Long-read sequencing for brain tumors.

Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.

A rare case of atypical intradural extramedullary glioblastoma diagnosed utilizing next-generation sequencing and methylation profiling: illustrative case.

BACKGROUND: Primary spinal cord tumors, especially primary spinal cord glioblastoma multiforme (PSC-GBM), are exceptionally rare, accounting for less than 1.5% of all spinal tumors. Their infrequency and aggressive yet atypical presentation make diagnosis challenging. In uncertain cases, a surgical approach for tissue diagnosis is often optimal. OBSERVATIONS: A 76-year-old male presented with a rapidly progressing clinical history marked by worsening extremity weakness, urinary retention, and periodic fecal incontinence alongside diffuse changes on neuraxis imaging. The patient, in whom subacute polyneuropathy was initially diagnosed, received multiple rounds of steroids and intravenous immunoglobulin without clinical improvement. Histopathological review of the biopsy tissue yielded an initial diagnosis of spindle cell neoplasm. Next-generation sequencing (NGS) is done routinely on all neuropathology specimens at the authors' institution, and methylation profiling is pursued in difficult cases. Ultimately, NGS and methylation profiling results were essential to an integrated final diagnosis of GBM. LESSONS: PSC-GBM is a rare but highly aggressive occurrence of this tumor. Prolonged back pain, rapid neurological decline, and imaging changes warrant the consideration of lesional biopsy for precise disease characterization. In inconclusive cases, NGS has proved invaluable for clinical clarification and diagnosis, underscoring its importance for integrated diagnoses in guiding appropriate treatment strategies.

Operative planning for a functional precision medicine assay of recurrent high-grade glioma: illustrative case.

BACKGROUND: Functional precision medicine (FPM) represents a personalized and efficacious modality for treating malignant neoplasms. However, acquiring sufficient live tissue to perform FPM analyses is complicated by both difficult identification on imaging and radiation necrosis, particularly in cases of recurrence. The authors describe a case of planning biopsy trajectories for an FPM assay in a patient with recurrent high-grade glioma. OBSERVATIONS: A 25-year-old male with a history of recurrent high-grade glioma was scheduled for laser ablation and biopsy with ChemoID assaying after regions of potential recurrence were identified on follow-up imaging. Preoperative magnetic resonance (MR) spectroscopy of the regions showed areas of high choline/creatine ratios within lesions of radiation necrosis, which helped in planning the biopsy trajectories to selectively target malignancies for FPM analysis. ChemoID results showed high tumor susceptibility to lomustine, which was implemented as adjuvant therapy. LESSONS: FPM therapy in the setting of recurrence is complicated by radiation necrosis, which can present as malignancy on imaging and interfere with tissue acquisition during biopsy or resection. Thus, operative approaches should be carefully planned with the assistance of imaging modalities such as MR spectroscopy to better ensure effective tissue acquisition for accurate FPM analysis and to promote more definitive treatment of recurrence.

Loss of BAP1 Protein Expression by Immunohistochemistry in the Salivary Duct Carcinoma Component of an Intracapsular Carcinoma ex Pleomorphic Adenoma of the Parotid Gland.

BACKGROUND: BRCA1-associated protein 1 (BAP1) is a tumor suppressor gene that is altered in a variety of neoplasms as well as in BAP1 tumor predisposition syndrome. BAP1 alterations are associated with aggressive behavior in some malignancies and may have treatment implications in future. We present the first documented case of loss of BAP1 protein expression by immunohistochemistry in the salivary duct carcinoma (SDC) component of an intracapsular carcinoma ex pleomorphic adenoma (CXPA) in the context of molecular loss of function of BAP1 in the neoplasm. METHODS: A woman of approximately 55 years of age presented with a deep parotid lobe mass, which was resected and found to be CXPA. BAP1 immunohistochemistry and next-generation sequencing was performed to further characterize the neoplasm. RESULTS: The neoplasm showed loss of BAP1 protein expression in the SDC component but retention in the residual pleomorphic adenoma (PA). Next-generation sequencing confirmed a BAP1 loss of function alteration in the neoplasm. CONCLUSION: This is the first documented case report of BAP1 protein expression loss in the SDC component of a CXPA. Future studies are needed to investigate the relevance of BAP1 alterations in SDC and CXPA, which may have prognostic and treatment implications.

DEK-AFF2 Carcinoma of the Sinonasal Region and Skull Base: Detailed Clinicopathologic Characterization of a Distinctive Entity.

A novel DEK-AFF2 fusion was recently reported in 4 nonkeratinizing squamous cell carcinomas of the sinonasal region and skull base, including 1 with exceptional response to immunotherapy, but it is not yet clear if this rearrangement defines a unique clinicopathologic category or represents a rare event. This study aims to characterize a larger cohort of carcinomas with DEK-AFF2 fusions to assess whether they truly constitute a distinctive entity. Among 27 sinonasal and skull base nonkeratinizing squamous cell carcinoma that were negative for human papillomavirus and Epstein-Barr virus, RNA sequencing identified DEK-AFF2 fusions in 13 cases (48%). Nine were centered in the nasal cavity, 2 in the middle ear/temporal bone, 1 in the nasopharynx, and 1 in the orbit. These tumors displayed recurrent histologic features including (1) complex endophytic and exophytic, frequently papilloma-like growth, (2) transitional epithelium with eosinophilic to amphophilic cytoplasm, (3) absent or minimal keratinization with occasional compact keratin pearls, (4) monotonous nuclei, and (5) prominent tumor-infiltrating neutrophils or stromal lymphocytes. This appearance not only overlaps with high-grade basaloid sinonasal carcinomas but also with benign papillomas and tumors reported as low-grade papillary Schneiderian carcinoma. However, DEK-AFF2 carcinomas showed frequent local recurrence, cervical lymph node metastases, and distant metastasis with 2 deaths from disease, confirming they are aggressive malignancies despite relatively bland histology. Overall, the distinctive molecular, histologic, and clinical features of DEK-AFF2 carcinomas suggest they represent a unique entity in the sinonasal region. This tumor merits increased pathologic recognition to better understand its prognostic and therapeutic implications.

What Every Neuropathologist Needs to Know: Practical Aspects and Pitfalls in Molecular Diagnosis of Brain Tumors.

Molecular testing has become part of the routine diagnostic workup of brain tumors after the implementation of integrated histomolecular diagnoses in the 2016 WHO classification update. It is important for every neuropathologist to be aware of practical preanalytical, analytical, and postanalytical factors that impact the performance and interpretation of molecular tests. Prior to testing, optimizing tumor purity and tumor amount increases the ability of the molecular test to detect the genetic alteration of interest. Recognizing basic molecular testing platform analytical characteristics allows selection of the optimal platform for each clinicopathological scenario. Finally, postanalytical considerations to properly interpret molecular test results include understanding the clinical significance of the detected genetic alteration, recognizing that detected clinically significant genetic alterations are occasionally germline constitutional rather than somatic tumor-specific, and being cognizant that recommended and commonly used genetic nomenclature may differ. Potential pitfalls in brain tumor molecular diagnosis are also discussed.

Global microRNA profiling identified miR-10b-5p as a regulator of neurofibromatosis 1 (NF1)-glioma migration.

AIMS: Neurofibromatosis 1 (NF1) is an autosomal-dominant cancer predisposition syndrome caused by loss of function alterations involving the NF1 locus on chromosome 17. The most common brain tumours encountered in affected patients are low-grade gliomas (pilocytic astrocytomas), although high-grade gliomas are also observed at increased frequency. While bi-allelic NF1 loss characterizes these tumours, previous studies have suggested noncoding RNA molecules (microRNA, miR) may have important roles in dictating glioma biology. METHODS: To explore the contributions of miRs in NF1-associated gliomas, we analysed five high-grade gliomas (NF1-HGG) and five PAs (NF1-PA) using global microRNA profiling with NanoString-based microarrays followed by functional experiments with glioma cell lines. RESULTS: miR-10b-5p, miR-135b-5p, miR-196a-5p, miR-196b-5p, miR-1247-5p and miR-320a (adjusted P < 0.05) were increased> 3-fold in NF1-HGG relative to NF1-PA tumours. In addition, miR-378b and miR-1305 were decreased 6.8- and 6-fold, respectively, whereas miR-451a was increased 2.7-fold (adjusted P < 0.05) in NF1-PAs compared to non-neoplastic NF1 patient brain specimens (n = 2). As miR-10b-5p was the microRNA overexpressed the most in NF1-high-grade glioma compared to NF1-low-grade glioma (5.76 fold), we examined its levels in glioma cell lines. miR-10b-5p levels were highest in adult glioma cell lines and lowest in paediatric low-grade glioma lines (P = 0.02). miR-10b-5p knockdown resulted in decreased invasion in NF1-deficient LN229 high-grade glioma line, whereas its overexpression in the NF1-PA derived line (JHH-NF1-PA1) led to increased invasion. There was no change in cell growth (viability and proliferation). CONCLUSIONS: These proof-of-concept experiments support a role for microRNA regulation in NF1-glioma biology.

Navigating small biopsies of salivary gland tumors: a pattern-based approach.

Diagnosis of salivary gland tumors on small biopsy can be difficult because of overlapping morphology, limited tissue availability, and technical artifact. Although a specific diagnosis is not feasible in all cases, a cautious and thoughtful approach to the differential diagnosis and a keen awareness of clinical consequences can facilitate the most complete and useful classification possible. In this review, we present a general strategy for the evaluation of small salivary biopsies, including consideration of clinical and radiographic information, systematic assessment of histologic patterns, and judicious use of immunohistochemistry and molecular studies. We then focus on the distinctive differential diagnoses raised by 6 specific histologic patterns: tubular and cribriform architecture, squamous differentiation, mucin and other secretions, high-grade cytology, epithelial and lymphoid elements, and oncocytic features. Throughout this systematic and pattern-based approach, we focus on practical and cost-effective strategies to overcome the most common diagnostic challenges in limited material.

An update on the central nervous system manifestations of neurofibromatosis type 1.

Neurofibromatosis 1 (NF1) is an autosomal dominant genetic disorder that presents with variable phenotypes as a result of mutations in the neurofibromatosis type 1 (NF1) gene and subsequently, abnormal function of the protein product, neurofibromin. Patients with NF1 are at increased risk for central nervous system (CNS) manifestations including structural, functional, and neoplastic disease. The mechanisms underlying the varied manifestations of NF1 are incompletely understood, but the loss of functional neurofibromin, resulting in sustained activation of the oncoprotein RAS, is responsible for tumorigenesis throughout the body, including the CNS. Much of our understanding of NF1-related CNS manifestations is from a combination of data from animal models and natural history studies of people with NF1 and CNS disease. Data from animal models suggest the importance of both Nf1 mutations and somatic genetic alterations, such as Tp53 loss, for development of neoplasms, as well as the role of the timing of the acquisition of such alterations on the variability of CNS manifestations. A variety of non-neoplastic structural (macrocephaly, hydrocephalus, aqueductal stenosis, and vasculopathy) and functional (epilepsy, impaired cognition, attention deficits, and autism spectrum disorder) abnormalities occur with variable frequency in individuals with NF1. In addition, there is increasing evidence that similar appearing CNS neoplasms in people with and without the NF1 syndrome are due to distinct oncogenic pathways. Gliomas in people with NF1 show alterations in the RAS/MAPK pathway, generally in the absence of BRAF alterations (common to sporadic pilocytic astrocytomas) or IDH or histone H3 mutations (common to diffuse gliomas subsets). A subset of low-grade astrocytomas in these patients remain difficult to classify using standard criteria, and occasionally demonstrate morphologic features resembling subependymal giant cell astrocytomas that afflict patients with tuberous sclerosis complex ("SEGA-like astrocytomas"). There is also emerging evidence that NF1-associated high-grade astrocytomas have frequent co-existing alterations such as ATRX mutations and an alternative lengthening of telomeres (ALT) phenotype responsible for unique biologic properties. Ongoing efforts are seeking to improve diagnostic accuracy for CNS neoplasms in the setting of NF1 versus sporadic tumors. In addition, MEK inhibitors, which act on the RAS/MAPK pathway, continue to be studied as rational targets for the treatment of NF1-associated tumors, including CNS tumors.

Malignant Peripheral Nerve Sheath Tumors Show Decreased Global DNA Methylation.

Malignant peripheral nerve sheath tumors (MPNST) are aggressive spindle cell neoplasms that may occur sporadically, often in association with radiation exposure, or in the clinical context of Neurofibromatosis type 1. MPNST are known to harbor genetic alterations affecting the function of polycomb repressive complex 2 (PRC2), resulting in profound changes to global H3K27me3 levels. Recent evidence suggests a link between the polycomb complex and DNA methylation. Given the established epigenetic alterations found in MPNST, we aimed to further explore global methylation changes including 5-methylcystosine (5mC), 5-hydroxymethylcytosine (5hmC), and H3K27me3 levels using previously validated immunolabeling protocols in a representative cohort of 28 peripheral nerve sheath tumors (MPNST [n = 8], localized cutaneous neurofibroma [n = 10], and plexiform neurofibroma [n = 10]). MPNST showed significantly decreased levels of H3K27me3 (p < 0.0002) and 5mC (p = 0.0001) with levels of 5hmC showing borderline statistical significance (p = 0.05) when compared to localized and plexiform neurofibromas. Immunohistochemical findings of decreased H3K27me3 and 5mC further our understanding of global epigenetic alterations observable in MPNST and may provide insight into the basis of tumor progression as well as prognostic and treatment implications in the future.

Dodecafluoropentane emulsion delays and reduces MRI markers of infarction in a rat stroke model: a preliminary report.

BACKGROUND: Dodecafluoropentane emulsion (DDFPe), an oxygen transport agent, has been shown to reduce infarct volume in animal models of acute ischemic stroke (AIS). Our study assesses the effect of DDFPe on MRI markers of infarct evolution in the early hours after vascular occlusion in a rat AIS model. We hypothesized that DDFPe will delay the development of MRI markers of AIS and/or reduce the extent of infarction. METHODS: Permanent, unilateral surgical occlusion of the middle cerebral and common carotid arteries was performed in control (n=4) and treatment (n = 10) rats. The treatment group received 1 IV dose of 2% w/v DDFPe at 0.6 mL/kg at 1 hour post-occlusion versus none. Diffusion-weighted (DWI) and inversion recovery (IR) MRI sequences were obtained over the 4 hours following occlusion. Infarct extent was quantified by number of abnormal MRI slices per sequence for each group and time point. Student's T-test was applied. RESULTS: DDFPe-treated rats demonstrated reduced infarct extent versus controls over combined time points on IR at 5.43 ± 0.40 (mean ± standard error) abnormal slices vs. 7.38 ± 0.58 (P = 0.01) and on DWI at 5.21 ± 0.54 vs. 9.00 ± 0.95 (P < 0.01). Development of abnormal MRI signal was delayed in the treatment group. CONCLUSIONS: DDFPe delays and reduces MRI markers of AIS in the early hours following vascular occlusion in a rat stroke model. Further investigation of DDFPe as a neuroprotectant is warranted.

Spinal bone marrow necrosis with vertebral compression fracture: differentiation of BMN from AVN.

Bone marrow necrosis (BMN) is a rare malignancy-associated hematologic disorder characterized by necrosis of myeloid and stromal marrow elements with preservation of cortical bone. Overlap between the imaging appearances of BMN and avascular necrosis (AVN) raises the potential for diagnostic confusion. We report a case of BMN presenting with a traumatic multi-level vertebral body collapse, and finding that may potentially confound distinction between the two entities. We discuss important pathophysiologic, clinical, and radiologic differences between BMN and AVN with emphasis on features important in the differential diagnosis.

Dodecafluoropentane Emulsion (DDFPe) Decreases Stroke Size and Improves Neurological Scores in a Permanent Occlusion Rat Stroke Model.

BACKGROUND: Dodecafluoropentane emulsion (DDFPe), given IV one hour after stroke, has been shown to greatly reduce the percent stroke volume (%SV) in rabbits. With repeated doses its effect continued for 24 hours. PURPOSE: Test DDFPe as neuroprotective agent in permanent occlusion rat stroke models in Sprague Dawley (SD) and Spontaneously Hypertensive Rats (SHR) measuring both %SV and neurological assessment scores (NAS). METHODS: The male rats received either saline (control), or one or four doses (1x or 4x) of DDFPe (0.6ml/kg IV) one hour post stroke. Treatment groups were SD (n=26) (control, 1x and 4x; n=12, 7 and 7) and SHR (n=14) (control, 1x and 4x; n=7, 3 and 4). The 4x doses were given at 1.5 hour intervals. At six hours post stroke, the rats received a NAS using standard tests for balance, reflexes, and motor performance. Then rats were euthanized and brains removed for TTC evaluation of %SV. RESULTS: For %SV analysis strain differences were not significant therefore strains were combined. DDFPe significantly decreased %SV in 1x and 4xDDFPe groups compared to control groups (2.59±1.81 and 0.98±0.88 vs. 9.24±6.06, p≤0.001 each; p≤0.0001 for the overall test for treatment effect). The 1x versus 4xDDFPe groups were not significantly different (p=0.40). In NAS analysis both strains showed significant improvement with 4xDDFPe therapy vs. controls, (SD: 5.00+2.45 vs. 9.36+3.56, p=0.01; SHR: 7.75+4.43 vs. 12.14+3.08, p=0.05). Differences between the 1x DDFPe group and controls were not significant (SD: 8.43+3.69; SHR: 9. 33+3.51). CONCLUSION: DDFPe treatment provides significant neuroprotection when assessed six hours post stroke.

Structure of MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) from Vibrio fischeri in complex with substrate UDP-N-acetylglucosamine and the drug fosfomycin.

The development of new antibiotics is necessitated by the rapid development of resistance to current therapies. UDP-N-acetylglucosamine enolpyruvyl transferase (MurA), which catalyzes the first committed step of bacterial peptidoglycan biosynthesis, is a prime candidate for therapeutic intervention. MurA is the target of the antibiotic fosfomycin, a natural product produced by Streptomyces. Despite possessing a high degree of sequence conservation with MurA enzymes from fosfomycin-susceptible organisms, recent microbiological studies suggest that MurA from Vibrio fischeri (VfiMurA) may confer fosfomycin resistance via a mechanism that is not yet understood. The crystal structure of VfiMurA in a ternary complex with the substrate UDP-N-acetylglucosamine (UNAG) and fosfomycin has been solved to a resolution of 1.93 Å. Fosfomycin is known to inhibit MurA by covalently binding to a highly conserved cysteine in the active site of the enzyme. A comparison of the title structure with the structure of fosfomycin-susceptible Haemophilus influenzae MurA (PDB entry 2rl2) revealed strikingly similar conformations of the mobile substrate-binding loop and clear electron density for a fosfomycin-cysteine adduct. Based on these results, there are no distinguishing sequence/structural features in VfiMurA that would translate to a diminished sensitivity to fosfomycin. However, VfiMurA is a robust crystallizer and shares high sequence identity with many clinically relevant bacterial pathogens. Thus, it would serve as an ideal system for use in the structure-guided optimization of new antibacterial agents.

Search for a light pseudoscalar particle in the decay K_{L};{0}-->pi;{0}pi;{0}X.

We performed a search for a light pseudoscalar particle X in the decay K_{L};{0}-->pi;{0}pi;{0}X, X-->gammagamma with the E391a detector at KEK. Such a particle with a mass of 214.3 MeV/c;{2} was suggested by the HyperCP experiment. We found no evidence for X and set an upper limit on the product branching ratio for K_{L};{0}-->pi;{0}pi;{0}X, X-->gammagamma of 2.4x10;{-7} at the 90% confidence level. Upper limits on the branching ratios in the mass region of X from 194.3 to 219.3 MeV/c;{2} are also presented.

Search for the Decay K L0-->pi0nu nu[over].

We performed a search for the K L0-->pi0nu nu[over] decay at the KEK 12-GeV proton synchrotron. No candidate events were observed. An upper limit on the branching ratio for the decay was set to be 6.7 x 10(-8) at the 90% confidence level.

Outcome of the current management of splenic injuries.

BACKGROUND: For patients > 55 years, nonoperative management (NOM) of blunt splenic injury remains controversial. Conflicting reports of excessively high or acceptably low failure rates have discouraged widespread application of NOM in these older patients. However, the small number of patients in these studies limits the impact of their conclusions. METHODS: We manage splenic injury nonoperatively in all appropriate patients without regard to age. We present the largest series of patients > 55 years who have been managed nonsurgically, in a retrospective review of all patients with blunt splenic injury admitted to our trauma center between 1996 and 1999. RESULTS: In 4 years, 542 patients were admitted with blunt splenic injury. Eighty-three patients were > 55 years, and 61 of these patients underwent NOM. Seven older patients failed NOM and required delayed splenectomy, yielding a failure rate of 11.4%. This failure rate was statistically equivalent to the 7% failure rate of patients < 55 years. This study has a power of 80% to detect a failure rate change from 7% to 20%. By multivariate analysis, the only factor that significantly increased the risk of NOM failure was splenic injury grade. Patients > 55 years had a higher mortality than younger patients regardless of NOM/operative treatment. Splenic injury did not directly cause any of the deaths in patients > 55 years who had NOM or failure of NOM. High-grade splenic injuries fail NOM in those > 55 years. CONCLUSION: Nonoperative management of lower grade splenic injuries in patients > 55 years can be accomplished with an acceptably low failure rate. Only grade of splenic injury, not patient age, increases the risk of NOM failure.

The 1.3 A crystal structure of a biotin-binding pseudoknot and the basis for RNA molecular recognition.

A pseudoknot-containing aptamer isolated from a pool of random sequence molecules has been shown previously to represent an optimal RNA solution to the problem of binding biotin. The affinity of this RNA molecule is nonetheless orders of magnitude weaker than that of its highly evolved protein analogs, avidin and streptavidin. To understand the structural basis for biotin binding and to compare directly strategies for ligand recognition available to proteins and RNA molecules, we have determined the 1.3 A crystal structure of the aptamer complexed with its ligand. Biotin is bound at the interface between the pseudoknot's stacked helices in a pocket defined almost entirely by base-paired nucleotides. In comparison to the protein avidin, the aptamer packs more tightly around the biotin headgroup and makes fewer contacts with its fatty acid tail. Whereas biotin is deeply buried within the hydrophobic core in the avidin complex, the aptamer relies on a combination of hydrated magnesium ions and immobilized water molecules to surround its ligand. In addition to demonstrating fundamentally different approaches to molecular recognition by proteins and RNA, the structure provides general insight into the mechanisms by which RNA function is mediated by divalent metals.