EPCT-15. RAPID EPIGENOMIC CLASSIFICATION OF BRAIN TUMORS ENABLES INTRAOPERATIVE NEUROSURGICAL RISK MODULATION

Abstract Background Clear identification of tumor subtype is the main predictor of patient outcome and ultimately what is considered an adequate level of surgical risk. At brain tumor resection, imaging modalities and intraoperative histology often give an ambigious diagnosis, complicating intraoperative surgical decision-making. Here, we report a nanopore DNA methylation analysis (NDMA) sequencing approach combined with machine learning for classification of tumor entities that could be used intraoperatively. Methods We analyzed 50 biopsies obtained from biobanked tissue (43, prospective) or sampled at surgery (7, intraoperative) from 20 female and 30 male patients with a median age of 8 years. DNA was extracted using spin columns, quantified on a Qubit fluorometer and assessed for purity using NanoDrop spectrophotometer. DNA was then barcoded with the Rapid Barcoding kit from Oxford Nanopore technologies and loaded onto a MinION flow cell. Sequencing was performed for 3 hours (intraoperative) and 24 hours (prospective). Raw reads were basecalled using the Guppy algorithm, then fed into a snakemake workflow (nanoDx pipeline). This generated a report showing the copy number profile, genome-wide methylation status and subclassification of the tumor according to the Heidelberg reference cohort. Results Twelve different tumor classes were discovered within our cohort spanning from WHO Grade I to Grade IV. The results generated by NDMA were concordant with standard neuropathological diagnosis in 43 out of 50 cases (86%). Of the discordant cases, six were due to the biological complexity of the tumor and one case was misclassified by the pipeline. NDMA enabled correct subclassification of 6/7 intraop cases within a mean of 129 minutes. Conclusion NDMA can accurately subclassify tumor entities intraoperatively and guide surgical procedures when preoperative imaging and frozen section evaluation are unclear.

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BIOM-19. DECIPHERING THE METHYLATION SIGNATURE OF CIRCULATING EXTRACELLULAR VESICLE DNA FOR CNS TUMOR CLASSIFICATION

Neuro-Oncology ◽

10.1093/neuonc/noab196.050 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi14-vi14

Author(s):

Franz Ricklefs ◽

Tammo Ricklefs ◽

Cecile Maire ◽

Amanda Salviano da Silva ◽

Kathrin Wollman ◽

...

Keyword(s):

Empirical Bayes ◽

Methylation Status ◽

Extracellular Vesicle ◽

Tumor Detection ◽

Tumor Classification ◽

Tumor Patients ◽

Cns Tumor ◽

Genome Wide ◽

Tumor Entities ◽

Methylation Profiling

Abstract Genome-wide methylation profiling has recently been developed into a tool that allows subtype tumor classification in central nervous system (CNS) tumors. We previously showed that extracellular vesicle (EV) DNA faithfully reflects the tumor methylation class, including information on the IDH mutation and MGMT promoter methylation status. Furthermore we showed that circulating plasma EVs are elevated in CNS tumor patients in comparison to non-tumor donors (HD) controls with tumor related protein profiles. We now investigated, whether the methylation signatures of circulating DNA (both EV and cfNDA) can be used in liquid biopsy approaches for CNS tumor detection and classification. We isolated DNA from circulating EVs (n=27), cfDNA (n=27) and tumor tissue DNA (n=90) of patients with glioblastoma (GBM), meningioma (MGN) and cerebral metastases (CM). Patients undergoing epilepsy surgery as well as aneurysm clipping were used as non-tumor controls (HD, n= 7). EVs were classified by nanoparticle analysis, immunoblotting, imaging flow cytometry and electron microscopy. Isolated EV-DNA comprised many sorts of molecular weight (up tp >10Kb) in comparison to cfDNA (130-140bp). Healthy donors and tumor patients showed not differences in their DNA size profiles. We performed genome-wide methylation profiling by 850k Illumina EPIC arrays for all DNA analytes and tumor entities. Linear models and empirical Bayes methods identified significant differentially methylated CpGs (GBM vs. HD, MGN, vs HD, CM vs. HD), that revealed tumor specific signatures to detect and discriminate different CNS tumor entities. Visualization of differentially methylated CPGs by dimension reduction (PCA, t-SNE, Umap) verified tumor specific clusters. cfDNA and EV-DNA exhibited distinctive individual CpG profiles. Our study shows that the methylation signature of circulating EV DNA and cfDNA can be used to separate healthy individuals from tumor patients and could potentially complement standard-of-care imaging to improve tumor detection, classification and surveillance.

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SURG-08. SARCOPENIA IS A PROGNOSTIC FACTOR OF 90-DAY MORTALITY AND OVERALL SURVIVAL IN ELDERLY PATIENTS WITH GLIOBLASTOMA

Neuro-Oncology ◽

10.1093/neuonc/noab196.778 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi196-vi196

Author(s):

Ramin Morshed ◽

Jacob Young ◽

Megan Casey ◽

Elaina Wang ◽

Manish K Aghi ◽

...

Keyword(s):

Overall Survival ◽

Radiation Therapy ◽

Life Expectancy ◽

Adjuvant Therapy ◽

Elderly Patients ◽

Tumor Resection ◽

Preoperative Imaging ◽

Imaging Features ◽

Who Grade ◽

Treatment Data

Abstract Elderly patients with glioblastoma (GBM) have worse overall prognosis compared to younger patients and are less likely to undergo tumor resection and adjuvant therapy. The goal of this study was to identify patient and treatment factors as well as preoperative imaging features associated with worse overall survival and death within 3 months of surgery in elderly GBM patients. A single-center retrospective study was conducted with patients who met the following inclusion criteria: 1) age ≥ 79 at surgery (past the average age of life expectancy), 2) underwent biopsy or resection of an IDH-wildtype WHO Grade IV GBM at the time of initial diagnosis, and 3) had no prior radiation or chemotherapy. Patient, imaging, and treatment data were collected retrospectively from the electronic medical record. Univariate and multivariate Cox proportional hazard and logistic regression analyses were performed to identify factors associated with overall survival and 90-day mortality. The cohort consisted of 110 patients with a mean age of 82.8 (range 79 to 94.1) at surgery and a median preoperative KPS of 80. Thirty-seven (33.6%) and 73 (66.4%) patients underwent biopsy and resection, respectively. Adjuvant chemo- and/or radiation therapy were used in 72.5% of cases. On multivariate analysis, age (HR 1.13 by year, p=0.01), increased masseter thickness (HR 0.88 by mm, p=0.049), adjuvant therapy (HR 0.05, p< .0001), and surgical resection rather than biopsy (HR 0.38, p=0.0007) were associated with improved survival. Decreased masseter thickness was the only preoperative factor on analysis that predicted 90-day mortality in the cohort (p=0.038). GBM patients past the average age of life expectancy still fare better when undergoing resection followed by adjuvant chemotherapy and radiation therapy. In addition to treatment factors that predict survival, smaller masseter diameter on preoperative imaging, a marker of sarcopenia, is associated with shorter survival and death within 90 days of surgery.

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Preoperative Imaging of Glioblastoma Patients using Hyperpolarized 13C Pyruvate: Potential Role in Clinical Decision Making

Neuro-Oncology Advances ◽

10.1093/noajnl/vdab092 ◽

2021 ◽

Author(s):

Jun Chen ◽

Toral R Patel ◽

Marco C Pinho ◽

Changho Choi ◽

Crystal E Harrison ◽

...

Keyword(s):

Clinical Decision Making ◽

Surgical Navigation ◽

Tumor Resection ◽

Lactate Production ◽

Spectroscopic Imaging ◽

Preoperative Imaging ◽

Dual Frequency ◽

Who Grade ◽

Hyperpolarized 13C ◽

Mr Spectroscopic Imaging

Abstract Background Glioblastoma remains incurable despite treatment with surgery, radiation therapy, and cytotoxic chemotherapy, prompting the search for a metabolic pathway unique to glioblastoma cells. 13C MR spectroscopic imaging with hyperpolarized pyruvate can demonstrate alterations in pyruvate metabolism in these tumors. Methods Three patients with diagnostic MRI suggestive of a glioblastoma were scanned at 3T 1-2 days prior to tumor resection using a 13C/ 1H dual-frequency RF coil and a 13C/ 1H-integrated MR protocol, which consists of a series of 1H MR sequences (T2 FLAIR, arterial spin labeling and contrast-enhanced (CE) T1) and 13C spectroscopic imaging with hyperpolarized [1- 13C]pyruvate. Dynamic spiral chemical shift imaging was used for 13C data acquisition. Surgical navigation was used to correlate the locations of tissue samples submitted for histology with the changes seen on the diagnostic MR scans and the 13C spectroscopic images. Results Each tumor was histologically confirmed to be a WHO grade IV glioblastoma with isocitrate dehydrogenase wild type. Total hyperpolarized 13C signals detected near the tumor mass reflected altered tissue perfusion near the tumor. For each tumor, a hyperintense [1- 13C]lactate signal was detected both within CE and T2-FLAIR regions on the 1H diagnostic images (p = 0.008). [ 13C]Bicarbonate signal was maintained or decreased in the lesion but the observation was not significant (p = 0.3). Conclusions Prior to surgical resection, 13C MR spectroscopic imaging with hyperpolarized pyruvate reveals increased lactate production in regions of histologically confirmed glioblastoma.

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Transcavernous Approach for Gross Total Resection of a Dumbbell-Shaped Giant Trigeminal Schwannoma

Journal of Neurological Surgery Part B Skull Base ◽

10.1055/s-0041-1729995 ◽

2021 ◽

Author(s):

Sima Sayyahmelli ◽

Emel Avci ◽

Burak Ozaydin ◽

Mustafa K. Başkaya

Keyword(s):

Skull Base ◽

Cavernous Sinus ◽

Tumor Resection ◽

Mass Effect ◽

World Health ◽

Gross Total Resection ◽

Petrous Apex ◽

Total Resection ◽

Who Grade ◽

Trigeminal Schwannoma

AbstractTrigeminal schwannomas are rare nerve sheet tumors that represent the second most common intracranial site of occurrence after vestibular nerve origins. Microsurgical resection of giant dumbbell-shaped trigeminal schwannomas often requires complex skull base approaches. The extradural transcavernous approach is effective for the resection of these giant tumors involving the cavernous sinus.The patient is a 72-year-old man with headache, dizziness, imbalance, and cognitive decline. Neurological examination revealed left-sided sixth nerve palsy, a diminished corneal reflex, and wasting of temporalis muscle. Magnetic resonance imaging (MRI) showed a giant homogeneously enhancing dumbbell-shaped extra-axial mass centered within the left cavernous sinus, Meckel's cave, and the petrous apex, with extension to the cerebellopontine angle. There was a significant mass effect on the brain stem causing hydrocephalus. Computed tomography (CT) scan showed erosion of the petrous apex resulting in partial anterior autopetrosectomy (Figs. 1 and 2).The decision was made to proceed with tumor resection using a transcavernous approach. Gross total resection was achieved. The surgery and postoperative course were uneventful, and the patient woke up the same as in the preoperative period. MRI confirmed gross total resection of the tumor. The histopathology was a trigeminal schwannoma, World Health Organization (WHO) grade I. The patient continues to do well without any recurrence at 15-month follow-up.This video demonstrates important steps of the microsurgical skull base techniques for resection of these challenging tumors.The link to the video can be found at https://youtu.be/TMK5363836M

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CTNI-20. PCV CHEMOTHERAPY ALONE IS ASSOCIATED WITH BETTER CLINICAL COURSE IN OLIGODENDROGLIOMA WHO GRADE II

Neuro-Oncology ◽

10.1093/neuonc/noaa215.187 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii46-ii46

Author(s):

Jonathan Weller ◽

Sophie Katzendobler ◽

Philipp Karschnia ◽

Stefanie Lietke ◽

Rupert Egensperger ◽

...

Keyword(s):

Stereotactic Biopsy ◽

Tumor Volume ◽

Treatment Guidelines ◽

Tumor Resection ◽

World Health ◽

Incomplete Resection ◽

Watch And Wait ◽

Who Grade ◽

Long Term Outcome ◽

Pcv Chemotherapy

Abstract BACKGROUND Current treatment guidelines for oligodendrogliomas (OD) recommend watch-and-wait strategies after gross total resection and radiation with subsequent chemotherapy (procarbazine, CCNU and vincristine (PCV)) after incomplete resection. The value of chemotherapy alone as an option to delay the risk of late cognitive deficits is not well defined yet. Here, we retrospectively investigated long-term outcome in OD WHO II with respect to initial therapy and tumor volume in magnetic resonance imaging (MRI). METHODS A total of 142 patients with OD WHO (World Health Organization) II according to WHO 2016 were retrospectively included. Patients either had watch and wait (W&W) after histological sampling through stereotactic biopsy (n=59) or tumor resection (n=27) or else stereotactic biopsy with subsequent temozolomide (TMZ) (n=26) or PCV (n=30). Pre- and post-therapeutic T2 tumor volumes were obtained. Progression-free survival (PFS), post-recurrence PFS (PR-PFS) and rate of secondary malignization after 10 years (MR-10yrs) were correlated with clinical and volumetric data. RESULTS PFS was significantly longer in the PCV cohort compared to TMZ (9.1 vs. 3.6 years, p = 0.04), even after matching patients according to age and initial tumor volume (9.1 vs 4.7 yrs, p = 0.03). PFS in the W&W cohort was 5.1 years and 4.4 years in those receiving tumor resection only. MR-10yrs was 4% in PCV cohort, 18% in the W&W cohort and 52% in the resection only cohort (p = 0.01). In the W&W cohort, patients treated with PCV at first relapse had a longer PR-PFS than those treated with TMZ (in years, 7.2 vs 4.0, p = 0.04). Multivariate analysis confirmed initial PCV therapy (p = 0.01) and initial T2 tumor volume (p = 0.02) to be prognostic. CONCLUSION In oligodendrogliomas WHO II PCV chemotherapy alone is superior in terms of PFS and rate of secondary malignization compared to TMZ chemotherapy alone or tumor resection only.

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Recurrent Sphenocavernous Meningioma

Journal of Neurological Surgery Part B Skull Base ◽

10.1055/s-0041-1725941 ◽

2021 ◽

Author(s):

Mizuho Inoue ◽

Mohamed Labib ◽

Alexander Yang ◽

A. Samy Youssef

Keyword(s):

Tumor Resection ◽

Intensity Modulated Radiotherapy ◽

Residual Tumor ◽

World Health ◽

Neurological Deficits ◽

Falciform Ligament ◽

Total Resection ◽

Anterior Clinoid Process ◽

Who Grade ◽

Health Organization

AbstractA case of a recurrent sphenocavernous meningioma is presented. The patient is a 42-year-old male who presented with an episode of transient right-sided numbness. A magnetic resonance imaging (MRI) revealed a large left sphenocavernous meningioma. The patient underwent a frontotemporal craniotomy for tumor resection. Near total resection was achieved with minimal residual in the left cavernous sinus (CS) and orbital apex. The pathology was consistent with meningioma, World Health Organization (WHO) grade I. A follow-up MRI was done 9 months after surgery and showed a growth of the residual tumor, which was treated with intensity modulated radiotherapy. Tumor growth was detected on serial imaging over a 4-year period. Surgical resection was offered. A left frontotemporal craniotomy with pretemporal transcavernous approach was performed. The bone flap was reopened and the dura was opened in a Y-shaped fashion. The roof of the optic canal was drilled off, and the falciform ligament was opened to decompress the optic nerve. The tumor was disconnected from the anterior clinoid region (the anterior clinoid process was eroded by the tumor) and reflected off the wall of the lateral CS. Tumor was adherent to the V2 fascicles (the lateral CS wall was resected in the first surgery) and was sharply dissected off. Gross total resection was achieved. The pathology was consistent with meningioma, WHO grade I. The patient had an unremarkable postoperative course without any new neurological deficits.The link to the video can be found at: https://youtu.be/KVBVw_86JqM.

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F-Box Genes in the Wheat Genome and Expression Profiling in Wheat at Different Developmental Stages

Genes ◽

10.3390/genes11101154 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1154

Author(s):

Min Jeong Hong ◽

Jin-Baek Kim ◽

Yong Weon Seo ◽

Dae Yeon Kim

Keyword(s):

Developmental Stages ◽

Brachypodium Distachyon ◽

Triticum Aestivum L ◽

Wheat Genome ◽

Post Translational Modification ◽

Genome Wide ◽

A Genome ◽

High Sequence Homology ◽

Wide Scale

Genes of the F-box family play specific roles in protein degradation by post-translational modification in several biological processes, including flowering, the regulation of circadian rhythms, photomorphogenesis, seed development, leaf senescence, and hormone signaling. F-box genes have not been previously investigated on a genome-wide scale; however, the establishment of the wheat (Triticum aestivum L.) reference genome sequence enabled a genome-based examination of the F-box genes to be conducted in the present study. In total, 1796 F-box genes were detected in the wheat genome and classified into various subgroups based on their functional C-terminal domain. The F-box genes were distributed among 21 chromosomes and most showed high sequence homology with F-box genes located on the homoeologous chromosomes because of allohexaploidy in the wheat genome. Additionally, a synteny analysis of wheat F-box genes was conducted in rice and Brachypodium distachyon. Transcriptome analysis during various wheat developmental stages and expression analysis by quantitative real-time PCR revealed that some F-box genes were specifically expressed in the vegetative and/or seed developmental stages. A genome-based examination and classification of F-box genes provide an opportunity to elucidate the biological functions of F-box genes in wheat.

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Cordotomy for patients with thoracic malignant astrocytoma

Journal of Neurosurgery Spine ◽

10.3171/2010.4.spine09901 ◽

2010 ◽

Vol 13 (4) ◽

pp. 418-423 ◽

Cited By ~ 8

Author(s):

Masaya Nakamura ◽

Osahiko Tsuji ◽

Kanehiro Fujiyoshi ◽

Kota Watanabe ◽

Takashi Tsuji ◽

...

Keyword(s):

Tumor Resection ◽

Radical Resection ◽

Subtotal Resection ◽

Optimal Management ◽

Malignant Astrocytoma ◽

Initial Operation ◽

Who Grade ◽

Kaplan Meier ◽

Malignant Astrocytomas ◽

Grade Ii

Object The optimal management of malignant astrocytomas remains controversial, and the prognosis of these lesions has been dismal regardless of the administered treatment. In this study the authors investigated the surgical outcomes of cordotomy in patients with thoracic malignant astrocytomas to determine the effectiveness of this procedure. Methods Cordotomy was performed in 5 patients with glioblastoma multiforme (GBM) and 2 with anaplastic astrocytoma (AA). A Kaplan-Meier survival analysis was performed, and the associations of the resection level with survival and postoperative complications were retrospectively examined. Results Cordotomy was performed in a single stage in 2 patients with GBM and in 2 stages in 3 patients with GBM and 2 patients with AA. In the 2 patients with GBM, cordotomy was performed 2 and 3 weeks after a partial tumor resection. In the 2 patients with AA, the initial treatment consisted of partial tumor resection and subtotal resection combined with radiotherapy, and rostral tumor growth and progressive paralysis necessitated cordotomy 2 and 28 months later. One patient with a secondary GBM underwent cordotomy; the GBM developed 1 year after subtotal resection and radiotherapy for a WHO Grade II astrocytoma. Four patients died 4, 5, 24, and 42 months after the initial operation due to CSF dissemination, and 3 patients (2 with GBM and 1 with AA) remain alive (16, 39, and 71 months). No metastasis to any other organs was noted. Conclusions One-stage cordotomy should be indicated for patients with thoracic GBM or AA presenting with complete paraplegia preoperatively. In patients with thoracic GBM, even if paralysis is incomplete, cordotomy should be performed before the tumor disseminates through the CSF. Radical resection should be attempted in patients with AA and incomplete paralysis. If the tumor persists, radiotherapy and chemotherapy are indicated, and cordotomy should be reserved for lesions growing progressively after such second-line treatments.

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Genome-Wide DNA Methylation Pattern of Cancer Stem Cells in Esophageal Cancer

Technology in Cancer Research & Treatment ◽

10.1177/1533033820983793 ◽

2020 ◽

Vol 19 ◽

pp. 153303382098379

Author(s):

Xiying Yu ◽

Ying Teng ◽

Xingran Jiang ◽

Hui Yuan ◽

Wei Jiang

Keyword(s):

Dna Methylation ◽

Stem Cells ◽

Esophageal Cancer ◽

Cancer Stem Cells ◽

Side Population ◽

Methylation Status ◽

Methylation Profile ◽

Cpg Dinucleotides ◽

Genome Wide ◽

Differentially Methylated Genes

Background: Cancer stem cells (CSCs) are considered the main cause of cancer recurrence and metastasis, and DNA methylation is involved in the maintenance of CSCs. However, the methylation profile of esophageal CSCs remains unknown. Methods: Side population (SP) cells were isolated from esophageal squamous cell carcinoma (ESCC) cell lines KYSE150 and EC109. Sphere-forming cells were collected from human primary esophageal cancer cells. SP cells and sphere-forming cells were used as substitutes for cancer stem-like cells. We investigated the genome-wide DNA methylation profile in esophageal cancer stem-like cells using reduced representation bisulfite sequencing (RRBS). Results: Methylated cytosine (mC) was found mostly in CpG dinucleotides, located mostly in the intronic, intergenic, and exonic regions. Forty intersected differentially methylated regions (DMRs) were identified in these 3 groups of samples. Thirteen differentially methylated genes with the same alteration trend were detected; these included OTX1, SPACA1, CD163L1, ST8SIA2, TECR, CADM3, GRM1, LRRK1, CHSY1, PROKR2, LINC00658, LOC100506688, and NKD2. DMRs covering ST8SIA2 and GRM1 were located in exons. These differentially methylated genes were involved in 10 categories of biological processes and 3 cell signaling pathways. Conclusions: When compared to non-CSCs, cancer stem-like cells have a differential methylation status, which provides an important biological base for understanding esophageal CSCs and developing therapeutic targets for esophageal cancer.

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