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1.
Nat Cancer ; 5(1): 147-166, 2024 Jan.
Article En | MEDLINE | ID: mdl-38172338

Glioblastoma is the most lethal primary brain tumor with glioblastoma stem cells (GSCs) atop a cellular hierarchy. GSCs often reside in a perivascular niche, where they receive maintenance cues from endothelial cells, but the role of heterogeneous endothelial cell populations remains unresolved. Here, we show that lymphatic endothelial-like cells (LECs), while previously unrecognized in brain parenchyma, are present in glioblastomas and promote growth of CCR7-positive GSCs through CCL21 secretion. Disruption of CCL21-CCR7 paracrine communication between LECs and GSCs inhibited GSC proliferation and growth. LEC-derived CCL21 induced KAT5-mediated acetylation of HMGCS1 on K273 in GSCs to enhance HMGCS1 protein stability. HMGCS1 promoted cholesterol synthesis in GSCs, favorable for tumor growth. Expression of the CCL21-CCR7 axis correlated with KAT5 expression and HMGCS1K273 acetylation in glioblastoma specimens, informing patient outcome. Collectively, glioblastomas contain previously unrecognized LECs that promote the molecular crosstalk between endothelial and tumor cells, offering potentially alternative therapeutic strategies.


Brain Neoplasms , Glioblastoma , Humans , Glioblastoma/therapy , Cytokines/metabolism , Endothelial Cells/metabolism , Receptors, CCR7/metabolism , Neoplastic Stem Cells/metabolism , Neoplastic Stem Cells/pathology , Cell Proliferation , Cholesterol/metabolism
2.
Acta Neuropathol Commun ; 11(1): 202, 2023 12 18.
Article En | MEDLINE | ID: mdl-38110981

Machine learning (ML) has increasingly been used to assist and expand current practices in neuropathology. However, generating large imaging datasets with quality labels is challenging in fields which demand high levels of expertise. Further complicating matters is the often seen disagreement between experts in neuropathology-related tasks, both at the case level and at a more granular level. Neurofibrillary tangles (NFTs) are a hallmark pathological feature of Alzheimer disease, and are associated with disease progression which warrants further investigation and granular quantification at a scale not currently accessible in routine human assessment. In this work, we first provide a baseline of annotator/rater agreement for the tasks of Braak NFT staging between experts and NFT detection using both experts and novices in neuropathology. We use a whole-slide-image (WSI) cohort of neuropathology cases from Emory University Hospital immunohistochemically stained for Tau. We develop a workflow for gathering annotations of the early stage formation of NFTs (Pre-NFTs) and mature intracellular (iNFTs) and show ML models can be trained to learn annotator nuances for the task of NFT detection in WSIs. We utilize a model-assisted-labeling approach and demonstrate ML models can be used to aid in labeling large datasets efficiently. We also show these models can be used to extract case-level features, which predict Braak NFT stages comparable to expert human raters, and do so at scale. This study provides a generalizable workflow for various pathology and related fields, and also provides a technique for accomplishing a high-level neuropathology task with limited human annotations.


Alzheimer Disease , Neurodegenerative Diseases , Humans , Neurofibrillary Tangles/pathology , Neurodegenerative Diseases/pathology , tau Proteins/metabolism , Workflow , Brain/pathology , Alzheimer Disease/pathology , Machine Learning
3.
J Ophthalmic Inflamm Infect ; 13(1): 35, 2023 Aug 17.
Article En | MEDLINE | ID: mdl-37589912

PURPOSE: Posterior uveitis is a common chorioretinal pathology affecting all ages worldwide and is a frequent reason for referral to the retina clinic. The spectrum of etiologies for uveitis is very broad and includes infectious and auto-immune diseases. Inflammation can be confined to the eye or may be a part of systemic disease. A useful outline is therefore proposed to aid in the correct diagnosis of these challenging entities. The situation is further complicated by the fact that many neoplastic conditions resemble features of posterior uveitis; they are known as "masqueraders of uveitis". Here, we summarize different posterior uveitides that present with rare findings, along with masqueraders that can be difficult to distinguish. These conditions pose a diagnostic dilemma resulting in delay in treatment because of diagnostic uncertainty. METHODS: An extensive literature search was performed on the MEDLINE/PUBMED, EBSCO and Cochrane CENTRAL databases from January 1985 to January 2022 for original studies and reviews of predetermined diagnoses that include posterior uveitic entities, panuveitis and masquerade syndromes. RESULTS: We described conditions that can present as mimickers of posterior uveitis (i.e., immune check-points inhibitors and Vogt-Koyanagi-Harada-like uveitis; leukemia and lymphoma associated posterior uveitis), inflammatory conditions that present as mimickers of retinal diseases (i.e., Purtscher-like retinopathy as a presentation of systemic lupus erythematosus; central serous chorioretinopathy masquerading inflammatory exudative retinal detachment), and uveitic conditions with rare and diagnostically challenging etiologies (i.e., paradoxical inflammatory effects of anti-TNF-α; post vaccination uveitis; ocular inflammation after intravitreal injection of antiangiogenic drugs). CONCLUSION: This review of unique posterior uveitis cases highlights the overlapping features of posterior uveitis (paradoxical inflammatory effects of anti -TNF α and uveitis; Purtscher-like retinopathy as a presentation of systemic lupus erythematosus, …) and the nature of retinal conditions (ischemic ocular syndrome, or central retinal vein occlusion, amyloidosis, inherited conditions like retinitis pigmentosa, autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV), etc.…) that may mimic them is represented. Careful review of past uveitis history, current medications and recent vaccinations, detailed examination of signs of past or present inflammation, eventually genetic testing and/ or multimodal retinal imaging (like fluorescein angiography, EDI-OCT, OCT-angiography for lupus Purtscher-like retinopathy evaluation, or ICG for central serous retinopathy, or retinal amyloid angiopathy) may aid in correct diagnosis.

4.
Cancer Res Commun ; 3(7): 1173-1188, 2023 07.
Article En | MEDLINE | ID: mdl-37426447

Glioblastoma (GBM) is the most common and malignant primary brain tumor in adults. Immunotherapy may be promising for the treatment of some patients with GBM; however, there is a need for noninvasive neuroimaging techniques to predict immunotherapeutic responses. The effectiveness of most immunotherapeutic strategies requires T-cell activation. Therefore, we aimed to evaluate an early marker of T-cell activation, CD69, for its use as an imaging biomarker of response to immunotherapy for GBM. Herein, we performed CD69 immunostaining on human and mouse T cells following in vitro activation and post immune checkpoint inhibitors (ICI) in an orthotopic syngeneic mouse glioma model. CD69 expression on tumor-infiltrating leukocytes was assessed using single-cell RNA sequencing (scRNA-seq) data from patients with recurrent GBM receiving ICI. Radiolabeled CD69 Ab PET/CT imaging (CD69 immuno-PET) was performed on GBM-bearing mice longitudinally to quantify CD69 and its association with survival following immunotherapy. We show CD69 expression is upregulated upon T-cell activation and on tumor-infiltrating lymphocytes (TIL) in response to immunotherapy. Similarly, scRNA-seq data demonstrated elevated CD69 on TILs from patients with ICI-treated recurrent GBM as compared with TILs from control cohorts. CD69 immuno-PET studies showed a significantly higher tracer uptake in the tumors of ICI-treated mice compared with controls. Importantly, we observed a positive correlation between survival and CD69 immuno-PET signals in immunotherapy-treated animals and established a trajectory of T-cell activation by virtue of CD69-immuno-PET measurements. Our study supports the potential use of CD69 immuno-PET as an immunotherapy response assessment imaging tool for patients with GBM. Significance: Immunotherapy may hold promise for the treatment of some patients with GBM. There is a need to assess therapy responsiveness to allow the continuation of effective treatment in responders and to avoid ineffective treatment with potential adverse effects in the nonresponders. We demonstrate that noninvasive PET/CT imaging of CD69 may allow early detection of immunotherapy responsiveness in patients with GBM.


Glioblastoma , Animals , Humans , Mice , Glioblastoma/diagnostic imaging , Immunotherapy , Neoplasm Recurrence, Local , Positron Emission Tomography Computed Tomography , Positron-Emission Tomography/methods , T-Lymphocytes/metabolism
5.
World Neurosurg ; 178: e540-e548, 2023 Oct.
Article En | MEDLINE | ID: mdl-37516146

OBJECTIVE: The current standard of care for patients with glioblastoma (GBM) is maximal safe resection followed by adjuvant radiation therapy with concurrent temozolomide chemotherapy. Previous studies that identified this treatment regimen focused on younger patients with GBM. The proportion of patients with GBM over the age of 80 years is increasing. We investigate whether elderly patients benefit from the current standard of care with additional maximal safe resection. METHODS: Clinical, operative, radiographic, demographic, genetic, and outcomes data were retrospectively collected for patients treated for histologically confirmed World Health Organization grade 4 GBM at University of Pittsburgh Medical Center from 2009 to 2020. Only patients 80 years and older were included (n = 123). Statistically significant values were set at P < 0.05. RESULTS: A univariate Cox proportional hazards analysis of GBM patients aged >80 years identified the use of temozolomide, radiation, Karnofsky Performance Status (KPS) > 70, and methylguanine DNA methyltransferase methylation with increased overall survival (OS). Further multivariate Cox proportional hazards model analysis showed that the variables identified in the univariate analysis passed multicollinearity testing, and that use of temozolomide, KPS >70, and gross total resection were shown to significantly impact survival. Survival analysis showed that patients with biopsy alone had a shorter median OS compared with patients who received resection, temozolomide, and radiation (P < 0.0001, median OS 1.6 vs. 7.5 months). Additionally, patients who underwent biopsy and then received temozolomide and radiation had a shorter median OS when compared with patients who received resection, temozolomide, and radiation (P = 0.0047, median OS 3.6 vs. 7.5 months). CONCLUSIONS: For elderly patients with KPS >70, GTR followed by radiation and temozolomide is associated with maximum OS.

6.
Semin Diagn Pathol ; 40(1): 47-51, 2023 Jan.
Article En | MEDLINE | ID: mdl-35843756

Germ cell tumors of the central nervous system (GCT-CNS) arise predominantly in midline locations of the CNS and affect young patients in their first to third decades of life. Involvement of the CNS is thought to be a sequelae of residual primordial germ cells with incomplete embryologic migration. Clinically, GCT-CNS present with symptoms of ventricular obstruction or compression of affected brain structures. Histologically, these tumors are analogous to their gonadal and extra-gonadal counterparts. Diagnosis relies heavily on morphology and immunohistochemical findings, and can be complicated by limited tumor sampling. There is currently only a limited role for molecular studies. Treatment of these lesions is made difficult by their involvement of deep and vital brain structures and accurate pathologic diagnosis is essential for appropriate therapy. Diagnosis should involve review of the clinical history, imaging studies, and assessment of serum and cerebrospinal fluid tumor markers. Current therapeutic strategies involving radiation therapy with or without chemotherapy are quite effective, in spite of the locational difficulties that often prevent gross total resection.


Brain Neoplasms , Central Nervous System Neoplasms , Neoplasms, Germ Cell and Embryonal , Humans , Central Nervous System Neoplasms/diagnosis , Central Nervous System Neoplasms/therapy , Central Nervous System Neoplasms/pathology , Neoplasms, Germ Cell and Embryonal/diagnosis , Neoplasms, Germ Cell and Embryonal/therapy , Biomarkers, Tumor , Brain Neoplasms/therapy
7.
Neurooncol Adv ; 4(1): vdab182, 2022.
Article En | MEDLINE | ID: mdl-35047821

BACKGROUND: Infiltrative astrocytic tumors with and without isocitrate dehydrogenase (IDH) mutation frequently contain mutations in the TP53 tumor suppressor gene. Disruption of normal p53 protein activity confers neoplastic cells with a number of oncogenic properties and is a common feature of aggressive malignancies. However, the high prevalence of TP53 mutation and its pathogenic role in IDH-mutant (IDHmut) astrocytoma is not well understood. METHODS: We performed a retrospective analysis of molecular and clinical data from patients with IDHmut astrocytoma at the University of Pittsburgh Medical Center between 2015 and 2019 as our initial cohort. We validated and expanded our findings using molecular and clinical data from The Cancer Genome Atlas. RESULTS: We show that the TP53 mutational spectrum in IDHmut astrocytomas is dominated by a single hotspot mutation that codes for the R273C amino acid change. This mutation is not enriched in IDH-wildtype astrocytomas. The high prevalence of TP53 R273C mutation is not readily explained by known mutagenic mechanisms, and TP53 R273C mutant tumors have lower transcriptional levels of proliferation-related genes compared to IDHmut astrocytomas harboring other forms of mutant p53. Despite lower proliferation, TP53 R273C mutant tumors tend to progress more quickly and have a shorter overall survival than those with other TP53 mutations, particularly in male patients. CONCLUSIONS: Our findings suggest that compared to other TP53 mutations, IDHmut astrocytomas may select for TP53 R273C mutations during tumorigenesis. The genotype, sex, and mutation-specific findings are clinically relevant and should prompt further investigation of TP53 R273C.

8.
Brain Pathol ; 32(5): e13050, 2022 09.
Article En | MEDLINE | ID: mdl-35014126

AIMS: Resource-strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings. METHODS: We used simple information theory calculations on a brain cancer simulation model and real-world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&E and Olig2 stained images obtained from digital slides. An auto-adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH-mutant tumors. RESULTS: Information theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH-mutant tumors. The predictive models may facilitate the reduction of false-positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing. CONCLUSIONS: We posit that this approach provides an improvement on the cIMPACT-NOW workflow recommendations for IDH-mutant tumors and a framework for future resource and testing allocation.


Brain Neoplasms , Glioma , Brain Neoplasms/pathology , Chromosome Aberrations , Chromosomes, Human, Pair 1 , Chromosomes, Human, Pair 19 , Ecosystem , Glioma/pathology , Humans , In Situ Hybridization, Fluorescence , Information Theory , Isocitrate Dehydrogenase/genetics , Mutation , Neuropathology , Tumor Suppressor Protein p53 , Workflow
9.
J Neurol Surg B Skull Base ; 82(6): 601-607, 2021 Dec.
Article En | MEDLINE | ID: mdl-34745826

Objective Previous work categorized skull base chordoma (SBC) into three genetic risk groups based on 1p36 and homozygous 9p21(p16) deletions, accounting for a wide variability in prognosis (A = low-risk, B = intermediate-risk, C = high-risk). However, it remains unclear how these groups could guide management. Study Design By integrating surgical outcome and adjuvant radiation (AdjXRT) information with genetic data on 152 tumors, we sought to develop an evidence-based management algorithm for SBC. Results Gross total resections (GTRs) were associated with improved progression free survival (PFS) in all genetic groups. For Group C tumors, GTR and AdjXRT independently contributed to PFS (multivariate Cox proportional hazard ratio [HR] = 0.14, p = 0.002, and HR = 0.40, p = 0.047, respectively). For Group B tumors, AdjXRT improved outcomes only when GTR was not feasible (log-rank p = 0.008), but not following GTR (log-rank p = 0.54). However, 24 of 25 Group A tumors underwent GTR, and AdjXRT for these did not confer any benefit (log-Rank p = 0.285). The high GTR rates in Group A could be explained by smaller tumor sizes (mean = 0.98cc/4.08cc/4.92cc for Group A/B/C, respectively, p = 0.031) and lack of invasiveness. Group A tumors were also more frequently diagnosed in young people ( p = 0.002) as asymptomatic lesions ( p = 0.001), suggesting that they could be precursors to tumors in higher risk groups. Conclusion Genotypic grouping by 1p36 and homozygous 9p21(p16) deletions can predict prognosis in SBC and guide management. GTR remains the cornerstone of SBC treatment and can be sufficient without AdjXRT in low and intermediate risk tumors. Low-risk tumors are associated with a less invasive phenotype, which makes them more amenable to GTR.

10.
J Med Case Rep ; 15(1): 446, 2021 Sep 05.
Article En | MEDLINE | ID: mdl-34481512

BACKGROUND: Immunoglobulin-G4-related hypophysitis is a rare inflammatory disease that can present as a tumefactive pituitary lesion mimicking hypophyseal neoplasms such as pituitary adenoma or craniopharyngioma. The literature on this entity is sparse, with fewer than 100 cases reported across 19 publications; a recent review found only 24 cases published from 2007 to 2018. Previous reports have described demographic differences, with immunoglobulin-G4-related hypophysitis in females tending to present in the second and third decades in association with other autoimmune disease, while males tend to present in the fifth and sixth decades of life without an autoimmune history. CASE PRESENTATION: In contrast to the reported demographic trends, here we describe a unique case of immunoglobulin-G4-related hypophysitis in a 63-year-old white female with no history of autoimmune disease who presented with a rapidly enlarging sellar and hypothalamic mass causing headaches and cranial nerve palsies, prompting biopsy for diagnosis. The patient experienced rapid response to treatment with high-dose steroids and rituximab. CONCLUSION: The case contributes to the growing clinicopathologic description of immunoglobulin-G4-related hypophysitis and illustrates that this diagnosis should be a consideration even outside the conventional demographic setting.


Craniopharyngioma , Hypophysitis , Pituitary Diseases , Female , Humans , Hypophysitis/diagnosis , Immunoglobulin G , Male , Middle Aged , Pituitary Diseases/diagnosis , Pituitary Gland
11.
Vox Sang ; 116(7): 831-840, 2021 Aug.
Article En | MEDLINE | ID: mdl-33491789

BACKGROUND: A risk assessment model for predicting the risk of haemolytic disease of the fetus and newborn (HDFN) in future pregnancies following the transfusion of Rh(D)-positive red blood cell (RBC)-containing products to females of childbearing potential (FCP) was developed, accounting for the age that the FCP is transfused in various countries. METHODS: The HDFN risk prediction model included the following inputs: risk of FCP death in trauma, Rh(D) alloimmunization rate following Rh(D)-positive RBC transfusion, expected number of live births following resuscitation, probability of carrying an Rh(D)-positive fetus, the probability of HDFN in an Rh(D)-positive fetus carried by an alloimmunized mother. The model was implemented in Microsoft R Open, and one million FCPs of each age between 18 and 49 years old were simulated. Published data from eight countries, including the United States, were utilized to generate country-specific HDFN risk estimates. RESULTS: The risk predictions showed similar characteristics for each country in that the overall risk of having a pregnancy affected by HDFN was higher if the FCP was younger when she received her Rh(D)-positive transfusion than if she was older. In the United States, the overall risk of HDFN if the FCP was transfused at age 18 was 3·4% (mild: 1·20%, moderate: 0·45%; severe: 1·15%; IUFD: 0·57%); the risk was approximately 0% if the FCP was 43 years or older at the time of transfusion. CONCLUSION: This model can be used to predict HDFN outcomes when establishing transfusion policies as it relates to the administration of Rh(D)-positive products for massively bleeding FCPs.


Erythroblastosis, Fetal , Rh-Hr Blood-Group System , Blood Transfusion , Erythrocytes , Female , Humans , Isoantibodies , Pregnancy
12.
Brain Pathol ; 31(1): 70-83, 2021 01.
Article En | MEDLINE | ID: mdl-32997853

The group of CNS mesenchymal (non-meningothelial) and primary glial/neuronal tumors in association with EWSR1-non-ETS rearrangements comprises a growing spectrum of entities, mostly reported in isolation with incomplete molecular profiling. Archival files from three pediatric institutions were queried for unusual cases of pediatric (≤21 years) CNS EWSR1-rearranged tumors confirmed by at least one molecular technique. Extra-axial tumors and cases with a diagnosis of Ewing sarcoma (EWSR1-ETS family fusions) were excluded. Additional studies, including anchored multiplex-PCR with next-generation sequencing and DNA methylation profiling, were performed as needed to determine fusion partner status and brain tumor methylation class, respectively. Five cases (median 17 years) were identified (M:F of 3:2). Location was parenchymal (n = 3) and undetermined (n = 2) with topographic distributions including posterior fossa (n = 1), frontal (n = 1), temporal (n = 1), parietal (n = 1) and occipital (n = 1) lobes. Final designation with fusion findings included desmoplastic small round cell tumor (EWSR1-WT1; n = 1) and tumors of uncertain histogenesis (EWSR1-CREM, n = 1; EWSR1-CREB1, n = 1; EWSR1-PLAGL1, n = 1; and EWSR1-PATZ1, n = 1). Tumors showed a wide spectrum of morphology and biologic behavior. For EWSR1-CREM, EWSR1-PLAGL1 and EWSR1-PATZ1 tumors, no significant methylation scores were reached in the known brain tumor classes. Available outcome (4/5) was reported as favorable (n = 2) and unfavorable (n = 2) with a median follow-up of 30 months. In conclusion, we describe five primary EWSR1-non-ETS fused CNS tumors exhibiting morphologic and biologic heterogeneity and we highlight the clinical importance of determining specific fusion partners to improve diagnostic accuracy, treatment and monitoring. Larger prospective clinicopathological and molecular studies are needed to determine the prognostic implications of histotypes, anatomical location, fusion partners, breakpoints and methylation profiles in patients with these rare tumors.


Brain Neoplasms/genetics , Brain Neoplasms/pathology , RNA-Binding Protein EWS/genetics , Adolescent , Child , Child, Preschool , Female , Humans , Male , Oncogene Fusion , Oncogene Proteins, Fusion/genetics , Young Adult
13.
Acta Neuropathol Commun ; 8(1): 169, 2020 10 20.
Article En | MEDLINE | ID: mdl-33081848

IDH-mutant astrocytomas have a more indolent natural history and better prognosis than their IDH-wild type counterparts, but are still graded according to schemes developed prior to the recognition of this type of neoplasm as a distinct entity. Homozygous deletion of CDKN2A has been proposed as a molecular correlate of aggressive behavior in these tumors, and may be incorporated into future grading systems in an effort to improve prognostic stratification. Fluorescence in situ hybridization (FISH) is a common ancillary testing modality used to assess CDKN2A status, but the specifics of how to best interpret FISH results for prognostication of gliomas have not been clearly defined in the literature. To address this issue, we performed a retrospective analysis of prospectively collected CDKN2A FISH data from 108 primary and 43 recurrent IDH-mutant astrocytomas diagnosed between 2007-2020 at the University of Pittsburgh Medical Center. High level CDKN2A homozygous deletion was rare in primary tumors and was identified more frequently in recurrent tumors. Multivariate Cox Proportional-Hazards analysis demonstrated that histologic grade and CDKN2A status are independent predictors of survival, and the prognostic value of CDKN2A is maximized by applying a threshold of ≥ 30% of tumor cells with homozygous deletion by FISH to define a positive result. At this threshold, CDKN2A deletion significantly stratified survival of histologic grade 4 tumors, but grade 2 and 3 tumors rarely exceeded this cutoff value and did not show worse survival. Lower thresholds identified additional lower grade tumors, but were not prognostically useful. Compared to prior studies, the lack of prognostic significance of CDKN2A homozygous deletion by FISH in grade 2-3 IDH-mutant astrocytomas may reflect differences in cohort populations or technical differences between testing modalities. Definitive criteria for determining CDKN2A homozygous deletion by various methodologies will be critical if this is to be included in future grading schemes.


Astrocytoma/genetics , Brain Neoplasms/genetics , Cyclin-Dependent Kinase Inhibitor p16/genetics , Gene Deletion , Adult , Aged , Astrocytoma/pathology , Brain Neoplasms/pathology , Female , Homozygote , Humans , In Situ Hybridization, Fluorescence , Isocitrate Dehydrogenase/genetics , Kaplan-Meier Estimate , Male , Middle Aged , Mutation , Neoplasm Grading , Prognosis , Proportional Hazards Models , Young Adult
14.
J Am Soc Cytopathol ; 8(5): 243-249, 2019.
Article En | MEDLINE | ID: mdl-31543223

INTRODUCTION: At our institution, almost all thyroid fine-needle aspiration (FNA) procedures are performed by either Endocrinology or Radiology personnel. In this study, we compared the cytology and molecular adequacy rates of these 2 thyroid FNA practices, which differ on several aspects of specimen procurement. MATERIALS AND METHODS: All thyroid FNA specimens from Endocrinology and Radiology practices between September 2008 and December 2016 were included. Over this time frame, the molecular testing modality transitioned from polymerase chain reaction (PCR)-based (7-gene panel era) to next generation sequencing (NGS)-based (ThyroSeq era). In measuring cytology adequacy, the Bethesda System unsatisfactory rate was determined. Molecular adequacy was categorized as Optimal, Limited Thyroid Epithelial Cells, Limited Nucleic Acids, or Failed. These parameters were compared for the 2 practices. RESULTS: The study cohorts comprised 5810 specimens from Endocrinology and 4597 from Radiology. More Endocrinology specimens were satisfactory for cytology diagnosis than those from Radiology (94.7% versus 90.0%, P < 0.001). For molecular adequacy, fewer Endocrinology specimens were optimal than specimens from Radiology for both the 7-gene panel era (76.2% versus 82.9%, P < 0.001) and the ThyroSeq era (88.1% versus 91.9%, P = 0.049). CONCLUSIONS: The 2 thyroid FNA practices varied inversely in their adequacy rates for cytology and molecular testing. Had one practice been superior for both cytology and molecular adequacy, a recommendation for the method of choice would have been straightforward. However, our results show that optimization of FNA practice for the current practice of thyroid cytology requires further investigation due to the complex nature of specimen procurement.


Cytodiagnosis/methods , Molecular Diagnostic Techniques , Specimen Handling , Thyroid Gland/pathology , Biopsy, Fine-Needle , Humans , Logistic Models
15.
J Mol Diagn ; 21(6): 985-993, 2019 11.
Article En | MEDLINE | ID: mdl-31382034

Visualization-driven data exploration is a highly effective modality for interpreting and discovering insights from high-throughput genomics data sets; however, it is vastly underutilized in routine workflows in clinical and translation settings. We have developed three open-source, browser-based, interactive genomics data visualization widgets that can be used as intuitive stand-alone applications or integrated with existing web-based laboratory information solutions. The widgets were developed in JavaScript using the D3.js library. These widgets run in any modern web browser across desktop and mobile devices for easy accessibility but are designed for client-side data processing to address data privacy concerns. jsProteinMapper plots the location of a variant of interest relative to the protein domains and multiple variant databases, assisting with clinical interpretation of sequence variants. jsComut generates a highly interactive and customizable comutation plot for visual exploration of genomic data sets with clinicopathologic annotations to reveal unique molecular profiles and clinical correlates. jsCodonWheel is an interactive version of the ubiquitous circular codon-to-amino acid translation table, which lets users quickly map nucleotide changes onto resulting amino acid differences. These open-source visualization tools may improve some of the key laboratory workflows that involve the review of large-scale genomics data sets in a high-volume setting. The intuitive and responsive user interface, highly customizable visualizations, and easy integration with existing web-based laboratory software are significant highlights of these tools.


Data Visualization , Genomics/methods , Web Browser , Clinical Laboratory Services , Codon , Cohort Studies , Computer Graphics , Gene Frequency , Humans , Protein Interaction Domains and Motifs , Protein Interaction Maps , Translational Research, Biomedical , User-Computer Interface
16.
Pediatr Neurosurg ; 54(5): 347-353, 2019.
Article En | MEDLINE | ID: mdl-31430747

Translocations between EWSR1 and members of the CREB family of transcription factors (CREB1, ATF1, and CREM) are rare genetic findings occurring in various sarcomas. Of these, the EWSR1-CREM translocation is the most rarely reported. We present the case of a 9-year-old boy who presented with a year of fatigue, weight loss, and abulia. A brain MRI revealed a frontal interhemispheric tumor arising from the falx. After resection, pathology demonstrated a myxoid mesenchymal tumor with an EWSR1-CREM translocation. A series of recent reports of similar tumors has generated ongoing debate in the literature over the classification of these tumors either as intracranial angiomatoid fibrous histiocytomas, which also harbor EWSR1-CREB family translocations, or as a novel diagnostic entity. The present case provides another example of the rare EWSR1-CREM fusion in an intracranial myxoid mesenchymal tumor that recurred in just 6 months despite gross total resection. The findings are discussed in the context of the existing literature and the ongoing effort to appropriately classify this type of tumor.


Brain Neoplasms/genetics , Cyclic AMP Response Element Modulator/genetics , Histiocytoma, Malignant Fibrous/genetics , Neoplasm Recurrence, Local/genetics , RNA-Binding Protein EWS/genetics , Translocation, Genetic/genetics , Brain Neoplasms/diagnostic imaging , Brain Neoplasms/surgery , Child , Histiocytoma, Malignant Fibrous/diagnostic imaging , Histiocytoma, Malignant Fibrous/surgery , Humans , Male , Neoplasm Recurrence, Local/diagnostic imaging , Neoplasm Recurrence, Local/surgery
17.
Science ; 337(6097): 984-8, 2012 Aug 24.
Article En | MEDLINE | ID: mdl-22821987

The kinematic strategy encoded in motor cortical areas for classic straight-line reaching is remarkably simple and consistent across subjects, despite the complicated musculoskeletal dynamics that are involved. As tasks become more challenging, however, different conscious strategies may be used to improve perceived behavioral performance. We identified additional spatial information that appeared both in single neurons and in the population code of monkey dorsal premotor cortex when obstacles impeded direct reach paths. The neural correlate of movement planning varied between subjects in a manner consistent with the use of different strategies to optimize task completion. These distinct planning strategies were manifested in the timing and strength of the information contained in the neural population code.


Arm/physiology , Motor Activity , Motor Cortex/physiology , Movement , Neurons/physiology , Psychomotor Performance , Animals , Arm/innervation , Biomechanical Phenomena , Brain Mapping , Cues , Hand/innervation , Hand/physiology , Macaca mulatta , Mental Processes
18.
J Neurosci Methods ; 189(1): 5-13, 2010 May 30.
Article En | MEDLINE | ID: mdl-20219536

To analyze the spatiotemporal dynamics of network activity in a brain tissue slice, it is useful to record simultaneously from multiple locations. When obtained from laminar structures such as the hippocampus or neocortex, multisite recordings also yield information about subcellular current distributions via current source density analysis. Multisite probes developed for in vivo recordings could serve these purposes in vitro, allowing recordings to be obtained from brain slices at sites deeper within the tissue than currently available surface recording methods permit. However, existing recording chambers do not allow for the insertion of lamina-spanning probes that enter through the edges of brain slices. Here, we present a novel brain slice recording chamber design that accomplishes this goal. The device provides a stable microfluidic perfusion environment in which tissue health is optimized by superfusing both surfaces of the slice. Multichannel electrodes can be inserted parallel to the surface of the slice, at any depth relative to the surface. Access is also provided from above for the insertion of additional recording or stimulating electrodes. We illustrate the utility of this recording configuration by measuring current sources and sinks during theta burst stimuli that lead to the induction of long-term potentiation in hippocampal slices.


Brain/physiology , Electrophysiology/instrumentation , Neurophysiology/instrumentation , Perfusion/instrumentation , Action Potentials/physiology , Animals , Brain/anatomy & histology , Diffusion Chambers, Culture/instrumentation , Diffusion Chambers, Culture/methods , Electric Stimulation/instrumentation , Electric Stimulation/methods , Electrodes/standards , Electronics, Medical/instrumentation , Electronics, Medical/methods , Electrophysiology/methods , Equipment Design/methods , Hippocampus/anatomy & histology , Hippocampus/physiology , Long-Term Potentiation/physiology , Male , Mice , Neurons/physiology , Neurophysiology/methods , Organ Culture Techniques/instrumentation , Organ Culture Techniques/methods , Perfusion/methods , Theta Rhythm
19.
Med J Aust ; 186(4): 192-6, 2007 Feb 19.
Article En | MEDLINE | ID: mdl-17309422

From July 2007, the Health Professions Registration Act 2005 (Vic) will significantly alter the medical disciplinary process in Victoria. For practitioners: Formal hearings for allegations of serious unprofessional conduct will be heard by the Victorian Civil and Administrative Tribunal (VCAT); There will be no right of appeal from a VCAT decision other than on a point of law; The maximum fine for serious unprofessional conduct will increase from $2000 to $50 000; Performance standards panels (PSPs) will be established to conduct informal hearings, with a power to impose conditions on registration; and Costs of the new system will cause an increase in annual registration fees. For complainants: There are new avenues for conciliation; There is a right to seek a review of certain Medical Practitioners Board of Victoria decisions; and Reasons for a PSP decision will be provided. Despite government argument that these changes will make the health complaints handling system fairer, the new Act has the potential to diminish the rights and interests of doctors.


Civil Rights/legislation & jurisprudence , Licensure/legislation & jurisprudence , Patient Rights/legislation & jurisprudence , Physicians/legislation & jurisprudence , Accreditation , Costs and Cost Analysis , Ethics, Medical , Health Care Reform , Humans , Peer Review, Health Care/legislation & jurisprudence , Physicians/ethics , Registries , Victoria
20.
Lab Chip ; 7(1): 30-40, 2007 Jan.
Article En | MEDLINE | ID: mdl-17180203

The field of neuroscience has always been attractive to engineers. Neurons and their connections, like tiny circuit elements, process and transmit information in a dramatic way that is intimately curious to researchers in the computer science and engineering fields. Of particular interest has been the recent push in applying microtechnology to the field of neuroscience. This review is meant to provide an overview of some of the subtle nuances of the nervous system and outline recent advances in lab on a chip applications in neurobiology. It also aims to highlight some of the challenges the field faces in the hopes of encouraging new engineering researchers to collaborate with neurobiologists to help advance our basic understanding of the nervous system and create novel applications based on neuroengineering principles.


Microarray Analysis , Microfluidic Analytical Techniques , Neurobiology , Neurons , Animals , Biomedical Engineering , Cells, Cultured , Electrochemistry , Humans , Microarray Analysis/instrumentation , Microarray Analysis/methods , Microfluidic Analytical Techniques/instrumentation , Microfluidic Analytical Techniques/methods , Models, Neurological , Neurobiology/instrumentation , Neurobiology/methods , Neurons/cytology , Neurons/metabolism , Neurons/physiology
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