.6%) were identified exclusively in CPP (p=0.019), predominantly grade 2 (4 of 5 cases), and exclusively in adult patients, with a median age of 48 years. DAXX mutations (n=4, 6.9%) were more common in CPC (n=3). Other alterations included PTEN (n=4, all adults) and MYCN amplification (n=3, all children &lt;6 years), both exclusively in CPC. In 21 cases, including 9 out of the 11 Grade 1 CPP, no known cancer mutation was detected.

CONCLUSION
This study provides comprehensive genomic profiling of CPTs, highlighting distinct genetic alterations associated with different histological grades and patient demographics. These findings may inform future research and therapeutic strategies targeting specific molecular pathways in CPTs.
PATH-51. CENTRAL NERVOUS SYSTEM METASTASES ARE GENOMICALLY DIVERGENT FROM THEIR RESPECTIVE EXTRACRANIAL SITES
Authors: Huang David , Bergagnini Isabella , Hajiyeva Sabina , Akerman Meredith , Wong Tamika , Boockvar Randy D’Amico John , Vojnic Morana 
Published: November 2024

Abstract

INTRODUCTION
Next-generation sequencing (NGS) has become standard of care in establishing the diagnosis and guiding treatment of cancers. Our understanding of genomic evolution of brain metastases (BM) and leptomeningeal disease (LMD) from solid tumor malignancies remains limited. Here we present updated data from our pilot study.

METHODS
We prospectively collected clinical data and NGS of seventeen patients undergoing craniotomy for symptomatic BM from solid tumor malignancies or cerebrospinal fluid (CSF) sampling for LMD. Matched systemic and CNS analyses were performed using a research-based NGS assay. When extracranial disease tissue was unavailable, liquid NGS served as a surrogate.

RESULTS
CNS metastases were present at initial diagnosis in 10/17 and 11/17 patients had not received systemic therapy prior to CNS tissue sampling. The predominant cancer type was NSCLC (n=11), followed by breast cancer (n=3), ovarian high grade serous carcinoma (n=1), GEJ adenocarcinoma (n=1), and basosquamous carcinoma of skin (n=1). The mean tumor mutational burden in extracranial samples was 3.65 (SD 3.34; SEM 0.97), in contrast to CNS samples 21.63 (SD 26.47; SEM 7.64). Concordant mutations in matched sampling had an increase in CNS variant allele frequency (VAF) (27.8% vs 17.3%; arithmetic difference = 10.5, p=0.054) and CNS gene copy number alterations (CNA) (2.4 copies vs 0.8 copies; arithmetic difference = 1.6, p=0.171). Known driver alterations in EGFR, KRAS and PIK3CA were retained. LMD was present in 4/17 patients, with two present at enrollment and two developing during the study.

CONCLUSIONS
Matched sequencing reveals CNS metastases to harbor a significantly higher TMB, retention of primary driver alterations with a trend towards higher VAF and CNA of concordant mutations. While limited by small sample size, these data indicate genetic evolution in CNS metastases regardless of prior treatment status.
PATH-53. DNA MUTATION SEQUENCING AND METHYLATION ANALYSIS OF SOMATICNF1 MUTANT IDH-WILDTYPE GLIOBLASTOMA IDENTIFIES THREE EPIGENETIC GROUPS ANDCDKN2A/B LOSS AS A NEGATIVE PROGNOSTIC BIOMARKER
Authors: Mirchia Kanish , Pan Sixuan , Payne Emily , Liu John , Peeran Zain , Shukla Poojan , Young Jacob , Gupta Rohit , Wu Jasper , Pak Joanna , Seo Kyounghee , Ozawa Tomoko , Na Brian , Reddy Alyssa , Braunstein Steve , Phillips Joanna , Chang Susan , Solomon David , Perry Arie , Raleigh David , Berger Mitchel , Abate Adam , Vasudevan Harish 
Published: November 2024

Abstract
The tumor suppressor NF1 is frequently mutated in IDH-wildtype glioblastoma. However, the molecular subgroups and clinically relevant biomarkers within somatic NF1 mutant, IDH-wildtype glioblastomas remain incompletely understood. Here, we combine methylation arrays and targeted DNA sequencing to identify epigenetic subgroups and clinical biomarkers within non-syndromic NF1 mutant IDH-wildtype glioblastoma. We identified 186 patients treated at the University of California San Francisco between 2016-2024 with newly diagnosed IDH-wildtype glioblastoma containing a somatic pathogenic NF1 mutation on a CLIA certified targeted DNA sequencing assay. Illumina EPIC DNA methylation arrays (n=129 patients) were processed using the minfi package and Heidelberg random forest classifier (v12.8). Downstream analyses including hierarchical clustering and survival analyses were performed in R. DNA sequencing identified 12 recurrently altered genes in greater than 10% of cases across cell cycle regulators (CDKN2A/B, TP53, RB1), PI3K signaling (PTEN, PIK3R1, PIK3CA), epigenetic modifiers (ATRX, SETD2), and growth factor signaling (EGFR, PDGFRA, PTPN11). DNA methylation analysis revealed three epigenetic subgroups. Group 1 showed lower median patient age and significantly increased TP53 co-mutation rate. Group 2 contained a significantly higher proportion of male patients and was significantly enriched for RB1 and TERT promoter alterations, with a majority of tumors classified as GBM-MES using the Heidelberg classifier. Group 3 showed a significantly higher proportion of female patients and was significantly enriched for homozygous CDKN2A/B deletion. Homozygous CDKN2A/B loss was associated with significantly worse overall survival across the entire non-syndromic NF1 mutant glioblastoma cohort but not in a propensity score matched NF1 wildtype glioblastoma cohort. DNA methylation profiling revealed three epigenetic subgroups characterized by distinct clinical features, co-mutation patterns, and reference DKFZ methylation classifier identities. CDKN2A/B loss may be a negative prognostic biomarker specifically in NF1 mutant glioblastomas; future multi-institutional studies are required to validate these findings and their therapeutic implications in a larger, representative cohort.
PATH-54. HIGH-THROUGHPUT SINGLE NUCLEAR DNA SEQUENCING OF HUMAN SPORADICNF1 MUTANT IDH-WILDTYPE GLIOBLASTOMAS REVEALS PATTERNS OF TUMOR EVOLUTION AND RECURRENCE
Authors: Mirchia Kanish , Pan Sixuan , Payne Emily , Agoglia Rachel , Arribas-Layton Marc , Vasudevan Harish 
Published: November 2024

Abstract
The advent of single cell techniques has advanced our understanding of glioblastoma (GBM) evolution and cell lineage relationships. However, study of mutational co-occurrence and clonal phylogeny has been hampered by limitations in single cell genotyping. Here, we perform semi-automated, rapid single nuclear dissociation followed by targeted single nucleus DNA sequencing (snDNA-seq) of eleven retrospectively identified somatic NF1 mutant IDH-wildtype glioblastomas. Bulk DNA sequencing was performed as part of routine clinical care using a CLIA-certified targeted sequencing panel. For snDNA-seq, tissue cores with greater than 30% tumor were dissociated on a S2 genomics S100 Singulator followed by snDNA-seq using a targeted 361 amplicon panel (Tapestri, Mission Bio, USA) to sequence for recurrently observed single nucleotide substitutions and copy number alterations. A mean of 3,661 cells were recovered per sample with a mean of 96 reads per cell per amplicon and 87% mean panel uniformity. SnDNA-seq validated point mutations and copy number alterations observed in bulk DNA-sequencing and revealed novel alterations and subclonal copy number alterations not detected on bulk analysis. Within individual samples, snDNA-seq based phylogenetic reconstruction identified mutually exclusive patterns of mutation between NF1 and PI3K signaling alterations, suggesting these events may occur in distinct tumor subclones. With regard to copy number alterations (CNAs), snDNA-seq demonstrated intra-tumoral heterogeneity for chromosome 9p loss, chromosome 7 gain, and chromosome 10 monosomy. Subclonal CNA clones not detected by bulk sequencing were identified in 5 samples. Analysis of a matched primary-recurrent tumor pair revealed expansion of a specific mutational clone (loss of 9p, 10p, gains of 1p, 7, 15, and 19q) at recurrence. SnDNA-seq recapitulated bulk DNA sequencing alterations and identified distinct patterns of mutational co-occurrence, CNAs, and tumor evolution over time. Reconstructing GBM phylogeny at single cell resolution has potential translational implications for understanding tumor evolution and treatment resistance.