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Mooney MA, Georges J, Yazdanabadi MI, Goehring KY, White WL, Little AS, Preul MC, Coons SW, Nakaji P, Eschbacher JM. Immediate ex-vivo diagnosis of pituitary adenomas using confocal reflectance microscopy: a proof-of-principle study. J Neurosurg 2017; 128:1072-1075. [PMID: 28548594 DOI: 10.3171/2016.11.jns161651] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The objective of this study was to evaluate the feasibility of using confocal reflectance microscopy (CRM) ex vivo to differentiate adenoma from normal pituitary gland in surgical biopsy specimens. CRM allows for rapid, label-free evaluation of biopsy specimens with cellular resolution while avoiding some limitations of frozen section analysis. METHODS Biopsy specimens from 11 patients with suspected pituitary adenomas were transported directly to the pathology department. Samples were immediately positioned and visualized with CRM using a confocal microscope located in the same area of the pathology department where frozen sections are prepared. An H & E-stained slide was subsequently prepared from imaged tissue. A neuropathologist compared the histopathological characteristics of the H & E-stained slide and the matched CRM images. A second neuropathologist reviewed images in a blinded fashion and assigned diagnoses of adenoma or normal gland. RESULTS For all specimens, CRM contrasted cellularity, tissue architecture, nuclear pleomorphism, vascularity, and stroma. Pituitary adenomas demonstrated sheets and large lobules of cells, similar to the matched H & E-stained slides. CRM images of normal tissue showed scattered small lobules of pituitary epithelial cells, consistent with matched H & E-stained images of normal gland. Blinded review by a neuropathologist confirmed the diagnosis in 15 (94%) of 16 images of adenoma versus normal gland. CONCLUSIONS CRM is a simple, reliable approach for rapidly evaluating pituitary adenoma specimens ex vivo. This technique can be used to accurately differentiate between pituitary adenoma and normal gland while preserving biopsy tissue for future permanent analysis, immunohistochemical studies, and molecular studies.
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Mooney MA, Hardesty DA, Sheehy JP, Bird R, Chapple K, White WL, Little AS. Interrater and intrarater reliability of the Knosp scale for pituitary adenoma grading. J Neurosurg 2017; 126:1714-1719. [DOI: 10.3171/2016.3.jns153044] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVEThe goal of this study was to determine the interrater and intrarater reliability of the Knosp grading scale for predicting pituitary adenoma cavernous sinus (CS) involvement.METHODSSix independent raters (3 neurosurgery residents, 2 pituitary surgeons, and 1 neuroradiologist) participated in the study. Each rater scored 50 unique pituitary MRI scans (with contrast) of biopsy-proven pituitary adenoma. Reliabilities for the full scale were determined 3 ways: 1) using all 50 scans, 2) using scans with midrange scores versus end scores, and 3) using a dichotomized scale that reflects common clinical practice. The performance of resident raters was compared with that of faculty raters to assess the influence of training level on reliability.RESULTSOverall, the interrater reliability of the Knosp scale was “strong” (0.73, 95% CI 0.56–0.84). However, the percent agreement for all 6 reviewers was only 10% (26% for faculty members, 30% for residents). The reliability of the middle scores (i.e., average rated Knosp Grades 1 and 2) was “very weak” (0.18, 95% CI −0.27 to 0.56) and the percent agreement for all reviewers was only 5%. When the scale was dichotomized into tumors unlikely to have intraoperative CS involvement (Grades 0, 1, and 2) and those likely to have CS involvement (Grades 3 and 4), the reliability was “strong” (0.60, 95% CI 0.39–0.75) and the percent agreement for all raters improved to 60%. There was no significant difference in reliability between residents and faculty (residents 0.72, 95% CI 0.55–0.83 vs faculty 0.73, 95% CI 0.56–0.84). Intrarater reliability was moderate to strong and increased with the level of experience.CONCLUSIONSAlthough these findings suggest that the Knosp grading scale has acceptable interrater reliability overall, it raises important questions about the “very weak” reliability of the scale's middle grades. By dichotomizing the scale into clinically useful groups, the authors were able to address the poor reliability and percent agreement of the intermediate grades and to isolate the most important grades for use in surgical decision making (Grades 3 and 4). Authors of future pituitary surgery studies should consider reporting Knosp grades as dichotomized results rather than as the full scale to optimize the reliability of the scale.
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Mooney MA, Oppenlander ME, Kakarla UK, Theodore N. Tumoral calcinosis of the craniovertebral junction as a cause of dysphagia with treatment by transoral decompression: case report. J Neurosurg Spine 2017; 26:567-571. [PMID: 28186471 DOI: 10.3171/2016.9.spine16469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Tumoral calcinosis is characterized by tumor-like deposition of calcium in periarticular soft tissue. Spinal involvement is rare, and perioperative diagnosis of tumoral calcinosis can be difficult because lesions may be confused with bony neoplasms. Symptoms of tumoral calcinosis result from bony involvement and/or direct compression of surrounding anatomical structures, for which treatment with surgical decompression can be highly successful. The craniovertebral junction is rarely affected by tumoral calcinosis, and patients with this condition may present with distinct symptoms. Herein, to their knowledge the authors present the first case of tumoral calcinosis affecting the craniovertebral junction in a patient who presented with severe dysphagia and required transoral decompression. Recognition of tumoral calcinosis by neurosurgeons is essential for facilitating diagnosis and treatment, and the transoral approach is an effective method for decompression in select patients.
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Mooney MA, Moon K, Gross BA, Ducruet AF, Albuquerque FC. Incidence of delivery wire recapture failure with the Pipeline Flex device. J Neurointerv Surg 2017; 9:571-573. [DOI: 10.1136/neurintsurg-2016-012856] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 11/04/2022]
Abstract
BackgroundThe Pipeline Flex embolization device has several advantages over the first-generation Pipeline embolization device (Covidien, Dublin, Republic of Ireland). Despite these advantages, we have observed frequent difficulty in recapturing the device's delivery wire.ObjectiveTo prospectively document the incidence of failure to recapture the delivery wire.MethodsWe tracked our experience in patients undergoing endovascular treatment with a flow-diverting stent for cerebral aneurysms between 1 May and 30 September 2016. Patient and lesion characteristics, device dimensions, and technical outcomes of delivery wire recapture were prospectively recorded for each device.ResultsEighteen devices were deployed in 15 patients by the senior author (FCA) during this period. Failure to recapture the delivery wire occurred in 10 of 18 (56%) cases. No adverse outcomes of delivery wire recapture failure were encountered in this series.ConclusionsThe incidence of delivery wire recapture failure with the Pipeline Flex device is high. Failure to recapture the delivery wire carries a theoretical risk of stent displacement when re-navigating across the device, and endovascular surgeons should be aware of this limitation. Authors are encouraged to report delivery wire recapture failure rates in future clinical series in which the Pipeline Flex device is used.
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Abstract
Developmental venous anomalies (DVAs) are relatively common lesions, present in up to 3% of the population. The defining characteristic of these lesions is the confluence of radially oriented veins into a single dilated venous channel. DVAs are also known as cerebral venous angiomas, cerebral venous malformations, and cerebral venous medullary malformations. They are the most common type of cerebral vascular malformation found on autopsy studies, and they are often encountered as incidental findings on neuroimaging studies. DVAs are congenital lesions thought to arise from aberrations that occur during venous development, but continue to provide the normal venous drainage to the cerebral territory in which they reside. Although the natural history of DVAs is benign, they may be associated with cavernous malformations or other vascular abnormalities, which can lead to hemorrhage in the vicinity of the DVA. Surgical or endovascular obliteration of DVAs carries a significant risk of venous infarction; thus, conservative management is the treatment of choice for patients with these lesions.
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Mooney MA, McWeeney SK, Faraone SV, Hinney A, Hebebrand J, Nigg JT, Wilmot B. Pathway analysis in attention deficit hyperactivity disorder: An ensemble approach. Am J Med Genet B Neuropsychiatr Genet 2016; 171:815-26. [PMID: 27004716 PMCID: PMC4983253 DOI: 10.1002/ajmg.b.32446] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/07/2016] [Indexed: 12/21/2022]
Abstract
Despite a wealth of evidence for the role of genetics in attention deficit hyperactivity disorder (ADHD), specific and definitive genetic mechanisms have not been identified. Pathway analyses, a subset of gene-set analyses, extend the knowledge gained from genome-wide association studies (GWAS) by providing functional context for genetic associations. However, there are numerous methods for association testing of gene sets and no real consensus regarding the best approach. The present study applied six pathway analysis methods to identify pathways associated with ADHD in two GWAS datasets from the Psychiatric Genomics Consortium. Methods that utilize genotypes to model pathway-level effects identified more replicable pathway associations than methods using summary statistics. In addition, pathways implicated by more than one method were significantly more likely to replicate. A number of brain-relevant pathways, such as RhoA signaling, glycosaminoglycan biosynthesis, fibroblast growth factor receptor activity, and pathways containing potassium channel genes, were nominally significant by multiple methods in both datasets. These results support previous hypotheses about the role of regulation of neurotransmitter release, neurite outgrowth and axon guidance in contributing to the ADHD phenotype and suggest the value of cross-method convergence in evaluating pathway analysis results. © 2016 Wiley Periodicals, Inc.
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Mooney MA, McWeeney SK, Faraone SV, Hinney A, Hebebrand J, Nigg JT, Wilmot B. Cover Image, Volume 171B, Number 6, September 2016. AMERICAN JOURNAL OF MEDICAL GENETICS PART B: NEUROPSYCHIATRIC GENETICS 2016. [DOI: 10.1002/ajmg.b.32490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Mooney MA, Simon ED, Little AS. Advancing Treatment of Pituitary Adenomas through Targeted Molecular Therapies: The Acromegaly and Cushing Disease Paradigms. Front Surg 2016; 3:45. [PMID: 27517036 PMCID: PMC4963385 DOI: 10.3389/fsurg.2016.00045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/12/2016] [Indexed: 11/14/2022] Open
Abstract
The current treatment of pituitary adenomas requires a balance of conservative management, surgical resection, and in select tumor types, molecular therapy. Acromegaly treatment is an evolving field where our understanding of molecular targets and drug therapies has improved treatment options for patients with excess growth hormone levels. We highlight the use of molecular therapies in this disease process and advances in this field, which may represent a paradigm shift for the future of pituitary adenoma treatment.
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Raygor KP, Mooney MA, Snyder LA, Levitt MR, Albuquerque FC, Spetzler RF. Pseudoaneurysm of Distal Anterior Cerebral Artery Branch Following External Ventricular Drain Placement. Oper Neurosurg (Hagerstown) 2016; 12:77-82. [PMID: 29506250 DOI: 10.1227/neu.0000000000001039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/17/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND External ventricular drains (EVDs) are routinely placed as part of the management of intracranial hypertension. Pseudoaneurysm formation after EVD placement is a rare complication that can occur as a result of direct trauma to the cerebral vasculature. Prompt recognition and treatment may prevent future rupture. OBJECTIVE To present our management strategy of a unique case of pseudoaneurysm formation in the context of the medical literature on these rare complications. METHODS An EVD was placed in a 58-year-old female patient who presented with intracranial hypertension after subarachnoid hemorrhage secondary to a ruptured posterior communicating artery aneurysm before coiling of the aneurysm. On postbleed day 10, a pseudoaneurysm was identified in the distal anterior cerebral artery adjacent to the EVD tract. RESULTS The pseudoaneurysm was successfully treated with surgical resection. CONCLUSION Pseudoaneurysm formation after EVD placement is a rare but serious complication. We do not recommend routine screening for this complication; however, further investigation may be warranted when a delayed EVD tract hemorrhage is encountered. Prompt treatment of pseudoaneurysms is necessary to prevent future hemorrhage.
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Mooney MA, Zaidi HA, Spetzler RF. Identifying Patients at Risk for Vasospasm After Aneurysmal Subarachnoid Hemorrhage Using Genetic Sequencing. World Neurosurg 2015; 84:1520-1. [DOI: 10.1016/j.wneu.2015.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/01/2015] [Indexed: 11/28/2022]
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Mooney MA, Wilmot B. Gene set analysis: A step-by-step guide. Am J Med Genet B Neuropsychiatr Genet 2015; 168:517-27. [PMID: 26059482 PMCID: PMC4638147 DOI: 10.1002/ajmg.b.32328] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/20/2015] [Indexed: 12/21/2022]
Abstract
To maximize the potential of genome-wide association studies, many researchers are performing secondary analyses to identify sets of genes jointly associated with the trait of interest. Although methods for gene-set analyses (GSA), also called pathway analyses, have been around for more than a decade, the field is still evolving. There are numerous algorithms available for testing the cumulative effect of multiple SNPs, yet no real consensus in the field about the best way to perform a GSA. This paper provides an overview of the factors that can affect the results of a GSA, the lessons learned from past studies, and suggestions for how to make analysis choices that are most appropriate for different types of data. © 2015 Wiley Periodicals, Inc.
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Mooney MA, Kalani MYS, Nakaji P, Albuquerque FC, McDougall CG, Spetzler RF, Zabramski JM. Long-term Patient Outcomes After Microsurgical Treatment of Blister-Like Aneurysms of the Basilar Artery. Oper Neurosurg (Hagerstown) 2015; 11 Suppl 3:387-93. [DOI: 10.1227/neu.0000000000000866] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Abstract
BACKGROUND
Blister-like aneurysms (BLAs) are challenging lesions that require unique microsurgical strategies. BLAs are predominantly found along the internal carotid artery; however, BLAs of the basilar artery are a rare subset that requires a modified treatment strategy.
OBJECTIVE
To discuss the microsurgical management and review the long-term outcomes of patients with BLAs of the basilar artery.
METHODS
We retrospectively reviewed the surgical technique, postoperative results, and long-term outcomes of all patients with basilar artery BLAs treated at our institution from 2005 to 2011.
RESULTS
Four patients with basilar artery BLAs were identified over this 6-year interval. All 4 patients were treated by direct microsurgical clipping. A thin layer of cotton reinforcement was used beneath the clip tines to minimize the risk of clip slippage in 2 of 4 patients; 1 patient required adjunctive endovascular stent placement for residual aneurysm after clipping. Complete obliteration of all aneurysms was achieved, and there has been no recurrence at mean clinical follow-up of 72 months (median, 74.5; range, 37-103) and imaging follow-up of 48 months (median, 54; range 12-72).
CONCLUSION
Direct clipping with or without cotton reinforcement can obliterate basilar BLAs with excellent long-term outcomes. Clip wrapping is not an option for these lesions given the proximity to perforating branches. Endovascular techniques provide a useful adjunctive strategy; however, risks with antiplatelet therapy in the acute subarachnoid hemorrhage period must be considered.
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Georges JF, Liu X, Eschbacher J, Nichols J, Mooney MA, Joy A, Spetzler RF, Feuerstein BG, Preul MC, Anderson T, Yan H, Nakaji P. Use of a conformational switching aptamer for rapid and specific ex vivo identification of central nervous system lymphoma in a xenograft model. PLoS One 2015; 10:e0123607. [PMID: 25876071 PMCID: PMC4398547 DOI: 10.1371/journal.pone.0123607] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 03/04/2015] [Indexed: 01/17/2023] Open
Abstract
Improved tools for providing specific intraoperative diagnoses could improve patient care. In neurosurgery, intraoperatively differentiating non-operative lesions such as CNS B-cell lymphoma from operative lesions can be challenging, often necessitating immunohistochemical (IHC) procedures which require up to 24-48 hours. Here, we evaluate the feasibility of generating rapid ex vivo specific labeling using a novel lymphoma-specific fluorescent switchable aptamer. Our B-cell lymphoma-specific switchable aptamer produced only low-level fluorescence in its unbound conformation and generated an 8-fold increase in fluorescence once bound to its target on CD20-positive lymphoma cells. The aptamer demonstrated strong binding to B-cell lymphoma cells within 15 minutes of incubation as observed by flow cytometry. We applied the switchable aptamer to ex vivo xenograft tissue harboring B-cell lymphoma and astrocytoma, and within one hour specific visual identification of lymphoma was routinely possible. In this proof-of-concept study in human cell culture and orthotopic xenografts, we conclude that a fluorescent switchable aptamer can provide rapid and specific labeling of B-cell lymphoma, and that developing aptamer-based labeling approaches could simplify tissue staining and drastically reduce time to histopathological diagnoses compared with IHC-based methods. We propose that switchable aptamers could enhance expeditious, accurate intraoperative decision-making.
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Ikard SJ, Rittgers J, Revil A, Mooney MA. Geophysical investigation of seepage beneath an earthen dam. GROUND WATER 2015; 53:238-250. [PMID: 24635516 DOI: 10.1111/gwat.12185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Accepted: 02/04/2014] [Indexed: 06/03/2023]
Abstract
A hydrogeophysical survey is performed at small earthen dam that overlies a confined aquifer. The structure of the dam has not shown evidence of anomalous seepage internally or through the foundation prior to the survey. However, the surface topography is mounded in a localized zone 150 m downstream, and groundwater discharges from this zone periodically when the reservoir storage is maximum. We use self-potential and electrical resistivity tomography surveys with seismic refraction tomography to (1) determine what underlying hydrogeologic factors, if any, have contributed to the successful long-term operation of the dam without apparent indicators of anomalous seepage through its core and foundation; and (2) investigate the hydraulic connection between the reservoir and the seepage zone to determine whether there exists a potential for this success to be undermined. Geophysical data are informed by hydraulic and geotechnical borehole data. Seismic refraction tomography is performed to determine the geometry of the phreatic surface. The hydro-stratigraphy is mapped with the resistivity data and groundwater flow patterns are determined with self-potential data. A self-potential model is constructed to represent a perpendicular profile extending out from the maximum cross-section of the dam, and self-potential data are inverted to recover the groundwater velocity field. The groundwater flow pattern through the aquifer is controlled by the bedrock topography and a preferential flow pathway exists beneath the dam. It corresponds to a sandy-gravel layer connecting the reservoir to the downstream seepage zone.
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Mooney MA, Nigg JT, McWeeney SK, Wilmot B. ‘Pitfalls in the application of gene set analysis to genetics studies’: a response. Trends Genet 2014; 30:514-5. [PMID: 25459302 PMCID: PMC4476633 DOI: 10.1016/j.tig.2014.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
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Mooney MA, Zehri AH, Georges JF, Nakaji P. Laser scanning confocal endomicroscopy in the neurosurgical operating room: a review and discussion of future applications. Neurosurg Focus 2014; 36:E9. [PMID: 24484262 DOI: 10.3171/2013.11.focus13484] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Laser scanning confocal endomicroscopy (LSCE) is an emerging technology for examining brain neoplasms in vivo. While great advances have been made in macroscopic fluorescence in recent years, the ability to perform confocal microscopy in vivo expands the potential of fluorescent tumor labeling, can improve intraoperative tissue diagnosis, and provides real-time guidance for tumor resection intraoperatively. In this review, the authors highlight the technical aspects of confocal endomicroscopy and fluorophores relevant to the neurosurgeon, provide a comprehensive summary of LSCE in animal and human neurosurgical studies to date, and discuss the future directions and potential for LSCE in neurosurgery.
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Georges J, Zehri A, Carlson E, Nichols J, Mooney MA, Martirosyan NL, Ghaffari L, Kalani MYS, Eschbacher J, Feuerstein B, Anderson T, Preul MC, Van Keuren-Jensen K, Nakaji P. Label-free microscopic assessment of glioblastoma biopsy specimens prior to biobanking [corrected]. Neurosurg Focus 2014; 36:E8. [PMID: 24484261 DOI: 10.3171/2013.11.focus13478] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Glioblastoma is the most common primary brain tumor with a median 12- to 15-month patient survival. Improving patient survival involves better understanding the biological mechanisms of glioblastoma tumorigenesis and seeking targeted molecular therapies. Central to furthering these advances is the collection and storage of surgical biopsies (biobanking) for research. This paper addresses an imaging modality, confocal reflectance microscopy (CRM), for safely screening glioblastoma biopsy samples prior to biobanking to increase the quality of tissue provided for research and clinical trials. These data indicate that CRM can immediately identify cellularity of tissue biopsies from animal models of glioblastoma. When screening fresh human biopsy samples, CRM can differentiate a cellular glioblastoma biopsy from a necrotic biopsy without altering DNA, RNA, or protein expression of sampled tissue. These data illustrate CRM's potential for rapidly and safely screening clinical biopsy samples prior to biobanking, which demonstrates its potential as an effective screening technique that can improve the quality of tissue biobanked for patients with glioblastoma.
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Mooney MA, Nigg JT, McWeeney SK, Wilmot B. Functional and genomic context in pathway analysis of GWAS data. Trends Genet 2014; 30:390-400. [PMID: 25154796 DOI: 10.1016/j.tig.2014.07.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/18/2014] [Accepted: 07/18/2014] [Indexed: 02/07/2023]
Abstract
Gene set analysis (GSA) is a promising tool for uncovering the polygenic effects associated with complex diseases. However, the available techniques reflect a wide variety of hypotheses about how genetic effects interact to contribute to disease susceptibility. The lack of consensus about the best way to perform GSA has led to confusion in the field and has made it difficult to compare results across methods. A clear understanding of the various choices made during GSA - such as how gene sets are defined, how single-nucleotide polymorphisms (SNPs) are assigned to genes, and how individual SNP-level effects are aggregated to produce gene- or pathway-level effects - will improve the interpretability and comparability of results across methods and studies. In this review we provide an overview of the various data sources used to construct gene sets and the statistical methods used to test for gene set association, as well as provide guidelines for ensuring the comparability of results.
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Zehri AH, Ramey W, Georges JF, Mooney MA, Martirosyan NL, Preul MC, Nakaji P. Neurosurgical confocal endomicroscopy: A review of contrast agents, confocal systems, and future imaging modalities. Surg Neurol Int 2014; 5:60. [PMID: 24872922 PMCID: PMC4033764 DOI: 10.4103/2152-7806.131638] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/13/2014] [Indexed: 01/15/2023] Open
Abstract
Background: The clinical application of fluorescent contrast agents (fluorescein, indocyanine green, and aminolevulinic acid) with intraoperative microscopy has led to advances in intraoperative brain tumor imaging. Their properties, mechanism of action, history of use, and safety are analyzed in this report along with a review of current laser scanning confocal endomicroscopy systems. Additional imaging modalities with potential neurosurgical utility are also analyzed. Methods: A comprehensive literature search was performed utilizing PubMed and key words: In vivo confocal microscopy, confocal endomicroscopy, fluorescence imaging, in vivo diagnostics/neoplasm, in vivo molecular imaging, and optical imaging. Articles were reviewed that discussed clinically available fluorophores in neurosurgery, confocal endomicroscopy instrumentation, confocal microscopy systems, and intraoperative cancer diagnostics. Results: Current clinically available fluorescent contrast agents have specific properties that provide microscopic delineation of tumors when imaged with laser scanning confocal endomicroscopes. Other imaging modalities such as coherent anti-Stokes Raman scattering (CARS) microscopy, confocal reflectance microscopy, fluorescent lifetime imaging (FLIM), two-photon microscopy, and second harmonic generation may also have potential in neurosurgical applications. Conclusion: In addition to guiding tumor resection, intraoperative fluorescence and microscopy have the potential to facilitate tumor identification and complement frozen section analysis during surgery by providing real-time histological assessment. Further research, including clinical trials, is necessary to test the efficacy of fluorescent contrast agents and optical imaging instrumentation in order to establish their role in neurosurgery.
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Lee SY, Mooney MA, Inra ML, Juluru K, Fox AN, Olsen SK, Brown RS, Emond JC, Cherqui D, Kluger MD. Exposure to ionizing radiation during liver transplantation evaluation, waitlist time, and in the postoperative period: a cause for concern. Hepatology 2014; 59:496-504. [PMID: 23904338 DOI: 10.1002/hep.26633] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/02/2013] [Accepted: 07/10/2013] [Indexed: 01/11/2023]
Abstract
UNLABELLED Substantial evidence has linked ionizing radiation exposure (RE) to oncogenesis. Patients evaluated for transplantation undergo extensive diagnostic imaging and have increased baseline cancer risk factors. The objective was to examine exposure in a cohort of patients undergoing evaluation and liver transplantation. Radiation exposure from all diagnostic examinations and procedures were retrospectively recorded. Radiation exposure is reported in mSv, a standardized measure of the detrimental biologic effect of radiation which allows for population-level comparisons. Seventy-four patients (69% male, mean 57 years) were evaluated, of which 13 of 35 subsequently listed patients were transplanted; an additional 18 previously evaluated patients were also transplanted during 2010. The most common indications were hepatitis C (55%) and hepatocellular carcinoma (HCC) (30%). The median observation period was 14 months. In all, 1,826 imaging examinations were performed, of which 408 (22%) involved considerable ionizing radiation and were the focus of investigation. Median annualized effective RE was 51 mSv (interquartile range [IQR]: 19,126), with 10% exposed to almost twice the amount of radiation recommended for a 5-year period. Patients with HCC received significantly (P < 0.00001) higher median annualized effective RE than patients without HCC, 137 mSv (IQR: 87,259) versus 32 mSv (IQR: 13,57), respectively. Computed tomography (CT) abdomen (23%) and chest (16%) accounted for the most common exposures, with CT abdomen accounting for 46% of overall cohort RE. CONCLUSION Patients undergoing evaluation and liver transplantation at our center are exposed to very high levels of ionizing radiation. Although long-term effects in these patients are yet to be defined, the theoretical increased risk of malignancy must be given its due consideration. Routine use of nonradiation imaging and reconsideration of indications may be preferred and justified in this population.
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Mooney MA, Wilmot B, McWeeney SK. The GA and the GWAS: using genetic algorithms to search for multilocus associations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2012; 9:899-910. [PMID: 22025762 PMCID: PMC3748153 DOI: 10.1109/tcbb.2011.145] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Enormous data collection efforts and improvements in technology have made large genome-wide association studies a promising approach for better understanding the genetics of common diseases. Still, the knowledge gained from these studies may be extended even further by testing the hypothesis that genetic susceptibility is due to the combined effect of multiple variants or interactions between variants. Here we explore and evaluate the use of a genetic algorithm to discover groups of SNPs (of size 2, 3, or 4) that are jointly associated with bipolar disorder. The algorithm is guided by the structure of a gene interaction network, and is able to find groups of SNPs that are strongly associated with the disease, while performing far fewer statistical tests than other methods.
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Walter NAR, Bottomly D, Laderas T, Mooney MA, Darakjian P, Searles RP, Harrington CA, McWeeney SK, Hitzemann R, Buck KJ. High throughput sequencing in mice: a platform comparison identifies a preponderance of cryptic SNPs. BMC Genomics 2009; 10:379. [PMID: 19686600 PMCID: PMC2743714 DOI: 10.1186/1471-2164-10-379] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 08/17/2009] [Indexed: 11/29/2022] Open
Abstract
Background Allelic variation is the cornerstone of genetically determined differences in gene expression, gene product structure, physiology, and behavior. However, allelic variation, particularly cryptic (unknown or not annotated) variation, is problematic for follow up analyses. Polymorphisms result in a high incidence of false positive and false negative results in hybridization based analyses and hinder the identification of the true variation underlying genetically determined differences in physiology and behavior. Given the proliferation of mouse genetic models (e.g., knockout models, selectively bred lines, heterogeneous stocks derived from standard inbred strains and wild mice) and the wealth of gene expression microarray and phenotypic studies using genetic models, the impact of naturally-occurring polymorphisms on these data is critical. With the advent of next-generation, high-throughput sequencing, we are now in a position to determine to what extent polymorphisms are currently cryptic in such models and their impact on downstream analyses. Results We sequenced the two most commonly used inbred mouse strains, DBA/2J and C57BL/6J, across a region of chromosome 1 (171.6 – 174.6 megabases) using two next generation high-throughput sequencing platforms: Applied Biosystems (SOLiD) and Illumina (Genome Analyzer). Using the same templates on both platforms, we compared realignments and single nucleotide polymorphism (SNP) detection with an 80 fold average read depth across platforms and samples. While public datasets currently annotate 4,527 SNPs between the two strains in this interval, thorough high-throughput sequencing identified a total of 11,824 SNPs in the interval, including 7,663 new SNPs. Furthermore, we confirmed 40 missense SNPs and discovered 36 new missense SNPs. Conclusion Comparisons utilizing even two of the best characterized mouse genetic models, DBA/2J and C57BL/6J, indicate that more than half of naturally-occurring SNPs remain cryptic. The magnitude of this problem is compounded when using more divergent or poorly annotated genetic models. This warrants full genomic sequencing of the mouse strains used as genetic models.
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Abstract
PURPOSE Prader-Willi syndrome (PWS) refers to a genetic disorder induced by an anomaly on chromosome 15 occurring with a frequency of one in 10,000 to 20,000. It is characterized by a unique set of features including infantile hypotonia, obesity in childhood, small hands and feet, hypogonadism, and mental retardation. Reported here are the results of ophthalmic examinations of persons with PWS, together with results from controls comparable in age, percentage of body fat, and intelligence. These data bear on the hypothesis that the ocular anomalies in PWS are unique to this syndrome. METHOD A comprehensive investigation of PWS brought children and adults to Vanderbilt University for extended testing, which included an ophthalmic examination. Genetic analysis determined unequivocally the PWS diagnosis and identified subgroups-deletion and maternal disomy. A group of persons without PWS but generally comparable in age, body composition, and intelligence served as controls. RESULTS Significant differences between the deletion and disomy subgroups were not found for the clinical ophthalmic measures. The incidence of anomalies in the combined PWS was similar to those reported in previous studies. A similar pattern was present in the control group except for myopia and stereopsis. An effect of genetic subgroup, however, was observed for random element stereopsis with the maternal disomy group having a greater degree of impairment. CONCLUSION The overall similarity between the PWS and control groups on all measures except myopia and stereopsis suggest that many of the anomalies in PWS found in prior studies are due to factors inherent in a general dysfunctional population, rather than reflective of an ocular signature unique to PWS.
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Mooney MA, Vaughn DM, Reinhart GA, Powers RD, Wright JC, Hoffman CE, Swaim SF, Baker HJ. Evaluation of the effects of omega-3 fatty acid-containing diets on the inflammatory stage of wound healing in dogs. Am J Vet Res 1998; 59:859-63. [PMID: 9659552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVES To ascertain the effects of dietary omega-3 (n-3) fatty acids on biochemical and histopathologic components of the inflammatory stage of wound healing. ANIMALS 30 purpose-bred Beagles. PROCEDURE Dogs were allotted to 5 groups of 6. Each group was fed a unique dietary fatty acid ratio of omega-6 to n-3--diet A, 5.3:1; diet B, 10.4:1; diet C, 24.1:1; diet D, 51.6:1; and diet E, 95.8:1. Dogs were fed once daily for 12 weeks, then biopsy specimens were taken from 4-day-old wounds of each dog and analyzed by gas chromatography-mass spectrometry for: prostaglandin E2 (PGE2) metabolites, and ratios of omega-6 to n-3 fatty acids, arachidonic acid (AA) to eicosapentaenoic acid (EPA), adrenic acid to docosahexaenoic acid, and PGE2 to prostaglandin E3 (PGE3) metabolites. RESULTS Qualitative analysis was carried out on AA, EPA, adrenic acid, docosahexaenoic acid, and the major metabolite from the PGE2 and PGE3 pathway. These molecules were further quantified with respect to diet to determine significant differences. By analysis of the AA-to-EPA ratio, diet A was different from diets D and E and diets B and C were different from diet E (P < 0.05). By analysis of the PGE2-to-PGE3 metabolite ratio, diet A was different from diet E (P < 0.05). Though biochemical analysis indicated dietary dependence, histopathologic data indicated no significant difference with respect to diet groups. CONCLUSION The biochemical component of the inflammatory stage of wound healing can be manipulated by diet. CLINICAL RELEVANCE Omega-3 fatty acid-enriched diets can be used to control inflammation associated with dermatologic conditions.
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Finno RJ, Harris WW, Mooney MA, Viggiani G. Strain Localization and Undrained Steady State of Sand. ACTA ACUST UNITED AC 1996. [DOI: 10.1061/(asce)0733-9410(1996)122:6(462)] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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