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Sung YJ, Yang C, Norton J, Johnson M, Fagan A, Bateman RJ, Perrin RJ, Morris JC, Farlow MR, Chhatwal JP, Schofield PR, Chui H, Wang F, Novotny B, Eteleeb A, Karch C, Schindler SE, Rhinn H, Johnson EC, Se-Hwee Oh H, Rutledge JE, Dammer EB, Seyfried NT, Wyss-Coray T, Harari O, Cruchaga C. Proteomics of brain, CSF, and plasma identifies molecular signatures for distinguishing sporadic and genetic Alzheimer's disease. Sci Transl Med 2023; 15:eabq5923. [PMID: 37406134 PMCID: PMC10803068 DOI: 10.1126/scitranslmed.abq5923] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/13/2023] [Indexed: 07/07/2023]
Abstract
Proteomic studies for Alzheimer's disease (AD) are instrumental in identifying AD pathways but often focus on single tissues and sporadic AD cases. Here, we present a proteomic study analyzing 1305 proteins in brain tissue, cerebrospinal fluid (CSF), and plasma from patients with sporadic AD, TREM2 risk variant carriers, patients with autosomal dominant AD (ADAD), and healthy individuals. We identified 8 brain, 40 CSF, and 9 plasma proteins that were altered in individuals with sporadic AD, and we replicated these findings in several external datasets. We identified a proteomic signature that differentiated TREM2 variant carriers from both individuals with sporadic AD and healthy individuals. The proteins associated with sporadic AD were also altered in patients with ADAD, but with a greater effect size. Brain-derived proteins associated with ADAD were also replicated in additional CSF samples. Enrichment analyses highlighted several pathways, including those implicated in AD (calcineurin and Apo E), Parkinson's disease (α-synuclein and LRRK2), and innate immune responses (SHC1, ERK-1, and SPP1). Our findings suggest that combined proteomics across brain tissue, CSF, and plasma can be used to identify markers for sporadic and genetically defined AD.
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Affiliation(s)
- Yun Ju Sung
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Chengran Yang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Joanne Norton
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Matt Johnson
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Anne Fagan
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Randall J. Bateman
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Richard J. Perrin
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO 63108, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - John C. Morris
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO 63108, USA
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Martin R. Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jasmeer P. Chhatwal
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Peter R. Schofield
- Neuroscience Research Australia, Randwick, NSW, 2031, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Helena Chui
- Department of Neurology, University of Southern California, Los Angeles, CA 90089, USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Brenna Novotny
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Abdallah Eteleeb
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Celeste Karch
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Suzanne E. Schindler
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Neurology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Herve Rhinn
- Department of Bioinformatics. Alector, Inc. 151 Oyster Point Blvd. #300 South San Francisco CA 94080, USA
| | - Erik C.B. Johnson
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Hamilton Se-Hwee Oh
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Jarod Evert Rutledge
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Eric B Dammer
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Nicholas T. Seyfried
- Goizueta Alzheimer’s Disease Research Center, Emory University School of Medicine, Atlanta, GA 30329, USA
- Department of Biochemistry, Emory School of Medicine, Atlanta, GA 30329, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO 63108, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO 63108, USA
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Chen HH, Eteleeb A, Wang C, Fernandez MV, Budde JP, Bergmann K, Norton J, Wang F, Ebl C, Morris JC, Perrin RJ, Bateman RJ, McDade E, Xiong C, Goate A, Farlow M, Chhatwal J, Schofield PR, Chui H, Harari O, Cruchaga C, Ibanez L. Circular RNA detection identifies circPSEN1 alterations in brain specific to autosomal dominant Alzheimer's disease. Acta Neuropathol Commun 2022; 10:29. [PMID: 35246267 PMCID: PMC8895634 DOI: 10.1186/s40478-022-01328-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/07/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Autosomal-dominant Alzheimer's disease (ADAD) is caused by pathogenic mutations in APP, PSEN1, and PSEN2, which usually lead to an early age at onset (< 65). Circular RNAs are a family of non-coding RNAs highly expressed in the nervous system and especially in synapses. We aimed to investigate differences in brain gene expression of linear and circular transcripts from the three ADAD genes in controls, sporadic AD, and ADAD. METHODS We obtained and sequenced RNA from brain cortex using standard protocols. Linear counts were obtained using the TOPMed pipeline; circular counts, using python package DCC. After stringent quality control (QC), we obtained the counts for PSEN1, PSEN2 and APP genes. Only circPSEN1 passed QC. We used DESeq2 to compare the counts across groups, correcting for biological and technical variables. Finally, we performed in-silico functional analyses using the Circular RNA interactome website and DIANA mirPath software. RESULTS Our results show significant differences in gene counts of circPSEN1 in ADAD individuals, when compared to sporadic AD and controls (ADAD = 21, AD = 253, Controls = 23-ADADvsCO: log2FC = 0.794, p = 1.63 × 10-04, ADADvsAD: log2FC = 0.602, p = 8.22 × 10-04). The high gene counts are contributed by two circPSEN1 species (hsa_circ_0008521 and hsa_circ_0003848). No significant differences were observed in linear PSEN1 gene expression between cases and controls, indicating that this finding is specific to the circular forms. In addition, the high circPSEN1 levels do not seem to be specific to PSEN1 mutation carriers; the counts are also elevated in APP and PSEN2 mutation carriers. In-silico functional analyses suggest that circPSEN1 is involved in several pathways such as axon guidance (p = 3.39 × 10-07), hippo signaling pathway (p = 7.38 × 10-07), lysine degradation (p = 2.48 × 10-05) or Wnt signaling pathway (p = 5.58 × 10-04) among other KEGG pathways. Additionally, circPSEN1 counts were able to discriminate ADAD from sporadic AD and controls with an AUC above 0.70. CONCLUSIONS Our findings show the differential expression of circPSEN1 is increased in ADAD. Given the biological function previously ascribed to circular RNAs and the results of our in-silico analyses, we hypothesize that this finding might be related to neuroinflammatory events that lead or that are caused by the accumulation of amyloid-beta.
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Affiliation(s)
- Hsiang-Han Chen
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Abdallah Eteleeb
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Ciyang Wang
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Maria Victoria Fernandez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - John P. Budde
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Kristy Bergmann
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Joanne Norton
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Fengxian Wang
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Curtis Ebl
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - John C. Morris
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Richard J. Perrin
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Randall J. Bateman
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Eric McDade
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Alison Goate
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Martin Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN USA
| | - Jasmeer Chhatwal
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
| | - Peter R. Schofield
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Helena Chui
- Department of Neurology, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Laura Ibanez
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
| | - Dominantly Inherited Alzheimer Network
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, 4444 Forest Park, Campus Box 8134, Saint Louis, MO 63110 USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Hope Center for Neurological Disorders, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- The Charles F. and Joanne Knight Alzheimer Disease Research Center, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Pathology and Immunology, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Division of Biostatistics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA USA
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences, University of New South Wales, Sydney, Australia
- Department of Neurology, Keck School of Medicine of University of Southern California, Los Angeles, CA USA
- Department of Genetics, Washington University in Saint Louis School of Medicine, Saint Louis, MO USA
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3
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Bigley TM, Xiong M, Ali M, Chen Y, Wang C, Serrano JR, Eteleeb A, Harari O, Yang L, Patel SJ, Cruchaga C, Yokoyama WM, Holtzman DM. Murine roseolovirus does not accelerate amyloid-β pathology and human roseoloviruses are not over-represented in Alzheimer disease brains. Mol Neurodegener 2022; 17:10. [PMID: 35033173 PMCID: PMC8760754 DOI: 10.1186/s13024-021-00514-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/22/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The role of viral infection in Alzheimer Disease (AD) pathogenesis is an area of great interest in recent years. Several studies have suggested an association between the human roseoloviruses, HHV-6 and HHV-7, and AD. Amyloid-β (Aβ) plaques are a hallmark neuropathological finding of AD and were recently proposed to have an antimicrobial function in response to infection. Identifying a causative and mechanistic role of human roseoloviruses in AD has been confounded by limitations in performing in vivo studies. Recent -omics based approaches have demonstrated conflicting associations between human roseoloviruses and AD. Murine roseolovirus (MRV) is a natural murine pathogen that is highly-related to the human roseoloviruses, providing an opportunity to perform well-controlled studies of the impact of roseolovirus on Aβ deposition. METHODS We utilized the 5XFAD mouse model to test whether MRV induces Aβ deposition in vivo. We also evaluated viral load and neuropathogenesis of MRV infection. To evaluate Aβ interaction with MRV, we performed electron microscopy. RNA-sequencing of a cohort of AD brains compared to control was used to investigate the association between human roseolovirus and AD. RESULTS We found that 5XFAD mice were susceptible to MRV infection and developed neuroinflammation. Moreover, we demonstrated that Aβ interacts with viral particles in vitro and, subsequent to this interaction, can disrupt infection. Despite this, neither peripheral nor brain infection with MRV increased or accelerated Aβ plaque formation. Moreover, -omics based approaches have demonstrated conflicting associations between human roseoloviruses and AD. Our RNA-sequencing analysis of a cohort of AD brains compared to controls did not show an association between roseolovirus infection and AD. CONCLUSION Although MRV does infect the brain and cause transient neuroinflammation, our data do not support a role for murine or human roseoloviruses in the development of Aβ plaque formation and AD.
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Affiliation(s)
- Tarin M. Bigley
- Division of Rheumatology, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Monica Xiong
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Division of Biology and Biomedical Sciences (DBBS), Washington University School of Medicine, St. Louis, MO 63110 USA
- Present address: Genentech, 1 DNA Way, South San Francisco, CA 94080 USA
| | - Muhammad Ali
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
| | - Yun Chen
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Division of Biology and Biomedical Sciences (DBBS), Washington University School of Medicine, St. Louis, MO 63110 USA
- Department of Pathology & Immunology, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Chao Wang
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Javier Remolina Serrano
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Abdallah Eteleeb
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - Oscar Harari
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - Liping Yang
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Swapneel J. Patel
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - Carlos Cruchaga
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
- Department Psychiatry, Washington University School of Medicine (WUSM), 660 S. Euclid Ave. B8134, St. Louis, MO 63110 USA
- NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, MO USA
| | - Wayne M. Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110 USA
| | - David M. Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer’s Disease Research Center, Washington University School of Medicine, St. Louis, MO 63110 USA
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Minaya M, Martinez R, Eteleeb A, Cruchaga C, Harari O, Karch CM. Impact of MAPT mutations on transcriptomic signatures of FTLD brains and patient-derived pluripotent cell models. Alzheimers Dement 2022. [PMID: 34971166 DOI: 10.1002/alz.058313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND Mutations in the microtubule-associated protein tau (MAPT) cause heterogeneous forms of frontotemporal lobar dementia with tau inclusions (FTLD-tau). Yet the pathogenic events linked to disease remain poorly understood. This study aimed to identify genes and pathways that lead to FTLD-tau. METHOD To identify the earliest genes and pathways that are dysregulated in FTLD-tau, we identified differentially expressed genes in RNA-seq data generated from induced pluripotent stem cell (iPSC)-derived cortical neurons carrying MAPT R406W, MAPT P301L, and MAPT IVS10+16 and isogenic, controls and brain tissue samples from progressive supranuclear palsy (PSP) and control brains. We then identified pathological pathways and drug targets that were enriched among the differentially expressed genes. RESULTS We identified 275 genes that were differentially expressed in iPSC-derived cortical neurons from MAPT R406W carriers compared to isogenic controls, MAPT IVS10+16 carriers compared to isogenic controls, and MAPT P301L carriers compared with isogenic controls. These commonly dysregulated genes were enriched for pathways involving synaptic function, neuronal development, and endolysosomal function. A subset of these genes were also changed in brains from human subjects with PSP compared to normal control brains. Finally, a subset of genes, enriched in glutamate receptor signaling, were altered across the mutant neurons and significantly changed with tau accumulation in a mouse model of tauopathy (Tau-P301L mice). CONCLUSION The results from this study demonstrate that iPSC-derived neurons capture molecular processes that occur in human brains and can be used to model disease and point to common molecular pathways driven by 3 distinct MAPT mutations.
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Affiliation(s)
| | | | | | - Carlos Cruchaga
- Washington University School of Medicine, St. Louis, MO, USA
| | | | - Celeste M Karch
- Washington University School of Medicine, St. Louis, MO, USA
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Ibanez L, Bergmann K, Eteleeb A, Wang F, Norton J, Gentsch J, Harari O, Cruchaga C. Prediction of Alzheimer disease using plasma RNA sequences from dementia genes. Alzheimers Dement 2021. [DOI: 10.1002/alz.049885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Laura Ibanez
- Washington University in St. Louis Saint Louis MO USA
- Neurogenomics and Informatics Saint Louis MO USA
| | | | | | - Fengxian Wang
- Washington University School of Medicine St. Louis MO USA
| | - Joanne Norton
- Washington University School of Medicine St. Louis MO USA
- Knight Alzheimer Disease Research Center St Louis MO USA
| | - Jen Gentsch
- Washington University School of Medicine St. Louis MO USA
- Knight Alzheimer Disease Research Center St Louis MO USA
| | - Oscar Harari
- Washington University School of Medicine St. Louis MO USA
| | - Carlos Cruchaga
- Washington University St. Louis MO USA
- Knight Alzheimer Disease Research Center Saint Louis MO USA
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Li F, Eteleeb A, Buchser W, Wang G, Xiong C, Payne PR, McDade E, Karch CM, Harari O, Cruchaga C. Weakly activated core inflammation pathways were identified as a central signaling mechanism contributing to the chronic neurodegeneration in Alzheimer's disease. bioRxiv 2021:2021.08.30.458295. [PMID: 34494019 PMCID: PMC8423192 DOI: 10.1101/2021.08.30.458295] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Neuro-inflammation signaling has been identified as an important hallmark of Alzheimer's disease (AD) in addition to amyloid β plaques (Aβ) and neurofibrillary tangles (NFTs). However, our knowledge of neuro-inflammation is very limited; and the core signaling pathways associated with neuro-inflammation are missing. From a novel perspective, i.e., investigating weakly activated molecular signals (rather than the strongly activated molecular signals), in this study, we uncovered the core neuro-inflammation signaling pathways in AD. Our novel hypothesis is that weakly activated neuro-inflammation signaling pathways can cause neuro-degeneration in a chronic process; whereas, strongly activated neuro-inflammation often cause acute disease progression like in COVID-19. Using the two large-scale genomics datasets, i.e., Mayo Clinic (77 control and 81 AD samples) and RosMap (97 control and 260 AD samples), our analysis identified 7 categories of signaling pathways implicated on AD and related to virus infection: immune response, x-core signaling, apoptosis, lipid dysfunctional, biosynthesis and metabolism, and mineral absorption signaling pathways. More interestingly, most of genes in the virus infection, immune response and x-core signaling pathways, are associated with inflammation molecular functions. Specifically, the x-core signaling pathways were defined as a group of 9 signaling proteins: MAPK, Rap1, NF-kappa B, HIF-1, PI3K-Akt, Wnt, TGF-beta, Hippo and TNF, which indicated the core neuro-inflammation signaling pathways responding to the low-level and weakly activated inflammation and hypoxia, and leading to the chronic neuro-degeneration. The core neuro-inflammation signaling pathways can be used as novel therapeutic targets for effective AD treatment and prevention.
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Affiliation(s)
- Fuhai Li
- Institute for Informatics (I2), Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Abdallah Eteleeb
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - William Buchser
- Department of Neuroscience, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Guoqiao Wang
- Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Chengjie Xiong
- Division of Biostatistics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Philip R. Payne
- Institute for Informatics (I2), Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Eric McDade
- Department of Neurology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Celeste M. Karch
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Department of Neurology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- Hope Center for Neurological Disorders, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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7
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Wani A, Zhu J, Ulrich JD, Eteleeb A, Sauerbeck AD, Reitz SJ, Arhzaouy K, Ikenaga C, Yuede CM, Pittman SK, Wang F, Li S, Benitez BA, Cruchaga C, Kummer TT, Harari O, Chou TF, Schröder R, Clemen CS, Weihl CC. Neuronal VCP loss of function recapitulates FTLD-TDP pathology. Cell Rep 2021; 36:109399. [PMID: 34289347 PMCID: PMC8383344 DOI: 10.1016/j.celrep.2021.109399] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
The pathogenic mechanism by which dominant mutations in VCP cause multisystem proteinopathy (MSP), a rare neurodegenerative disease that presents as fronto-temporal lobar degeneration with TDP-43 inclusions (FTLD-TDP), remains unclear. To explore this, we inactivate VCP in murine postnatal forebrain neurons (VCP conditional knockout [cKO]). VCP cKO mice have cortical brain atrophy, neuronal loss, autophago-lysosomal dysfunction, and TDP-43 inclusions resembling FTLD-TDP pathology. Conditional expression of a single disease-associated mutation, VCP-R155C, in a VCP null background similarly recapitulates features of VCP inactivation and FTLD-TDP, suggesting that this MSP mutation is hypomorphic. Comparison of transcriptomic and proteomic datasets from genetically defined patients with FTLD-TDP reveal that progranulin deficiency and VCP insufficiency result in similar profiles. These data identify a loss of VCP-dependent functions as a mediator of FTLD-TDP and reveal an unexpected biochemical similarity with progranulin deficiency.
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Affiliation(s)
- Abubakar Wani
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Jiang Zhu
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason D Ulrich
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Abdallah Eteleeb
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew D Sauerbeck
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Sydney J Reitz
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Khalid Arhzaouy
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Chiseko Ikenaga
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Carla M Yuede
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Sara K Pittman
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Feng Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bruno A Benitez
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Terrance T Kummer
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Oscar Harari
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rolf Schröder
- Institute of Neuropathology, University Hospital Erlangen, Friedrich Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Christoph S Clemen
- Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany; Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Conrad C Weihl
- Department of Neurology, Hope Center for Neurological Diseases, Washington University School of Medicine, St. Louis, MO, USA.
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8
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Silva-Fisher JM, Dang HX, White NM, Strand MS, Krasnick BA, Rozycki EB, Jeffers GGL, Grossman JG, Highkin MK, Tang C, Cabanski CR, Eteleeb A, Mudd J, Goedegebuure SP, Luo J, Mardis ER, Wilson RK, Ley TJ, Lockhart AC, Fields RC, Maher CA. Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression. Nat Commun 2020; 11:2156. [PMID: 32358485 PMCID: PMC7195452 DOI: 10.1038/s41467-020-15547-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/16/2020] [Indexed: 01/14/2023] Open
Abstract
Colorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of patients develop metastatic disease (mCRC). Despite our understanding of long non-coding RNAs (lncRNAs) in primary colon cancer, their role in mCRC and treatment resistance remains poorly characterized. Therefore, through transcriptome sequencing of normal, primary, and distant mCRC tissues we find 148 differentially expressed RNAs Associated with Metastasis (RAMS). We prioritize RAMS11 due to its association with poor disease-free survival and promotion of aggressive phenotypes in vitro and in vivo. A FDA-approved drug high-throughput viability assay shows that elevated RAMS11 expression increases resistance to topoisomerase inhibitors. Subsequent experiments demonstrate RAMS11-dependent recruitment of Chromobox protein 4 (CBX4) transcriptionally activates Topoisomerase II alpha (TOP2α). Overall, recent clinical trials using topoisomerase inhibitors coupled with our findings of RAMS11-dependent regulation of TOP2α supports the potential use of RAMS11 as a biomarker and therapeutic target for mCRC.
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Affiliation(s)
- Jessica M Silva-Fisher
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ha X Dang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- The McDonnell Genome Institute, St. Louis, MO, USA
| | - Nicole M White
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew S Strand
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley A Krasnick
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily B Rozycki
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gejae G L Jeffers
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Julie G Grossman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Maureen K Highkin
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Tang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Abdallah Eteleeb
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Jingqin Luo
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Timothy J Ley
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Ryan C Fields
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- The McDonnell Genome Institute, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA.
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9
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Maher CA, Silva-Fisher J, Eteleeb A, Tang C, Perou C, Reis-Filho JS, Mardis ER, Ellis MJ. Abstract GS2-01: Discovery and characterization of an estrogen bound LncRNA in late-Stage breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-gs2-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Breast cancer is the second most common newly diagnosed cancer and the second leading cause of cancer death among women in the United States. Despite the proven benefits of adjuvant endocrine therapy in women with hormone receptor positive breast cancer, relapses still occur over 5 years after initial treatment with endocrine therapy, referred to as late-stage relapse. Currently, the mechanisms of driving late-stage relapse are poorly characterized. To date, breast cancer research has primarily focused on protein-coding genes thereby missing the emerging class of long intergenic non-coding RNAs (lncRNAs) that may serve as critical regulators of relapse. Furthermore, the current understanding of lncRNA function is still in its infancy representing a critical gap for translating lncRNA discoveries into real-world applications to benefit patient care. Several well-described examples indicate that lncRNAs may be master epigenetic regulators in cancer biology through their interactions with proteins regulating target gene expression. Therefore, we hypothesize that lncRNAs may interact with estrogen receptor alpha 1 (ESR1) to regulate genes promoting late-stage relapse. To address this, we performed a transcriptome analysis of tumors from a unique cohort of 24 patients that had late-stage relapse to discover a novel set of lncRNAs, most of which have not yet been characterized. Next, we used RNA Immunoprecipitation coupled with transcriptome sequencing (RIP-Seq) to identify transcripts bound to ESR1 in T47D cells. We discovered 217 lncRNAs bound to ESR1 of which 50 were up-regulated in late-stage breast cancer. We chose to focus the most up-regulated lncRNA in late-stage relapse. Since it is an unannotated lncRNA we will refer to it as 'LAte-Stage relapse ESR1-Bound lncRNA 1', or LASER-1. To further understand the interplay between LASER-1 and ESR1, cells endogenously expressing LASER-1 were subjected to partial digestion to preserve lncRNA and protein interactions. Protected RNA fragments were subsequently immunoprecipitated with ESR1 and quantified by qPCR to reveal specific ESR1 interaction sites within LASER-1. Next, we observed increased expression of LASER-1 in ER+ breast cancer cell lines. Notably, LASER-1 expression was elevated in MCF7 long-term estrogen deprived (MCF7 LTED) cells -- that have amplified ESR1 -- relative to parental MCF7 cells. To demonstrate that LASER-1 promotes oncogenic phenotypes we transiently silenced LASER-1 in two cell lines with high endogenous expression of LASER-1 (including MCF LTED) and observed a decrease in cellular proliferation and invasion. Subsequent gene expression analysis after silencing LASER-1 altered mRNA and protein levels of critical cell cycle genes (i.e., p27). Overall, this is the first study to discover ESR1 bound lncRNAs that may be contributing to late-stage relapse in breast cancer. In the short-term, our ongoing research may lead to significant breakthroughs establishing the importance of LASER-1 as a master regulator in late-stage relapse. In the longer-term, we envision this research may lead to the development of novel therapeutics targeting LASER-1 with the potential for rapid clinical translation.
Citation Format: Maher CA, Silva-Fisher J, Eteleeb A, Tang C, Perou C, Reis-Filho JS, Mardis ER, Ellis MJ. Discovery and characterization of an estrogen bound LncRNA in late-Stage breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS2-01.
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Affiliation(s)
- CA Maher
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - J Silva-Fisher
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - A Eteleeb
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - C Tang
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - C Perou
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - JS Reis-Filho
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - ER Mardis
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
| | - MJ Ellis
- Washington University School of Medicine in St. Louis; The McDonnell Genome Institute; University of North Carolina at Chapel Hill; Memorial Sloan Kettering Cancer Center; Nationwide Children's Hospital, Institute for Genomic Medicine; Baylor College of Medicine in Houston
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10
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Harrison BJ, Flight RM, Eteleeb A, Rouchka EC, Petruska JC. RNASeq profiling of UTR expression during neuronal plasticity. BMC Bioinformatics 2012. [PMCID: PMC3409041 DOI: 10.1186/1471-2105-13-s12-a4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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