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Chatrath A, Lemieux M, Patel RP, Roberts KF, Dahiya S, Pennicooke B. Spinal calcifying pseudoneoplasms of the neuraxis: A case report and review of the literature. World Neurosurg X 2024; 23:100312. [PMID: 38497058 PMCID: PMC10937954 DOI: 10.1016/j.wnsx.2024.100312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Calcifying pseudoneoplasms of the neuraxis (CAPNON) are rare, non-neoplastic, slow-growing tumors that can present anywhere throughout the central nervous system. While the etiology of these lesions remains unknown, the mainstay of treatment is surgical excision. We describe a case of CAPNON at our institution in a 66 year-old female patient who presented with 5 months of pain and burning sensation in her thigh. On MRI, an intradural extramedullary lesion was identified at the level of T11-T12. The mass was surgically excised and the patient reported resolution of her symptoms by her six week follow-up appointment. We reviewed 79 spinal CAPNON cases, covering all cases reported in the literature thus far. In summary, we find that spinal CAPNON are most commonly lumbar and extradural in location, with pain as the most common presenting symptom. Lesions are well-defined and hypointense on T1 and T2 MRI sequence. The majority of cases had favorable surgical outcomes with near complete resolution of pain and associated symptoms.
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Affiliation(s)
- Ajay Chatrath
- Department of Neurosurgery, Washington University School of Medicine in St. Louis, MO, USA
| | - Mackenzie Lemieux
- Department of Neurosurgery, Washington University School of Medicine in St. Louis, MO, USA
| | - Rujvee P. Patel
- Department of Neurosurgery, Washington University School of Medicine in St. Louis, MO, USA
| | - Kaleigh F. Roberts
- Department of Pathology & Immunology, Division of Neuropathology, Washington University School of Medicine in St. Louis, MO, USA
| | - Sonika Dahiya
- Department of Pathology & Immunology, Division of Neuropathology, Washington University School of Medicine in St. Louis, MO, USA
| | - Brenton Pennicooke
- Department of Neurosurgery, Washington University School of Medicine in St. Louis, MO, USA
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Chatrath A, Kosyakovsky J, Patel P, Ahn J, Elsarrag M, Young LC, Wu A, Sokolowski JD, Taylor D, Jane JA, Lopes MBS. Impact of histopathological classification of non-functioning adenomas on long term outcomes: comparison of the 2004 and 2017 WHO classifications. Pituitary 2022; 25:988-996. [PMID: 36261697 DOI: 10.1007/s11102-022-01281-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/23/2022] [Indexed: 10/24/2022]
Abstract
PURPOSE Outcomes of patients with non-functioning pituitary adenomas categorized using the 2004 and 2017 WHO classification systems are understudied. We report outcomes from the University of Virginia of patients with non-functioning pituitary adenomas categorized using both systems. METHODS We constructed a database from all 239 patients who underwent resection of a non-functioning pituitary adenoma between 2003 and 2015 and had at least 5 years of follow-up. Pathologic diagnosis was determined under both the 2004 and 2017 WHO classification systems. We compared the rates of recurrence and progression between subtypes using univariate and multivariate Cox regression analyses. RESULTS Nearly 30% of the tumors in our database were classified as null cell adenomas under the 2004 classification system, whereas only 10% of the tumors were classified as null cell adenomas using the 2017 classification system. Most of these tumors were reclassified as either corticotroph or gonadotroph adenomas. Despite our relatively large cohort and average follow-up of nearly 9 years, we did not detect a significant difference in recurrence and progression between subtypes. CONCLUSIONS The majority of null cell adenomas diagnosed under the 2004 WHO classification system are reclassified as gonadotroph or corticotroph adenomas under the 2017 WHO classification system. Rates of progression and recurrence between subtypes are not as different as previously believed at our institution and require a larger cohort to further investigate.
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Affiliation(s)
- Ajay Chatrath
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacob Kosyakovsky
- Department of Neurological Surgery, University of Virginia Health System, P.O. Box 800212, Charlottesville, VA, 22908-0711, USA
| | - Parantap Patel
- Department of Neurological Surgery, University of Maryland, Baltimore, MD, USA
| | - Jungeun Ahn
- Department of Neurological Surgery, University of Virginia Health System, P.O. Box 800212, Charlottesville, VA, 22908-0711, USA
| | - Mazin Elsarrag
- Department of Ophthalmology, MedStar Washington Hospital Center, Washington, DC, USA
| | - Lena C Young
- Department of Pathology, University of Virginia Health System, P.O. Box 800214, Charlottesville, VA, 22908-0214, USA
| | - Angela Wu
- Department of Pathology, University of Virginia Health System, P.O. Box 800214, Charlottesville, VA, 22908-0214, USA
| | - Jennifer D Sokolowski
- Department of Neurological Surgery, University of Virginia Health System, P.O. Box 800212, Charlottesville, VA, 22908-0711, USA
| | - Davis Taylor
- Naval Medical Center Portsmouth, Portsmouth, VA, USA
| | - John A Jane
- Department of Neurological Surgery, University of Virginia Health System, P.O. Box 800212, Charlottesville, VA, 22908-0711, USA.
| | - M Beatriz S Lopes
- Department of Neurological Surgery, University of Virginia Health System, P.O. Box 800212, Charlottesville, VA, 22908-0711, USA.
- Department of Pathology, University of Virginia Health System, P.O. Box 800214, Charlottesville, VA, 22908-0214, USA.
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Sahu D, Chatrath A, Ratan A, Dutta A. Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer. STAR Protoc 2022; 3:101273. [PMID: 35403010 PMCID: PMC8987392 DOI: 10.1016/j.xpro.2022.101273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Germline Variants (GVs) are effective in predicting cancer risk and may be relevant in predicting patient outcomes. Here we provide a bioinformatic pipeline to identify GVs from the TCGA lower grade glioma cohort in Genomics Data Commons. We integrate paired whole exome sequences from normal and tumor samples and RNA sequences from tumor samples to determine a patient’s GV status. We then identify the subset of GVs that are predictive of patient outcomes by Cox regression. For complete details on the use and execution of this protocol, please refer to Chatrath et al. (2019) and Chatrath et al. (2020). Integration of whole-exome and RNA sequences to determine Germline Variants (GVs) Whole-exome and RNA sequences from tumors resolve low coverage issue in normal samples High correlation of GV allele frequencies between patient data and the GnomAD database GVs predict patient cancer outcome
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Sienkiewicz K, Chen J, Chatrath A, Lawson JT, Sheffield NC, Zhang L, Ratan A. Detecting molecular subtypes from multi-omics datasets using SUMO. Cell Rep Methods 2022; 2:100152. [PMID: 35211690 PMCID: PMC8865426 DOI: 10.1016/j.crmeth.2021.100152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 08/27/2021] [Accepted: 12/21/2021] [Indexed: 12/31/2022]
Abstract
We present a data integration framework that uses non-negative matrix factorization of patient-similarity networks to integrate continuous multi-omics datasets for molecular subtyping. It is demonstrated to have the capability to handle missing data without using imputation and to be consistently among the best in detecting subtypes with differential prognosis and enrichment of clinical associations in a large number of cancers. When applying the approach to data from individuals with lower-grade gliomas, we identify a subtype with a significantly worse prognosis. Tumors assigned to this subtype are hypomethylated genome wide with a gain of AP-1 occupancy in demethylated distal enhancers. The tumors are also enriched for somatic chromosome 7 (chr7) gain, chr10 loss, and other molecular events that have been suggested as diagnostic markers for "IDH wild type, with molecular features of glioblastoma" by the cIMPACT-NOW consortium but have yet to be included in the World Health Organization (WHO) guidelines.
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Affiliation(s)
- Karolina Sienkiewicz
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jinyu Chen
- Department of Mathematics and Computational Biology Program, National University of Singapore, Singapore 119076, Singapore
| | - Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - John T. Lawson
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
| | - Nathan C. Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Cancer Center, Charlottesville, VA 22908, USA
| | - Louxin Zhang
- Department of Mathematics and Computational Biology Program, National University of Singapore, Singapore 119076, Singapore
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
- University of Virginia Cancer Center, Charlottesville, VA 22908, USA
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Shepard MJ, Xu Z, Kearns K, Li C, Chatrath A, Sheehan K, Sheehan D, Faramand A, Niranjan A, Kano H, Gurewitz J, Bernstein K, Liscak R, Guseynova K, Grills IS, Parzen JS, Cifarelli CP, Rehman AA, Atik A, Bakhsheshian J, Zada G, Chang E, Giannotta S, Speckter H, Wu HM, Kondziolka D, Golfinos JG, Mathieu D, Lee CC, Warnick RE, Lunsford LD, Sheehan JP. Stereotactic Radiosurgery for Atypical (World Health Organization II) and Anaplastic (World Health Organization III) Meningiomas: Results From a Multicenter, International Cohort Study. Neurosurgery 2021. [DOI: 10.1093/neuros/nyaa553_s121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Shepard MJ, Xu Z, Kearns K, Li C, Chatrath A, Sheehan K, Sheehan D, Faramand A, Niranjan A, Kano H, Gurewitz J, Bernstein K, Liscak R, Guseynova K, Grills IS, Parzen JS, Cifarelli CP, Rehman AA, Atik A, Bakhsheshian J, Zada G, Chang E, Giannotta S, Speckter H, Wu HM, Kondziolka D, Golfinos JG, Mathieu D, Lee CC, Warnick RE, Lunsford LD, Sheehan JP. Stereotactic Radiosurgery for Atypical (World Health Organization II) and Anaplastic (World Health Organization III) Meningiomas: Results From a Multicenter, International Cohort Study. Neurosurgery 2021; 88:980-988. [PMID: 33469655 DOI: 10.1093/neuros/nyaa553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/04/2020] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Atypical and anaplastic meningiomas have reduced progression-free/overall survival (PFS/OS) compared to benign meningiomas. Stereotactic radiosurgery (SRS) for atypical meningiomas (AMs) and anaplastic meningiomas (malignant meningiomas, MMs) has not been adequately described. OBJECTIVE To define clinical/radiographic outcomes for patients undergoing SRS for AM/MMs. METHODS An international, multicenter, retrospective cohort study was performed to define clinical/imaging outcomes for patients receiving SRS for AM/MMs. Tumor progression was assessed with response assessment in neuro-oncology (RANO) criteria. Factors associated with PFS/OS were assessed using Kaplan-Meier analysis and a Cox proportional hazards model. RESULTS A total of 271 patients received SRS for AMs (n = 233, 85.9%) or MMs (n = 38, 14.0%). Single-fraction SRS was most commonly employed (n = 264, 97.4%) with a mean target dose of 14.8 Gy. SRS was used as adjuvant treatment (n = 85, 31.4%), salvage therapy (n = 182, 67.2%), or primary therapy (1.5%). The 5-yr PFS/OS rate was 33.6% and 77.0%, respectively. Increasing age (hazard ratio (HR) = 1.01, P < .05) and a Ki-67 index > 15% (HR = 1.66, P < .03) negatively correlated with PFS. MMs (HR = 3.21, P < .05), increased age (HR = 1.04, P = .04), and reduced KPS (HR = 0.95, P = .04) were associated with shortened OS. Adjuvant versus salvage SRS did not impact PFS/OS. A shortened interval between surgery and SRS improved PFS for AMs (HR = 0.99, P = .02) on subgroup analysis. Radiation necrosis occurred in 34 (12.5%) patients. Five-year rates of repeat surgery/radiation were 33.8% and 60.4%, respectively. CONCLUSION AM/MMs remain challenging tumors to treat. Elevated proliferative indices are associated with tumor recurrence, while MMs have worse survival. SRS can control AM/MMs in the short term, but the 5-yr PFS rates are low, underscoring the need for improved treatment options for these patients.
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Affiliation(s)
- Matthew J Shepard
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia.,MD Anderson Cancer Center, Houston, Texas
| | - Zhiyuan Xu
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Kathryn Kearns
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Chelsea Li
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Ajay Chatrath
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Kimball Sheehan
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Darrah Sheehan
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
| | - Andrew Faramand
- Center of Image Guided Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Ajay Niranjan
- Center of Image Guided Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Hideyuki Kano
- Center of Image Guided Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | - Roman Liscak
- Department of Stereotactic and Radiation Neurosurgery, Na Homolce Hospital, Prague, Czech Republic
| | - Khumar Guseynova
- Department of Stereotactic and Radiation Neurosurgery, Na Homolce Hospital, Prague, Czech Republic
| | - Inga S Grills
- Department of Radiation Oncology, Beaumont Health, Royal Oak, Michigan
| | - Jacob S Parzen
- Department of Radiation Oncology, Beaumont Health, Royal Oak, Michigan
| | | | - Azeem A Rehman
- Department of Neurologic Surgery, West Virginia University, Morgantown, West Virginia
| | - Ahmet Atik
- Department of Neurologic Surgery, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Joshua Bakhsheshian
- Departments of Neurologic Surgery, University of Southern California, Los Angeles, California
| | - Gabriel Zada
- Departments of Neurologic Surgery, University of Southern California, Los Angeles, California
| | - Eric Chang
- Department of Radiation Oncology, University of Southern California, Los Angeles, California
| | - Steven Giannotta
- Departments of Neurologic Surgery, University of Southern California, Los Angeles, California
| | - Herwin Speckter
- Centro Gamma Knife Dominicano, CEDIMAT, Plaza de la Salud, Santo Domingo, Dominican Republic
| | - Hsiu-Mei Wu
- Department of Radiology, Taipei Veteran General Hospital, Taipei, Taiwan.,National Yang-Ming University School of Medicine, Taipei, Taiwan
| | | | | | - David Mathieu
- Department of Neurosurgery, Université de Sherbrooke, Centre de recherche du CHUS, Sherbrooke, Québec, Canada
| | - Cheng-Chia Lee
- Department of Neurosurgery, Taipei Veteran General Hospital, Taipei, Taiwan.,National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Ronald E Warnick
- Department of Neurologic Surgery, Mayfield Clinic, Cincinnati, Ohio
| | - L Dade Lunsford
- Center of Image Guided Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Jason P Sheehan
- Department of Neurologic Surgery, University of Virginia Health System, Charlottesville, Virginia
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Elsarrag M, Patel PD, Chatrath A, Taylor D, Jane JA. Genomic and molecular characterization of pituitary adenoma pathogenesis: review and translational opportunities. Neurosurg Focus 2021; 48:E11. [PMID: 32480367 DOI: 10.3171/2020.3.focus20104] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/09/2020] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Innovations in genomics, epigenomics, and transcriptomics now lay the groundwork for therapeutic interventions against neoplastic disease. In the past 30 years, the molecular pathogenesis of pituitary adenomas has been characterized. This enhanced understanding of the biology of pituitary tumors has potential to impact current treatment paradigms, and there exists significant translational potential for these results. In this review the authors summarize the results of genomics and molecular biology investigations into pituitary adenoma pathogenesis and behavior and discuss opportunities to translate basic science findings into clinical benefit. METHODS The authors searched the PubMed and MEDLINE databases by using combinations of the keywords "pituitary adenoma," "genomics," "pathogenesis," and "epigenomics." From the initial search, additional articles were individually evaluated and selected. RESULTS Pituitary adenoma growth is primarily driven by unrestrained cell cycle progression, deregulation of growth and proliferation pathways, and abnormal epigenetic regulation of gene expression. These pathways may be amenable to therapeutic intervention. A significant number of studies have attempted to establish links between gene mutations and tumor progression, but a thorough mechanistic understanding remains elusive. CONCLUSIONS Although not currently a prominent aspect in the clinical management of pituitary adenomas, genomics and epigenomic studies may become essential in refining patient care and developing novel pharmacological agents. Future basic science investigations should aim at elucidating mechanistic understandings unique to each pituitary adenoma subtype, which will facilitate rational drug design.
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Chatrath A, Ratan A, Dutta A. Germline variants predictive of tumor mutational burden and immune checkpoint inhibitor efficacy. iScience 2021; 24:102248. [PMID: 33786423 PMCID: PMC7988326 DOI: 10.1016/j.isci.2021.102248] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 01/25/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022] Open
Abstract
High tumor mutational burden (TMB) is associated with response to checkpoint blockade in several cancers. We identify pathogenic germline variants associated with increased TMB (GVITMB). GVITMB were found in 7 genes using a pan-cancer approach (APC, FANCL, SLC25A13, ERCC3, MSH6, PMS2, and TP53) and 38 gene sets (e.g., those involved in DNA repair and programmed cell death). GVITMB were also associated with mutational signatures related to the dysfunction of the gene carrying the variant, somatic mutations that further affect the gene or pathway with the variant, or transcriptomic changes concordant with the expected effect of the variant. In a validation cohort of 140 patients with cutaneous melanoma, we found that patients with GVITMB had prolonged progression-free survival (p = 0.0349, hazard ratio = 0.688) and responded favorably (p = 0.0341, odds = 1.842) when treated with immune checkpoint inhibitors. Our results suggest that germline variants can influence the molecular phenotypes of tumors and predict the response to immune checkpoint inhibitors. GVITMB were found in 7 genes and 38 gene sets GVITMB influence the somatic mutation and gene expression profiles of tumors GVITMB predict immune checkpoint inhibitory efficacy in SKCM
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1240 Pinn Hall, Charlottesville, VA 22908, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, 1240 Pinn Hall, Charlottesville, VA 22908, USA
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Chatrath A, Ratan A, Dutta A. Germline Variants That Affect Tumor Progression. Trends Genet 2020; 37:433-443. [PMID: 33203571 DOI: 10.1016/j.tig.2020.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 01/31/2023]
Abstract
Germline variants have a rich history of being studied in the context of cancer risk. Emerging studies now suggest that germline variants contribute not only to cancer risk but to tumor progression as well. In this opinion article, we discuss the initial discoveries associating germline variants with patient outcome and the mechanisms by which germline variants affect molecular pathways. Germline variants affect molecular pathways through amino acid changes, alteration of splicing patterns or expression of genes, influencing the selection for somatic mutations, and causing genome-wide mutational enrichment. These molecular alterations can lead to tumor phenotypes that become clinically apparent such as metastasis, alterations to the immune microenvironment, and modulation of therapeutic response. Overall, the growing body of evidence suggests that germline variants play a larger role in tumor progression than has been previously appreciated and that germline variation holds substantial potential for improving personalized medicine and patient outcomes.
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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10
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Mullis A, Lu Z, Zhan Y, Wang TY, Rodriguez J, Rajeh A, Chatrath A, Lin Z. Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance. Mol Biol Evol 2020; 37:455-468. [PMID: 31589316 PMCID: PMC6993855 DOI: 10.1093/molbev/msz229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ribosomal protein (RP) genes encode structural components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78–80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. The mechanisms by which the RP genes were duplicated and maintained and their functional significance are poorly understood. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication events for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages: budding yeasts, fission yeasts, and Mucoromycota. The RP gene duplicates in budding yeasts and Mucoromycota were mainly created by whole genome duplication events. However, duplicate RP genes in fission yeasts were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs have been homogenized by repeated gene conversion in each species, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased their transcript abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consume sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.
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Affiliation(s)
- Alison Mullis
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhaolian Lu
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Yu Zhan
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Judith Rodriguez
- Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO
| | - Ahmad Rajeh
- Department of Biology, Saint Louis University, St. Louis, MO.,Program of Bioinformatics and Computational Biology, Saint Louis University, St. Louis, MO
| | - Ajay Chatrath
- Department of Biology, Saint Louis University, St. Louis, MO
| | - Zhenguo Lin
- Department of Biology, Saint Louis University, St. Louis, MO
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11
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Soldozy S, Norat P, Elsarrag M, Chatrath A, Costello JS, Sokolowski JD, Tvrdik P, Kalani MYS, Park MS. The biophysical role of hemodynamics in the pathogenesis of cerebral aneurysm formation and rupture. Neurosurg Focus 2020; 47:E11. [PMID: 31261115 DOI: 10.3171/2019.4.focus19232] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 04/18/2019] [Indexed: 11/06/2022]
Abstract
The pathogenesis of intracranial aneurysms remains complex and multifactorial. While vascular, genetic, and epidemiological factors play a role, nascent aneurysm formation is believed to be induced by hemodynamic forces. Hemodynamic stresses and vascular insults lead to additional aneurysm and vessel remodeling. Advanced imaging techniques allow us to better define the roles of aneurysm and vessel morphology and hemodynamic parameters, such as wall shear stress, oscillatory shear index, and patterns of flow on aneurysm formation, growth, and rupture. While a complete understanding of the interplay between these hemodynamic variables remains elusive, the authors review the efforts that have been made over the past several decades in an attempt to elucidate the physical and biological interactions that govern aneurysm pathophysiology. Furthermore, the current clinical utility of hemodynamics in predicting aneurysm rupture is discussed.
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12
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Chatrath A, Soldozy S, Sokolowski JD, Burke RM, Schultz JG, Rannigan ZC, Park MS. Endovascular and Surgical Treatment Is Predictive of Readmission Risk After Aneurysmal Subarachnoid Hemorrhage. World Neurosurg 2020; 142:e494-e501. [PMID: 32693223 DOI: 10.1016/j.wneu.2020.07.079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 01/01/2023]
Abstract
BACKGROUND Aneurysmal subarachnoid hemorrhage (aSAH) is a debilitating disease process accounting for 5% of strokes. Although improvements in care have reduced the case-fatality rates, patients have an increased risk of neurological and medical complications after discharge. Additionally, the readmission rates have been increasingly used as a metric for patient care quality. METHODS In the present study, we reviewed the medical records of 206 patients who had been treated for aSAH at the University of Virginia from 2011 to 2018 to identify the causes and predictors of readmission. RESULTS The all-cause readmission rate was 9.8%, 15.3%, and 21.3% within 30, 60, and 180 days, respectively. The readmission rate for neurologic causes was 7.7%, 12.6%, and 18.0% within 30, 60, and 180 days, respectively. The neurologic causes of readmission included aneurysm retreatment, cranioplasty, a fall, hydrocephalus, stroke symptoms, and syncope. Surgical treatment (odds ratio [OR], 4.11-6.30) and endovascular treatment (OR, 3.79-8.33) of vasospasm were associated with an increased risk of all-cause readmission. Endovascular aneurysm treatment (OR, 0.22) was associated with a decreased risk of all-cause readmission. The average interval to the first follow-up appointment at our institution was 55.3 ± 63.3 days. Of the patients who had been readmitted from the emergency room, 65% had not had follow-up contact with physicians at our institution until their readmission. CONCLUSIONS To the best of our knowledge, the present study is the first to have examined the readmission rates for subarachnoid hemorrhage >90 days after treatment. Our results have suggested that the readmission rates >90 days after treatment could still be predicted by the hospital and treatment course during admission and that follow-up appointments with patients earlier in the clinic could identify those patients with a greater risk of readmission.
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Affiliation(s)
- Ajay Chatrath
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Sauson Soldozy
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Jennifer D Sokolowski
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Rebecca M Burke
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Julianne G Schultz
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Zuseen C Rannigan
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Min S Park
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia, USA.
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Kumar P, Kiran S, Saha S, Su Z, Paulsen T, Chatrath A, Shibata Y, Shibata E, Dutta A. ATAC-seq identifies thousands of extrachromosomal circular DNA in cancer and cell lines. Sci Adv 2020; 6:eaba2489. [PMID: 32440553 PMCID: PMC7228742 DOI: 10.1126/sciadv.aba2489] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/06/2020] [Indexed: 05/17/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are somatically mosaic and contribute to intercellular heterogeneity in normal and tumor cells. Because short eccDNAs are poorly chromatinized, we hypothesized that they are sequenced by tagmentation in ATAC-seq experiments without any enrichment of circular DNA. Indeed, ATAC-seq identified thousands of eccDNAs in cell lines that were validated by inverse PCR and by metaphase FISH. ATAC-seq in gliomas and glioblastomas identify hundreds of eccDNAs, including one containing the well-known EGFR gene amplicon from chr7. More than 18,000 eccDNAs, many carrying known cancer driver genes, are identified in a pan-cancer analysis of ATAC-seq libraries from 23 tumor types. Somatically mosaic eccDNAs are identified by ATAC-seq even before amplification is recognized by genome-wide copy number variation measurements. Thus, ATAC-seq is a sensitive method to detect eccDNA present in a tumor at the pre-amplification stage and can be used to predict resistance to therapy.
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Affiliation(s)
- Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Shashi Kiran
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yoshiyuki Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Etsuko Shibata
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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14
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Mastorakos P, Xu Z, Yu J, Hess J, Qian J, Chatrath A, Taylor DG, Kondziolka D, Warnick R, Chiang V, Sheehan J. BRAF V600 Mutation and BRAF Kinase Inhibitors in Conjunction With Stereotactic Radiosurgery for Intracranial Melanoma Metastases: A Multicenter Retrospective Study. Neurosurgery 2020; 84:868-880. [PMID: 29846702 DOI: 10.1093/neuros/nyy203] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 04/17/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The BRAF mutation has been identified as a potent target for the treatment of metastatic melanoma and BRAF inhibitors (BRAFi) have demonstrated promising results against melanoma brain metastases (BM). OBJECTIVE To further investigate the effectiveness of this combined treatment regimen. METHODS In this multicenter retrospective cohort study, 198 patients with known BRAF mutation status and treated with stereotactic radiosurgery (SRS) between 2011 and 2015 were identified. Kaplan-Meier methodology and multivariate regression analysis was then used to compare survival based on each parameter. RESULTS The median survival after the diagnosis of BM in patients with BRAF mutation who received BRAFi was increased compared to survival in patients with wild-type BRAF (BRAF wt). In multivariate analysis, the BRAF mutation was an independent, positive prognostic factor with a hazard ratio of 0.59. BRAF mutated Patients who received BRAFi following SRS had improved survival compared to patients who received it before (P < .001) or concurrently (P = .007). PD-1 inhibitors improved survival, with more pronounced effect in patients not carrying the BRAF mutation. Among the patients who were treated with BRAFi, 10.4% developed intracerebral hematoma (ICH), in comparison to 3% of patients who were not treated with BRAFi (P = .03). CONCLUSION In the setting of widespread use of BRAFi, the presence of a BRAF mutation is an independent predictor of better prognosis in patients with melanoma BM that underwent SRS. The effect of BRAFi is optimal when treatment is initiated at least 1 wk following SRS. BRAFi may increase the frequency of asymptomatic ICH.
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Affiliation(s)
- Panagiotis Mastorakos
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia.,Department of Neurological Surgery, National Institutes of Health, Bethesda, Maryland
| | - Zhiyuan Xu
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia
| | - James Yu
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut
| | - Judith Hess
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Jack Qian
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut
| | - Ajay Chatrath
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia
| | - Davis G Taylor
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia
| | | | - Ronald Warnick
- Department of Neurosurgery, University of Cincinnati, Cincinnati, Ohio
| | - Veronica Chiang
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
| | - Jason Sheehan
- Department of Neurological Surgery, University of Virginia, Charlottesville, Virginia.,Department of Radiation Oncology, University of Virginia, Charlottesville, Virginia
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15
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Taylor DG, Chatrath A, Mastorakos P, Paisan G, Chen CJ, Buell TJ, Jane JA. Cerebrospinal fluid area and syringogenesis in Chiari malformation type I. J Neurosurg 2020; 134:825-830. [PMID: 32084641 DOI: 10.3171/2019.11.jns191439] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 11/26/2019] [Indexed: 11/06/2022]
Abstract
OBJECTIVE Syringogenesis in Chiari malformation type I (CM-I) is thought to occur secondary to impaction of the cerebellar tonsils within the foramen magnum (FM). However, the correlation between the CSF area and syringogenesis has yet to be elucidated. The authors sought to determine whether the diminution in subarachnoid space is associated with syringogenesis. Further, the authors sought to determine if syrinx resolution was associated with the degree of expansion of subarachnoid spaces after surgery. METHODS The authors performed a retrospective review of all patients undergoing posterior fossa decompression for CM-I from 2004 to 2016 at the University of Virginia Health System. The subarachnoid spaces at the FM and at the level of the most severe stenosis were measured before and after surgery by manual delineation of the canal and neural tissue area on MRI and verified through automated CSF intensity measurements. Imaging and clinical outcomes were then compared. RESULTS Of 68 patients, 26 had a syrinx at presentation. Syrinx patients had significantly less subarachnoid space at the FM (13% vs 19%, p = 0.0070) compared to those without syrinx. Following matching based on degree of tonsillar herniation and age, the subarachnoid space was significantly smaller in patients with a syrinx (12% vs 19%, p = 0.0015). Syrinx resolution was associated with an increase in patients' subarachnoid space after surgery compared with those patients without resolution (23% vs 10%, p = 0.0323). CONCLUSIONS Syrinx development in CM-I patients is correlated with the degree to which the subarachnoid CSF spaces are diminished at the cranial outlet. Successful syrinx reduction is associated with the degree to which the subarachnoid spaces are increased following surgery.
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Affiliation(s)
- Davis G Taylor
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and
| | - Ajay Chatrath
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and
| | - Panagiotis Mastorakos
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and.,2Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Gabriella Paisan
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and
| | - Ching-Jen Chen
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and
| | - Thomas J Buell
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and
| | - John A Jane
- 1Department of Neurological Surgery, University of Virginia Health System, Charlottesville, Virginia; and
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16
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Chatrath A, Przanowska R, Kiran S, Su Z, Saha S, Wilson B, Tsunematsu T, Ahn JH, Lee KY, Paulsen T, Sobierajska E, Kiran M, Tang X, Li T, Kumar P, Ratan A, Dutta A. The pan-cancer landscape of prognostic germline variants in 10,582 patients. Genome Med 2020; 12:15. [PMID: 32066500 PMCID: PMC7027124 DOI: 10.1186/s13073-020-0718-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/31/2020] [Indexed: 02/08/2023] Open
Abstract
Background While clinical factors such as age, grade, stage, and histological subtype provide physicians with information about patient prognosis, genomic data can further improve these predictions. Previous studies have shown that germline variants in known cancer driver genes are predictive of patient outcome, but no study has systematically analyzed multiple cancers in an unbiased way to identify genetic loci that can improve patient outcome predictions made using clinical factors. Methods We analyzed sequencing data from the over 10,000 cancer patients available through The Cancer Genome Atlas to identify germline variants associated with patient outcome using multivariate Cox regression models. Results We identified 79 prognostic germline variants in individual cancers and 112 prognostic germline variants in groups of cancers. The germline variants identified in individual cancers provide additional predictive power about patient outcomes beyond clinical information currently in use and may therefore augment clinical decisions based on expected tumor aggressiveness. Molecularly, at least 12 of the germline variants are likely associated with patient outcome through perturbation of protein structure and at least five through association with gene expression differences. Almost half of these germline variants are in previously reported tumor suppressors, oncogenes or cancer driver genes with the other half pointing to genomic loci that should be further investigated for their roles in cancers. Conclusions Germline variants are predictive of outcome in cancer patients and specific germline variants can improve patient outcome predictions beyond predictions made using clinical factors alone. The germline variants also implicate new means by which known oncogenes, tumor suppressor genes, and driver genes are perturbed in cancer and suggest roles in cancer for other genes that have not been extensively studied in oncology. Further studies in other cancer cohorts are necessary to confirm that germline variation is associated with outcome in cancer patients as this is a proof-of-principle study. Electronic supplementary material The online version of this article (10.1186/s13073-020-0718-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Roza Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Shashi Kiran
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Zhangli Su
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Takaaki Tsunematsu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Ji-Hye Ahn
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Kyung Yong Lee
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Ewelina Sobierajska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Xiwei Tang
- Department of Statistics, University of Virginia, Charlottesville, VA, USA
| | - Tianxi Li
- Department of Statistics, University of Virginia, Charlottesville, VA, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1240 Pinn Hall, Charlottesville, VA, 22908, USA.
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17
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Saha S, Kiran M, Kuscu C, Chatrath A, Wotton D, Mayo MW, Dutta A. Long Noncoding RNA DRAIC Inhibits Prostate Cancer Progression by Interacting with IKK to Inhibit NF-κB Activation. Cancer Res 2020; 80:950-963. [PMID: 31900260 DOI: 10.1158/0008-5472.can-19-3460] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022]
Abstract
DRAIC is a 1.7 kb spliced long noncoding RNA downregulated in castration-resistant advanced prostate cancer. Decreased DRAIC expression predicts poor patient outcome in prostate and seven other cancers, while increased DRAIC represses growth of xenografted tumors. Here, we show that cancers with decreased DRAIC expression have increased NF-κB target gene expression. DRAIC downregulation increased cell invasion and soft agar colony formation; this was dependent on NF-κB activation. DRAIC interacted with subunits of the IκB kinase (IKK) complex to inhibit their interaction with each other, the phosphorylation of IκBα, and the activation of NF-κB. These functions of DRAIC mapped to the same fragment containing bases 701-905. Thus, DRAIC lncRNA inhibits prostate cancer progression through suppression of NF-κB activation by interfering with IKK activity. SIGNIFICANCE: A cytoplasmic tumor-suppressive lncRNA interacts with and inhibits a major kinase that activates an oncogenic transcription factor in prostate cancer. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/5/950/F1.large.jpg.
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Affiliation(s)
- Shekhar Saha
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Manjari Kiran
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Canan Kuscu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - David Wotton
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Marty W Mayo
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.
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18
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Chatrath A, Kiran M, Kumar P, Ratan A, Dutta A. The Germline Variants rs61757955 and rs34988193 Are Predictive of Survival in Lower Grade Glioma Patients. Mol Cancer Res 2019; 17:1075-1086. [PMID: 30651372 DOI: 10.1158/1541-7786.mcr-18-0996] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/22/2018] [Accepted: 01/07/2019] [Indexed: 01/01/2023]
Abstract
Lower grade gliomas are invasive brain tumors that are difficult to completely resect neurosurgically. They often recur following resection and progress, resulting in death. Although previous studies have shown that specific germline variants increase the risk of tumor formation, no previous study has screened many germline variants to identify variants predictive of survival in patients with glioma. In this study, we present an approach to identify the small fraction of prognostic germline variants from the pool of over four million variants that we variant called in The Cancer Genome Atlas whole-exome sequencing and RNA sequencing datasets. We identified two germline variants that are predictive of poor patient outcomes by Cox regression, controlling for eleven covariates. rs61757955 is a germline variant found in the 3' UTR of GRB2 associated with increased KRAS signaling, CIC mutations, and 1p/19q codeletion. rs34988193 is a germline variant found in the tumor suppressor gene ANKDD1a that causes an amino acid change from lysine to glutamate. This variant was found to be predictive of poor prognosis in two independent lower grade glioma datasets and is predicted to be within the top 0.06% of deleterious mutations across the human genome. The wild-type residue is conserved in all 22 other species with a homologous protein. IMPLICATIONS: This is the first study presenting an approach to screening many germline variants to identify variants predictive of survival and our application of this methodology revealed the germline variants rs61757955 and rs34988193 as being predictive of survival in patients with lower grade glioma.
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Affiliation(s)
- Ajay Chatrath
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Manjari Kiran
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.
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19
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Chatrath A, Mastorakos P, Mehta GU, Wildeman M, Moosa S, Jane JA. Ganglioglioma Arising from the Septum Pellucidum: Case Report and Review of the Literature. Pediatr Neurosurg 2019; 54:36-45. [PMID: 30620941 DOI: 10.1159/000495043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/27/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND Gangliogliomas are low-grade neoplasms that typically affect patients under the age of 30 and present with epilepsy and symptoms of mass effect. Here, we report a case of an intraventricular ganglioglioma involving the septum pellucidum in a pediatric patient with history of optic glioma. Only one other pediatric intraventricular ganglioglioma arising from the septum pellucidum has been reported previously. CASE REPORT The patient initially presented at 9 months of age with a pilocytic astrocytoma centered on the optic chiasm, treated with chemotherapy and radiation at 3 years of age. Routine follow-up imaging at 13 years of age revealed the development of a mass in the septum pellucidum, which was subtotally resected endoscopically because of its proximity to the fornices. Pathology confirmed a ganglioglioma positive for the BRAF V600E mutation. The tumor residual progressed and was treated with stereotactic radiosurgery. The patient was asymptomatic at her 6-month follow-up visit and the size of the nodule remained stable. LITERATURE REVIEW Our review of the 25 previously reported intraventricular gangliogliomas found that their pre-surgical diagnoses were often incorrect, reflecting the difficulty of making the diagnosis with signs, symptoms, and imaging alone. Patients can be reassured that the prognosis is generally favorable following uncomplicated neurosurgical resection.
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Affiliation(s)
- Ajay Chatrath
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, USA
| | - Panagiotis Mastorakos
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, USA.,Department of Neurological Surgery, NIH/NINDS, Bethesda, Maryland, USA
| | - Gautam U Mehta
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, USA.,Department of Neurological Surgery, NIH/NINDS, Bethesda, Maryland, USA.,Department of Neurosurgery, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Miriam Wildeman
- Department of Pathology, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, USA
| | - Shayan Moosa
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, USA
| | - John A Jane
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, USA,
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20
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Bauer-Nilsen K, Chatrath A, Ruiz-Garcia H, Marchan E, Peterson J, Sheehan J, Trifiletti D. Stereotactic Radiosurgery for Hemorrhagic Brain Metastases from Malignant Melanoma. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Mastorakos P, Mehta GU, Chatrath A, Moosa S, Lopes MB, Payne SC, Jane JA. Tumor to Cerebellar Peduncle T2-Weighted Imaging Intensity Ratio Fails to Predict Pituitary Adenoma Consistency. J Neurol Surg B Skull Base 2018; 80:252-257. [PMID: 31143567 DOI: 10.1055/s-0038-1668516] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/07/2018] [Indexed: 10/28/2022] Open
Abstract
Object The consistency of pituitary macroadenomas affects the complexity of surgical resection. On T2-weighted (T2W) imaging, the intensity ratio of the tumor to the cerebellar peduncle (tumor to cerebellar peduncle T2-weighted imaging intensity [TCTI] ratio) correlates with meningioma consistency. We aimed to determine the correlation of this radiographic finding with pituitary macroadenoma consistency and to determine whether it can be used for preoperative planning. Methods We performed a retrospective evaluation of 196 patients with macroadenomas who underwent endoscopic transsphenoidal resection from January 2012 to June 2017. Macroadenoma consistency was determined by one senior neurosurgeon at the time of surgery. Axial and coronal T2W magnetic resonance imaging images were evaluated retrospectively, and adenoma size, Knosp grade, suprasellar extension and TCTI were calculated. Results The mean TCTI ratio was 1.70 (95% confidence interval [CI]: 1.65-1.75). Intraoperatively, 140 (71.4%) adenomas were classified as soft and 48 (24.5%) as fibrous. Gross total resection was achieved in 66.7% of fibrous adenomas and in 86.4% of soft adenomas ( p = 0.007). The mean ratio was 1.68 (95% CI: 1.62-1.74) for soft tumors and 1.76 (95%CI: 1.67-1.84) for fibrous tumors. There was no difference in the mean TCTI ratio between groups. Lactotroph and somatotroph adenomas had a lower mean TCTI ratio compared with other functioning and nonfunctioning adenomas with a mean TCTI of 1.52 compared with 1.77. Conclusions In this retrospective cohort study, we found that the TCTI ratio does not correlate with tumor consistency. We also noted that the TCTI ratio is increased in prolactin and growth hormone-secreting adenomas.
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Affiliation(s)
- Panagiotis Mastorakos
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States.,Department of Neurological Surgery, NIH/NINDS, Bethesda, Maryland, United States
| | - Gautam U Mehta
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States.,Department of Neurological Surgery, NIH/NINDS, Bethesda, Maryland, United States.,Department of Neurosurgery, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States
| | - Ajay Chatrath
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States
| | - Shayan Moosa
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States
| | - Maria-Beatriz Lopes
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States.,Department of Neuroathology, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States
| | - Spencer C Payne
- Department of Otolaryngology, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States
| | - John A Jane
- Department of Neurological Surgery, University of Virginia Health Science Center, University of Virginia, Charlottesville, Virginia, United States
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22
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Bauer-Nilsen K, Trifiletti DM, Chatrath A, Ruiz-Garcia H, Marchan E, Peterson J, May BC, Sheehan JP. Stereotactic radiosurgery for brain metastases from malignant melanoma and the impact of hemorrhagic metastases. J Neurooncol 2018; 140:83-88. [PMID: 29926319 DOI: 10.1007/s11060-018-2933-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/14/2018] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Stereotactic radiosurgery (SRS) is a common treatment modality among patients with brain metastases, particularly from malignant melanoma. Our objective was to investigate the difference in local control, toxicity, and survival among patients with hemorrhagic and solid melanoma brain metastases. METHODS We collected demographic, treatment, local control, toxicity, and survival for 134 patients with a total of 936 intracranial melanoma metastases who underwent SRS between 1998 and 2015. Pre-radiosurgical diagnostic imaging was reviewed for evidence of hemorrhage (melanin-containing or clearly hemorrhagic). RESULTS The cohort consisted of 92 men and 42 women with a mea age of 61.7 years (range 21.2-84.9) at the time of radiosurgery. Overall survival of patients with brain metastases from malignant melanoma was 42, 31, 12% at 12, 24, and 72 months from date of first SRS. At 6 months, 43% of the patients with hemorrhagic metastases had local tumor control compared to 83% of solid melanoma metastases (p < 0.001). No significant difference in toxicity was noted between the two groups. Factors that were significantly associated with time to local tumor progression on multivariate analysis include prior WBRT (HR 1.62, p = 0.003), prior chemotherapy (HR 0.69, p = 0.011), margin dose (HR 0.88, p < 0.001) and radiographic features of melanin deposition (HR 3.73, p < 0.001), or clear hemorrhage (HR 2.20, p < 0.001). CONCLUSIONS Our findings demonstrate that hemorrhagic intracranial melanoma metastases are associated with inferior local tumor control when treated with SRS, as compared to solid tumors. These results highlight the importance of early radiosurgery among patients with melanoma brain metastases before hemorrhage occurs.
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Affiliation(s)
| | - Daniel M Trifiletti
- Department of Radiation Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA. .,Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, USA.
| | - Ajay Chatrath
- Department of Neurological Surgery, University of Virginia, Charlottesville, VA, USA
| | - Henry Ruiz-Garcia
- Department of Radiation Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Eduardo Marchan
- Department of Radiation Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Jennifer Peterson
- Department of Radiation Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA.,Department of Neurological Surgery, Mayo Clinic, Jacksonville, FL, USA
| | - Byron C May
- Department of Radiation Oncology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL, 32224, USA
| | - Jason P Sheehan
- Department of Radiation Oncology, University of Virginia, Charlottesville, VA, USA.,Department of Neurological Surgery, University of Virginia, Charlottesville, VA, USA
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23
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Hawasli AH, Khalifeh JM, Chatrath A, Yarbrough CK, Ray WZ. Minimally invasive transforaminal lumbar interbody fusion with expandable versus static interbody devices: radiographic assessment of sagittal segmental and pelvic parameters. Neurosurg Focus 2018; 43:E10. [PMID: 28760032 DOI: 10.3171/2017.5.focus17197] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF) has been adopted as an alternative technique to hasten recovery and minimize postoperative morbidity. Advances in instrumentation technologies and operative techniques have evolved to maximize patient outcomes as well as radiographic results. The development of expandable interbody devices allows a surgeon to perform MIS-TLIF with minimal tissue disruption. However, sagittal segmental and pelvic radiographic outcomes after MIS-TLIF with expandable interbody devices are not well characterized. The object of this study is to evaluate the radiographic sagittal lumbar segmental and pelvic parameter outcomes of MIS-TLIF performed using an expandable interbody device. METHODS A retrospective review of MIS-TLIFs performed between 2014 and 2016 at a high-volume center was performed. Radiographic measurements were performed on lateral radiographs before and after MIS-TLIF with static or expandable interbody devices. Radiographic measurements included disc height, foraminal height, fused disc angle, lumbar lordosis, pelvic incidence, sacral slope, and pelvic tilt. Mismatch between pelvic incidence and lumbar lordosis were calculated for each radiograph. RESULTS A total of 48 MIS-TLIFs were performed, predominantly at the L4-5 level, in 44 patients. MIS-TLIF with an expandable interbody device led to a greater and more sustained increase in disc height when compared with static interbody devices. Foraminal height increased after MIS-TLIF with expandable but not with static interbody devices. MIS-TLIF with expandable interbody devices increased index-level segmental lordosis more than with static interbody devices. The increase in segmental lordosis was sustained in the patients with expandable interbody devices but not in patients with static interbody devices. For patients with a collapsed disc space, MIS-TLIF with an expandable interbody device provided superior and longer-lasting increases in disc height, foraminal height, and index-level segmental lordosis than in comparison with patients with static interbody devices. Using an expandable interbody device improved the Oswestry Disability Index scores more than using a static interbody device, and both disc height and segmental lordosis were correlated with improved clinical outcome. Lumbar MIS-TLIF with expandable or static interbody devices had no effect on overall lumbar lordosis, pelvic parameters, or pelvic incidence-lumbar lordosis mismatch. CONCLUSIONS Performing MIS-TLIF with an expandable interbody device led to a greater and longer-lasting restoration of disc height, foraminal height, and index-level segmental lordosis than MIS-TLIF with a static interbody device, especially for patients with a collapsed disc space. However, neither technique had any effect on radiographic pelvic parameters.
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Affiliation(s)
- Ammar H Hawasli
- Departments of 1 Neurological Surgery and.,Orthopedic Surgery, Washington University School of Medicine, Saint Louis, Missouri; and
| | | | | | - Chester K Yarbrough
- Department of Neurosurgery, University of Utah School of Medicine, Salt Lake City, Utah
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